WO2006029389A2

WO2006029389A2 - Tryptophan-processing enzymes, nucleic acids encoding them and methods for making and using them

Info

Publication number: WO2006029389A2
Application number: PCT/US2005/032383
Authority: WO
Inventors: David Blum; Justin T. Stege; Gordana Djordjevic; Amit Vasavada; Peter Williams
Original assignee: Diversa Corporation; Sygenta Participations Ag
Priority date: 2004-09-09
Filing date: 2005-09-09
Publication date: 2006-03-16
Also published as: WO2006029389A9

Abstract

The invention provides tryptophan-processing enzymes, polynucleotides encoding these enzymes, the use of such polynucleotides and polypeptides. In one aspect, the invention provides foods or feeds comprising at least one polypeptide of the invention. In one aspect the invention provides compositions, e.g., feeds and foods, feed and food additives, drugs, dietary supplements, and methods for degrading or otherwise processing tryptophan to reduce or eliminate skatole accumulation in an animal. In one aspect the invention provides compositions and methods to reduce skatole accumulation in animal fat. In one aspect the invention provides compositions and methods for controlling boar taint and improving the efficiency of pig production and flavor of cooked pork meat.

Description

TRYPTOPHAN-PROCESSING ENZYMES, NUCLEIC ACIDS ENCODING THEM AND METHODS FOR MAKING

AND USING THEM

Cross-Reference to Related Applications This application claims benefit of U.S. provisional patent application

60/608,242, filed September 09, 2004. The contents of this document are expressly incorporated herein by reference in its entirety for all purposes.

FIELD OF THE INVENTION This invention relates to the fields of enzymology and animal farming. The invention provides tryptophan-processing (tryptophan-degrading) enzymes, polynucleotides encoding these enzymes, the use of such polynucleotides and polypeptides. In one aspect, the invention provides a method for the enzymatic degradation of tryptophan, e.g., using a novel tryptophan-processing enzymes of the invention. In one aspect the invention provides compositions, e.g., feeds, foods, dietary supplements, liquids, formulations including capsules, tablets, powders and the like, and methods for degrading, modifying and/or hydrolyzing tryptophan to reduce or eliminate skatole (3-methylindole) accumulation in an animal, e.g., the animal's fat.

BACKGROUND

For pigs, there are nine essential amino acids that need to be supplied in feed. These essential amino acids are lysine, methionine, tryptophan, isoleucine, histidine, phenylalanine, threonine, leucine and valine. Ingested protein derived from animal feed is first digested in the stomach then the small intestine with most amino acid absorption occurring in the small intestine. Proteins are hydrolyzed to free amino acids (FAA) as well as di- and tri- peptides. Studies have shown that di- and tri- peptides are absorbed more rapidly than FAAs. A large portion (~80%) of the amino acid uptake in pigs may be via di- and tri- peptides. FAAs that are not absorbed move into the large intestine where increasing microbial populations and decreasing supplies of nutrients force the bacteria to ferment compounds to derive energy.

This phenomenon leads to the production of skatole (3-methylindole) from tryptophan. Skatole has an offensive odor. In pigs in combination with the male hormone androsterone it causes "boar taint". Skatole (3-methylindole) is a volatile lipophilic compound produced by microbial degradation of L-tryptophan in rumen, caecum and colon of monogastric animals. L-tryptophan, derived from diet or from turnover of epithelial cells in upper intestine, can be degraded directly to indole or converted to indole-3 -acetate (IAA) and then to skatole. Once formed, skatole can remain in intestine, be excreted, or absorbed by intestinal mucosa and metabolized in liver. Skatole that is not metabolized deposits in adipose (fat) tissue. Besides animal intestine, formation of skatole (and indole) by microbial activity can be detected during cheese ripening.

Skatole has major harmful consequences for beef and pork industries. It is highly toxic to ruminants, for example, it causes fatal acute bovine pulmonary edema and emphysema, ABPE. Although it is not toxic to pigs, unmetabolized intestinal skatole accumulates in liver, kidneys and fat tissue of uncastrated male pigs. Together with a sex steroid androstenone, skatole is responsible for foul taste and offensive odor of cooked boar meat (boar taint). Skatole does not accumulate in pig stomach or small intestine. It starts to accumulate in caecum and proximal colon in low amounts and progressively increases in distal colon, which is the main accumulation site. Amount of skatole accumulated in pig intestine is estimated to about 54 mg/day in the entire gut of a 100 kg live pig or to 200μmol/L (26 mg/L) of intestinal contents. Accepted amount of skatole accumulated in fat is estimated to 0.25 μg/g fat (threshold for detection by human population).

Formation of skatole in pig intestine is related to metabolism of androstenone. According to literature evidence, testicular synthesis of androstenone is more responsible for the relationship between the two compounds in adipose tissue than the metabolism of androstenone and skatole in liver. Also, it appears that skatole could play predominant role in producing boar taint due to genetic determination of the ability to smell androstenone in human population (56% of men and 92% of women can detect androstenone; in contrast, most people can detect skatole).

Only six known bacterial species produce skatole: Clostridium scatologenes (the only known strain which produces skatole directly from tryptophan), Clostridium nauseum, Pseudomonas sp., Rhizobium sp., Lactobacillus helveticus and Lactobacillus sp. strain 11201. Among these organisms, Lactobacillus sp. strain 11201 and Clostridia are primarily responsible for skatole production in pig colon. Generally, skatole-producing bacteria comprise less than 0.01% of total intestinal flora. In Lactobacillus sp. strain 11201, enzyme believed to be involved in skatole production is cell wall associated and inducible by IAA and several other indolic compounds. Exact nature of the enzymatic activity is not known, but it is non-competitively inhibited by skatole. Bacterial-mediated production of skatole is sensitive to antibiotics (e.g. monesin, polyether antibiotics). Because of its lipophilic properties, skatole has bacteriostatic effect on ciliated protozoa and gram-negative bacteria (e.g. Escherichia, Shigella, Proteus, Salmonella Eberthella, Aerobacter).

Tryptophanase (E.G. 4.1.99.1) catalyzes the β-elimination of tryptophan resulting in three products: indole, ammonia and pyruvate. Tryptophanases are produced by bacteria and several gene sequences are in the NCBI database. A tryptophanase from E. coli has been well studied and exists as a tetramer of molecular weight 220,000. This enzyme also has been shown to utilize the amino acids serine and cysteine as substrates.

SUMMARY

The invention provides polypeptides having tryptophan-processing activity (which includes tryptophan-modifying, tryptophan-degrading and tryptophan-hydrolyzing activity), e.g., enzymes having tryptophan-processing activity, and polynucleotides encoding these enzymes, and uses of these polynucleotides and polypeptides. In one aspect, the polypeptides having tryptophan-processing activity of the invention convert the free amino acid tryptophan to indole; i.e., in this aspect, polypeptides of the invention catalyze the degradation of tryptophan to indole, pyruvate, and ammonia, and in one aspect (optionally), the reverse reaction of indole, pyruvate, and ammonia to tryptophan (particularly at high concentrations of pyruvate and ammonia). In one aspect, enzymes of the invention are active in the physiological conditions of the hindgut (e.g., colon, rumen, caecum) of an animal. In alternative aspects the tryptophan-processing (tryptophan- degrading) polypeptides of the invention have tryptophanase, tryptophan decarboxylase, tryptophan dioxygenase, tryptophan transaminase activity, tryptophan side chain oxidase and/or tyrosine phenol lyase activity.

The invention provides compositions and methods for the enzymatic degradation, modification or hydrolysis of tryptophan, e.g., using at least one tryptophan- processing (tryptophan-modifying, tryptophan-degrading or tryptophan-hydrolyzing) enzyme of the invention. In one aspect, these methods comprise use of a polypeptide having tryptophan-processing (tryptophan-modifying, tryptophan-degrading or tryptophan-hydrolyzing) activity to decrease the amount of free tryptophan in the gut of an animal, and in one aspect, to decrease the amount of free tryptophan in the hindgut (including the rumen, caecum and/or colon) of an animal, e.g., a pig or hog (versus the stomach or intestine).

By decreasing or otherwise processing the amount of free tryptophan in the gut of an animal, the invention also provides compositions (e.g., feeds, foods, liquids, powders, sprays, drugs, capsules, dietary supplements, food and feed additives) and methods for reducing or eliminating skatole accumulation in an animal, e.g., by reducing or eliminating the amount of skatole produced in the animals gut. Thus, in one aspect, the invention provides compositions and methods for reducing or eliminating the amount of skatole in a hindgut (including the rumen, caecum and/or colon) of an animal, such as a pig or hog. In one aspect, this is accomplished by the invention providing various formulations of feeds, foods, liquids, powders, sprays, aerosols, drugs, capsules, tablets, dietary supplements and the like. In alternative aspects, these formulations comprise enzymes of the invention and/or compound that inhibit the formation of skatole, e.g., indole-3-carbinol (BC) and indole-3-acetonytril (BA), and similar inhibitory compounds. In one aspect, these formulations are processed such that a tryptophan- processing polypeptide of the invention has most or substantially all of its activity in the hindgut, versus the stomach or intestine. In one aspect, a polypeptide of the invention is formulated such that a clinically or industrially significant percentage, e.g., at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or most of its activity or substantially all of its tryptophan-processing activity is in the hindgut (including the rumen, caecum and/or the colon) or remains active after passage through the upper gastrointestinal tract (e.g., the stomach or small intestine).

In one aspect, by decreasing the amount of skatole produced in the gut of an animal, the compositions and methods of the invention decrease the amount of skatole accumulation in the meat of an animal, e.g., a domestic animal, such as a hog or pig, bred for consumption. Thus, the invention also provides methods of decreasing the amount of skatole absorbed from the digestive tract of an animal comprising feeding or otherwise administering at least one skatole-binding composition, e.g., a hydrophobic polypeptide, to the animal. Any composition that can slow or eliminate skatole absorption from the gut by the animal can be used in the methods of the animal. Thus, the invention provides compositions and methods to increase the palatability of an animal's meat, thereby increasing the value of the animal, e.g., a domestic animal, such as a hog or pig, by decreasing the amount of skatole in the animal (e.g., in the animal's fat). These compositions can be formulated in a variety of forms, e.g., as liquids, sprays, aerosols, powders, food, feed pellets, tablets or as capsules (encapsulated forms), as a daily oral supplement, as a drench, as a slow release bolus, or as a rectal pessary. These formulations can be used to deliver tryptophan-processing (tryptophan- degrading) enzyme (e.g., an enzyme of the invention) to man or animal. Alternatively, tryptophan-processing (tryptophan-degrading) enzyme (e.g., an enzyme of the invention) can be delivered simply by adding to the drinking water or other liquid.

The invention also provides formulations (e.g., encapsulated forms) that only release the tryptophan-processing (tryptophan-degrading) enzyme, or only release an active form of the enzyme, in the hindgut (e.g., rumen, caecum and colon of monogastric animals). In one aspect, the enzyme is only active in hindgut conditions (e.g., rumen, caecum, colon conditions), e.g., the enzyme is only active, or is relatively more active (e.g., is substantially active only) at certain alkaline pHs, e.g., under pH conditions similar or the same as a rumen, caecum and colon, e.g., of a monogastric animal. In one aspect, a polypeptide of the invention, either inherently (e.g., because of sequence or structure) or because of its formulation is relatively active, substantially active or is only active under conditions (including pH or other specific conditions) similar or the same as a rumen, caecum and colon, e.g., of a monogastric animal, such as a pig.

The compositions and methods of the invention can be practiced on any animal, e.g., a domestic or wild (or zoo) animal, e.g., any farm animal, e.g., a pig

(including all swine, hogs and related animals), a cow, a sheep, a horse. In one aspect the invention provides compositions and methods to reduce skatole accumulation in the animal, e.g., in the animal's fat.

In one aspect the invention provides compositions (e.g., feeds, drugs, dietary supplements) and methods for converting skatole to a compound that cannot be absorbed from the lumen of the digestive tract (skatole does not accumulate in pig stomach or small intestine, it accumulates in caecum and proximal colon in low amounts and progressively increases in amount in the distal colon, which is the main accumulation (or absorption) site of skatole), or, converting skatole to derivatives that are not problematic, e.g., non-toxic, have acceptable pallatability, no regulatory issues. In one aspect, enzymes that can modify skatole (e.g., such that it cannot be absorbed by an animal, e.g., preventing absorption from the colon into the body) are administered in conjunction with polypeptides (e.g., enzymes, antibodies) of the invention, or with other treatment methods of the invention (e.g., administration of tryptophan or skatole binding proteins, probiotics, probiotic bacteria, etc, as discussed herein). These compositions can be formulated in a variety of forms, e.g., as liquids, sprays, aerosols, powders, food, feed pellets, capsules, tablets, or encapsulated forms.

In one aspect, the invention provides methods for reducing or eliminating skatole accumulation in an animal (e.g., swine, hogs, pigs and related animals) by administration of skatole-degrading enzymes, including enzymes that can modify or degrade skatole precursors (intermediates), such as indolacetate or indolepyruvate. Removal of skatole precursors (intermediates) can also reduce or eliminate skatole accumulation in an animal. In one aspect, the skatole-degrading enzyme has an activity comprising the removal of a 3 -methyl group from skatole (to generate indole). In one aspect, the enzymatic removal of a 3 -methyl group from skatole also involves an oxidative enzyme requiring co-factors. In one aspect, enzymes that can modify or degrade skatole precursors are administered in conjunction with polypeptides (e.g., enzymes, antibodies) of the invention, or with other treatment methods of the invention (e.g., administration of tryptophan or skatole binding proteins, probiotics, probiotic bacteria, etc, as discussed herein).

In one aspect the invention provides compositions, e.g., feeds, and methods for binding or "sequestering" skatole in the digestive tract (e.g., rumen, caecum and colon of monogastric animals) of an animal by administering hydrophobic proteins that specifically or generally (e.g., albumin) bind skatole. In one aspect, the hydrophobic proteins are applied at low concentrations. In one aspect, the invention provides methods for removing skatole from pig colon using proteins which specifically (or generally) bind skatole. In one aspect, these hydrophobic proteins are co-administered with an enzyme and/or an antibody (e.g., an anti-skatole antibody) of the invention. The invention provides isolated or recombinant nucleic acids comprising a nucleic acid sequence having at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more, or complete (100%) sequence identity to an exemplary nucleic acid of the invention, e.g., SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID

NO:31, SEQ ID NO:33, SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67 or SEQ ID NO:69 (hereinafter referred to as the exemplary nucleic acid sequences of the invention), over a region of at least about 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650, 1700, 1750, 1800, 1850, 1900, 1950, 2000, 2050, 2100, 2200, 2250, 2300, 2350, 2400, 2450, 2500, or more residues, encodes at least one polypeptide having a tryptophan-degrading or a tryptophanase activity, e.g., catalysis of the beta-elimination of a tryptophan, and, in one aspect, the sequence identities are determined by analysis with a sequence comparison algorithm or by a visual inspection. In alternative aspects, the invention provides isolated or recombinant nucleic acids comprising a nucleic acid sequence having at least about 65% sequence identity to an exemplary polypeptide of the invention, e.g., SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5 or SEQ ID NO:6, etc (see explanation, below). In alternative aspects, the invention provides isolated or recombinant nucleic acids comprising a nucleic acid sequence having at least about 75% sequence identity to SEQ ID NO:7 or SEQ ID NO:8. In alternative aspects, the invention provides isolated or recombinant nucleic acids comprising a nucleic acid sequence having at least about 55% sequence identity to SEQ ID NO:9 or SEQ ID NO: 10.

Exemplary nucleic acids of the invention also include isolated or recombinant nucleic acids encoding a polypeptide having a sequence as set forth in SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68 or SEQ ID NO:70 (hereinafter referred to as exemplary polypeptides of the invention), and subsequences thereof and variants thereof. In one aspect, the polypeptide has a tryptophan-degrading or a tryptophanase activity.

In one aspect, the invention also provides tryptophanase-encoding nucleic acids with a common novelty in that they are derived from mixed cultures. The invention provides tryptophan-degrading enzyme-encoding nucleic acids isolated from mixed cultures comprising a polynucleotide of the invention, e.g., a sequence having at least about 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, ^' 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more, or complete (100%) sequence identity to an exemplary nucleic acid of the invention (e.g., SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO.13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, SEQ ID NO:69), over a region of at least about 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, or more, and sequences complementary thereto (collectively referred to as nucleic acids of the invention).

In one aspect, the invention provides tryptophan-degrading enzyme- encoding nucleic acids, including the exemplary sequences of the invention (e.g., SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, etc.) and the polypeptides encoded by them, including the exemplary polypeptide sequences of the invention (e.g., SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO: 10, etc.) with a common novelty in that they are derived from a common source, e.g., an environmental source, or a bacterial source (see discussion below). In one aspect, the invention also provides tryptophan-processing (tryptophan-degrading) enzyme-encoding nucleic acids with a common novelty in that they are derived from environmental sources, e.g., mixed environmental sources.

In one aspect, the sequence comparison algorithm is a BLAST version 2.2.2 algorithm where a filtering setting is set to blastall -p blastp -d "nr pataa" -F F, and all other options are set to default. The nucleic acids of the invention also comprise isolated or recombinant nucleic acids comprising at least 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650, 1700, 1750, 1800, 1850, 1900, 1950, 2000, 2050, 2100, 2200, 2250, 2300, 2350, 2400, 2450, 2500, or more consecutive bases of a nucleic acid sequence of the invention, sequences substantially identical thereto, and the sequences complementary thereto.

In one aspect, the isolated or recombinant nucleic acid encodes a polypeptide having a tryptophan-processing activity that is thermostable. The polypeptide can retain a tryptophan-processing activity under conditions comprising a temperature range of between about 37⁰C to about 95⁰C; between about 55°C to about 85°C, between about 7O⁰C to about 95°C, or, between about 9O⁰C to about 95⁰C, 96°C, 97⁰C, 98°C or 99⁰C.

In another aspect, the isolated or recombinant nucleic acid encodes a polypeptide having a tryptophan-processing activity that is thermotolerant. The polypeptide can retain a tryptophan-processing activity after exposure to a temperature in the range from greater than 37°C to about 95⁰C, 96⁰C, 97°C, 98°C or 99°C or anywhere in the range from greater than 55⁰C to about 85°C. The polypeptide can retain a tryptophan- processing activity after exposure to a temperature in the range between about I⁰C to about 5⁰C, between about 5°C to about 15°C, between about 15⁰C to about 25⁰C, between about 25⁰C to about 37⁰C, between about 37⁰C to about 95°C, 96°C, 97°C, 98⁰C or 99⁰C, between about 55°C to about 85°C, between about 70⁰C to about 75⁰C, or between about 90⁰C to about 95⁰C, or more. In one aspect, the polypeptide retains a tryptophan- processing activity after exposure to a temperature in the range from greater than 9O⁰C to about 95⁰C, 96⁰C, 97°C, 98°C or 99⁰C at about pH 4.5.

The invention provides isolated or recombinant nucleic acids comprising a sequence that hybridizes under stringent conditions to a nucleic acid comprising a sequence of the invention, e.g., an exemplary nucleic acid sequence of the invention (e.g., SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, etc.) or fragments or subsequences thereof. In one aspect, the nucleic acid encodes a polypeptide having a tryptophan-processing activity. The nucleic acid can be at least about 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200 or more residues in length or the full length of the gene or transcript. In one aspect, the stringent conditions include a wash step comprising a wash in 0.2X SSC at a temperature of about 65⁰C for about 15 minutes.

The invention provides a nucleic acid probe for identifying a nucleic acid encoding a polypeptide having a tryptophan-processing activity, wherein the probe comprises at least about 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90,

95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000 or more, consecutive bases of a sequence comprising a sequence of the invention, or fragments or subsequences thereof, wherein the probe identifies the nucleic acid by binding or hybridization. The probe can comprise an oligonucleotide comprising at least about 10 to 50, about 20 to 60, about 30 to 70, about 40 to 80, or about 60 to 100 consecutive bases of a sequence comprising a sequence of the invention, or fragments or subsequences thereof.

The invention provides a nucleic acid probe for identifying a nucleic acid encoding a polypeptide having a tryptophan-processing activity, wherein the probe comprises a nucleic acid comprising a sequence at least about 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000 or more residues having at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more, or complete (100%) sequence identity to an exemplary nucleic acid of the invention. In one aspect, the sequence identities are determined by analysis with a sequence comparison algorithm or by visual inspection. In alternative aspects, the probe can comprise an oligonucleotide comprising at least about 10 to 50, about 20 to 60, about 30 to 70, about 40 to 80, or about 60 to 100 consecutive bases of a nucleic acid sequence of the invention, or a subsequence thereof.

The invention provides an amplification primer pair for amplifying a nucleic acid encoding a polypeptide having a tryptophan-processing activity, wherein the primer pair is capable of amplifying a nucleic acid comprising a sequence of the invention, or fragments or subsequences thereof. One or each member of the amplification primer sequence pair can comprise an oligonucleotide comprising at least about 10 to 50, or more, consecutive bases of the sequence, or about 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,- 24, 25, 26, 27, 28, 29, 30 or more consecutive bases of the sequence.

The invention provides amplification primer pairs, wherein the primer pair comprises a first member having a sequence as set forth by about the first (the 5') 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36 or more residues of a nucleic acid of the invention, and a second member having a sequence as set forth by about the first (the 5') 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36 or more residues of the complementary strand of the first member.

The invention provides tryptophan-degrading enzyme-encoding nucleic acids generated by amplification, e.g., polymerase chain reaction (PCR), using an amplification primer pair of the invention. The invention provides tryptophan-processing enzyme-encoding nucleic acids generated by amplification, e.g., polymerase chain reaction (PCR), using an amplification primer pair of the invention. The invention provides methods of making a tryptophan-processing enzyme by amplification, e.g., polymerase chain reaction (PCR), using an amplification primer pair of the invention. In one aspect, the amplification primer pair amplifies a nucleic acid from a library, e.g., a gene library, such as an environmental library.

The invention provides methods of amplifying a nucleic acid encoding a polypeptide having a tryptophan-processing enzyme activity, comprising amplification of a template nucleic acid with an amplification primer sequence pair capable of amplifying a nucleic acid sequence of the invention, or fragments or subsequences thereof.

The invention provides expression cassettes comprising a nucleic acid of the invention or a subsequence thereof. In one aspect, the expression cassette can comprise the nucleic acid that is operably linked to a promoter. The promoter can be a viral, bacterial, mammalian or plant promoter. In one aspect, the plant promoter can be a potato, rice, corn, wheat, tobacco or barley promoter. The promoter can be a constitutive promoter. The constitutive promoter can comprise CaMV35S. In another aspect, the promoter can be an inducible promoter. In one aspect, the promoter can be a tissue- specific promoter or an environmentally regulated or a developmentally regulated promoter. Thus, the promoter can be, e.g., a seed-specific, a leaf-specific, a root-specific, a stem-specific or an abscission-induced promoter. In one aspect, the expression cassette can further comprise a plant or plant virus expression vector.

The invention provides cloning vehicles comprising an expression cassette (e.g., a vector) of the invention or a nucleic acid of the invention. The cloning vehicle can be a viral vector, a plasmid, a phage, a phagemid, a cosmid, a fosmid, a bacteriophage or an artificial chromosome. The viral vector can comprise an adenovirus vector, a retroviral vector or an adeno-associated viral vector. The cloning vehicle can comprise a bacterial artificial chromosome (BAC), a plasmid, a bacteriophage Pl -derived vector (PAC), a yeast artificial chromosome (YAC), or a mammalian artificial chromosome

(MAC). The invention provides transformed cell comprising a nucleic acid of the invention or an expression cassette (e.g., a vector) of the invention, or a cloning vehicle of the invention. In one aspect, the transformed cell can be a bacterial cell, a mammalian cell, a fungal cell, a yeast cell, an insect cell or a plant cell. In one aspect, the plant cell can be a cereal, a potato, wheat, rice, corn, tobacco or barley cell.

The invention provides transgenic non-human animals comprising a nucleic acid of the invention or an expression cassette (e.g., a vector) of the invention. In one aspect, the animal is a mouse, a rat, a pig, a goat or a sheep.

The invention provides transgenic plants comprising a nucleic acid of the invention or an expression cassette (e.g., a vector) of the invention. The transgenic plant can be a cereal plant, a corn plant, a potato plant, a tomato plant, a wheat plant, an oilseed plant, a rapeseed plant, a soybean plant, a rice plant, a barley plant or a tobacco plant.

The invention provides transgenic seeds comprising a nucleic acid of the invention or an expression cassette (e.g., a vector) of the invention. The transgenic seed can be a cereal plant, a corn seed, a wheat kernel, an oilseed, a rapeseed, a soybean seed, a palm kernel, a sunflower seed, a sesame seed, a peanut or a tobacco plant seed.

The invention provides an antisense oligonucleotide comprising a nucleic acid sequence complementary to or capable of hybridizing under stringent conditions to a nucleic acid of the invention. The invention provides methods of inhibiting the translation of a tryptophan-processing enzyme message in a cell comprising administering to the cell or expressing in the cell an antisense oligonucleotide comprising a nucleic acid sequence complementary to or capable of hybridizing under stringent conditions to a nucleic acid of the invention. In one aspect, the antisense oligonucleotide is between about 10 to 50, about 20 to 60, about 30 to 70, about 40 to 80, or about 60 to 100 bases in length, e.g., 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 or more bases in length.

The invention provides methods of inhibiting the translation of a tryptophan-processing enzyme message in a cell comprising administering to the cell or expressing in the cell an antisense oligonucleotide comprising a nucleic acid sequence complementary to or capable of hybridizing under stringent conditions to a nucleic acid of the invention. The invention provides double-stranded inhibitory RNA (RNAi) molecules comprising a subsequence of a sequence of the invention. In one aspect, the RNAi is about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,

35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 or more duplex nucleotides in length. The invention provides methods of inhibiting the expression of a tryptophan- processing enzyme in a cell comprising administering to the cell or expressing in the cell a double-stranded inhibitory RNA (iRNA), wherein the RNA comprises a subsequence of a sequence of the invention. The invention provides an isolated, synthetic or recombinant polypeptide comprising an amino acid sequence having at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more, or complete (100%) sequence identity to an exemplary polypeptide or peptide of the invention over a region of at least about 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350 or more residues, or over the full length of the polypeptide. In one aspect, the sequence identities are determined by analysis with a sequence comparison algorithm or by a visual inspection. Exemplary polypeptide or peptide sequences of the invention include SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68 or SEQ ID NO:70, and subsequences thereof and variants thereof. Exemplary polypeptides also include fragments of at least about 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600 or more residues in length, or over the full length of an enzyme.

Polypeptide and peptide sequences of the invention include sequences encoded by a nucleic acid of the invention. Polypeptide and peptide sequences of the invention include subsequences and variants of exemplary polypeptides of the invention and of polypeptides of the invention (e.g., polypeptides having at least about 50% or more sequence identity to an exemplary polypeptide sequence of the invention). For example, exemplary polypeptides and peptides also include fragments of polypeptides of the invention of at least about 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600 or more residues in length, or over the full length of an enzyme of the invention. Exemplary polypeptide or peptide sequences of the invention include polypeptides or peptides specifically bound by an antibody of the invention. Exemplary polypeptide or peptide sequences of the invention include epitopes or immunogens capable of generating an antibody of the invention. Another aspect of the invention is an isolated, synthetic or recombinant peptide including at least 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, 80, 85, 90, 95, 100, 150 or more consecutive bases of a polypeptide or peptide sequence of the invention, sequences substantially identical thereto, and the sequences complementary thereto.

In one aspect, a polypeptide of the invention has at least one tryptophan- processing enzyme activity. In alternative aspects the tryptophan-processing (tryptophan- degrading) polypeptides of the invention have tryptophanase, tryptophan decarboxylase, tryptophan dioxygenase, tryptophan transaminase activity, tryptophan side chain oxidase and/or tyrosine phenol lyase activity.

In one aspect, the tryptophan-processing enzyme activity is thermostable. The polypeptide can retain a tryptophan-processing enzyme activity under conditions comprising a temperature range of between about 1°C to about 5⁰C, between about 5°C to about 15°C, between about 15⁰C to about 25⁰C, between about 25°C to about 37°C, between about 37⁰C to about 95⁰C, between about 55°C to about 85⁰C, between about 7O⁰C to about 75°C, or between about 9O⁰C to about 95⁰C, or more. In another aspect, the tryptophan-processing enzyme activity can be thermotolerant. The polypeptide can retain a tryptophan-processing enzyme activity after exposure to a temperature in the range from greater than 37⁰C to about 95°C, or in the range from greater than 55°C to about 85°C. In one aspect, the polypeptide can retain a tryptophan-processing enzyme activity after exposure to a temperature in the range from greater than 9O⁰C to about 95⁰C at pH 4.5. Another aspect of the invention provides an isolated or recombinant polypeptide or peptide including at least 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or 100 or more consecutive bases of a polypeptide or peptide sequence of the invention, sequences substantially identical thereto, and the sequences complementary thereto. The peptide can be, e.g., an immunogenic fragment, a motif (e.g., a binding site), a signal sequence, a prepro sequence or an active site.

The invention provides isolated or recombinant nucleic acids comprising a sequence encoding a polypeptide having a tryptophan-processing enzyme activity and a signal sequence, wherein the nucleic acid comprises a sequence of the invention. The signal sequence can be derived from another tryptophan-processing enzyme or a non- tryptophan-processing enzyme (a heterologous) enzyme. The invention provides isolated or recombinant nucleic acids comprising a sequence encoding a polypeptide having a tryptophan-processing enzyme activity, wherein the sequence does not contain a signal sequence and the nucleic acid comprises a sequence of the invention. In one aspect, the invention provides an isolated or recombinant polypeptide comprising a polypeptide of the invention lacking all or part of a signal sequence. In one aspect, the isolated or recombinant polypeptide can comprise the polypeptide of the invention comprising a heterologous signal sequence, such as a heterologous tryptophan-processing enzyme signal sequence or non-tryptophan-processing enzyme signal sequence. In one aspect, the invention provides chimeric proteins comprising a first domain comprising a signal sequence of the invention and at least a second domain. The protein can be a fusion protein. The second domain can comprise an enzyme. The enzyme can be a tryptophan-processing enzyme.

The invention provides chimeric polypeptides comprising at least a first domain comprising signal peptide (SP), a prepro sequence and/or a catalytic domain (CD) of the invention and at least a second domain comprising a heterologous polypeptide or peptide, wherein the heterologous polypeptide or peptide is not naturally associated with the signal peptide (SP), prepro sequence and/ or catalytic domain (CD). In one aspect, the heterologous polypeptide or peptide is not a tryptophan-processing enzyme. The heterologous polypeptide or peptide can be amino terminal to, carboxy terminal to or on both ends of the signal peptide (SP), prepro sequence and/or catalytic domain (CD).

The invention provides isolated or recombinant nucleic acids encoding a chimeric polypeptide, wherein the chimeric polypeptide comprises at least a first domain comprising signal peptide (SP), a prepro domain and/or a catalytic domain (CD) of the invention and at least a second domain comprising a heterologous polypeptide or peptide, wherein the heterologous polypeptide or peptide is not naturally associated with the signal peptide (SP), prepro domain and/ or catalytic domain (CD).

The invention provides isolated or recombinant signal sequences (e.g., signal peptides) consisting of or comprising a sequence as set forth in residues 1 to 14, 1 to 15, 1 to 16, 1 to 17, 1 to 18, 1 to 19, 1 to 20, 1 to 21, 1 to 22, 1 to 23, 1 to 24, 1 to 25, 1 to 26, 1 to 27, 1 to 28, 1 to 28, 1 to 30, 1 to 31, 1 to 32, 1 to 33, 1 to 34, 1 to 35, 1 to 36, 1 to 37, 1 to 38, 1 to 40, 1 to 41, 1 to 42, 1 to 43, 1 to 44, 1 to 45, 1 to 46 or 1 to 47, of a polypeptide of the invention, e.g., SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID

NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO.44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68 or SEQ ID NO:70. In one aspect, the invention provides signal sequences comprising the first 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 61, 68, 69, 70 or more amino terminal residues of a polypeptide of the invention.

In one aspect, the tryptophan-processing enzyme activity comprises a specific activity at about 37⁰C in the range from about 1 to about 1200 units per milligram of protein, or, about 100 to about 1000 units per milligram of protein. In another aspect, the tryptophan-processing enzyme activity comprises a specific activity from about 100 to about 1000 units per milligram of protein, or, from about 500 to about 750 units per milligram of protein. Alternatively, the tryptophan-processing enzyme activity comprises a specific activity at 37⁰C in the range from about 1 to about 750 units per milligram of protein, or, from about 500 to about 1200 units per milligram of protein. In one aspect, the tryptophan-processing enzyme activity comprises a specific activity at 37°C in the range from about 1 to about 500 units per milligram of protein, or, from about 750 to about 1000 units per milligram of protein. In another aspect, the tryptophan-processing enzyme activity comprises a specific activity at 37°C in the range from about 1 to about 250 units per milligram of protein. Alternatively, the tryptophan-processing enzyme activity comprises a specific activity at 37°C in the range from about 1 to about 100 units per milligram of protein.

In another aspect, the thermotolerance comprises retention of at least half of the specific activity of the tryptophan-processing enzyme at 37⁰C after being heated to the elevated temperature. Alternatively, the thermotolerance can comprise retention of specific activity at 37°C in the range from about 1 to about 1200 units per milligram of protein, or, from about 500 to about 1000 units per milligram of protein, after being heated to the elevated temperature. In another aspect, the thermotolerance can comprise retention of specific activity at 37⁰C in the range from about 1 to about 500 units per milligram of protein after being heated to the elevated temperature. The invention provides the isolated or recombinant polypeptide of the invention, wherein the polypeptide comprises at least one glycosylation site. In one aspect, glycosylation can be an N-linked glycosylation. In one aspect, the polypeptide can be glycosylated after being expressed in a P. pastoris or a S. pombe. 5 In one aspect, the polypeptide can retain tryptophan-processing enzyme activity under conditions comprising about pH 6.5, pH 6, pH 5.5, pH 5, pH 4.5 or pH 4. In another aspect, the polypeptide can retain a tryptophan-processing enzyme activity under conditions comprising about pH 7, pH 7.5 pH 8.0, pH 8.5, pH 9, pH 9.5, pH 10, pH 10.5 or pH 11. In one aspect, the polypeptide can retain a tryptophan-processing enzyme o activity after exposure to conditions comprising about pH 6.5, pH 6, pH 5.5, pH 5, pH 4.5 or pH 4. In another aspect, the polypeptide can retain a tryptophan-processing enzyme activity after exposure to conditions comprising about pH 7, pH 7.5 pH 8.0, pH 8.5, pH 9, pH 9.5, pH 10, pH 10.5 or pH 11.

In one aspect, the tryptophan-processing enzyme of the invention has 5 activity at under alkaline conditions, e.g., the alkaline conditions of the gut, e.g., the small intestine. In one aspect, the polypeptide can retains activity after exposure to the acidic pH of the stomach.

The invention provides protein preparations comprising a polypeptide of the invention, wherein the protein preparation comprises a liquid, a solid or a gel. 0 The invention provides heterodimers comprising a polypeptide of the invention and a second protein or domain. The second member of the heterodimer can be a different tryptophan-processing enzyme, a different enzyme or another protein. In one aspect, the second domain can be a polypeptide and the heterodimer can be a fusion protein. In one aspect, the second domain can be an epitope or a tag. In one aspect, the 5 invention provides homodimers comprising a polypeptide of the invention.

The invention provides immobilized polypeptides having tryptophan- processing enzyme activity, wherein the polypeptide comprises a polypeptide of the invention, a polypeptide encoded by a nucleic acid of the invention, or a polypeptide comprising a polypeptide of the invention and a second domain. In one aspect, the 0 polypeptide can be immobilized on a cell, a metal, a resin, a polymer, a ceramic, a glass, a microelectrode, a graphitic particle, a bead, a gel, a plate, an array or a capillary tube.

The invention provides arrays comprising an immobilized nucleic acid of the invention. The invention provides arrays comprising an antibody of the invention. The invention provides isolated or recombinant antibodies that specifically bind to a polypeptide of the invention or to a polypeptide encoded by a nucleic acid of the invention. In another aspect, the invention provides antibodies that bind to skatole, and these antibodies can be co-administered with an enzyme of the invention and/or a hydrophobic protein that specifically or generally binds to skatole. These antibodies of the invention can be a monoclonal or a polyclonal antibody. The invention provides hybridomas comprising an antibody of the invention, e.g., an antibody that specifically binds to a polypeptide of the invention or to a polypeptide encoded by a nucleic acid of the invention. The invention provides nucleic acids encoding these antibodies. The invention provides method of isolating or identifying a polypeptide having tryptophan-processing enzyme activity comprising the steps of: (a) providing an antibody of the invention; (b) providing a sample comprising polypeptides; and (c) contacting the sample of step (b) with the antibody of step (a) under conditions wherein the antibody can specifically bind to the polypeptide, thereby isolating or identifying a polypeptide having a tryptophan-processing enzyme activity.

The invention provides methods of making an anti-tryptophan-processing enzyme antibody comprising administering to a non-human animal a nucleic acid of the invention or a polypeptide of the invention or subsequences thereof in an amount sufficient to generate a humoral immune response, thereby making an anti-tryptophan- processing enzyme antibody. The invention provides methods of making an anti- tryptophan-processing enzyme immune comprising administering to a non-human animal a nucleic acid of the invention or a polypeptide of the invention or subsequences thereof in an amount sufficient to generate an immune response.

The invention provides methods of producing a recombinant polypeptide comprising the steps of: (a) providing a nucleic acid of the invention operably linked to a promoter; and (b) expressing the nucleic acid of step (a) under conditions that allow expression of the polypeptide, thereby producing a recombinant polypeptide. In one aspect, the method can further comprise transforming a host cell with the nucleic acid of step (a) followed by expressing the nucleic acid of step (a), thereby producing a recombinant polypeptide in a transformed cell.

The invention provides methods for identifying a polypeptide having tryptophan-processing enzyme activity comprising the following steps: (a) providing a polypeptide of the invention; or a polypeptide encoded by a nucleic acid of the invention;

(b) providing tryptophan-processing enzyme substrate; and (c) contacting the polypeptide or a fragment or variant thereof of step (a) with the substrate of step (b) and detecting a decrease in the amount of substrate or an increase in the amount of a reaction product, wherein a decrease in the amount of the substrate or an increase in the amount of the reaction product detects a polypeptide having a tryptophan-processing enzyme activity. In one aspect, the substrate is. tryptophan or a tryptophan-comprising compound.

The invention provides methods for identifying tryptophan-processing enzyme substrate comprising the following steps: (a) providing a polypeptide of the invention; or a polypeptide encoded by a nucleic acid of the invention; (b) providing a test substrate; and (c) contacting the polypeptide of step (a) with the test substrate of step (b) and detecting a decrease in the amount of substrate or an increase in the amount of reaction product, wherein a decrease in the amount of the substrate or an increase in the amount of a reaction product identifies the test substrate as a tryptophan-processing enzyme substrate.

The invention provides methods of determining whether a test compound specifically binds to a polypeptide comprising the following steps: (a) expressing a nucleic acid or a vector comprising the nucleic acid under conditions permissive for translation of the nucleic acid to a polypeptide, wherein the nucleic acid comprises a nucleic acid of the invention, or, providing a polypeptide of the invention; (b) providing a test compound; (c) contacting the polypeptide with the test compound; and (d) determining whether the test compound of step (b) specifically binds to the polypeptide.

The invention provides methods for identifying a modulator of a tryptophan-processing enzyme activity comprising the following steps: (a) providing a polypeptide of the invention or a polypeptide encoded by a nucleic acid of the invention; (b) providing a test compound; (c) contacting the polypeptide of step (a) with the test compound of step (b) and measuring an activity of the tryptophan-processing enzyme, wherein a change in the tryptophan-processing enzyme activity measured in the presence of the test compound compared to the activity in the absence of the test compound provides a determination that the test compound modulates the tryptophan-processing enzyme activity. In one aspect, the tryptophan-processing enzyme activity can be measured by providing a tryptophan-processing enzyme substrate and detecting a decrease in the amount of the substrate or an increase in the amount of a reaction product, or, an increase in the amount of the substrate or a decrease in the amount of a reaction product. A decrease in the amount of the substrate or an increase in the amount of the reaction product with the test compound as compared to the amount of substrate or reaction product without the test compound identifies the test compound as an activator of tryptophan-processing enzyme activity. An increase in the amount of the substrate or a decrease in the amount of the reaction product with the test compound as compared to the amount of substrate or reaction product without the test compound identifies the test compound as an inhibitor of tryptophan-processing enzyme activity.

The invention provides computer systems comprising a processor and a data storage device wherein said data storage device has stored thereon a polypeptide sequence or a nucleic acid sequence of the invention (e.g., a polypeptide encoded by a nucleic acid of the invention). In one aspect, the computer system can further comprise a sequence comparison algorithm and a data storage device having at least one reference sequence stored thereon. In another aspect, the sequence comparison algorithm comprises a computer program that indicates polymorphisms. In one aspect, the computer system can further comprise an identifier that identifies one or more features in said sequence. The invention provides computer readable media having stored thereon a polypeptide sequence or a nucleic acid sequence of the invention. The invention provides methods for identifying a feature in a sequence comprising the steps of: (a) reading the sequence using a computer program which identifies one or more features in a sequence, wherein the sequence comprises a polypeptide sequence or a nucleic acid sequence of the invention; and (b) identifying one or more features in the sequence with the computer program. The invention provides methods for comparing a first sequence to a second sequence comprising the steps of: (a) reading the first sequence and the second sequence through use of a computer program which compares sequences, wherein the first sequence comprises a polypeptide sequence or a nucleic acid sequence of the invention; and (b) determining differences between the first sequence and the second sequence with the computer program. The step of determining differences between the first sequence and the second sequence can further comprise the step of identifying polymorphisms. In one aspect, the method can further comprise an identifier that identifies one or more features in a sequence. Li another aspect, the method can comprise reading the first sequence using a computer program and identifying one or more features in the sequence. The invention provides methods for isolating or recovering a nucleic acid encoding a polypeptide having a tryptophan-processing enzyme activity from an environmental sample comprising the steps of: (a) providing an amplification primer sequence pair for amplifying a nucleic acid encoding a polypeptide having a tryptophan- processing enzyme activity, wherein the primer pair is capable of amplifying a nucleic acid of the invention; (b) isolating a nucleic acid from the environmental sample or treating the environmental sample such that nucleic acid in the sample is accessible for hybridization to the amplification primer pair; and, (c) combining the nucleic acid of step (b) with the amplification primer pair of step (a) and amplifying nucleic acid from the environmental sample, thereby isolating or recovering a nucleic acid encoding a polypeptide having a tryptophan-processing enzyme activity from an environmental sample. One or each member of the amplification primer sequence pair can comprise an oligonucleotide comprising an amplification primer sequence pair of the invention, e.g., having at least about 10 to 50 consecutive bases of a sequence of the invention. The invention provides methods for isolating or recovering a nucleic acid encoding a polypeptide having a tryptophan-processing enzyme activity from an environmental sample comprising the steps of: (a) providing a polynucleotide probe comprising a nucleic acid of the invention or a subsequence thereof; (b) isolating a nucleic acid from the environmental sample or treating the environmental sample such that nucleic acid in the sample is accessible for hybridization to a polynucleotide probe of step (a); (c) combining the isolated nucleic acid or the treated environmental sample of step (b) with the polynucleotide probe of step (a); and (d) isolating a nucleic acid that specifically hybridizes with the polynucleotide probe of step (a), thereby isolating or recovering a nucleic acid encoding a polypeptide having a tryptophan-processing enzyme activity from an environmental sample. The environmental sample can comprise a water sample, a liquid sample, a soil sample, an air sample or a biological sample. In one aspect, the biological sample can be derived from a bacterial cell, a protozoan cell, an insect cell, a yeast cell, a plant cell, a fungal cell or a mammalian cell.

The invention provides methods of generating a variant of a nucleic acid encoding a polypeptide having a tryptophan-processing enzyme activity comprising the steps of: (a) providing a template nucleic acid comprising a nucleic acid of the invention; and (b) modifying, deleting or adding one or more nucleotides in the template sequence, or a combination thereof, to generate a variant of the template nucleic acid. In one aspect, the method can further comprise expressing the variant nucleic acid to generate a variant tryptophan-processing enzyme polypeptide. The modifications, additions or deletions can be introduced by a method comprising error-prone PCR, shuffling, oligonucleotide- directed mutagenesis, assembly PCR, sexual PCR mutagenesis, in vivo mutagenesis, cassette mutagenesis, recursive ensemble mutagenesis, exponential ensemble mutagenesis, site-specific mutagenesis, gene reassembly, Gene Site Saturation Mutagenesis (GSSM), synthetic ligation reassembly (SLR) or a combination thereof. In another aspect, the modifications, additions or deletions are introduced by a method comprising recombination, recursive sequence recombination, phosphothioate-modifϊed DNA mutagenesis, uracil-containing template mutagenesis, gapped duplex mutagenesis, point mismatch repair mutagenesis, repair-deficient host strain mutagenesis, chemical mutagenesis, radiogenic mutagenesis, deletion mutagenesis, restriction-selection mutagenesis, restriction-purification mutagenesis, artificial gene synthesis, ensemble mutagenesis, chimeric nucleic acid multimer creation and a combination thereof.

The invention provides modified, or "improved" enzymes of the invention having stability or protease resistance in a gastric fluid, e.g., a stomach, small or large intestine, caecum, rumen or colon fluid (natural environment) by removing one, several or all protease cleavage sites in the enzyme of the invention. In one aspect, the invention encompasses modified versions of all enzymes of the invention wherein at least one, several, or all protease cleavage sites have been "engineered" out. For example, the invention provides for enzymes of the invention wherein one, several or all cathepsin B, an aminopeptidase, serine protease, aspartyl protease, pepsin, trypsin and/or chymotrypsin cleavage sites have been "engineered" out. The invention also provides methods for making modified, or an "improved" tryptophanases using, for example, GSSM or any other technology, e.g., as described herein. For example, an exemplary method for making a tryptophanase resistant to protease digestion comprises (a) providing a polypeptide having tryptophanase activity comprising a sequence of the invention; (b) identifying at least one protease cleavage site in the sequence of the polypeptide of (a); and (c) modifying at least one protease cleavage site in the sequence of the polypeptide of (a) such that the protease no longer cleaves the polypeptide at that at least one modified sequence. In one aspect, one, several or all cathepsin B, peptidase (e.g., aminopeptidase), serine protease, aspartyl protease, pepsin, trypsin and/or chymotrypsin cleavage sites have been "engineered" out (which can include a reduction in the ability of a protease to recognize and cleave a tryptophanase enzyme, in addition to complete eliminating the ability of the protease to hydrolyze/ cleave a tryptophanase enzyme).

In one aspect, the method can be iteratively repeated until a tryptophan- processing enzyme having an altered or different activity or an altered or different stability from that of a polypeptide encoded by the template nucleic acid is produced. In one aspect, the variant tryptophan-processing enzyme polypeptide is thermotolerant, and retains some activity after being exposed to an elevated temperature. In another aspect, the variant tryptophan-processing enzyme polypeptide has increased glycosylation as compared to the tryptophan-processing enzyme encoded by a template nucleic acid. Alternatively, the variant tryptophan-processing enzyme polypeptide has a tryptophan- processing enzyme activity under a high temperature, wherein the tryptophan-processing enzyme encoded by the template nucleic acid is not active under the high temperature. In one aspect, the method can be iteratively repeated until a tryptophan-processing enzyme coding sequence having an altered codon usage from that of the template nucleic acid is produced. In another aspect, the method can be iteratively repeated until a tryptophan- processing enzyme gene having higher or lower level of message expression or stability from that of the template nucleic acid is produced.

The invention provides methods for modifying codons in a nucleic acid encoding a polypeptide having a tryptophan-processing enzyme activity to increase its expression in a host cell, the method comprising the following steps: (a) providing a nucleic acid of the invention encoding a polypeptide having a tryptophan-processing enzyme activity; and, (b) identifying a non-preferred or a less preferred codon in the nucleic acid of step (a) and replacing it with a preferred or neutrally used codon encoding the same amino acid as the replaced codon, wherein a preferred codon is a codon over- represented in coding sequences in genes in the host cell and a non-preferred or less preferred codon is a codon under-represented in coding sequences in genes in the host cell, thereby modifying the nucleic acid to increase its expression in a host cell.

The invention provides methods for modifying codons in a nucleic acid encoding a polypeptide having a tryptophan-processing enzyme activity; the method comprising the following steps: (a) providing a nucleic acid of the invention; and, (b) identifying a codon in the nucleic acid of step (a) and replacing it with a different codon encoding the same amino acid as the replaced codon, thereby modifying codons in a nucleic acid encoding a tryptophan-processing enzyme.

The invention provides methods for modifying codons in a nucleic acid encoding a polypeptide having a tryptophan-processing enzyme activity to increase its expression in a host cell, the method comprising the following steps: (a) providing a nucleic acid of the invention encoding a tryptophan-processing enzyme polypeptide; and, (b) identifying a non-preferred or a less preferred codon in the nucleic acid of step (a) and replacing it with a preferred or neutrally used codon encoding the same amino acid as the replaced codon, wherein a preferred codon is a codon over-represented in coding sequences in genes in the host cell and a non-preferred or less preferred codon is a codon under-represented in coding sequences in genes in the host cell, thereby modifying the nucleic acid to increase its expression in a host cell.

The invention provides methods for modifying a codon in a nucleic acid encoding a polypeptide having a tryptophan-processing enzyme activity to decrease its expression in a host cell, the method comprising the following steps: (a) providing a nucleic acid of the invention; and (b) identifying at least one preferred codon in the nucleic acid of step (a) and replacing it with a non-preferred or less preferred codon encoding the same amino acid as the replaced codon, wherein a preferred codon is a codon over-represented in coding sequences in genes in a host cell and a non-preferred or less preferred codon is a codon under-represented in coding sequences in genes in the host cell, thereby modifying the nucleic acid to decrease its expression in a host cell. In one aspect, the host cell can be a bacterial cell, a fungal cell, an insect cell, a yeast cell, a plant cell or a mammalian cell. The invention provides methods for producing a library of nucleic acids encoding a plurality of modified tryptophan-processing enzyme active sites or substrate binding sites, wherein the modified active sites or substrate binding sites are derived from a first nucleic acid comprising a sequence encoding a first active site or a first substrate binding site the method comprising the following steps: (a) providing a first nucleic acid encoding a first active site or first substrate binding site, wherein the first nucleic acid sequence comprises a sequence that hybridizes under stringent conditions to a nucleic acid of the invention, and the nucleic acid encodes a tryptophan-processing enzyme active site or a tryptophan-processing enzyme substrate binding site; (b) providing a set of mutagenic oligonucleotides that encode naturally-occurring amino acid variants at a plurality of targeted codons in the first nucleic acid; and, (c) using the set of mutagenic oligonucleotides to generate a set of active site-encoding or substrate binding site- encoding variant nucleic acids encoding a range of amino acid variations at each amino acid codon that was mutagenized, thereby producing a library of nucleic acids encoding a plurality of modified tryptophan-processing enzyme active sites or substrate binding sites. In one aspect, the method comprises mutagenizing the first nucleic acid of step (a) by a method comprising an optimized directed evolution system, Gene Site Saturation Mutagenesis (GSSM), synthetic ligation reassembly (SLR), error-prone PCR, shuffling, oligonucleotide-directed mutagenesis, assembly PCR, sexual PCR mutagenesis, in vivo mutagenesis, cassette mutagenesis, recursive ensemble mutagenesis, exponential ensemble mutagenesis, site-specific mutagenesis, gene reassembly, and a combination thereof. In another aspect, the method comprises mutagenizing the first nucleic acid of step (a) or variants by a method comprising recombination, recursive sequence recombination, phosphothioate-modified DNA mutagenesis, uracil-containing template mutagenesis, gapped duplex mutagenesis, point mismatch repair mutagenesis, repair- deficient host strain mutagenesis, chemical mutagenesis, radiogenic mutagenesis, deletion mutagenesis, restriction-selection mutagenesis, restriction-purification mutagenesis, artificial gene synthesis, ensemble mutagenesis, chimeric nucleic acid multimer creation and a combination thereof. The invention provides methods for making a small molecule comprising the following steps: (a) providing a plurality of biosynthetic enzymes capable of synthesizing or modifying a small molecule, wherein one of the enzymes comprises a tryptophan-processing enzyme encoded by a nucleic acid of the invention; (b) providing a substrate for at least one of the enzymes of step (a); and (c) reacting the substrate of step (b) with the enzymes under conditions that facilitate a plurality of biocatalytic reactions to generate a small molecule by a series of biocatalytic reactions. The invention provides methods for modifying a small molecule comprising the following steps: (a) providing a tryptophan-processing enzyme, wherein the enzyme comprises a polypeptide of the invention, or, a polypeptide encoded by a nucleic acid of the invention, or a subsequence thereof; (b) providing a small molecule; and (c) reacting the enzyme of step (a) with the small molecule of step (b) under conditions that facilitate an enzymatic reaction catalyzed by the tryptophan-processing enzyme, thereby modifying a small molecule by a tryptophan-processing enzymatic reaction. In one aspect, the method can comprise a plurality of small molecule substrates for the enzyme of step (a), thereby generating a library of modified small molecules produced by at least one enzymatic reaction catalyzed by the tryptophan-processing enzyme. In one aspect, the method can comprise a plurality of additional enzymes under conditions that facilitate a plurality of biocatalytic reactions by the enzymes to form a library of modified small molecules produced by the plurality of enzymatic reactions. In another aspect, the method can further comprise the step of testing the library to determine if a particular modified small molecule that exhibits a desired activity is present within the library. The step of testing the library can further comprise the steps of systematically eliminating all but one of the biocatalytic reactions used to produce a portion of the plurality of the modified small molecules within the library by testing the portion of the modified small molecule for the presence or absence of the particular modified small molecule with a desired activity, and identifying at least one specific biocatalytic reaction that produces the particular modified small molecule of desired activity.

The invention provides methods for determining a functional fragment of a tryptophan-processing enzyme comprising the steps of: (a) providing a tryptophan- processing enzyme, wherein the enzyme comprises a polypeptide of the invention, or a polypeptide encoded by a nucleic acid of the invention, or a subsequence thereof; and (b) deleting a plurality of amino acid residues from the sequence of step (a) and testing the remaining subsequence for a tryptophan-processing enzyme activity, thereby determining a functional fragment of a tryptophan-processing enzyme. In one aspect, the tryptophan- processing enzyme activity is measured by providing a tryptophan-processing enzyme substrate and detecting a decrease in the amount of the substrate or an increase in the amount of a reaction product.

The invention provides methods for whole cell engineering of new or modified phenotypes by using real-time metabolic flux analysis, the method comprising the following steps: (a) making a modified cell by modifying the genetic composition of a cell, wherein the genetic composition is modified by addition to the cell of a nucleic acid of the invention; (b) culturing the modified cell to generate a plurality of modified cells; (c) measuring at least one metabolic parameter of the cell by monitoring the cell culture of step (b) in real time; and, (d) analyzing the data of step (c) to determine if the measured parameter differs from a comparable measurement in an unmodified cell under similar conditions, thereby identifying an engineered phenotype in the cell using real-time metabolic flux analysis. In one aspect, the genetic composition of the cell can be modified by a method comprising deletion of a sequence or modification of a sequence in the cell, or, knocking out the expression of a gene. In one aspect, the method can further comprise selecting a cell comprising a newly engineered phenotype. In another aspect, the method can comprise culturing the selected cell, thereby generating a new cell strain comprising a newly engineered phenotype.

The invention provides methods of increasing thermotolerance or thermostability of a tryptophan-processing enzyme polypeptide, the method comprising glycosylating a tryptophan-processing enzyme polypeptide, wherein the polypeptide comprises at least thirty contiguous amino acids of a polypeptide of the invention; or a polypeptide encoded by a nucleic acid sequence of the invention, thereby increasing the thermotolerance or thermostability of the tryptophan-processing polypeptide. In one aspect, the tryptophan-processing enzyme specific activity can be thermostable or thermotolerant at a temperature in the range from greater than about 37⁰C to about 95°C.

The invention provides methods for overexpressing a recombinant tryptophan-processing polypeptide in a cell comprising expressing a vector comprising a nucleic acid comprising a nucleic acid of the invention or a nucleic acid sequence of the invention, wherein the sequence identities are determined by analysis with a sequence comparison algorithm or by visual inspection, wherein overexpression is effected by use of a high activity promoter, a dicistronic vector or by gene amplification of the vector.

The invention provides methods of making a transgenic plant comprising the following steps: (a) introducing a heterologous nucleic acid sequence into the cell, wherein the heterologous nucleic sequence comprises a nucleic acid sequence of the invention, thereby producing a transformed plant cell; and (b) producing a transgenic plant from the transformed cell. In one aspect, the step (a) can further comprise introducing the heterologous nucleic acid sequence by electroporation or microinjection of plant cell protoplasts. In another aspect, the step (a) can further comprise introducing the heterologous nucleic acid sequence directly to plant tissue by DNA particle bombardment. Alternatively, the step (a) can further comprise introducing the heterologous nucleic acid sequence into the plant cell DNA using an Agrobacterium tumefaciens host. In one aspect, the plant cell can be a potato, corn, rice, wheat, tobacco, or barley cell.

The invention provides methods of expressing a heterologous nucleic acid sequence in a plant cell comprising the following steps: (a) transforming the plant cell with a heterologous nucleic acid sequence operably linked to a promoter, wherein the heterologous nucleic sequence comprises a nucleic acid of the invention; (b) growing the plant under conditions wherein the heterologous nucleic acids sequence is expressed in the plant cell. The invention provides methods of expressing a heterologous nucleic acid sequence in a plant cell comprising the following steps: (a) transforming the plant cell with a heterologous nucleic acid sequence operably linked to a promoter, wherein the heterologous nucleic sequence comprises a sequence of the invention; (b) growing the plant under conditions wherein the heterologous nucleic acids sequence is expressed in the plant cell.

The invention provides feeds or foods comprising a polypeptide of the invention, or a polypeptide encoded by a nucleic acid of the invention. In one aspect, the invention provides a food, feed, a food or feed additive, a liquid, e.g., a beverage (such as a fruit juice, any drink, or a beer), a bread or a dough or a bread product, or a beverage precursor (e.g., a wort), comprising a polypeptide of the invention. The invention provides food or nutritional supplements for an animal comprising a polypeptide of the invention, e.g., a polypeptide encoded by the nucleic acid of the invention. In one aspect, the polypeptide in the food or nutritional supplement can be glycosylated. The invention provides edible enzyme delivery matrices comprising a polypeptide of the invention, e.g., a polypeptide encoded by the nucleic acid of the invention. In one aspect, the delivery matrix comprises a pellet. In one aspect, the polypeptide can be glycosylated. In one aspect, the tryptophan-processing enzyme activity is thermotolerant. In another aspect, the tryptophan-processing enzyme activity is thermostable.

The invention provides a food, a feed or a nutritional supplement comprising a polypeptide of the invention. The invention provides methods for utilizing a tryptophan-processing enzyme as a nutritional supplement in an animal diet, the method comprising: preparing a nutritional supplement containing a tryptophan-processing enzyme comprising at least thirty contiguous amino acids of a polypeptide of the invention; and administering the nutritional supplement to an animal. The animal can be a human, a ruminant or a monogastric animal. The tryptophan-processing enzyme can be prepared by expression of a polynucleotide encoding the tryptophan-processing enzyme in an organism selected from the group consisting of a bacterium, a yeast, a plant, an insect, a fungus and an animal. The organism can be selected from the group consisting of an S. pombe, S. cerevisiae, Pichiapastoris, E. coli, Streptomyces sp., Bacillus sp. and Lactobacillus sp.

The invention provides edible enzyme delivery matrix comprising a thermostable recombinant tryptophan-processing enzyme, e.g., a polypeptide of the invention. The invention provides methods for delivering a tryptophan-processing enzyme supplement to an animal, the method comprising: preparing an edible enzyme delivery matrix in the form of pellets comprising a granulate edible carrier and a thermostable recombinant tryptophan-processing enzyme, wherein the pellets readily disperse the tryptophan-processing enzyme contained therein into aqueous media, and administering the edible enzyme delivery matrix to the animal. The recombinant tryptophan-processing enzyme can comprise a polypeptide of the invention. The tryptophan-processing enzyme can be glycosylated to provide thermostability at pelletizing conditions. The delivery matrix can be formed by pelletizing a mixture comprising a grain germ and a tryptophan-processing enzyme. The pelletizing conditions can include application of steam. The pelletizing conditions can comprise application of a temperature in excess of about 80⁰C for about 5 minutes and the enzyme retains a specific activity of at least 350 to about 900 units per milligram of enzyme. In one aspect, invention provides a pharmaceutical composition comprising a tryptophan-processing enzyme of the invention, or a polypeptide encoded by a nucleic acid of the invention. In one aspect, the pharmaceutical composition acts as a digestive aid.

In certain aspects of this aspect, tryptophan is contacted a polypeptide of the invention having a tryptophan-processing enzyme (e.g., tryptophanase) activity at a pH in the range of between about pH 3.0 to 9.0, 10.0, 11.0 or more. In other aspects, tryptophan is present at a concentration of at least 0.1%, 0.2%, 0.3%, 0.4%, 0.5%, 0.6%, 0.7%, 0.8%, 0.9%, 1.0% (v/v) or more when contacted with the tryptophan-processing enzyme. In other aspects, tryptophan is contacted with the tryptophan-processing enzyme at a temperature of about 55°C, 60⁰C, 65⁰C, 7O⁰C, 75°C, 8O⁰C, 85°C, 9O⁰C, or more.

The invention also provides pharmaceutical or dietary supplement composition, or any composition comprising a formulation of a tryptophanase (for human, animal, animal husbandry, and other related uses) comprising a polypeptide having a tryptophanase activity. The pharmaceutical or dietary supplement composition can be formulated as an edible delivery agent or an orally deliverable formulation, or, can be formulated to comprise a feed, a food, a liquid, an elixir, an aerosol, a spray, a powder, a tablet, a pill, a capsule, a gel, a geltab, a nanosuspension, a nanoparticle, a microgel or a suppository. The pharmaceutical or dietary supplement composition can comprise any polypeptide having a tryptophanase activity, e.g., comprise a polypeptide having a sequence of the invention.

The invention also provides methods for delivering a tryptophan- processing enzyme supplement to an animal, the method comprising: (a) providing a cell that recombinantly generates a polypeptide having a tryptophanase activity, or a formulation of the recombinantly generated polypeptide; and (b) administering the cell or the recombinantly generated polypeptide to the animal. The cell can be a plant cell, a bacterial cell, a yeast cell, an insect cell or an animal cell. The cell can be selected from the group consisting of a Schizosaccharomyces sp., Saccharomyces sp., Pichia sp., Escherichia sp., Streptomyces sp., Bacillus sp. and Lactobacillus sp., and optionally the cell is Saccharomyces pombe, Saccharomyces cerevisiae, Pichia pastoris, Escherichia coli, or Bacillus cereus. The recombinantly generated polypeptide can be a polypeptide of the invention.

The invention also provides methods for decreasing the amount of skatole in the meat or fat of an animal, the method comprising: (a) providing a cell that recombinantly generates a polypeptide having tryptophanase activity, and (b) administering the cell or the recombinantly generated polypeptide to the animal. The administered cell can recombinantly generate a polypeptide of the invention. The administered cell can comprise at least one microorganism, e.g., a Schizosaccharomyces sp., a Saccharomyces sp., a Pichia sp., an Escherichia sp., a Streptomyces sp., a Bacillus sp. or a Lactobacillus sp. In one aspect, the animal is a pig, a swine, a boar or a hog, and the method is effective in controlling boar taint and in one aspect (optionally) improves the efficiency of animal production and the flavor of cooked pork meat derived from the animal.

The invention also provides methods for identifying an inhibitor of skatole production comprising the following steps: (a) providing a polypeptide of the invention; (b) providing a test compound; (c) providing an in vitro or in vivo test system comprising tryptophan as a substrate, wherein the in vitro or in vivo test system can synthesize skatole; and (c) contacting the polypeptide of step (a) and the test compound of step (b) with the in vitro or in vivo test system and measuring the amount of skatole synthesized, wherein a decrease in the amount of skatole synthesized measured in the presence of the test compound compared to the amount of skatole synthesized in the absence of the test compound provides a determination that the test compound is an inhibitor of skatole production. The test compound can comprise a small molecule, a polysaccharide, a protein, a fat, a nucleic acid and the like. The in vitro or in vivo test system can comprise a cell.

The invention provides methods for decreasing the amount of skatole absorbed from the digestive tract of an animal comprising feeding or otherwise administering at least one skatole-binding composition to the animal, wherein optionally the skatole-binding composition comprises at least one hydrophobic composition, e.g., a small molecule, a polysaccharide, a protein, a fat, a nucleic acid and the like. The invention provides methods for decreasing the amount of skatole absorbed from the digestive tract of an animal (e.g., including decreasing about 1%, 2%, 5%, 10%, 20%, 30%, 40%, 50% or more of the skatole that otherwise would have been absorbed in the digestive tract of the animal) comprising feeding or otherwise administering to the animal an effective amount of at least one polypeptide having a tryptophanase activity. The invention provides methods for decreasing the amount of skatole in the digestive tract of an animal (e.g., including decreasing about 1%, 2%, 5%, 10%, 20%, 30%, 40%, 50% or more of the skatole that otherwise would have accumulated in the digestive tract of the animal) comprising feeding or otherwise administering to the animal an effective amount of at least one polypeptide having a tryptophanase activity. The invention provides methods for decreasing the amount of skatole in the fat of an animal (e.g., including decreasing about 1%, 2%, 5%, 10%, 20%, 30%, 40%, 50% or more of the skatole that otherwise would have accumulated in the fat of the animal) comprising feeding or otherwise administering to the animal an effective amount of at least one polypeptide having a tryptophanase activity. In one aspect, the at least one polypeptide having a tryptophanase activity comprises a polypeptide of the invention. In one aspect, the at least one polypeptide having a tryptophanase activity is formulated such that it all or some of its activity (e.g., about 1%, 2%, 5%, 10%, 20%, 30%, 40%, 50% or more activity) in the digestive tract of the animal, wherein optionally the digestive tract of the animal comprises a rumen, caecum or colon of the animal. The at least one polypeptide having a tryptophanase activity can be formulated such that it is substantially more active in a rumen, caecum or colon of the animal than in the foregut (e.g., intestine, stomach, or both) of the animal. The invention provides methods for decreasing the amount of skatole absorbed from the digestive tract of an animal comprising feeding or otherwise administering to the animal an effective amount of at least one polypeptide having a skatole-degrading activity. The invention provides methods for decreasing the amount of skatole absorbed from the digestive tract of an animal comprising feeding or otherwise administering to the animal an effective amount of at least one polypeptide having skatole-binding activity. The at least one polypeptide having skatole-binding activity comprises a skatole binding antibody (anti-skatole antibody, including antibody binding sites, single-stranded antibodies and the like).

The invention provides methods for decreasing the amount of skatole absorbed from the digestive tract of an animal (e.g., decreasing by about 1%, 2%, 5%, 10%, 20%, 30%, 40%, 50% or more) comprising feeding or otherwise administering at least one polypeptide of the invention and at least one anti-skatole antibody to the animal. The invention provides methods for decreasing the amount of skatole in the fat of an animal (e.g., decreasing by about 1%, 2%, 5%, 10%, 20%, 30%, 40%, 50% or more) comprising feeding or otherwise administering at least one skatole-binding hydrophobic polypeptide to the animal. The invention provides methods for decreasing the amount of skatole in the fat of an animal (e.g., decreasing by about 1%, 2%, 5%, 10%, 20%, 30%, 40%, 50% or more) comprising feeding or otherwise administering at least one polypeptide of the invention and at least one skatole-binding hydrophobic polypeptide to the animal. The invention provides methods for decreasing the amount of skatole in the fat of an animal (e.g., decreasing by about 1%, 2%, 5%, 10%, 20%, 30%, 40%, 50% or more) comprising feeding or otherwise administering at least one polypeptide of the invention and at least one anti-skatole antibody to the animal. The invention provides compositions comprising a formulation of a tryptophanase, wherein the formulation causes the tryptophanase to be only active, or substantially more active, in a rumen, caecum or colon of an animal, as compared to its activity in the intestine of the animal, e.g., comprising an encapsulated formulation of at least one tryptophanase. The formulation can comprise a feed, a food, a liquid, an elixir, an aerosol, a spray, a powder, a tablet, a pill, a capsule, a gel, a geltab, a nanosuspension, a nanoparticle, a microgel or a suppository. The composition can comprise at least one polypeptide or nucleic acid of the invention. The composition or formulation can further comprising an enzyme that can modify or degrade a skatole precursor, a probiotic, a probiotic bacteria, an indole-3-carbinol (I3C) or indole-3-acetonytril (DA), anti-skatole antibody or a skatole-binding polypeptide or a combination thereof. In one aspect, the animal is a monogastric animal, and optionally the monogastric animal is a pig, boar, swine or hog.

The invention provides a food or feed comprising (a) at least one polypeptide having a tryptophanase activity; (b) an enzyme that can modify or degrade a skatole precursor, a probiotic, a probiotic bacteria, an indole-3-carbinol (I3C) or an indole-3-acetonytril (I3A), an anti-skatole antibody or a skatole-binding polypeptide; or (c) a combination thereof. The food or feed can be formulated as a liquid, an elixir, an aerosol, a spray, a powder, a tablet, a pill, a capsule, a gel, a geltab, a nanosuspension, a nanoparticle, a microgel or a suppository. In one aspect, at least one polypeptide having a tryptophanase activity comprises at least one polypeptide of the invention.

The details of one or more aspects of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the description and drawings, and from the claims.

All publications, patents, patent applications, GenBank sequences and ATCC deposits, cited herein are hereby expressly incorporated by reference for all purposes.

BRIEF DESCRIPTION OF DRAWINGS

The following drawings are illustrative of aspects of the invention and are not meant to limit the scope of the invention as encompassed by the claims.

Figure 1 is a block diagram of a computer system. Figure 2 is a flow diagram illustrating one aspect of a process for comparing a new nucleotide or protein sequence with a database of sequences in order to determine the homology levels between the new sequence and the sequences in the database.

Figure 3 is a flow diagram illustrating one aspect of a process in a computer for determining whether two sequences are homologous. Figure 4 is a flow diagram illustrating one aspect of an identifier process

300 for detecting the presence of a feature in a sequence.

Figure 5 A is illustration of a reaction used in an exemplary assay of the invention, where 1-Naphthyl isocyanate reacts with FAA, peptide, and ammonia to produce naphthyl derivatives, and Figure 5B demonstrates the specificity of this assay, as described in detail in Example 1, below.

Figures 6 A and 6B illustrate the results of tryptophanase assays using an exemplary tryptophanase of the invention, as described in detail in Example 1, below.

Figure 7 illustrates the results of tryptophanase assays using an exemplary tryptophanase of the invention, as described in detail in Example 1, below. Figure 8 illustrates alternative routes of tryptophan processing used by compositions and methods of the invention.

Figure 9 illustrates data from an activity assay for tryptophanase in cecal fluid, as described in detail in Example 5, below.

Figure 10 illustrates data from a study to understand how diet affects skatole levels where two test diets: alfalfa and wheat/canola, and one control diet, corn/soy, were used, as described in detail in Example 6, below. Figure 11 illustrates data from an in vitro colon conditions simulation assay that analyzed tryptophanase fermentation parameters and indole production at various time points, as described in detail in Example 6, below.

Figure 12 illustrates data from an in vitro colon conditions simulation assay that analyzed tryptophanase fermentation parameters and skatole production at various time points, as described in detail in Example 6, below.

Figure 13 illustrates data from an in vitro colon conditions simulation assay that sums up the residual concentrations of indole and skatole at different time points, as described in detail in Example 6, below. Figure 14 illustrates data from an in vitro colon conditions simulation assay that summarizes pH in the simulation assay at different time points, as described in detail in Example 6, below.

Figure 15 illustrates data from an in vitro colon conditions simulation assay that summarizes gas production in the simulation assay at different time points, as described in detail in Example 6, below.

Figure 16 and Figure 17 illustrate data from an in vitro colon conditions simulation assay that summarizes the amount of indole and skatole produced, respectively, after addition of varying amounts of tryptophan to the assay, as described in detail in Example 6, below. Figure 18 illustrates data from an in vitro colon conditions simulation assay that summarizes the overall yield of indole + skatole from tryptophan as a function of the concentration of tryptophan, as described in detail in Example 6, below.

Figure 19 illustrates data from an in vitro colon conditions simulation assay that summarizes the effect of added tryptophan on final pH, as described in detail in Example 6, below.

Figure 20 illustrates data from an in vitro colon conditions simulation assay that summarizes the effect of added tryptophan on total gas production, as described in detail in Example 6, below.

Figure 21, Figure 22 and Figure 23 illustrate data from an in vitro colon conditions simulation assay that show correlations between the level of added tryptophan and the residual concentration of indole, skatole and the sum of the two after the 68 hour simulation, respectively, as described in detail in Example 6, below.

Figure 24A, Figure 24B and Figure 24C illustrate data from an in vitro colon conditions simulation assay that show the effect on gas production by addition of an exemplary tryptophanase enzyme of the invention added before, during or after the inoculation of microbial flora to the assay, respectively, as described in detail in Example 6, below.

Figure 25A, Figure 25B and Figure 25C illustrate data from an in vitro colon conditions simulation assay that show the effect on indole production by addition of an exemplary tryptophanase enzyme of the invention added before, during or after the inoculation of microbial flora to the assay, respectively, as described in detail in Example 6, below.

Figure 26A, Figure 26B and Figure 26C illustrate data from an in vitro colon conditions simulation assay that show the effect on skatole production by addition of an exemplary tryptophanase enzyme of the invention added before, during or after the inoculation of microbial flora to the assay, respectively, as described in detail in Example 6, below.

Figure 27A, Figure 27B and Figure 27C illustrate data from an in vitro colon conditions simulation assay that show the effect on skatole and indole production by addition of an exemplary tryptophanase enzyme of the invention added before, during or after the inoculation of microbial flora to the assay, respectively, as described in detail in Example 6, below.

Figure 28 illustrates data from an in vitro colon conditions simulation assay that shows the effect of addition of an exemplary tryptophanase enzyme of the invention at different times, in anaerobic buffer with colon extract and inoculum, on levels of indole and skatole yield, as described in detail in Example 6, below.

Figure 29 illustrates data from an in vitro colon conditions simulation assay that shows the effect of addition of an exemplary tryptophanase enzyme of the invention at different times, in anaerobic buffer with colon extract, inoculum and reductant, on levels of indole and skatole yield, as described in detail in Example 6, below.

Figure 30 illustrates data from an in vitro colon conditions simulation assay that shows the effect of addition of pH on tryptophanase activity, as described in detail in Example 6, below.

Figure 31 illustrates data from an in vitro colon conditions simulation assay that shows the effect of addition of tryptophanase on indole and skatole yield, in anaerobic buffer, as described in detail in Example 6, below. Figure 32 illustrates data from an in vitro colon conditions simulation assay that shows the effect of addition of tryptophanase on indole and skatole yield, in anaerobic buffer and reductant, as described in detail in Example 6, below.

Figure 33 illustrates data from an in vitro colon conditions simulation assay that shows the effect of addition of tryptophanase on indole and skatole yield, in anaerobic buffer with colon extract, as described in detail in Example 6, below.

Figure 34 illustrates data from an in vitro colon conditions simulation assay that shows the effect of addition of tryptophanase on indole and skatole yield, in anaerobic buffer with colon extract and reductant, as described in detail in Example 6, below.

Figure 35 illustrates data from an in vitro colon conditions simulation assay that shows the effect of various medium components on redox potential in the assay, as described in detail in Example 6, below.

Figure 36 illustrates data from an in vitro colon conditions simulation assay that shows the effect of pre-existing indole on the activity of different concentrations of an exemplary tryptophanase of the invention, as described in detail in Example 6, below.

Figure 37 illustrates data from an in vitro colon conditions simulation assay that shows the effect of increasing proportions of colon extract on the activity of an exemplary tryptophanase of the invention, as described in detail in Example 6, below.

Figure 38 illustrates data from simulated gastric fluid (SGF) and simulated intestinal fluid (SIF) studies on exemplary tryptophanases of the invention, as described in detail in Example 5, below.

Figure 39A and 39B illustrates an image of an SDS-PAGE gel showing the results of stability studies of exemplary tryptophanases of the invention, as described in detail in Example 5, below.

Figure 40 illustrates the results of stability studies of exemplary tryptophanases after treatment in simulated gastric fluid and simulated intestinal fluid, as described in detail in Example 5, below. Figure 41 illustrates the results of thermotolerance studies of exemplary tryptophanases of the invention, as described in detail in Example 7, below.

Figure 42 is an illustration of Western analysis of exemplary tryptophanases of the invention, as described in detail in Example 7, below. Figure 43 is an illustration of a protocol for detecting tryptophanases in vivo using, e.g., antibodies of the invention as described in detail in Example 1, below. Like reference symbols in the various drawings indicate like elements.

DETAILED DESCRIPTION The invention provides polypeptides with tryptophan-processing

(tryptophan-degrading) activity, polynucleotides encoding them, and methods of making and using these polynucleotides and polypeptides. In alternative aspects the tryptophan- processing (tryptophan-degrading) polypeptides of the invention have tryptophanase, tryptophan decarboxylase, tryptophan dioxygenase, tryptophan transaminase activity, tryptophan side chain oxidase and/or tyrosine phenol lyase activity.

The invention provides compositions (e.g., enzymes, formulations) and methods for processing or degrading tryptophan to reduce or eliminate skatole accumulation in the digestive tract (e.g., rumen, caecum or colon) of an animal, e.g., a farm animal, such as a pig (including all swine, hogs and related animals), and thus, to reduce skatole accumulation in the animal's tissues, particularly fat tissue. In one aspect, the invention provides methods for decreasing the amount of skatole absorbed by an animal (from the gut), or, decreasing the amount of skatole in the fat of an animal, comprising feeding or otherwise administering to the animal an effective amount of at least one polypeptide having a tryptophanase activity, e.g., an enzyme of the invention. Removal of tryptophan in an animal's rumen, caecum or colon (e.g., a pig colon) will lead to a decrease in gut microbial skatole production and reduce accumulation of skatole in the fat (e.g., back fat) of the animal. For example, the value of eliminating or reducing skatole below detectable levels can be estimated as a minimum of 4% improvement in the efficiency of production of male pigs. To benchmark this value, antibiotics, which are currently being banned as growth promotants, would give a 5% improvement in efficiency of pig production.

By providing compositions and method for removing or reducing tryptophan levels in an animal's hindgut, e.g., rumen, caecum or colon (e.g., a pig colon), thereby reducing skatole accumulation in the animal's tissues, particularly fat tissue, the invention also provides methods for producing lean pork meat in an efficient manner. It is a frequent industry practice to castrate pigs to prevent boar taint, an unpleasant characteristic smell and flavor of the meat from some pigs. Castrated pigs are allowed to grow to up to approx 110 kg carcass weight in the knowledge that boar taint is not a problem. However, castration of male pigs causes serious animal welfare concerns and reduces feed conversion and live weight gain due to removal of the source of natural anabolic androgens that stimulate lean growth. The loss of productive efficiency as a result of castration is recognized as being of the order of 15%. This can be evaluated in terms of the extra feed used. In the US cost of additional feed given to pigs to overcome this problem is estimated at $280 million per year. The improved efficiency of boars compared with castrates results in reduced environmental impact of pig production with improved efficiency of nitrogen, phosphorus and energy utilization. Thus production of entire males is viewed as environmental friendly and is the preferred future method of production. Accordingly the compositions and method, by preventing or reducing the severity of boar taint, allow (promote) production of uncastrated pigs, thereby providing an efficient and environmentally friendly method for raising pigs (the term including any swine, hog, boar, barrow or related animal).

Thus, the invention provides methods for decreasing the amount of tryptophan in a composition comprising the following steps: (a) providing a polypeptide having a tryptophan-processing enzyme activity of the invention, or a polypeptide encoded by a nucleic acid of the invention; (b) providing a composition comprising tryptophan; and (c) contacting the polypeptide of step (a) with the composition of step (b) under conditions wherein the tryptophan-processing enzyme hydrolyzes, breaks up or otherwise processes the tryptophan in the composition. The method can comprise use of a composition comprising an animal food or feed, e.g., a pellet, liquid, any formulation, e.g., as described herein, and the like. The invention also provides methods for decreasing the amount of tryptophan in the digestive tract of an animal comprising feeding or otherwise administering at least one polypeptide of the invention to the animal. The invention also provides methods for decreasing the amount of skatole in the digestive tract of an animal comprising feeding or otherwise administering at least one polypeptide of the invention to the animal. The invention also provides methods for decreasing the amount of skatole in the fat of an animal comprising feeding or otherwise administering at least one polypeptide of the invention to the animal. In one aspect, the animal comprises a pig, a goat or a sheep.

Thus, in one aspect, the invention also provides enzymes that are active in an animal's hindgut (rumen, caecum or colon, e.g., a pig colon); and in an alternative aspect the enzymes remain active after exposure to conditions of the foregut (e.g., stomach, intestine). Enzymes of the invention have been selected for their survival in a robust sequential in vitro gastric and intestinal stability assay whereby enzymes are subjected to a gastric (low pH and pepsin) and then an intestinal (pancreatin plus bile salts) simulation before residual activity is measured. These enzymes retained a significant activity after a 4 h treatment in the stability assay. Other enzymes survived a 1.5 h treatment, but had greatly reduced or no activity after the 4 h treatment.

The methods of the invention can also comprise processing (removal) of tryptophan from the diet of the animal, a pig; this will not significantly affect the animal's health. However, it should directly affect the levels of skatole in the animal's hindgut (rumen, caecum or colon), e.g., a rumen, caecum or colon of a monogastric animal such as a pig, and ultimately result in significantly lower levels of tryptophan in the animal' s tissues, e.g., in the animal's fat, such as in the back fat of pigs.

Removal of (or decreasing the levels of) tryptophan from the free amino acids (FAAs) pool in an animal's gut (the result of practicing some aspects of the methods of the invention), particularly the hindgut, will not significantly affect the health of an animal (e.g., a pig), but should directly affect the levels of skatole in the hindgut

(e.g., pig colon) by eliminating or reducing the amount of its precursor (tryptophan); this ultimately results in significantly lower levels of skatole in the fat of the animal, e.g., in the back fat of a pig. Ingested protein derived from animal feed is first digested in the stomach then the small intestine, with most amino acid absorption occurring in the small intestine. Proteins are hydrolyzed to free amino acids (FAA) as well as di- and tri- peptides. Studies have shown that di- and tri- peptides are absorbed more rapidly than FAAs and the majority of dietary tryptophan is derived from di- and tri-peptides. FAAs that are not absorbed move into the hindgut (e.g., colon, large intestine) where microbial populations ferment FAAs to derive energy. This phenomenon leads to the production of skatole from tryptophan, and it is blocked or reduced in various aspects of the invention. Some polypeptides of the invention having tryptophanase activity also have activity against the amino acids serine and cysteine (as do some known tryptophanases); however, because these two amino acids are not essential (essential amino acids are lysine, methionine, tryptophan, isoleucine, histidine, phenylalanine, threonine, leucine and valine), there should not be a problem in their removal.

In one aspect the invention provides compositions, e.g., feeds, and methods for processing (degrading) tryptophan to reduce or eliminate skatole accumulation in an animal, including farm animals. The animal can be any farm animal, e.g., a pig (including all swine, hogs and related animals), a cow, a sheep, a horse. In one aspect the invention provides compositions and methods to reduce skatole accumulation in animal fat. In one aspect the invention provides compositions and methods for controlling boar taint; by decreasing boar taint, the compositions and methods of the invention improve the efficiency of pig production and flavor of cooked pork meat. The invention provides compositions and methods comprising use of probiotic bacteria and/or probiotics (e.g., fructo-oligosaccharides (FOS); galacto- oligosaccharides (GOS)), in the reduction or elimination of skatole precursors (e.g. tryptophan) and in reduction of its accumulation in animal digestive tracts (e.g., pig colon) and fat. In one aspect, the probiotic bacteria and/or probiotics are used in conjunction with polypeptides of the invention, including the tryptophan-processing enzymes of the invention and/or the antibodies of the invention. In one aspect, the probiotic bacteria and/or probiotics are used in conjunction with skatole-binding polypeptides.

The invention provides compositions (e.g., formulations, such as feeds, etc.) and methods comprising use of any compound that can selectively inhibit formation of skatole, e.g., compounds that can selectively inhibit conversion of IAA to skatole, e.g., metabolites formed during skatole degradation, such as indole-3-carbinol (DC) and indole-3-acetonytril (BA). These compounds can selectively inhibit conversion of IAA to skatole (with no effect on IAA formation from tryptophan) and are used in formulations and methods of the invention as inhibitory agents to reduce skatole formation in colon. In one aspect, indole-3-carbinol (I3C) and indole-3-acetonytril (I3A) and related compounds are used in conjunction with polypeptides of the invention, including the tryptophan-processing enzymes of the invention and/or the antibodies of the invention. In one aspect, indole-3-carbinol (I3C) and indole-3-acetonytril (I3A) and related compounds are used in conjunction with probiotic bacteria and/or probiotics. In one aspect, indole-3-carbinol (I3C) and indole-3-acetonytril (I3A) and related compounds are used in conjunction with skatole-binding polypeptides.

In one aspect, a polypeptide of the invention catalyzes the β-elimination of tryptophan, resulting in three products: indole, ammonia and pyruvate. In one aspect, a polypeptide of the invention forms a tetramer, and is enzymatically (catalytically) active as a tetramer. In one aspect, a polypeptide of the invention utilizes the amino acids serine and cysteine as substrates. Since serine and cysteine are not essential amino acids, there should not be a problem for the animal in their removal from the animal's diet. Assays for measuring tryptophanase activity, e.g., for determining if a polypeptide has tryptophanase activity and is within the scope of the invention, are well known in the art; see, e.g., the LDH-coupled tryptophanase assay described by Phillips and Gollnick (1989) J. Biol. Chem. 264(18) 10627-10632; the SOPC assay described by Suelter (1976) FEBS Lett. 66:230-232. An exemplary amino acid analysis assay and tryptophanase selection modified protocol based on nitrilase screen are also described herein.

The pH of reaction conditions utilized by the invention is another variable parameter for which the invention provides. In certain aspects, the pH of the reaction is conducted in the range of about 3.0 to about 9.0. In other aspects, the pH is about 4.5 or the pH is about 7.5 or the pH is about 9. Reaction conditions conducted under alkaline conditions are particularly advantageous, as basic conditions promote the conversion of the hydroperoxide intermediate to nootkatone.

The invention provides for tryptophan-processing polypeptides of the invention in a variety of forms and formulations. In the methods of the invention, tryptophan-processing polypeptides of the invention are used in a variety of forms and formulations. For example, purified tryptophan-processing polypeptides can be utilized to contact digestive matter in animals for the conversion of tryptophan, e.g., to process tryptophan such that it cannot be converted to skatole, or any related compound. Alternatively, the tryptophan-processing polypeptide can be expressed in a microorganism using procedures known in the art. In other aspects, the tryptophan- processing polypeptides of the invention can be immobilized on a solid support prior to use in the methods of the invention. Methods for immobilizing enzymes on solid supports are commonly known in the art, for example J. MoI. Cat. B: Enzymatic 6 (1999) 29-39; Chivata et al. Biocatalysis: Immobilized cells and enzymes, J MoI. Cat. 37 (1986) 1-24: Sharma et al., Immobilized Biomaterials Techniques and Applications, Angew. Chem. Int. Ed. Engl. 21 (1982) 837-54: Laskin (Ed.), Enzymes and Immobilized Cells in Biotechnology.

Definitions The terms "array" or "microarray" or "biochip" or "chip" as used herein is a plurality of target elements, each target element comprising a defined amount of one or more polypeptides (including antibodies) or nucleic acids immobilized onto a defined area of a substrate surface, as discussed in further detail, below. As used herein, the terms "computer," "computer program" and "processor" are used in their broadest general contexts and incorporate all such devices, as described in detail, below. A "coding sequence of or a "sequence encodes" a particular polypeptide or protein, is a nucleic acid sequence which is transcribed and translated into a polypeptide or protein when placed under the control of appropriate regulatory sequences.

The term "expression cassette" as used herein refers to a nucleotide sequence which is capable of affecting expression of a structural gene (i.e., a protein coding sequence, such as a tryptophan-processing enzyme of the invention) in a host compatible with such sequences. Expression cassettes include at least a promoter operably linked with the polypeptide coding sequence; and, optionally, with other sequences, e.g., transcription termination signals. Additional factors necessary or helpful in effecting expression may also be used, e.g., enhancers, alpha-factors. Thus, expression cassettes also include plasmids, expression vectors, recombinant viruses, any form of recombinant "naked DNA" vector, and the like. A "vector" comprises a nucleic acid which can infect, transfect, transiently or permanently transduce a cell. It will be recognized that a vector can be a naked nucleic acid, or a nucleic acid complexed with protein or lipid. The vector optionally comprises viral or bacterial nucleic acids and/or proteins, and/or membranes (e.g., a cell membrane, a viral lipid envelope, etc.). Vectors include, but are not limited to replicons (e.g., RNA replicons, bacteriophages) to which fragments of DNA may be attached and become replicated. Vectors thus include, but are not limited to RNA, autonomous self-replicating circular or linear DNA or RNA (e.g., plasmids, viruses, and the like, see, e.g., U.S. Patent No. 5,217,879), and include both the expression and non-expression plasmids. Where a recombinant microorganism or cell culture is described as hosting an "expression vector" this includes both extra- chromosomal circular and linear DNA and DNA that has been incorporated into the host chromosome(s). Where a vector is being maintained by a host cell, the vector may either be stably replicated by the cells during mitosis as an autonomous structure, or is incorporated within the host's genome. As used herein, the term "promoter" includes all sequences capable of driving transcription of a coding sequence in a cell, e.g., a plant cell. Thus, promoters used in the constructs of the invention include cώ-acting transcriptional control elements and regulatory sequences that are involved in regulating or modulating the timing and/or rate of transcription of a gene. For example, a promoter can be a cώ-acting transcriptional control element, including an enhancer, a promoter, a transcription terminator, an origin of replication, a chromosomal integration sequence, 5' and 3' untranslated regions, or an intronic sequence, which are involved in transcriptional regulation. These cis-acting sequences typically interact with proteins or other biomolecules to carry out (turn on/off, regulate, modulate, etc.) transcription.

"Constitutive" promoters are those that drive expression continuously under most environmental conditions and states of development or cell differentiation. "Inducible" or "regulatable" promoters direct expression of the nucleic acid of the invention under the influence of environmental conditions or developmental conditions. Examples of environmental conditions that may affect transcription by inducible promoters include anaerobic conditions, elevated temperature, drought, or the presence of light.

"Tissue-specific" promoters are transcriptional control elements that are only active in particular cells or tissues or organs, e.g., in plants or animals. Tissue- specific regulation may be achieved by certain intrinsic factors which ensure that genes encoding proteins specific to a given tissue are expressed. Such factors are known to exist in mammals and plants so as to allow for specific tissues to develop.

"Plasmids" can be commercially available, publicly available on an unrestricted basis, or can be constructed from available plasmids in accord with published procedures. Equivalent plasmids to those described herein are known in the art and will be apparent to the ordinarily skilled artisan.

"Amino acid" or "amino acid sequence" as used herein refer to an oligopeptide, peptide, polypeptide, or protein sequence, or to a fragment, portion, or subunit of any of these and to naturally occurring or synthetic molecules.

"Amino acid" or "amino acid sequence" include an oligopeptide, peptide, polypeptide, or protein sequence, or to a fragment, portion, or subunit of any of these, and to naturally occurring or synthetic molecules. The term "polypeptide" as used herein, refers to amino acids joined to each other by peptide bonds or modified peptide bonds, i.e., peptide isosteres and may contain modified amino acids other than the 20 gene- encoded amino acids. The polypeptides may be modified by either natural processes, such as post-translational processing, or by chemical modification techniques which are well known in the art. Modifications can occur anywhere in the polypeptide, including the peptide backbone, the amino acid side-chains and the amino or carboxyl termini. It will be appreciated that the same type of modification may be present in the same or varying degrees at several sites in a given polypeptide. Also a given polypeptide may have many types of modifications. Modifications include acetylation, acylation, ADP- ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of a phosphytidylinositol, cross-linking cyclization, disulfide bond formation, demethylation, formation of covalent cross-links, formation of cysteine, formation of pyroglutamate, formylation, gamma-carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristolyation, oxidation, pegylation, glucan hydrolase processing, phosphorylation, prenylation, racemization, selenoylation, sulfation and transfer-RNA mediated addition of amino acids to protein such as arginylation. (See Creighton, T.E., Proteins - Structure and Molecular Properties 2nd Ed., W.H. Freeman and Company, New York (1993); Posttranslational Covalent Modification of Proteins, B.C. Johnson, Ed., Academic Press, New York, pp. 1-12 (1983)). The peptides and polypeptides of the invention also include all "mimetic" and "peptidomimetic" forms, as described in further detail, below. As used herein, the term "isolated" means that the material is removed from its original environment (e.g., the natural environment if it is naturally occurring). For example, a naturally-occurring polynucleotide or polypeptide present in a living animal is not isolated, but the same polynucleotide or polypeptide, separated from some or all of the coexisting materials in the natural system, is isolated. Such polynucleotides could be part of a vector and/or such polynucleotides or polypeptides could be part of a composition and still be isolated in that such vector or composition is not part of its natural environment. As used herein, the term "purified" does not require absolute purity; rather, it is intended as a relative definition. Individual nucleic acids obtained from a library have been conventionally purified to electrophoretic homogeneity. The sequences obtained from these clones could not be obtained directly either from the library or from total human DNA. The purified nucleic acids of the invention have been purified from the remainder of the genomic DNA in the organism by at least 10⁴-10⁶ fold. However, the term "purified" also includes nucleic acids which have been purified from the remainder of the genomic DNA or from other sequences in a library or other environment by at least one order of magnitude, typically two or three orders and more typically four or five orders of magnitude.

As used herein, the term "recombinant" means that the nucleic acid is adjacent to a "backbone" nucleic acid to which it is not adjacent in its natural environment. Additionally, to be "enriched" the nucleic acids will represent 5% or more of the number of nucleic acid inserts in a population of nucleic acid backbone molecules. Backbone molecules according to the invention include nucleic acids such as expression vectors, self- replicating nucleic acids, viruses, integrating nucleic acids and other vectors or nucleic acids used to maintain or manipulate a nucleic acid insert of interest. Typically, the enriched nucleic acids represent 15% or more of the number of nucleic acid inserts in the population of recombinant backbone molecules. More typically, the enriched nucleic acids represent 50% or more of the number of nucleic acid inserts in the population of recombinant backbone molecules. In a one aspect, the enriched nucleic acids represent 90% or more of the number of nucleic acid inserts in the population of recombinant backbone molecules. "Recombinant" polypeptides or proteins refer to polypeptides or proteins produced by recombinant DNA techniques; i. e. , produced from cells transformed by an exogenous DNA construct encoding the desired polypeptide or protein. "Synthetic" polypeptides or protein are those prepared by chemical synthesis. Solid-phase chemical peptide synthesis methods can also be used to synthesize the polypeptide or fragments of the invention. Such method have been known in the art since the early 1960's (Merrifield, R. B., J. Am. Chem. Soc, 85:2149-2154, 1963) (See also Stewart, J. M. and Young, J. D., SoUd

Phase Peptide Synthesis, 2nd Ed., Pierce Chemical Co., Rockford, III, pp. 11-12)) and have recently been employed in commercially available laboratory peptide design and synthesis kits (Cambridge Research Biochemicals). Such commercially available laboratory kits have generally utilized the teachings of H. M. Geysen et al, Proc. Natl. Acad. ScL, USA, £1:3998 (1984) and provide for synthesizing peptides upon the tips of a multitude of "rods" or "pins" all of which are connected to a single plate.

A promoter sequence is "operably linked to" a coding sequence when RNA polymerase which initiates transcription at the promoter will transcribe the coding sequence into mRNA. The phrase "substantially identical" in the context of two nucleic acids or polypeptides, refers to two or more sequences that have, e.g., at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more nucleotide or amino acid residue (sequence) identity, when compared and aligned for maximum correspondence, as measured using one of the known sequence comparison algorithms or by visual inspection. In alternative aspects, the substantial identity exists over a region of at least about 100 or more residues and most commonly the sequences are substantially identical over at least about 150 to 200 or more residues. In some aspects, the sequences are substantially identical over the entire length of the coding regions.

Additionally a "substantially identical" amino acid sequence is a sequence that differs from a reference sequence by one or more conservative or non-conservative amino acid substitutions, deletions, or insertions. In one aspect, the substitution occurs at a site that is not the active site of the molecule, or, alternatively the substitution occurs at a site that is the active site of the molecule, provided that the polypeptide essentially retains its functional (enzymatic) properties. A conservative amino acid substitution, for example, substitutes one amino acid for another of the same class (e.g., substitution of one hydrophobic amino acid, such as isoleucine, valine, leucine, or methionine, for another, or substitution of one polar amino acid for another, such as substitution of arginine for lysine, glutamic acid for aspartic acid or glutamine for asparagine). One or more amino acids can be deleted, for example, from a tryptophan-processing polypeptide, resulting in modification of the structure of the polypeptide, without significantly altering its biological activity. For example, amino- or carboxyl-terminal amino acids that are not required for tryptophan-processing enzyme biological activity can be removed. Modified polypeptide sequences of the invention can be assayed for tryptophan-processing enzyme biological activity by any number of methods, including contacting the modified polypeptide sequence with a substrate and determining whether the modified polypeptide decreases the amount of specific substrate in the assay or increases the bioproducts of the enzymatic reaction of a functional tryptophan-processing polypeptide with the substrate. "Fragments" as used herein are a portion of a naturally occurring protein which can exist in at least two different conformations. Fragments can have the same or substantially the same amino acid sequence as the naturally occurring protein. Fragments which have different three dimensional structures as the naturally occurring protein are also included. An example of this, is a "pro-form" molecule, such as a low activity proprotein that can be modified by cleavage to produce a mature enzyme with significantly higher activity.

"Hybridization" refers to the process by which a nucleic acid strand joins with a complementary strand through base pairing. Hybridization reactions can be sensitive and selective so that a particular sequence of interest can be identified even in samples in which it is present at low concentrations. Suitably stringent conditions can be defined by, for example, the concentrations of salt or formamide in the prehybridization and hybridization solutions, or by the hybridization temperature and are well known in the art. In particular, stringency can be increased by reducing the concentration of salt, increasing the concentration of formamide, or raising the hybridization temperature. In alternative aspects, nucleic acids of the invention are defined by their ability to hybridize under various stringency conditions (e.g., high, medium, and low), as set forth herein. For example, hybridization under high stringency conditions could occur in about 50% formamide at about 37°C to 42°C. Hybridization could occur under reduced stringency conditions in about 35% to 25% formamide at about 3O⁰C to 35°C. In one aspect, hybridization occurs under high stringency conditions, e.g., at 42°C in 50% formamide, 5X SSPE, 0.3% SDS and 200 n/ml sheared and denatured salmon sperm DNA. Hybridization could occur under these reduced stringency conditions, but in 35% formamide at a reduced temperature of 35°C. The temperature range corresponding to a particular level of stringency can be further narrowed by calculating the purine to pyrimidine ratio of the nucleic acid of interest and adjusting the temperature accordingly. Variations on the above ranges and conditions are well known in the art. The term "variant" refers to polynucleotides or polypeptides of the invention modified at one or more base pairs, codons, iαtrons, exons, or amino acid residues (respectively) yet still retain the biological activity of a tryptophan-processing of the invention. Variants can be produced by any number of means included methods such as, for example, error-prone PCR, shuffling, oligonucleotide-directed mutagenesis, assembly PCR, sexual PCR mutagenesis, in vivo mutagenesis, cassette mutagenesis, recursive ensemble mutagenesis, exponential ensemble mutagenesis, site-specific mutagenesis, gene reassembly, GSSM and any combination thereof.

The term "saturation mutagenesis", Gene Site Saturation Mutagenesis, or "GSSM" includes a method that uses degenerate oligonucleotide primers to introduce point mutations into a polynucleotide, as described in detail, below.

The term "optimized directed evolution system" or "optimized directed evolution" includes a method for reassembling fragments of related nucleic acid sequences, e.g., related genes, and explained in detail, below.

The term "synthetic ligation reassembly" or "SLR" includes a method of ligating oligonucleotide fragments in a non-stochastic fashion, and explained in detail, below. Nucleic Acids

The invention provides nucleic acids (e.g., gpe SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9; nucleic acids encoding polypeptides as set forth in SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68 or SEQ ID NO:70) including expression cassettes such as expression vectors, encoding the polypeptides of the invention. The invention also includes methods for discovering new tryptophan- processing polypeptide sequences using the nucleic acids of the invention. The invention also includes methods for inhibiting the expression of tryptophan-processing enzyme genes, transcripts and polypeptides using the nucleic acids of the invention. Also provided are methods for modifying the nucleic acids of the invention by, e.g., synthetic ligation reassembly, optimized directed evolution system and/or saturation mutagenesis.

The nucleic acids of the invention can be made, isolated and/or manipulated by, e.g., cloning and expression of cDNA libraries, amplification of message or genomic DNA by PCR, and the like. For example, exemplary sequences of the invention were initially derived from environmental sources, for example:

SEQ ID

NO: Source

1, 2 Escherichia coli MG1655

15, 16 Unknown

11, 12 Unknown

39, 40 Unknown

41 , 42 Unknown

7, 8 Unknown

9, 10 Unknown

5, 6 Unknown

3, 4 Unknown

55, 56 Unknown

57, 58 Unknown

13, 14 Unknown

19, 20 Unknown

17, 18 Unknown

21 , 22 Unknown

69, 70 Unknown 59, 60 Unknown

31 , 32 Unknown

23, 24 Unknown

33, 34 Unknown

37, 38 Unknown

29, 30 Unknown

25, 26 Unknown

35, 36 Unknown

27, 28 Unknown

65, 66 Unknown

45, 46 Fusobacterium nucleatum ATCC 25586 61 , 62 Fusobacterium nucleatum ATCC 25586

49, 50 Halobacterium sp. ATCC 700922 43, 44 Proteus vulgaris ATCC 9920

51 , 52 Desulfovibrio vulgaris ATCC 29579 47, 48 Aeropyrum pernix ATCC 700893

53, 54 Fusarium verticillioides GZ3639 (ATCC 38932) 67, 68 Unknown 63, 64 Unknown

In one aspect, the invention provides tryptophan-degrading enzyme- encoding nucleic acids, and the polypeptides encoded by them, with a common novelty in that they are derived from a common source, e.g., an environmental or a bacterial source. In practicing the methods of the invention, homologous genes can be modified by manipulating a template nucleic acid, as described herein. The invention can be practiced in conjunction with any method or protocol or device known in the art, which are well described in the scientific and patent literature.

The phrases "nucleic acid" or "nucleic acid sequence" as used herein refer to an oligonucleotide, nucleotide, polynucleotide, or to a fragment of any of these, to DNA or RNA of genomic or synthetic origin which may be single-stranded or double- stranded and may represent a sense or antisense (complementary) strand, to peptide nucleic acid (PNA), or to any DNA-like or RNA-like material, natural or synthetic in origin. The phrases "nucleic acid" or "nucleic acid sequence" includes oligonucleotide, nucleotide, polynucleotide, or to a fragment of any of these, to DNA or RNA (e.g., mRNA, rRNA, tRNA, iRNA) of genomic or synthetic origin which may be single- stranded or double-stranded and may represent a sense or antisense strand, to peptide nucleic acid (PNA), or to any DNA-like or RNA-like material, natural or synthetic in origin, including, e.g., iRNA, ribonucleoproteins (e.g., e.g., double stranded iRNAs, e.g., iRNPs). The term encompasses nucleic acids, i.e., oligonucleotides, containing known analogues of natural nucleotides. The term also encompasses nucleic-acid-like structures with synthetic backbones, see e.g., Mata (1997) Toxicol. Appl. Pharmacol. 144:189-197; Strauss-Soukup (1997) Biochemistry 36:8692-8698; Samstag (1996) Antisense Nucleic Acid Drug Dev 6: 153-156. "Oligonucleotide" includes either a single stranded polydeoxynucleotide or two complementary polydeoxynucleotide strands which may be chemically synthesized. Such synthetic oligonucleotides have no 5' phosphate and thus will not ligate to another oligonucleotide without adding a phosphate with an ATP in the presence of a kinase. A synthetic oligonucleotide can ligate to a fragment that has not been dephosphorylated.

A "coding sequence of or a "nucleotide sequence encoding" a particular polypeptide or protein, is a nucleic acid sequence which is transcribed and translated into a polypeptide or protein when placed under the control of appropriate regulatory sequences.

The term "gene" means the segment of DNA involved in producing a polypeptide chain; it includes regions preceding and following the coding region (leader and trailer) as well as, where applicable, intervening sequences (interns) between individual coding segments (exons). "Operably linked" as used herein refers to a functional relationship between two or more nucleic acid (e.g., DNA) segments.

Typically, it refers to the functional relationship of transcriptional regulatory sequence to a transcribed sequence. For example, a promoter is operably linked to a coding sequence, such as a nucleic acid of the invention, if it stimulates or modulates the transcription of the coding sequence in an appropriate host cell or other expression system. Generally, promoter transcriptional regulatory sequences that are operably linked to a transcribed sequence are physically contiguous to the transcribed sequence, i.e., they are cis-acting. However, some transcriptional regulatory sequences, such as enhancers, need not be physically contiguous or located in close proximity to the coding sequences whose transcription they enhance. One aspect of the invention is an isolated nucleic acid comprising one of the sequences of the invention, or a fragment comprising at least 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, 150, 200, 300, 400, or 500 or more consecutive bases of a nucleic acid of the invention. The isolated, nucleic acids may comprise DNA, including cDNA, genomic

DNA and synthetic DNA. The DNA may be double-stranded or single-stranded and if single stranded may be the coding strand or non-coding (anti-sense) strand. Alternatively, the isolated nucleic acids may comprise RNA.

The isolated nucleic acids of the invention may be used to prepare one of the polypeptides of the invention, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 or more consecutive amino acids of one of the polypeptides of the invention. Accordingly, another aspect of the invention is an isolated nucleic acid which encodes one of the polypeptides of the invention, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 or more consecutive amino acids of one of the polypeptides of the invention. The coding sequences of these nucleic acids may be identical to one of the coding sequences of one of the nucleic acids of the invention or may be different coding sequences which encode one of the of the invention having at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 or more consecutive amino acids of one of the polypeptides of the invention, as a result of the redundancy or degeneracy of the genetic code. The genetic code is well known to those of skill in the art and can be obtained, e.g., on page 214 of B. Lewin, Genes VI, Oxford University Press, 1997.

The isolated nucleic acid which encodes one of the polypeptides of the invention, but is not limited to: only the coding sequence of a nucleic acid of the invention and additional coding sequences, such as leader sequences or proprotein sequences and non-coding sequences, such as introns or non-coding sequences 5' and/or 3' of the coding sequence. Thus, as used herein, the term "polynucleotide encoding a polypeptide" encompasses a polynucleotide which includes only the coding sequence for the polypeptide as well as a polynucleotide which includes additional coding and/or non- coding sequence.

Alternatively, the nucleic acid sequences of the invention, may be mutagenized using conventional techniques, such as site directed mutagenesis, or other techniques familiar to those skilled in the art, to introduce silent changes into the polynucleotides o of the invention. As used herein, "silent changes" include, for example, changes which do not alter the amino acid sequence encoded by the polynucleotide. Such changes may be desirable in order to increase the level of the polypeptide produced by host cells containing a vector encoding the polypeptide by introducing codons or codon pairs which occur frequently in the host organism.

The invention also relates to polynucleotides which have nucleotide changes which result in amino acid substitutions, additions, deletions, fusions and truncations in the polypeptides of the invention. Such nucleotide changes may be introduced using techniques such as site directed mutagenesis, random chemical mutagenesis, exonuclease III deletion and other recombinant DNA techniques. Alternatively, such nucleotide changes may be naturally occurring allelic variants which are isolated by identifying nucleic acids which specifically hybridize to probes comprising at least 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, 150, 200, 300, 400, or 500 consecutive bases of one of the sequences of the invention (or the sequences complementary thereto) under conditions of high, moderate, or low stringency as provided herein.

General Techniques The nucleic acids used to practice this invention, whether RNA, iRNA, antisense nucleic acid, cDNA, genomic DNA, vectors, viruses or hybrids thereof, may be isolated from a variety of sources, genetically engineered, amplified, and/or expressed/ generated recombinantly. Recombinant polypeptides (e.g., tryptophan-processing enzymes) generated from these nucleic acids can be individually isolated or cloned and tested for a desired activity. Any recombinant expression system can be used, including bacterial, mammalian, yeast, insect or plant cell expression systems.

Alternatively, these nucleic acids can be synthesized in vitro by well- known chemical synthesis techniques, as described in, e.g., Adams (1983) J. Am. Chem. Soc. 105:661; Belousov (1997) Nucleic Acids Res. 25:3440-3444; Frenkel (1995) Free Radic. Biol. Med. 19:373-380; Blommers (1994) Biochemistry 33:7886-7896; Narang (1979) Meth. Enzymol. 68:90; Brown (1979) Meth. Enzymol. 68:109; Beaucage (1981) Tetra. Lett. 22:1859; U.S. Patent No. 4,458,066.

Techniques for the manipulation of nucleic acids, such as, e.g., subcloning, labeling probes (e.g., random-primer labeling using Klenow polymerase, nick translation, amplification), sequencing, hybridization and the like are well described in the scientific and patent literature, see, e.g., Sambrook, ed., MOLECULAR CLONING: A LABORATORY MANUAL (2ND ED.), VoIs. 1-3, Cold Spring Harbor Laboratory, (1989); CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, Ausubel, ed. John Wiley & Sons, Inc., New York (1997); LABORATORY TECHNIQUES IN BIOCHEMISTRY AND MOLECULAR BIOLOGY: HYBRIDIZATION WITH

NUCLEIC ACID PROBES, Part I. Theory and Nucleic Acid Preparation, Tijssen, ed. Elsevier, NY. (1993). Another useful means of obtaining and manipulating nucleic acids used to practice the methods of the invention is to clone from genomic samples, and, if desired, screen and re-clone inserts isolated or amplified from, e.g., genomic clones or cDNA clones. Sources of nucleic acid used in the methods of the invention include genomic or cDNA libraries contained in, e.g., mammalian artificial chromosomes (MACs), see, e.g., U.S. Patent Nos. 5,721,118; 6,025,155; human artificial chromosomes, see, e.g., Rosenfeld (1997) Nat. Genet. 15:333-335; yeast artificial chromosomes (YAC); bacterial artificial chromosomes (BAC); Pl artificial chromosomes, see, e.g., Woon (1998) Genomics 50:306-316; Pl-derived vectors (PACs), see, e.g., Kern (1997) Biotechniques 23:120-124; cosmids, recombinant viruses, phages or plasmids.

In one aspect, a nucleic acid encoding a polypeptide of the invention is assembled in appropriate phase with a leader sequence capable of directing secretion of the translated polypeptide or fragment thereof.

The invention provides fusion proteins and nucleic acids encoding them. A polypeptide of the invention can be fused to a heterologous peptide or polypeptide, such as N-terminal identification peptides which impart desired characteristics, such as increased stability or simplified purification. Peptides and polypeptides of the invention can also be synthesized and expressed as fusion proteins with one or more additional domains linked thereto for, e.g., producing a more immunogenic peptide, to more readily isolate a recombinantly synthesized peptide, to identify and isolate antibodies and antibody-expressing B cells, and the like. Detection and purification facilitating domains include, e.g., metal chelating peptides such as polyhistidine tracts and histidine- tryptophan modules that allow purification on immobilized metals, protein A domains that allow purification on immobilized immunoglobulin, and the domain utilized in the FLAGS extension/affinity purification system (Immunex Corp, Seattle WA). The inclusion of a cleavable linker sequences such as Factor Xa or enterokinase (Invitrogen, San Diego CA) between a purification domain and the motif-comprising peptide or polypeptide to facilitate purification. For example, an expression vector can include an epitope-encoding nucleic acid sequence linked to six histidine residues followed by a thioredoxin and an enterokinase cleavage site (see e.g., Williams (1995) Biochemistry 34:1787-1797; Dobeli (1998) Protein Expr. Purif. 12:404-414). The histidine residues facilitate detection and purification while the enterokinase cleavage site provides a means for purifying the epitope from the remainder of the fusion protein. Technology pertaining to vectors encoding fusion proteins and application of fusion proteins are well described in the scientific and patent literature, see e.g., Kroll (1993) DNA Cell. Biol., 12:441-53.

Transcriptional and translational control sequences

The invention provides nucleic acid (e.g., DNA) sequences of the invention operatively linked to expression (e.g., transcriptional or translational) control sequence(s), e.g., promoters or enhancers, to direct or modulate KNA synthesis/ expression. The expression control sequence can be in an expression vector. Exemplary bacterial promoters include lad, lacZ, T3, T7, gpt, lambda PR, PL and tip. Exemplary eukaryotic promoters include CMV immediate early, HSV thymidine kinase, early and late SV40, LTRs from retrovirus, and mouse metallothionein I.

Promoters suitable for expressing a polypeptide in bacteria include the E. coli lac or trp promoters, the lad promoter, the lacZ promoter, the T3 promoter, the T7 promoter, the gpt promoter, the lambda PR promoter, the lambda PL promoter, promoters from operons encoding glycolytic enzymes such as 3-phosphoglycerate kinase (PGK), and the acid phosphatase promoter. Eukaryotic promoters include the CMV immediate early promoter, the HSV thymidine kinase promoter, heat shock promoters, the early and late SV40 promoter, LTRs from retroviruses, and the mouse metallothionein-I promoter. Other promoters known to control expression of genes in prokaryotic or eukaryotic cells or their viruses may also be used. Promoters suitable for expressing the polypeptide or fragment thereof in bacteria include the E. coli lac or trp promoters, the /αc/ promoter, the lacZ promoter, the T3 promoter, the 77 promoter, the gpt promoter, the lambda P_R promoter, the lambda P_L promoter, promoters from operons encoding glycolytic enzymes such as 3-phosphoglycerate kinase (PGK) and the acid phosphatase promoter. Fungal promoters include the α-factor promoter. Eukaryotic promoters include the CMV immediate early promoter, the HSV thymidine kinase promoter, heat shock promoters, the early and late SV40 promoter, LTRs from retroviruses and the mouse metallothionein-I promoter. Other promoters known to control expression of genes in prokaryotic or eukaryotic cells or their viruses may also be used.

Tissue-Specific Plant Promoters The invention provides expression cassettes that can be expressed in a tissue-specific manner, e.g., that can express a tryptophan-processing enzyme of the invention in a tissue-specific manner. The invention also provides plants or seeds that express a tryptophan-processing enzyme of the invention in a tissue-specific manner. The tissue-specificity can be seed specific, stem specific, leaf specific, root specific, fruit specific and the like.

The term "plant" includes whole plants, plant parts (e.g., leaves, stems, flowers, roots, etc.), plant protoplasts, seeds and plant cells and progeny of same. The class of plants which can be used in the method of the invention is generally as broad as the class of higher plants amenable to transformation techniques, including angiosperms (monocotyledonous and dicotyledonous plants), as well as gymnosperms. It includes plants of a variety of ploidy levels, including polyploid, diploid, haploid and hemizygous states. As used herein, the term "transgenic plant" includes plants or plant cells into which a heterologous nucleic acid sequence has been inserted, e.g., the nucleic acids and various recombinant constructs (e.g., expression cassettes) of the invention.

In one aspect, a constitutive promoter such as the CaMV 35S promoter can be used for expression in specific parts of the plant or seed or throughout the plant. For example, for overexpression, a plant promoter fragment can be employed which will direct expression of a nucleic acid in some or all tissues of a plant, e.g., a regenerated plant. Such promoters are referred to herein as "constitutive" promoters and are active under most environmental conditions and states of development or cell differentiation. Examples of constitutive promoters include the cauliflower mosaic virus (CaMV) 35S transcription initiation region, the 1'- or 2'- promoter derived from T-DNA of Agi'obacterium tumefaciens, and other transcription initiation regions from various plant genes known to those of skill. Such genes include, e.g., ACTIl from Arabidopsis (Huang (1996) Plant MoI. Biol. 33:125-139); Cat3 from Arabidopsis (GenBankNo. U43147, Zhong (1996) MoI. Gen. Genet. 251:196-203); the gene encoding stearoyl-acyl carrier protein desaturase from Brassica napus (Genbank No. X74782, Solocombe (1994) Plant Physiol. 104:1167-1176); GPcI from maize (GenBank No. X15596; Martinez (1989) J. MoI. Biol 208:551-565); the Gpc2 from maize (GenBank No. U45855, Manjunath (1997) Plant MoI. Biol. 33:97-112); plant promoters described in U.S. Patent Nos. 4,962,028; 5,633,440.

The invention uses tissue-specific or constitutive promoters derived from viruses which can include, e.g. , the tobamovirus subgenomic promoter (Kumagai (1995) Proc. Natl. Acad. Sci. USA 92:1679-1683; the rice tungro bacilliform virus (RTBV), which replicates only in phloem cells in infected rice plants, with its promoter which drives strong phloem-specific reporter gene expression; the cassava vein mosaic virus (CVMV) promoter, with highest activity in vascular elements, in leaf mesophyll cells, and in root tips (Verdaguer (1996) Plant MoI. Biol. 31:1129-1139).

Alternatively, the plant promoter may direct expression of tryptophan- processing enzyme-expressing nucleic acid in a specific tissue, organ or cell type (i.e. tissue-specific promoters) or may be otherwise under more precise environmental or developmental control or under the control of an inducible promoter. Examples of environmental conditions that may affect transcription include anaerobic conditions, elevated temperature, the presence of light, or sprayed with chemicals/hormones. For example, the invention incorporates the drought-inducible promoter of maize (Busk (1997) supra); the cold, drought, and high salt inducible promoter from potato (Kirch (1997) Plant MoI. Biol. 33:897 909).

Tissue-specific promoters can promote transcription only within a certain time frame of developmental stage within that tissue. See, e.g., Blazquez (1998) Plant Cell 10:791-800, characterizing the Arabidopsis LEAFY gene promoter. See also Cardon (1997) Plant J 123- 61-11, describing the transcription factor SPL3, which recognizes a conserved sequence motif in the promoter region of the A. thaliana floral meristem identity gene API; and Mandel (1995) Plant Molecular Biology, Vol. 29, pp 995-1004, describing the meristem promoter eIF4. Tissue specific promoters which are active throughout the life cycle of a particular tissue can be used. In one aspect, the nucleic acids of the invention are operably linked to a promoter active primarily only in cotton fiber cells. In one aspect, the nucleic acids of the invention are operably linked to a promoter active primarily during the stages of cotton fiber cell elongation, e.g., as described by Rinehart (1996) supra. The nucleic acids can be operably linked to the Fbl2A gene promoter to be preferentially expressed in cotton fiber cells (Ibid) . See also, John (1997) Proc. Natl. Acad. Sci. USA 89:5769-5773; John, et al., U.S. Patent Nos.

5,608,148 and 5,602,321, describing cotton fiber-specific promoters and methods for the construction of transgenic cotton plants. Root-specific promoters may also be used to express the nucleic acids of the invention. Examples of root-specific promoters include the promoter from the alcohol dehydrogenase gene (DeLisle (1990) Int. Rev. Cytol. 123:39-60). Other promoters that can be used to express the nucleic acids of the invention include, e.g., ovule-specific, embryo-specific, endosperm-specific, integument- specific, seed coat-specific promoters, or some combination thereof; a leaf-specific promoter (see, e.g., Busk (1997) Plant J. 11:1285 1295, describing a leaf-specific promoter in maize); the ORF 13 promoter from Agrobacterium rhizogenes (which exhibits high activity in roots, see, e.g., Hansen (1997) supra); a maize pollen specific promoter (see, e.g., Guerrero (1990) MoI. Gen. Genet. 224:161 168); a tomato promoter active during fruit ripening, senescence and abscission of leaves and, to a lesser extent, of flowers can be used (see, e.g., Blume (1997) Plant J. 12:731 746); a pistil-specific promoter from the potato SK2 gene (see, e.g., Ficker (1997) Plant MoI. Biol. 35:425

431); the Blec4 gene from pea, which is active in epidermal tissue of vegetative and floral shoot apices of transgenic alfalfa making it a useful tool to target the expression of foreign genes to the epidermal layer of actively growing shoots or fibers; the ovule- specific BELl gene (see, e.g., Reiser (1995) Cell 83:735-742, GenBankNo. U39944); and/or, the promoter in Klee, U.S. Patent No. 5,589,583, describing a plant promoter region is capable of conferring high levels of transcription in meristematic tissue and/or rapidly dividing cells.

Alternatively, plant promoters which are inducible upon exposure to plant hormones, such as auxins, are used to express the nucleic acids of the invention. For example, the invention can use the auxin-response elements El promoter fragment

(AuxREs) in the soybean (Glycine max L.) (Liu (1997) Plant Physiol. 115:397-407); the auxin-responsive Arabidopsis GST6 promoter (also responsive to salicylic acid and hydrogen peroxide) (Chen (1996) Plant J. 10: 955-966); the auxin-inducible parC promoter from tobacco (Sakai (1996) 37:906-913); a plant biotin response element (Streit (1997) MoI. Plant Microbe Interact. 10:933-937); and, the promoter responsive to the stress hormone abscisic acid (Sheen (1996) Science 274:1900-1902).

The nucleic acids of the invention can also be operably linked to plant promoters which are inducible upon exposure to chemicals reagents which can be applied to the plant, such as herbicides or antibiotics. For example, the maize In2-2 promoter, activated by benzenesulfonamide herbicide safeners, can be used (De Veylder (1997) Plant Cell Physiol. 38:568-577); application of different herbicide safeners induces distinct gene expression patterns, including expression in the root, hydathodes, and the shoot apical meristem. Coding sequence can be under the control of, e.g., a tetracycline-inducible promoter, e.g., as described with transgenic tobacco plants containing the Avena sativa L. (oat) arginine decarboxylase gene (Masgrau (1997) Plant J. 11:465-473); or, a salicylic acid-responsive element (Stange (1997) Plant J. 11:1315-1324). Using chemically- {e.g., hormone- or pesticide-) induced promoters, i.e., promoter responsive to a chemical which can be applied to the transgenic plant hi the field, expression of a polypeptide of the invention can be induced at a particular stage of development of the plant. Thus, the invention also provides for transgenic plants containing an inducible gene encoding for polypeptides of the invention whose host range is limited to target plant species, such as corn, rice, barley, wheat, potato or other crops, inducible at any stage of development of the crop. One of skill will recognize that a tissue-specific plant promoter may drive expression of operably linked sequences in tissues other than the target tissue. Thus, a tissue-specific promoter is one that drives expression preferentially in the target tissue or cell type, but may also lead to some expression in other tissues as well.

The nucleic acids of the invention can also be operably linked to plant promoters which are inducible upon exposure to chemicals reagents. These reagents include, e.g., herbicides, synthetic auxins, or antibiotics which can be applied, e.g., sprayed, onto transgenic plants. Inducible expression of the tryptophan-processing enzyme-producing nucleic acids of the invention will allow the grower to select plants with the optimal tryptophan-processing enzyme expression and/or activity. The development of plant parts can thus controlled. In this way the invention provides the means to facilitate the harvesting of plants and plant parts. For example, in various embodiments, the maize In2-2 promoter, activated by benzenesulfonamide herbicide safeners, is used (De Veylder (1997) Plant Cell Physiol. 38:568-577); application of different herbicide safeners induces distinct gene expression patterns, including expression in the root, hydathodes, and the shoot apical meristem. Coding sequences of the invention are also under the control of a tetracycline-inducible promoter, e.g., as described with transgenic tobacco plants containing the Avena sativa L. (oat) arginine decarboxylase gene (Masgrau (1997) Plant J. 11:465-473); or, a salicylic acid-responsive element (Stange (1997) Plant J. 11:1315-1324). In some aspects, proper polypeptide expression may require polyadenylation region at the 3'-end of the coding region. The polyadenylation region can be derived from the natural gene, from a variety of other plant (or animal or other) genes, or from genes in the Agrobacterial T-DNA.

Expression vectors and cloning vehicles The invention provides expression vectors and cloning vehicles comprising nucleic acids of the invention, e.g., sequences encoding the tryptophan- processing enzymes of the invention. Expression vectors and cloning vehicles of the invention can comprise viral particles, baculovirus, phage, plasmids, phagemids, cosmids, fosmids, bacterial artificial chromosomes, viral DNA (e.g., vaccinia, adenovirus, foul pox virus, pseudorabies and derivatives of SV40), Pl -based artificial chromosomes, yeast plasmids, yeast artificial chromosomes, and any other vectors specific for specific hosts of interest (such as bacillus, Aspergillus and yeast). Vectors of the invention can include chromosomal, non-chromosomal and synthetic DNA sequences. Large numbers of suitable vectors are known to those of skill in the art, and are commercially available. Exemplary vectors are include: bacterial: pQE vectors (Qiagen), pBLUESCRIPT plasmids, pNH vectors, (lambda-ZAP vectors (Stratagene); ptrc99a, pKK223-3, pDR540, pRIT2T (Pharmacia); Eukaryotic: pXTl, pSG5 (Stratagene), pSVK3, pBPV, pMSG, pSVLSV40 (Pharmacia). However, any other plasmid or other vector may be used so long as they are replicable and viable in the host. Low copy number or high copy number vectors may be employed with the present invention.

The expression vector can comprise a promoter, a ribosome binding site for translation initiation and a transcription terminator. The vector may also include appropriate sequences for amplifying expression. Mammalian expression vectors can comprise an origin of replication, any necessary ribosome binding sites, a polyadenylation site, splice donor and acceptor sites, transcriptional termination sequences, and 5' flanking non-transcribed sequences. In some aspects, DNA sequences derived from the SV40 splice and polyadenylation sites may be used to provide the required non-transcribed genetic elements.

In one aspect, the expression vectors contain one or more selectable marker genes to permit selection of host cells containing the vector. Such selectable markers include genes encoding dihydrofolate reductase or genes conferring neomycin resistance for eukaryotic cell culture, genes conferring tetracycline or ampicillin resistance in E. coli, and the S. cerevisiae TRPl gene. Promoter regions can be selected from any desired gene using chloramphenicol transferase (CAT) vectors or other vectors with selectable markers.

Vectors for expressing the polypeptide or fragment thereof in eukaryotic cells can also contain enhancers to increase expression levels. Enhancers are cis-acting elements of DNA that can be from about 10 to about 300 bp in length. They can act on a promoter to increase its transcription. Exemplary enhancers include the SV40 enhancer on the late side of the replication origin bp 100 to 270, the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and the adenovirus enhancers. A nucleic acid sequence can be inserted into a vector by a variety of procedures. In general, the sequence is ligated to the desired position in the vector following digestion of the insert and the vector with appropriate restriction endonucleases. Alternatively, blunt ends in both the insert and the vector may be ligated. A variety of cloning techniques are known in the art, e.g., as described in Ausubel and

Sambrook. Such procedures and others are deemed to be within the scope of those skilled in the art.

The vector can be in the form of a plasmid, a viral particle, or a phage. Other vectors include chromosomal, non-chromosomal and synthetic DNA sequences, derivatives of SV40; bacterial plasmids, phage DNA, baculovirus, yeast plasmids, vectors derived from combinations of plasmids and phage DNA, viral DNA such as vaccinia, adenovirus, fowl pox virus, and pseudorabies. A variety of cloning and expression vectors for use with prokaryotic and eukaryotic hosts are described by, e.g., Sambrook. Particular bacterial vectors which can be used include the commercially available plasmids comprising genetic elements of the well known cloning vector pBR322 (ATCC 37017), pKK223-3 (Pharmacia Fine Chemicals, Uppsala, Sweden), GEMl (Promega Biotec, Madison, WI, USA) pQE70, pQE60, pQE-9 (Qiagen), pDIO, psiX174 pBLUESCRIPT II KS, pNH8A, pNH16a, pNH18A, pNH46A (Stratagene), ptrc99a, pKK223-3, pKK233-3, DR540, pRIT5 (Pharmacia), pKK232-8 andpCM7. Particular eukaryotic vectors include pSV2CAT, pOG44, pXTl , pSG (Stratagene) pSVK3, pBPV, pMSG, and pSVL (Pharmacia). However, any other vector may be used as long as it is replicable and viable in the host cell.

The nucleic acids of the invention can be expressed in expression cassettes, vectors or viruses and transiently or stably expressed in plant cells and seeds. One exemplary transient expression system uses episomal expression systems, e.g., cauliflower mosaic virus (CaMV) viral RNA generated in the nucleus by transcription of an episomal mini-chromosome containing supercoiled DNA, see, e.g., Covey (1990) Proc. Natl. Acad. Sci. USA 87:1633-1637. Alternatively, coding sequences, i.e., all or sub-fragments of sequences of the invention can be inserted into a plant host cell genome becoming an integral part of the host chromosomal DNA. Sense or antisense transcripts can be expressed in this manner. A vector comprising the sequences (e.g., promoters or coding regions) from nucleic acids of the invention can comprise a marker gene that confers a selectable phenotype on a plant cell or a seed. For example, the marker may encode biocide resistance, particularly antibiotic resistance, such as resistance to kanamycin, G418, bleomycin, hygromycin, or herbicide resistance, such as resistance to chlorosulfuron or Basta.

Expression vectors capable of expressing nucleic acids and proteins in plants are well known in the art, and can include, e.g., vectors from Agrobacterium spp., potato virus X (see, e.g., Angell (1997) EMBO J. 16:3675-3684), tobacco mosaic virus (see, e.g., Casper (1996) Gene 173:69-73), tomato bushy stunt virus (see, e.g., Hillman (1989) Virology 169:42-50), tobacco etch virus (see, e.g., Dolja (1997) Virology 234:243-252), bean golden mosaic virus (see, e.g., Morinaga (1993) Microbiol Immunol. 37:471-476), cauliflower mosaic virus (see, e.g., Cecchini (1997) MoI. Plant Microbe Interact. 10:1094-1101), maize Ac/Ds transposable element (see, e.g., Rubin (1997) MoI. Cell. Biol. 17:6294-6302; Kunze (1996) Curr. Top. Microbiol. Immunol. 204:161-194), and the maize suppressor-mutator (Spm) transposable element (see, e.g., Schlappi (1996) Plant MoI. Biol. 32:717-725); and derivatives thereof.

In one aspect, the expression vector can have two replication systems to allow it to be maintained in two organisms, for example in mammalian or insect cells for expression and in a prokaryotic host for cloning and amplification. Furthermore, for integrating expression vectors, the expression vector can contain at least one sequence homologous to the host cell genome. It can contain two homologous sequences which flank the expression construct. The integrating vector can be directed to a specific locus in the host cell by selecting the appropriate homologous sequence for inclusion in the vector. Constructs for integrating vectors are well known in the art.

Expression vectors of the invention may also include a selectable marker gene to allow for the selection of bacterial strains that have been transformed, e.g., genes which render the bacteria resistant to drugs such as ampicillin, chloramphenicol, erythromycin, kanamycin, neomycin and tetracycline. Selectable markers can also include biosynthetic genes, such as those in the histidine, tryptophan and leucine biosynthetic pathways.

The DNA sequence in the expression vector is operatively linked to an appropriate expression control sequence(s) (promoter) to direct RNA synthesis. Particular named bacterial promoters include lad, lacZ, T3, Tl, gpt, lambda P_R, P_L and trp.

Eukaryotic promoters include CMV immediate early, HSV thymidine kinase, early and late SV40, LTRs from retrovirus and mouse metallothionein-I. Selection of the appropriate vector and promoter is well within the level of ordinary skill in the art. The expression vector also contains a ribosome binding site for translation initiation and a transcription terminator. The vector may also include appropriate sequences for amplifying expression. Promoter regions can be selected from any desired gene using chloramphenicol transferase (CAT) vectors or other vectors with selectable markers. In addition, the expression vectors in one aspect contain one or more selectable marker genes to provide a phenotypic trait for selection of transformed host cells such as dihydrofolate reductase or neomycin resistance for eukaryotic cell culture, or such as tetracycline or ampicillin resistance in. E. coli.

Mammalian expression vectors may also comprise an origin of replication, any necessary ribosome binding sites, a polyadenylation site, splice donor and acceptor sites, transcriptional termination sequences and 5' flanking nontranscribed sequences. In some aspects, DNA sequences derived from the SV40 splice and polyadenylation sites may be used to provide the required nontranscribed genetic elements.

Vectors for expressing the polypeptide or fragment thereof in eukaryotic cells may also contain enhancers to increase expression levels. Enhancers are cis-acting elements of DNA, usually from about 10 to about 300 bp in length that act on a promoter to increase its transcription. Examples include the SV40 enhancer on the late side of the replication origin bp 100 to 270, the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin and the adenovirus enhancers. In addition, the expression vectors typically contain one or more selectable marker genes to permit selection of host cells containing the vector. Such selectable markers include genes encoding dihydrofolate reductase or genes conferring neomycin resistance for eukaryotic cell culture, genes conferring tetracycline or ampicillin resistance in E. coli and the S. cerevisiae TRPl gene.

In some aspects, the nucleic acid encoding one of the polypeptides of the invention, or fragments comprising at least about 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof is assembled in appropriate phase with a leader sequence capable of directing secretion of the translated polypeptide or fragment thereof. Optionally, the nucleic acid can encode a fusion polypeptide in which one of the polypeptides of the invention, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof is fused to heterologous peptides or polypeptides, such as N-terminal identification peptides which impart desired characteristics, such as increased stability or simplified purification.

The appropriate DNA sequence may be inserted into the vector by a variety of procedures. In general, the DNA sequence is ligated to the desired position in the vector following digestion of the insert and the vector with appropriate restriction endonucleases. Alternatively, blunt ends in both the insert and the vector may be ligated. A variety of cloning techniques are disclosed in Ausubel et al. Current Protocols in Molecular Biology, John Wiley 503 Sons, Inc. 1997 and Sambrook et al, Molecular Cloning: A Laboratory Manual 2nd Ed., Cold Spring Harbor Laboratory Press (1989. Such procedures and others are deemed to be within the scope of those skilled in the art.

The vector may be, for example, in the form of a plasmid, a viral particle, or a phage. Other vectors include chromosomal, nonchromosomal and synthetic DNA sequences, derivatives of SV40; bacterial plasmids, phage DNA, baculovirus, yeast plasmids, vectors derived from combinations of plasmids and phage DNA, viral DNA such as vaccinia, adenovirus, fowl pox virus and pseudorabies. A variety of cloning and expression vectors for use with prokaryotic and eukaryotic hosts are described by Sambrook, et al, Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor, N. Y., (1989). Host cells and transformed cells

The invention also provides a transformed cell comprising a nucleic acid sequence of the invention, e.g., a sequence encoding a tryptophan-processing enzyme of the invention, or a vector of the invention. The host cell may be any of the host cells familiar to those skilled in the art, including prokaryotic cells, eukaryotic cells, such as bacterial cells, fungal cells, yeast cells, mammalian cells, insect cells, or plant cells.

Exemplary bacterial cells include E. coli, Streptomyces, Bacillus subtilis, Bacillus cereus, Salmonella typhimuήum and various species within the genera Streptomyces and Staphylococcus. Exemplary insect cells include Drosophila S2 and Spodoptera S/9. Exemplary animal cells include CHO, COS or Bowes melanoma or any mouse or human cell line. The selection of an appropriate host is within the abilities of those skilled in the art. Techniques for transforming a wide variety of higher plant species are well known and described in the technical and scientific literature. See, e.g., Weising (1988) Ann. Rev. Genet. 22:421-477; U.S. Patent No. 5,750,870.

The vector can be introduced into the host cells using any of a variety of techniques, including transformation, transfection, transduction, viral infection, gene guns, or Ti-mediated gene transfer. Particular methods include calcium phosphate transfection, DEAE-Dextran mediated transfection, lipofection, or electroporation (Davis, L., Dibner, M., Battey, L, Basic Methods in Molecular Biology, (1986)). In one aspect, the nucleic acids or vectors of the invention are introduced into the cells for screening, thus, the nucleic acids enter the cells in a manner suitable for subsequent expression of the nucleic acid. The method of introduction is largely dictated by the targeted cell type. Exemplary methods include CaPO₄ precipitation, liposome fusion, lipofection (e.g., LIPOFECTIN™), electroporation, viral infection, etc. The candidate nucleic acids may stably integrate into the genome of the host cell (for example, with retroviral introduction) or may exist either transiently or stably in the cytoplasm (i.e. through the use of traditional plasmids, utilizing standard regulatory sequences, selection markers, etc.). As many pharmaceutically important screens require human or model mammalian cell targets, retroviral vectors capable of transfecting such targets can be used.

Where appropriate, the engineered host cells can be cultured in conventional nutrient media modified as appropriate for activating promoters, selecting transformants or amplifying the genes of the invention. Following transformation of a suitable host strain and growth of the host strain to an appropriate cell density, the selected promoter may be induced by appropriate means (e.g., temperature shift or chemical induction) and the cells may be cultured for an additional period to allow them to produce the desired polypeptide or fragment thereof.

Cells can be harvested by centrifugation, disrupted by physical or chemical means, and the resulting crude extract is retained for further purification. Microbial cells employed for expression of proteins can be disrupted by any convenient method, including freeze-thaw cycling, sonication, mechanical disruption, or use of cell lysing agents. Such methods are well known to those skilled in the art. The expressed polypeptide or fragment thereof can be recovered and purified from recombinant cell cultures by methods including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography and lectin chromatography. Protein refolding steps can be used, as necessary, in completing configuration of the polypeptide. If desired, high performance liquid chromatography (HPLC) can be employed for final purification steps.

The constructs in host cells can be used in a conventional manner to produce the gene product encoded by the recombinant sequence. Depending upon the host employed in a recombinant production procedure, the polypeptides produced by host cells containing the vector may be glycosylated or may be non-glycosylated. Polypeptides of the invention may or may not also include an initial methionine amino acid residue.

Cell-free translation systems can also be employed to produce a polypeptide of the invention. Cell-free translation systems can use mRNAs transcribed from a DNA construct comprising a promoter operably linked to a nucleic acid encoding the polypeptide or fragment thereof. In some aspects, the DNA construct may be linearized prior to conducting an in vitro transcription reaction. The transcribed mRNA is then incubated with an appropriate cell-free translation extract, such as a rabbit reticulocyte extract, to produce the desired polypeptide or fragment thereof. The expression vectors can contain one or more selectable marker genes to provide a phenotypic trait for selection of transformed host cells such as dihydrofolate reductase or neomycin resistance for eukaryotic cell culture, or such as tetracycline or ampicillin resistance in E. coli.

Host cells containing the polynucleotides of interest, e.g., nucleic acids of the invention, can be cultured in conventional nutrient media modified as appropriate for activating promoters, selecting transformants or amplifying genes. The culture conditions, such as temperature, pH and the like, are those previously used with the host cell selected for expression and will be apparent to the ordinarily skilled artisan. The clones which are identified as having the specified enzyme activity may then be sequenced to identify the polynucleotide sequence encoding an enzyme having the enhanced activity.

The invention provides a method for overexpressing a recombinant tryptophan-processing enzyme in a cell comprising expressing a vector comprising a nucleic acid of the invention, e.g., a nucleic acid comprising a nucleic acid sequence with at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more sequence identity to an exemplary sequence of the invention over a region of at least about 100 residues, wherein the sequence identities are determined by analysis with a sequence comparison algorithm or by visual inspection, or, a nucleic acid that hybridizes under stringent conditions to a nucleic acid sequence of the invention. The overexpression can be effected by any means, e.g., use of a high activity promoter, a dicistronic vector or by gene amplification of the vector. The nucleic acids of the invention can be expressed, or overexpressed, in any in vitro or in vivo expression system. Any cell culture systems can be employed to express, or over-express, recombinant protein, including bacterial, insect, yeast, fungal or mammalian cultures. Over-expression can be effected by appropriate choice of 5 promoters, enhancers, vectors (e.g., use of replicon vectors, dicistronic vectors (see, e.g., Gurtu (1996) Biochem. Biophys. Res. Commun. 229:295-8), media, culture systems and the like. In one aspect, gene amplification using selection markers, e.g., glutamine synthetase (see, e.g., Sanders (1987) Dev. Biol. Stand. 66:55-63), in cell systems are used to overexpress the polypeptides of the invention. o The host cell may be any of the host cells familiar to those skilled in the art, including prokaryotic cells, eukaryotic cells, mammalian cells, insect cells, or plant cells. As representative examples of appropriate hosts, there may be mentioned: bacterial cells, such as E. coli, Streptomyces, Bacillus subtilis, Bacillus cereus, Salmonella typhimurium and various species within the genera Streptomyces and Staphylococcus, 5 fungal cells, such as yeast, insect cells such as Drosophila S2 and Spodoptera Sf9, animal cells such as CHO, COS or Bowes melanoma and adenoviruses. The selection of an appropriate host is within the abilities of those skilled in the art.

The vector may be introduced into the host cells using any of a variety of techniques, including transformation, transfection, transduction, viral infection, gene guns, 0 . or Ti-mediated gene transfer. Particular methods include calcium phosphate transfection, DEAE-Dextran mediated transfection, lipofection, or electroporation (Davis, L., Dibner, M., Battey, L, Basic Methods in Molecular Biology, (1986)).

Where appropriate, the engineered host cells can be cultured in conventional nutrient media modified as appropriate for activating promoters, selecting 5 transformants or amplifying the genes of the invention. Following transformation of a suitable host strain and growth of the host strain to an appropriate cell density, the selected promoter may be induced by appropriate means {e.g., temperature shift or chemical induction) and the cells may be cultured for an additional period to allow them to produce the desired polypeptide or fragment thereof. 0 Cells are typically harvested by centrifugation, disrupted by physical or chemical means and the resulting crude extract is retained for further purification. Microbial cells employed for expression of proteins can be disrupted by any convenient method, including freeze-thaw cycling, sonication, mecham^'cal disruption, or use of cell lysing agents. Such methods are well known to those skilled in the art. The expressed polypeptide or fragment thereof can be recovered and purified from recombinant cell cultures by methods including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography and lectin chromatography. Protein refolding steps can be used, as necessary, in completing configuration of the polypeptide. If desired, high performance liquid chromatography (HPLC) can be employed for final purification steps.

Various mammalian cell culture systems can also be employed to express recombinant protein. Examples of mammalian expression systems include the COS-7 lines of monkey kidney fibroblasts (described by Gluzman, Cell, 23_:175, 1981) and other cell lines capable of expressing proteins from a compatible vector, such as the C127, 3T3, CHO, HeLa and BHK cell lines.

Alternatively, the polypeptides of the invention, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 or more consecutive amino acids thereof can be synthetically produced by conventional peptide synthesizers. In other aspects, fragments or portions of the polypeptides may be employed for producing the corresponding full-length polypeptide by peptide synthesis; therefore, the fragments may be employed as intermediates for producing the full-length polypeptides.

Cell-free translation systems can also be employed to produce one of the polypeptides of the invention, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35,

40, 50, 75, 100, or 150 or more consecutive amino acids thereof using mRNAs transcribed from a DNA construct comprising a promoter operably linked to a nucleic acid encoding the polypeptide or fragment thereof. In some aspects, the DNA construct may be linearized prior to conducting an in vitro transcription reaction. The transcribed mRNA is then incubated with an appropriate cell-free translation extract, such as a rabbit reticulocyte extract, to produce the desired polypeptide or fragment thereof. Amplification of Nucleic Acids

In practicing the invention, nucleic acids of the invention and nucleic acids encoding the tryptophan-processing enzymes of the invention, or modified nucleic acids of the invention, can be reproduced by amplification. Amplification can also be used to clone or modify the nucleic acids of the invention. Thus, the invention provides amplification primer sequence pairs for amplifying nucleic acids of the invention. One of skill in the art can design amplification primer sequence pairs for any part of or the full length of these sequences.

In one aspect, the invention provides a nucleic acid amplified by a primer pair of the invention, e.g., a primer pair as set forth by about the first (the 5') 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 or more residues of a nucleic acid of the invention, and about the first (the 5') 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 or more residues of the complementary strand.

The invention provides an amplification primer sequence pair for amplifying a nucleic acid encoding a polypeptide having a tryptophan-processing enzyme activity, wherein the primer pair is capable of amplifying a nucleic acid comprising a sequence of the invention, or fragments or subsequences thereof. One or each member of the amplification primer sequence pair can comprise an oligonucleotide comprising at least about 10 to 50 or more consecutive bases of the sequence, or about 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 or more consecutive bases of the sequence. The invention provides amplification primer pairs, wherein the primer pair comprises a first member having a sequence as set forth by about the first (the 5') 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 or more residues of a nucleic acid of the invention, and a second member having a sequence as set forth by about the first (the 5') 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 or more residues of the complementary strand of the first member. The invention provides tryptophan-processing enzymes generated by amplification, e.g., polymerase chain reaction (PCR), using an amplification primer pair of the invention. The invention provides methods of making a tryptophan-processing enzyme by amplification, e.g., polymerase chain reaction (PCR), using an amplification primer pair of the invention. In one aspect, the amplification primer pair amplifies a nucleic acid from a library, e.g., a gene library, such as an environmental library.

Amplification reactions can also be used to quantify the amount of nucleic acid in a sample (such as the amount of message in a cell sample), label the nucleic acid

(e.g., to apply it to an array or a blot), detect the nucleic acid, or quantify the amount of a specific nucleic acid in a sample. In one aspect of the invention, message isolated from a cell or a cDNA library are amplified.

The skilled artisan can select and design suitable oligonucleotide amplification primers. Amplification methods are also well known in the art, and include, e.g., polymerase chain reaction, PCR (see, e.g., PCR PROTOCOLS, A GUIDE TO

METHODS AND APPLICATIONS, ed. Innis, Academic Press, N. Y. (1990) and PCR STRATEGIES (1995), ed. Innis, Academic Press, Inc., N.Y., ligase chain reaction (LCR) (see, e.g., Wu (1989) Genomics 4:560; Landegren (1988) Science 241:1077; Barringer (1990) Gene 89: 117); transcription amplification (see, e.g., Kwoh (1989) Proc. Natl. Acad. Sci. USA 86: 1173); and, self-sustained sequence replication (see, e.g., Guatelli (1990) Proc. Natl. Acad. Sci. USA 87:1874); Q Beta replicase amplification (see, e.g., Smith (1997) J. Clin. Microbiol. 35:1477-1491), automated Q-beta replicase amplification assay (see, e.g., Burg (1996) MoI. Cell. Probes 10:257-271) and other RNA polymerase mediated techniques (e.g., NASBA, Cangene, Mississauga, Ontario); see also Berger (1987) Methods Enzymol. 152:307-316; Sambrook; Ausubel; U.S. Patent Nos. 4,683,195 and 4,683,202; Sooknanan (1995) Biotechnology 13:563-564.

Determining the degree of sequence identity

The invention provides nucleic acids comprising sequences having at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more, or complete (100%) sequence identity (homology) to an exemplary nucleic acid of the invention (e.g., SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9) over a region of at least about 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550 or more, residues. The invention provides polypeptides comprising sequences having at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more, or complete (100%) sequence identity to an exemplary polypeptide of the invention (e.g., SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34₃ SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68 or SEQ ID NO:70). The extent of sequence identity (homology) may be determined using any computer program and associated parameters, including those described herein, such as BLAST 2.2.2. or FASTA version 3.0t78, with the default parameters.

Nucleic acid sequences of the invention can comprise at least 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, 150, 200, 300, 400, or 500 or more consecutive nucleotides of an exemplary sequence of the invention and sequences substantially identical thereto. Homologous sequences and fragments of nucleic acid sequences of the invention can refer to a sequence having at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more sequence identity (homology) to these sequences. Homology (sequence identity) may be determined using any of the computer programs and parameters described herein, including FASTA version 3.0t78 with the default parameters. Homologous sequences also include RNA sequences in which uridines replace the thymines in the nucleic acid sequences of the invention. The homologous sequences may be obtained using any of the procedures described herein or may result from the correction of a sequencing error. It will be appreciated that the nucleic acid sequences of the invention can be represented in the traditional single character format (See the inside back cover of Stryer, Lubert. Biochemistry, 3rd Ed., W. H Freeman & Co., New York.) or in any other format which records the identity of the nucleotides in a sequence.

Various sequence comparison programs identified elsewhere in this patent specification are particularly contemplated for use in this aspect of the invention. Protein and/or nucleic acid sequence homologies may be evaluated using any of the variety of sequence comparison algorithms and programs known in the art. Such algorithms and programs include, but are by no means limited to, TBLASTN, BLASTP, FASTA, TFASTA and CLUSTALW (see, e.g., Pearson and Lipman, Proc. Natl. Acad. Sci. USA 85(8):2444-2448, 1988; Altschul et al, J. MoI. Biol. 215(3):403-410, 1990; Thompson

Nucleic Acids Res. 22(2):4673-4680, 1994; Higgins et al, Methods En∑ymol. 266:383- 402, 1996; Altschul et al, J. MoI. Biol. 215(3):403-410, 1990; Altschul et al, Nature Genetics 3:266-272, 1993).

Homology or identity is often measured using sequence analysis software {e.g., Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology Center, 1710 University Avenue, Madison, WI 53705). Such software matches similar sequences by assigning degrees of homology to various deletions, substitutions and other modifications. The terms "homology" and "identity" in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same when compared and aligned for maximum correspondence over a comparison window or designated region as measured using any number of sequence comparison algorithms or by manual alignment and visual inspection.

For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary and sequence algorithm program parameters are designated. Default program parameters can be used, or alternative parameters can be designated. The sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters.

A "comparison window", as used herein, includes reference to a segment of any one of the number of contiguous positions selected from the group consisting of from 20 to 600, usually about 50 to about 200, more usually about 100 to about 150 in which a sequence maybe compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned. Methods of alignment of sequence for comparison are well-known in the art. Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482, 1981, by the homology alignment algorithm of Needleman & Wunsch, J. MoI. Biol 48:443, 1970, by the search for similarity method of person & Lipman, Proc. Natl. Acad. Sci. USA 85:2444, 1988, by computerized implementations of these algorithms (GAP, BESTFIT, FASTA and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, WI), or by manual alignment and visual inspection. Other algorithms for determining homology or identity include, for example, in addition to a BLAST program (Basic Local Alignment Search Tool at the National Center for Biological Information), ALIGN, AMAS (Analysis of Multiply Aligned Sequences), AMPS (Protein Multiple Sequence Alignment), ASSET (Aligned Segment Statistical Evaluation Tool), BANDS, BESTSCOR, BIOSCAN (Biological Sequence Comparative Analysis Node), BLIMPS (BLocks IMProved Searcher), FASTA, Intervals & Points, BMB, CLUSTAL V, CLUSTAL W, CONSENSUS, LCONSENSUS, WCONSENSUS, Smith-Waterman algorithm, DARWIN, Las Vegas algorithm, FNAT (Forced Nucleotide Alignment Tool), Framealign, Framesearch, DYNAMIC, FILTER, FSAP (Fristensky Sequence Analysis Package), GAP (Global Alignment Program), GENAL, GIBBS, GenQuest, ISSC (Sensitive Sequence Comparison), LALIGN (Local Sequence Alignment), LCP (Local Content Program), MACAW (Multiple Alignment Construction & Analysis Workbench), MAP (Multiple Alignment Program), MBLKP, MBLKN, PIMA (Pattern-Induced Multi-sequence Alignment), SAGA (Sequence Alignment by Genetic Algorithm) and WHAT-IF. Such alignment programs can also be used to screen genome databases to identify polynucleotide sequences having substantially identical sequences. A number of genome databases are available, for example, a substantial portion of the human genome is available as part of the Human Genome Sequencing Project (Gibbs, 1995). At least twenty-one other genomes have already been sequenced, including, for example, M. genitalium (Fraser et al, 1995), M. jannaschii (BuIt et al, 1996), H. influenzae (Fleischmann et al., 1995), E. coli (Blattner et al, 1997) and yeast (S. cerevisiae) (Mewes et al, 1997) and D. melanogaster (Adams et al, 2000). Significant progress has also been made in sequencing the genomes of model organism, such as mouse, C. elegans and Arabadopsis sp. Several databases containing genomic information annotated with some functional information are maintained by different organizations and may be accessible via the internet. One example of a useful algorithm is BLAST and BLAST 2.0 algorithms, which are described in Altschul et al, Nuc. Acids Res. 25:3389-3402, 1977 and Altschul et al, J. MoI. Biol. 215:403-410, 1990, respectively. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information. This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al, supra). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, M=5, N=-4 and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength of 3 and expectations (E) of 10 and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89:10915, 1989) alignments (B) of 50, expectation (E) of 10, M=5, N= -4 and a comparison of both strands. The BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, Proc. Natl. Acad. Sci. USA 90:5873, 1993). One measure of similarity provided by BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a references sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.2, more in one aspect less than about 0.01 and most in one aspect less than about 0.001.

In one aspect, protein and nucleic acid sequence homologies are evaluated using the Basic Local Alignment Search Tool ("BLAST") In particular, five specific BLAST programs are used to perform the following task:

(1) BLASTP and BLAST3 compare an amino acid query sequence against a protein sequence database;

(2) BLASTN compares a nucleotide query sequence against a nucleotide sequence database; (3) BLASTX compares the six-frame conceptual translation products of a query nucleotide sequence (both strands) against a protein sequence database; (4) TBLASTN compares a query protein sequence against a nucleotide sequence database translated in all six reading frames (both strands); and

(5) TBLASTX compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.

The BLAST programs identify homologous sequences by identifying similar segments, which are referred to herein as "high-scoring segment pairs," between a query amino or nucleic acid sequence and a test sequence which is in one aspect obtained from a protein or nucleic acid sequence database. High-scoring segment pairs are in one aspect identified (i.e., aligned) by means of a scoring matrix, many of which are known in the art. In one aspect, the scoring matrix used is the BLOSUM62 matrix (Gonnet (1992) Science 256:1443-1445; Henikoff and Henikoff (1993) Proteins 17:49-61). Less in one aspect, the PAM or PAM250 matrices may also be used (see, e.g., Schwartz and Dayhoff, eds., 1978, Matrices for Detecting Distance Relationships: Atlas of Protein Sequence and Structure, Washington: National Biomedical Research Foundation). BLAST programs are accessible through the U.S. National Library of Medicine.

The parameters used with the above algorithms may be adapted depending on the sequence length and degree of homology studied. In some aspects, the parameters may be the default parameters used by the algorithms in the absence of instructions from the user.

Computer systems and computer program products

To determine and identify sequence identities, structural homologies, motifs and the like in silico, a nucleic acid or polypeptide sequence of the invention can be stored, recorded, and mam^'pulated on any medium which can be read and accessed by a computer.

Accordingly, the invention provides computers, computer systems, computer readable mediums, computer programs products and the like recorded or stored thereon the nucleic acid and polypeptide sequences of the invention. As used herein, the words "recorded" and "stored" refer to a process for storing information on a computer medium. A skilled artisan can readily adopt any known methods for recording information on a computer readable medium to generate manufactures comprising one or more of the nucleic acid and/or polypeptide sequences of the invention. The polypeptides of the invention include the polypeptide sequences of the invention, e.g., the exemplary sequences of the invention, and sequences substantially identical thereto, and fragments of any of the preceding sequences. Substantially identical, or homologous, polypeptide sequences refer to a polypeptide sequence having at least 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more, or complete (100%) sequence identity (homology) to an exemplary sequence of the invention. Homology (sequence identity) may be determined using any of the computer programs and parameters described herein. A nucleic acid or polypeptide sequence of the invention can be stored, recorded and manipulated on any medium which can be read and accessed by a computer. As used herein, the words "recorded" and "stored" refer to a process for storing information on a computer medium. A skilled artisan can readily adopt any of the presently known methods for recording information on a computer readable medium to generate manufactures comprising one or more of the nucleic acid sequences of the invention, one or more of the polypeptide sequences of the invention. Another aspect of the invention is a computer readable medium having recorded thereon at least 2, 5, 10, 15, or 20 or more nucleic acid or polypeptide sequences of the invention. Another aspect of the invention is a computer readable medium having recorded thereon one or more of the nucleic acid sequences of the invention. Another aspect of the invention is a computer readable medium having recorded thereon one or more of the polypeptide sequences of the invention. Another aspect of the invention is a computer readable medium having recorded thereon at least 2, 5, 10, 15, or 20 or more of the nucleic acid or polypeptide sequences as set forth above.

Computer readable media include magnetically readable media, optically readable media, electronically readable media and magnetic/optical media. For example, the computer readable media may be a hard disk, a floppy disk, a magnetic tape, CD-ROM, Digital Versatile Disk (DVD), Random Access Memory (RAM), or Read Only Memory (ROM) as well as other types of other media known to those skilled in the art.

Aspects of the invention include systems {e.g., internet based systems), particularly computer systems which store and manipulate the sequence information described herein. One example of a computer system 100 is illustrated in block diagram form in Figure 1. As used herein, "a computer system" refers to the hardware components, software components and data storage components used to analyze a nucleotide sequence of a nucleic acid sequence of the invention, or a polypeptide sequence of the invention. The computer system 100 typically includes a processor for processing, accessing and manipulating the sequence data. The processor 105 can be any well-known type of central processing unit, such as, for example, the Pentium in from Intel Corporation, or similar processor from Sun, Motorola, Compaq, AMD or International Business Machines. Typically the computer system 100 is a general purpose system that comprises the processor 105 and one or more internal data storage components 110 for storing data and one or more data retrieving devices for retrieving the data stored on the data storage components. A skilled artisan can readily appreciate that any one of the currently available computer systems are suitable.

In one particular aspect, the computer system 100 includes a processor 105 connected to a bus which is connected to a main memory 115 (in one aspect implemented as RAM) and one or more internal data storage devices 110, such as a hard drive and/or other computer readable media having data recorded thereon. In some aspects, the computer system 100 further includes one or more data retrieving device 118 for reading the data stored on the internal data storage devices 110.

The data retrieving device 118 may represent, for example, a floppy disk drive, a compact disk drive, a magnetic tape drive, or a modem capable of connection to a remote data storage system (e.g., via the internet) etc. In some aspects, the internal data storage device 110 is a removable computer readable medium such as a floppy disk, a compact disk, a magnetic tape, etc. containing control logic and/or data recorded thereon. The computer system 100 may advantageously include or be programmed by appropriate software for reading the control logic and/or the data from the data storage component once inserted in the data retrieving device.

The computer system 100 includes a display 120 which is used to display output to a computer user. It should also be noted that the computer system 100 can be linked to other computer systems 125a-c in a network or wide area network to provide centralized access to the computer system 100. Software for accessing and processing the nucleotide sequences of a nucleic acid sequence of the invention, or a polypeptide sequence of the invention, (such as search tools, compare tools and modeling tools etc.) may reside in main memory 115 during execution. In some aspects, the computer system 100 may further comprise a sequence comparison algorithm for comparing a nucleic acid sequence of the invention, or a polypeptide sequence of the invention, stored on a computer readable medium to a reference nucleotide or polypeptide sequence(s) stored on a computer readable medium. A "sequence comparison algorithm" refers to one or more programs which are implemented (locally or remotely) on the computer system 100 to compare a nucleotide sequence with other nucleotide sequences and/or compounds stored within a data storage means. For example, the sequence comparison algorithm may compare the nucleotide sequences of a nucleic acid sequence of the invention, or a polypeptide sequence of the invention, stored on a computer readable medium to reference sequences stored on a computer readable medium to identify homologies or structural motifs.

Figure 2 is a flow diagram illustrating one aspect of a process 200 for comparing a new nucleotide or protein sequence with a database of sequences in order to determine the homology levels between the new sequence and the sequences in the database. The database of sequences can be a private database stored within the computer system 100, or a public database such as GENBANK that is available through the Internet.

The process 200 begins at a start state 201 and then moves to a state 202 wherein the new sequence to be compared is stored to a memory in a computer system 100. As discussed above, the memory could be any type of memory, including RAM or an internal storage device.

The process 200 then moves to a state 204 wherein a database of sequences is opened for analysis and comparison. The process 200 then moves to a state 206 wherein the first sequence stored in the database is read into a memory on the computer. A comparison is then performed at a state 210 to determine if the first sequence is the same as the second sequence. It is important to note that this step is not limited to performing an exact comparison between the new sequence and the first sequence in the database. Well- known methods are known to those of skill in the art for comparing two nucleotide or protein sequences, even if they are not identical. For example, gaps can be introduced into one sequence in order to raise the homology level between the two tested sequences. The parameters that control whether gaps or other features are introduced into a sequence during comparison are normally entered by the user of the computer system.

Once a comparison of the two sequences has been performed at the state 210, a determination is made at a decision state 210 whether the two sequences are the same. Of course, the term "same" is not limited to sequences that are absolutely identical. Sequences that are within the homology parameters entered by the user will be marked as "same" in the process 200.

If a determination is made that the two sequences are the same, the process 200 moves to a state 214 wherein the name of the sequence from the database is displayed to the user. This state notifies the user that the sequence with the displayed name fulfills the homology constraints that were entered. Once the name of the stored sequence is displayed to the user, the process 200 moves to a decision state 218 wherein a determination is made whether more sequences exist in the database. If no more sequences exist in the database, then the process 200 terminates at an end state 220. However, if more sequences do exist in the database, then the process 200 moves to a state 224 wherein a pointer is moved to the next sequence in the database so that it can be compared to the new sequence. In this manner, the new sequence is aligned and compared with every sequence in the database.

It should be noted that if a determination had been made at the decision state 212 that the sequences were not homologous, then the process 200 would move immediately to the decision state 218 in order to determine if any other sequences were available in the database for comparison.

Accordingly, one aspect of the invention is a computer system comprising a processor, a data storage device having stored thereon a nucleic acid sequence of the invention, or a polypeptide sequence of the invention, a data storage device having retrievably stored thereon reference nucleotide sequences or polypeptide sequences to be compared to a nucleic acid sequence of the invention, or a polypeptide sequence of the invention and a sequence comparer for conducting the comparison. The sequence comparer may indicate a homology level between the sequences compared or identify structural motifs in the above described nucleic acid code a nucleic acid sequence of the invention, or a polypeptide sequence of the invention, or it may identify structural motifs in sequences which are compared to these nucleic acid codes and polypeptide codes. In some aspects, the data storage device may have stored thereon the sequences of at least 2, 5, 10, 15, 20, 25, 30 or 40 or more of the nucleic acid sequences of the invention, or the polypeptide sequences of the invention. Another aspect of the invention is a method for determining the level of homology between a nucleic acid sequence of the invention, or a polypeptide sequence of the invention and a reference nucleotide sequence. The method including reading the nucleic acid code or the polypeptide code and the reference nucleotide or polypeptide sequence through the use of a computer program which determines homology levels and determining homology between the nucleic acid code or polypeptide code and the reference nucleotide or polypeptide sequence with the computer program. The computer program may be any of a number of computer programs for determining homology levels, including those specifically enumerated herein, (e.g., BLAST2N with the default parameters or with any modified parameters). The method may be implemented using the computer systems described above. The method may also be performed by reading at least 2, 5, 10, 15, 20, 25, 30 or 40 or more of the above described nucleic acid sequences of the invention, or the polypeptide sequences of the invention through use of the computer program and determining homology between the nucleic acid codes or polypeptide codes and reference nucleotide sequences or polypeptide sequences.

Figure 3 is a flow diagram illustrating one aspect of a process 250 in a computer for determining whether two sequences are homologous. The process 250 begins at a start state 252 and then moves to a state 254 wherein a first sequence to be compared is stored to a memory. The second sequence to be compared is then stored to a memory at a state 256. The process 250 then moves to a state 260 wherein the first character in the first sequence is read and then to a state 262 wherein the first character of the second sequence is read. It should be understood that if the sequence is a nucleotide sequence, then the character would normally be either A, T, C, G or U. If the sequence is a protein sequence, then it is in one aspect in the single letter amino acid code so that the first and sequence sequences can be easily compared.

A determination is then made at a decision state 264 whether the two characters are the same. If they are the same, then the process 250 moves to a state 268 wherein the next characters in the first and second sequences are read. A determination is then made whether the next characters are the same. If they are, then the process 250 continues this loop until two characters are not the same. If a determination is made that the next two characters are not the same, the process 250 moves to a decision state 274 to determine whether there are any more characters either sequence to read.

If there are not any more characters to read, then the process 250 moves to a state 276 wherein the level of homology between the first and second sequences is displayed to the user. The level of homology is determined by calculating the proportion of characters between the sequences that were the same out of the total number of sequences in the first sequence. Thus, if every character in a first 100 nucleotide sequence aligned with a every character in a second sequence, the homology level would be 100%. Alternatively, the computer program may be a computer program which compares the nucleotide sequences of a nucleic acid sequence as set forth in the invention, to one or more reference nucleotide sequences in order to determine whether the nucleic acid code of the invention, differs from a reference nucleic acid sequence at one or more positions. Optionally such a program records the length and identity of inserted, deleted or substituted nucleotides with respect to the sequence of either the reference polynucleotide or a nucleic acid sequence of the invention. In one aspect, the computer program may be a program which determines whether a nucleic acid sequence of the invention, contains a single nucleotide polymorphism (SNP) with respect to a reference nucleotide sequence. Accordingly, another aspect of the invention is a method for determining whether a nucleic acid sequence of the invention, differs at one or more nucleotides from a reference nucleotide sequence comprising the steps of reading the nucleic acid code and the reference nucleotide sequence through use of a computer program which identifies differences between nucleic acid sequences and identifying differences between the nucleic acid code and the reference nucleotide sequence with the computer program. In some aspects, the computer program is a program which identifies single nucleotide polymorphisms. The method may be implemented by the computer systems described above and the method illustrated in Figure 3. The method may also be performed by reading at least 2, 5, 10, 15, 20, 25, 30, or 40 or more of the nucleic acid sequences of the invention and the reference nucleotide sequences through the use of the computer program and identifying differences between the nucleic acid codes and the reference nucleotide sequences with the computer program.

In other aspects the computer based system may further comprise an identifier for identifying features within a nucleic acid sequence of the invention or a polypeptide sequence of the invention.

An "identifier" refers to one or more programs which identifies certain features within a nucleic acid sequence of the invention, or a polypeptide sequence of the invention. In one aspect, the identifier may comprise a program which identifies an open reading frame in a nucleic acid sequence of the invention. Figure 4 is a flow diagram illustrating one aspect of an identifier process

300 for detecting the presence of a feature in a sequence. The process 300 begins at a start state 302 and then moves to a state 304 wherein a first sequence that is to be checked for features is stored to a memory 115 in the computer system 100. The process 300 then moves to a state 306 wherein a database of sequence features is opened. Such a database would include a list of each feature's attributes along with the name of the feature. For example, a feature name could be "Initiation Codon" and the attribute would be "ATG". Another example would be the feature name "TAATAA Box" and the feature attribute would be "TAATAA". An example of such a database is produced by the University of Wisconsin Genetics Computer Group. Alternatively, the features may be structural polypeptide motifs such as alpha helices, beta sheets, or functional polypeptide motifs such as en2ymatic active sites, helix-turn-helix motifs or other motifs known to those skilled in the art.

Once the database of features is opened at the state 306, the process 300 moves to a state 308 wherein the first feature is read from the database. A comparison of the attribute of the first feature with the first sequence is then made at a state 310. A determination is then made at a decision state 316 whether the attribute of the feature was found in the first sequence. If the attribute was found, then the process 300 moves to a state 318 wherein the name of the found feature is displayed to the user. The process 300 then moves to a decision state 320 wherein a determination is made whether move features exist in the database. If no more features do exist, then the process 300 terminates at an end state 324. However, if more features do exist in the database, then the process 300 reads the next sequence feature at a state 326 and loops back to the state 310 wherein the attribute of the next feature is compared against the first sequence. It should be noted, that if the feature attribute is not found in the first sequence at the decision state 316, the process 300 moves directly to the decision state 320 in order to determine if any more features exist in the database.

Accordingly, another aspect of the invention is a method of identifying a feature within a nucleic acid sequence of the invention, or a polypeptide sequence of the invention, comprising reading the nucleic acid code(s) or polypeptide code(s) through the use of a computer program which identifies features therein and identifying features within the nucleic acid code(s) with the computer program. In one aspect, computer program comprises a computer program which identifies open reading frames. The method may be performed by reading a single sequence or at least 2, 5, 10, 15, 20, 25, 30, or 40 of the nucleic acid sequences of the invention, or the polypeptide sequences of the invention, through the use of the computer program and identifying features within the nucleic acid codes or polypeptide codes with the computer program.

A nucleic acid sequence of the invention, or a polypeptide sequence of the invention, may be stored and manipulated in a variety of data processor programs in a variety of formats. For example, a nucleic acid sequence of the invention, or a polypeptide sequence of the invention, may be stored as text in a word processing file, such as Microsoft WORD™ or WORDPERFECT™ or as an ASCII file in a variety of database programs familiar to those of skill in the art, such as DB2™, SYBASE™, or ORACLE™. In addition, many computer programs and databases may be used as sequence comparison algorithms, identifiers, Or sources of reference nucleotide sequences or polypeptide sequences to be compared to a nucleic acid sequence of the invention, or a polypeptide sequence of the invention. The following list is intended not to limit the invention but to provide guidance to programs and databases which are useful with the nucleic acid sequences of the invention, or the polypeptide sequences of the invention.

The programs and databases which may be used include, but are not limited to: MacPattern (EMBL), DiscoveryBase (Molecular Applications Group), GeneMine (Molecular Applications Group), Look (Molecular Applications Group), MacLook (Molecular Applications Group), BLAST and BLAST2 (NCBI), BLASTN and BLASTX (Altschul et al, J. MoI. Biol. 215: 403, 1990), FASTA (Pearson and Lipman, Proc. Natl.

Acad. Sci. USA, 85: 2444, 1988), FASTDB (Brutlag et al. Comp. App. Biosci. 6:237-245, 1990), Catalyst (Molecular Simulations Inc.), Catalysf SHAPE (Molecular Simulations Inc.), Cerius².DBAccess (Molecular Simulations Inc.), HypoGen (Molecular Simulations Inc.), Insight π, (Molecular Simulations Inc.), Discover (Molecular Simulations Inc.), CHARMm (Molecular Simulations Inc.), Felix (Molecular Simulations Inc.), DelPhi, (Molecular Simulations Inc.), QuanteMM, (Molecular Simulations Inc.), Homology (Molecular Simulations Inc.), Modeler (Molecular Simulations Inc.), ISIS (Molecular Simulations Inc.), Quanta/Protein Design (Molecular Simulations Inc.), WebLab (Molecular Simulations Inc.), WebLab Diversity Explorer (Molecular Simulations Inc.), Gene Explorer (Molecular Simulations Inc.), SeqFold (Molecular Simulations Inc.), the MDL Available Chemicals Directory database, the MDL Drug Data Report data base, the Comprehensive Medicinal Chemistry database, Derwents's World Drug Index database, the BioByteMasterFile database, the Genbank database and the Genseqn database. Many other programs and data bases would be apparent to one of skill in the art given the present disclosure. Motifs which may be detected using the above programs include sequences encoding leucine zippers, helix-turn-helix motifs, glycosylation sites, ubiquitination sites, alpha helices and beta sheets, signal sequences encoding signal peptides which direct the secretion of the encoded proteins, sequences implicated in transcription regulation such as homeoboxes, acidic stretches, enzymatic active sites, substrate binding sites and enzymatic cleavage sites.

Hybridization of nucleic acids

The invention provides isolated or recombinant nucleic acids that hybridize under stringent conditions to an exemplary sequence of the invention (e.g., SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, etc.). The stringent conditions can be highly stringent conditions, medium stringent conditions and/or low stringent conditions, including the high and reduced stringency conditions described herein. In one aspect, it is the stringency of the wash conditions that set forth the conditions which determine whether a nucleic acid is within the scope of the invention, as discussed below.

In alternative aspects, nucleic acids of the invention as defined by their ability to hybridize under stringent conditions can be between about five residues and the full length of nucleic acid of the invention; e.g., they can be at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 55, 60, 65, 70, 75, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, or more, residues in length. Nucleic acids shorter than full length are also included. These nucleic acids can be useful as, e.g., hybridization probes, labeling probes, PCR oligonucleotide probes, iRNA (single or double stranded), antisense or sequences encoding antibody binding peptides (epitopes), motifs, active sites and the like. In one aspect, nucleic acids of the invention are defined by their ability to hybridize under high stringency comprises conditions of about 50% formamide at about 37°C to 42°C. In one aspect, nucleic acids of the invention are defined by their ability to hybridize under reduced stringency comprising conditions in about 35% to 25% formamide at about 30⁰C to 35°C. Alternatively, nucleic acids of the invention are defined by their ability to hybridize under high stringency comprising conditions at 42°C in 50% formamide, 5X SSPE, 0.3% SDS, and a repetitive sequence blocking nucleic acid, such as cot-1 or salmon sperm DNA (e.g., 200 n/ml sheared and denatured salmon sperm DNA). In one aspect, nucleic acids of the invention are defined by their ability to hybridize under reduced stringency conditions comprising 35% formamide at a reduced temperature of 35°C.

In nucleic acid hybridization reactions, the conditions used to achieve a particular level of stringency will vary, depending on the nature of the nucleic acids being hybridized. For example, the length, degree of complementarity, nucleotide sequence composition (e.g., GC v. AT content) and nucleic acid type (e.g., RNA v. DNA) of the hybridizing regions of the nucleic acids can be considered in selecting hybridization conditions. An additional consideration is whether one of the nucleic acids is immobilized, for example, on a filter.

Hybridization may be carried out under conditions of low stringency, moderate stringency or high stringency. As an example of nucleic acid hybridization, a polymer membrane containing immobilized denatured nucleic acids is first prehybridized for 30 minutes at 45°C in a solution consisting of 0.9 M NaCl, 50 mM NaH₂PO₄, pH 7.0, 5.0 mM Na₂EDTA, 0.5% SDS, 1OX Denhardt's and 0.5 mg/ml polyriboadenylic acid. Approximately 2 X 10⁷ cpm (specific activity 4-9 X lO⁸ cpm/ug) Of³²P end-labeled oligonucleotide probe are then added to the solution. After 12-16 hours of incubation, the membrane is washed for 30 minutes at room temperature in IX SET (150 mM NaCl, 20 mM Tris hydrochloride, pH 7.8, 1 mM Na₂EDTA) containing 0.5% SDS, followed by a 30 minute wash in fresh IX SET at T_m-10°C for the oligonucleotide probe. The membrane is then exposed to auto-radiographic film for detection of hybridization signals.

All of the foregoing hybridizations would be considered to be under conditions of high stringency. Following hybridization, a filter can be washed to remove any non- specifically bound detectable probe. The stringency used to wash the filters can also be varied depending on the nature of the nucleic acids being hybridized, the length of the nucleic acids being hybridized, the degree of complementarity, the nucleotide sequence composition (e.g., GC v. AT content) and the nucleic acid type (e.g., RNA v. DNA). Examples of progressively higher stringency condition washes are as follows: 2X SSC, 0.1% SDS at room temperature for 15 minutes (low stringency); 0.1X SSC, 0.5% SDS at room temperature for 30 minutes to 1 hour (moderate stringency); 0.1X SSC, 0.5% SDS for 15 to 30 minutes at between the hybridization temperature and 68⁰C (high stringency); and 0.15M NaCl for 15 minutes at 72°C (very high stringency). A final low stringency wash can be conducted in 0. IX SSC at room temperature. The examples above are merely illustrative of one set of conditions that can be used to wash filters. One of skill in the art would know that there are numerous recipes for different stringency washes. Some other examples are given below. In one aspect, hybridization conditions comprise a wash step comprising a wash for 30 minutes at room temperature in a solution comprising IX 150 mM NaCl, 20 mM Tris hydrochloride, pH 7.8, 1 mM Na₂EDTA, 0.5% SDS, followed by a 30 minute wash in fresh solution. Nucleic acids which have hybridized to the probe are identified by autoradiography or other conventional techniques.

The above procedure may be modified to identify nucleic acids having decreasing levels of homology to the probe sequence. For example, to obtain nucleic acids of decreasing homology to the detectable probe, less stringent conditions may be used. For example, the hybridization temperature may be decreased in increments of 5°C from 68°C to 42⁰C in a hybridization buffer having a Na+ concentration of approximately IM. Following hybridization, the filter may be washed with 2X SSC, 0.5% SDS at the temperature of hybridization. These conditions are considered to be "moderate" conditions above 50⁰C and "low" conditions below 5O⁰C. A specific example of "moderate" hybridization conditions is when the above hybridization is conducted at 55°C. A specific example of "low stringency" hybridization conditions is when the above hybridization is conducted at 45°C.

Alternatively, the hybridization may be carried out in buffers, such as 6X SSC, containing formamide at a temperature of 42°C. In this case, the concentration of formamide in the hybridization buffer may be reduced in 5% increments from 50% to 0% to identify clones having decreasing levels of homology to the probe. Following hybridization, the filter may be washed with 6X SSC, 0.5% SDS at 50⁰C. These conditions are considered to be "moderate" conditions above 25% formamide and "low" conditions below 25% formamide. A specific example of "moderate" hybridization conditions is when the above hybridization is conducted at 30% formamide. A specific example of "low stringency" hybridization conditions is when the above hybridization is conducted at 10% formamide. However, the selection of a hybridization format is not critical - it is the stringency of the wash conditions that set forth the conditions which determine whether a nucleic acid is within the scope of the invention. Wash conditions used to identify nucleic acids within the scope of the invention include, e.g.: a salt concentration of about 0.02 molar at pH 7 and a temperature of at least about 50⁰C or about 55°C to about 60⁰C; or, a salt concentration of about 0.15 M NaCl at 72°C for about 15 minutes; or, a salt concentration of about 0.2X SSC at a temperature of at least about 50⁰C or about 55⁰C to about 6O⁰C for about 15 to about 20 minutes; or, the hybridization complex is washed twice with a solution with a salt concentration of about 2X SSC containing 0.1% SDS at room temperature for 15 minutes and then washed twice by 0.1X SSC containing 0.1% SDS at 68oC for 15 minutes; or, equivalent conditions. See Sambrook, Tijssen and Ausubel for a description of SSC buffer and equivalent conditions. These methods may be used to isolate nucleic acids of the invention. For example, the preceding methods may be used to isolate nucleic acids having a sequence with at least about 97%, at least 95%, at least 90%, at least 85%, at least 80%, at least , 75%, at least 70%, at least 65%, at least 60%, at least 55%, or at least 50% sequence identity (homology) to a nucleic acid sequence selected from the group consisting of one of the sequences of the invention, or fragments comprising at least about 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, 150, 200, 300, 400, or 500 consecutive bases thereof and the sequences complementary thereto. Sequence identity (homology) may be measured using the alignment algorithm. For example, the homologous polynucleotides may have a coding sequence which is a naturally occurring allelic variant of one of the coding sequences described herein. Such allelic variants may have a substitution, deletion or addition of one or more nucleotides when compared to the nucleic acids of the invention. Additionally, the above procedures may be used to isolate nucleic acids which encode polypeptides having at least about 99%, 95%, at least 90%, at least 85%, at least 80%, at least 75%, at least 70%, at least 65%, at least 60%, at least 55%, or at least 50% sequence identity (homology) to a polypeptide of the invention, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof as determined using a sequence alignment algorithm (e.g., such as the FASTA version 3.0t78 algorithm with the default parameters).

Oligonucleotides probes and methods for using them The invention also provides nucleic acid probes that can be used, e.g., for identifying nucleic acids encoding a polypeptide with a tryptophan-processing enzyme activity or fragments thereof or for identifying tryptophan-processing enzyme genes. In one aspect, the probe comprises at least 10 consecutive bases of a nucleic acid of the invention. Alternatively, a probe of the invention can be at least about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 130, 150 or about 10 to 50, about 20 to 60 about 30 to 70, consecutive bases of a sequence as set forth in a nucleic acid of the invention. The probes identify a nucleic acid by binding and/or hybridization. The probes can be used in arrays of the invention, see discussion below, including, e.g., capillary arrays. The probes of the invention can also be used to isolate other nucleic acids or polypeptides.

The isolated nucleic acids of the invention, the sequences complementary thereto, or a fragment comprising at least 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, 150, 200, 300, 400, or 500 consecutive bases of one of the sequences of the invention, or the sequences complementary thereto may also be used as probes to determine whether a biological sample, such as a soil sample, contains an organism having a nucleic acid sequence of the invention or an organism from which the nucleic acid was obtained. In such procedures, a biological sample potentially harboring the organism from which the nucleic acid was isolated is obtained and nucleic acids are obtained from the sample. The nucleic acids are contacted with the probe under conditions which permit the probe to specifically hybridize to any complementary sequences from wlήch are present therein.

Where necessary, conditions which permit the probe to specifically hybridize to complementary sequences may be determined by placing the probe in contact with complementary sequences from samples known to contain the complementary sequence as well as control sequences which do not contain the complementary sequence. Hybridization conditions, such as the salt concentration of the hybridization buffer, the formamide concentration of the hybridization buffer, or the hybridization temperature, may be varied to identify conditions which allow the probe to hybridize specifically to complementary nucleic acids.

If the sample contains the organism from which the nucleic acid was isolated, specific hybridization of the probe is then detected. Hybridization may be detected by labeling the probe with a detectable agent such as a radioactive isotope, a fluorescent dye or an enzyme capable of catalyzing the formation of a detectable product. Many methods for using the labeled probes to detect the presence of complementary nucleic acids in a sample are familiar to those skilled in the art. These include Southern Blots, Northern Blots, colony hybridization procedures and dot blots. Protocols for each of these procedures are provided in Ausubel et al. Current Protocols in Molecular Biology, John Wiley 503 Sons, Inc. (1997) and Sambrook et al, Molecular Cloning: A Laboratory Manual 2nd Ed., Cold Spring Harbor Laboratory Press (1989. Alternatively, more than one probe (at least one of which is capable of specifically hybridizing to any complementary sequences which are present in the nucleic acid sample), may be used in an amplification reaction to determine whether the sample contains an organism containing a nucleic acid sequence of the invention {e.g., an organism from which the nucleic acid was isolated). Typically, the probes comprise oligonucleotides. In one aspect, the amplification reaction may comprise a PCR reaction. PCR protocols are described in Ausubel and Sambrook, supra. Alternatively, the amplification may comprise a ligase chain reaction, 3SR, or strand displacement reaction. (See Barany, F., "The Ligase Chain Reaction in a PCR World", PCR Methods and

Applications 1:5-16, 1991; E. Fahy et ah, "Self-sustained Sequence Replication (3SR): An Isothermal Transcription-based Amplification System Alternative to PCR", PCi? Methods and Applications 1:25-33, 1991; and Walker G.T. et ah, "Strand Displacement Amplification-an Isothermal in vitro DNA Amplification Technique", Nucleic Acid Research 20: 1691-1696, 1992) . hi such procedures, the nucleic acids in the sample are contacted with the probes, the amplification reaction is performed and any resulting amplification product is detected. The amplification product may be detected by performing gel electrophoresis on the reaction products and staining the gel with an intercalator such as ethidium bromide. Alternatively, one or more of the probes may be labeled with a radioactive isotope and the presence of a radioactive amplification product may be detected by autoradiography after gel electrophoresis.

Probes derived from sequences near the ends of the sequences of the invention, may also be used in chromosome walking procedures to identify clones containing genomic sequences located adjacent to the sequences of the invention. Such methods allow the isolation of genes which encode additional proteins from the host organism.

The isolated nucleic acids of the invention, the sequences complementary thereto, or a fragment comprising at least 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, 150, 200, 300, 400, or 500 consecutive bases of one of the sequences of the invention, or the sequences complementary thereto may be used as probes to identify and isolate related nucleic acids. In some aspects, the related nucleic acids may be cDNAs or genomic DNAs from organisms other than the one from which the nucleic acid was isolated. For example, the other organisms may be related organisms. In such procedures, a nucleic acid sample is contacted with the probe under conditions which permit the probe to specifically hybridize to related sequences. Hybridization of the probe to nucleic acids from the related organism is then detected using any of the methods described above.

By varying the stringency of the hybridization conditions used to identify nucleic acids, such as cDNAs or genomic DNAs, which hybridize to the detectable probe, nucleic acids having different levels of homology to the probe can be identified and isolated. Stringency may be varied by conducting the hybridization at varying temperatures below the melting temperatures of the probes. The melting temperature, T_m, is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly complementary probe. Very stringent conditions are selected to be equal to or about 5°C lower than the T_m for a particular probe. The melting temperature of the probe may be calculated using the following formulas:

For probes between 14 and 70 nucleotides in length the melting temperature (T_m) is calculated using the formula: T_m=81.5+16.6(log [Na+])+0.41(fraction G+C)- (600/N) where N is the length of the probe. If the hybridization is carried out in a solution containing formamide, the melting temperature may be calculated using the equation: T_m=81.5+16.6(log [Na+])+0.41(fraction G+C)-(0.63% formamide)-(600/N) where N is the length of the probe. Prehybridization may be carried out in 6X SSC, 5X Denhardt's reagent, 0.5% SDS, lOOμg denatured fragmented salmon sperm DNA or 6X SSC, 5X Denhardt's reagent, 0.5% SDS, lOOμg denatured fragmented salmon sperm DNA, 50% formamide. The formulas for SSC and Denhardt's solutions are listed in Sambrook et al, supra. Hybridization is conducted by adding the detectable probe to the prehybridization solutions listed above. Where the probe comprises double stranded DNA, it is denatured before addition to the hybridization solution. The filter is contacted with the hybridization solution for a sufficient period of time to allow the probe to hybridize to cDNAs or genomic DNAs containing sequences complementary thereto or homologous thereto. For probes over 200 nucleotides in length, the hybridization may be carried out at 15-25°C below the T_m. For shorter probes, such as oligonucleotide probes, the hybridization may be conducted at 5-1O⁰C below the T_m. In one aspect, for hybridizations in 6X SSC, the hybridization is conducted at approximately 68⁰C. Usually, for hybridizations in 50% formamide containing solutions, the hybridization is conducted at approximately 42°C.

Inhibiting Expression of Tryptophan-processing enzymes

The invention provides nucleic acids complementary to (e.g., antisense sequences to) the nucleic acids of the invention, e.g., tryptophan-degrading enzyme- encoding nucleic acids, e.g., nucleic acids comprising antisense, iRNA, ribozymes. Nucleic acids of the invention comprising antisense sequences can be capable of inhibiting the transport, splicing or transcription of tryptophan-degrading enzyme- encoding genes. The inhibition can be effected through the targeting of genomic DNA or messenger RNA. The transcription or function of targeted nucleic acid can be inhibited, for example, by hybridization and/or cleavage. One particularly useful set of inhibitors provided by the present invention includes oligonucleotides which are able to either bind tryptophan-processing enzyme gene or message, in either case preventing or inhibiting the production or function of a tryptophan-processing enzyme. The association can be through sequence specific hybridization. Another useful class of inhibitors includes oligonucleotides which cause inactivation or cleavage of tryptophan-processing enzyme message. The oligonucleotide can have enzyme activity which causes such cleavage, such as ribozymes. The oligonucleotide can be chemically modified or conjugated to an enzyme or composition capable of cleaving the complementary nucleic acid. A pool of many different such oligonucleotides can be screened for those with the desired activity. Thus, the invention provides various compositions for the inhibition of tryptophan- processing enzyme expression on a nucleic acid and/or protein level, e.g., antisense, iRNA and ribozymes comprising tryptophan-processing enzyme sequences of the invention and the anti-tryptophan-processing enzyme antibodies of the invention.

Inhibition of tryptophan-processing enzyme expression can have a variety of industrial applications. For example, inhibition of tryptophan-processing enzyme expression can slow or prevent spoilage. In one aspect, use of compositions of the invention that inhibit the expression and/or activity of tryptophan-processing enzymes, e.g., antibodies, antisense oligonucleotides, ribozymes and RNAi, are used to slow or prevent spoilage. Thus, in one aspect, the invention provides methods and compositions comprising application onto a plant or plant product (e.g., a cereal, a grain, a fruit, seed, root, leaf, etc.) antibodies, antisense oligonucleotides, ribozymes and RNAi of the invention to slow or prevent spoilage. These compositions also can be expressed by the plant (e.g., a transgenic plant) or another organism (e.g., a bacterium or other microorganism transformed with a tryptophan-processing enzyme gene of the invention).

The compositions of the invention for the inhibition of tryptophan- processing enzyme expression (e.g., antisense, iRNA, ribozymes, antibodies) can be used as pharmaceutical compositions, e.g., as anti-pathogen agents or in other therapies, e.g., as anti-microbials for, e.g., Salmonella. Antisense Oligonucleotides

The invention provides antisense oligonucleotides capable of binding tryptophan-processing enzyme message which, in one aspect, can inhibit tryptophan- processing enzyme activity by targeting mRNA. Strategies for designing antisense oligonucleotides are well described in the scientific and patent literature, and the skilled artisan can design such tryptophan-processing enzyme oligonucleotides using the novel reagents of the invention. For example, gene walking/ RNA mapping protocols to screen for effective antisense oligonucleotides are well known in the art, see, e.g., Ho (2000) Methods Enzymol. 314:168-183, describing an RNA mapping assay, which is based on standard molecular techniques to provide an easy and reliable method for potent antisense sequence selection. See also Smith (2000) Eur. J. Pharm. Sci. 11:191-198.

Naturally occurring nucleic acids are used as antisense oligonucleotides. The antisense oligonucleotides can be of any length; for example, in alternative aspects, the antisense oligonucleotides are between about 5 to 100, about 10 to 80, about 15 to 60, about 18 to 40. The optimal length can be determined by routine screening. The antisense oligonucleotides can be present at any concentration. The optimal concentration can be determined by routine screening. A wide variety of synthetic, non- naturally occurring nucleotide and nucleic acid analogues are known which can address this potential problem. For example, peptide nucleic acids (PNAs) containing non-ionic backbones, such as N-(2-aminoethyl) glycine units can be used. Antisense oligonucleotides having phosphorothioate linkages can also be used, as described in WO 97/03211; WO 96/39154; Mata (1997) Toxicol Appl Pharmacol 144:189-197; Antisense Therapeutics, ed. Agrawal (Humana Press, Totowa, NJ., 1996). Antisense oligonucleotides having synthetic DNA backbone analogues provided by the invention can also include phosphoro-dithioate, methylphosphonate, phosphoramidate, alkyl phosphotriester, sulfamate, 3'-thioacetal, methylene(methylimino), 3'-N-carbamate, and morpholino carbamate nucleic acids, as described above.

Combinatorial chemistry methodology can be used to create vast numbers of oligonucleotides that can be rapidly screened for specific oligonucleotides that have appropriate binding affinities and specificities toward any target, such as the sense and antisense tryptophan-processing enzyme sequences of the invention (see, e.g., Gold (1995) J. of Biol. Chem. 270:13581-13584). Inhibitory Ribozymes

The invention provides ribo2ymes capable of binding tryptophan- processing enzyme message. These ribozymes can inhibit tryptophan-processing enzyme activity by, e.g., targeting mRNA. Strategies for designing ribozymes and selecting the tryptophan-processing enzyme-specific antisense sequence for targeting are well described in the scientific and patent literature, and the skilled artisan can design such ribozymes using the novel reagents of the invention. Ribozymes act by binding to a target RNA through the target RNA binding portion of a ribozyme which is held in close proximity to an enzymatic portion of the RNA that cleaves the target RNA. Thus, the ribozyme recognizes and binds a target RNA through complementary base-pairing, and once bound to the correct site, acts enzymatically to cleave and inactivate the target RNA. Cleavage of a target RNA in such a manner will destroy its ability to direct synthesis of an encoded protein if the cleavage occurs in the coding sequence. After a ribozyme has bound and cleaved its RNA target, it can be released from that RNA to bind and cleave new targets repeatedly.

In some circumstances, the enzymatic nature of a ribozyme can be advantageous over other technologies, such as antisense technology (where a nucleic acid molecule simply binds to a nucleic acid target to block its transcription, translation or association with another molecule) as the effective concentration of ribozyme necessary to effect a therapeutic treatment can be lower than that of an antisense oligonucleotide. This potential advantage reflects the ability of the ribozyme to act enzymatically. Thus, a single ribozyme molecule is able to cleave many molecules of target RNA. In addition, a ribozyme is typically a highly specific inhibitor, with the specificity of inhibition depending not only on the base pairing mechanism of binding, but also on the mechanism by which the molecule inhibits the expression of the RNA to which it binds. That is, the inhibition is caused by cleavage of the RNA target and so specificity is defined as the ratio of the rate of cleavage of the targeted RNA over the rate of cleavage of non-targeted RNA. This cleavage mechanism is dependent upon factors additional to those involved in base pairing. Thus, the specificity of action of a ribozyme can be greater than that of antisense oligonucleotide binding the same RNA site.

The ribozyme of the invention, e.g., an enzymatic ribozyme RNA molecule, can be formed in a hammerhead motif, a hairpin motif, as a hepatitis delta virus motif, a group I intron motif and/or an RNaseP-like RNA in association with an RNA guide sequence. Examples of hammerhead motifs are described by, e.g., Rossi (1992) Aids Research and Human Retroviruses 8:183; hairpin motifs by Hampel (1989) Biochemistry 28:4929, and Hampel (1990) Nuc. Acids Res. 18:299; the hepatitis delta virus motif by Perrotta (1992) Biochemistry 31:16; the RNaseP motif by Gueπϊer-Takada (1983) Cell 35:849; and the group I intron by Cech U.S. Pat. No. 4,987,071. The recitation of these specific motifs is not intended to be limiting. Those skilled in the art will recognize that a ribozyme of the invention, e.g., an enzymatic RNA molecule of this invention, can have a specific substrate binding site complementary to one or more of the target gene RNA regions. A ribozyme of the invention can have a nucleotide sequence within or surrounding that substrate binding site which imparts an RNA cleaving activity to the molecule.

RNA interference (RNAi)

In one aspect, the invention provides an RNA inhibitory molecule, a so- called "RNAi" molecule, comprising a tryptophan-processing enzyme sequence of the invention. The RNAi molecule comprises a double-stranded RNA (dsRNA) molecule. The RNAi can inhibit expression of a tryptophan-processing enzyme gene. In one aspect, the RNAi is about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more duplex nucleotides in length. While the invention is not limited by any particular mechanism of action, the RNAi can enter a cell and cause the degradation of a single-stranded RNA (ssRNA) of similar or identical sequences, including endogenous mRNAs. When a cell is exposed to double-stranded RNA (dsRNA), mRNA from the homologous gene is selectively degraded by a process called RNA interference (RNAi). A possible basic mechanism behind RNAi is the breaking of a double-stranded RNA (dsRNA) matching a specific gene sequence into short pieces called short interfering RNA, which trigger the degradation of mRNA that matches its sequence. In one aspect, the RNAi' s of the invention are used in gene-silencing therapeutics, see, e.g., Shuey (2002) Drug Discov.

Today 7:1040-1046. In one aspect, the invention provides methods to selectively degrade RNA using the RNAi' s of the invention. The process may be practiced in vitro, ex vivo or in vivo. In one aspect, the RNAi molecules of the invention can be used to generate a loss-of-function mutation in a cell, an organ or an animal. Methods for making and using RNAi molecules for selectively degrade RNA are well known in the art, see, e.g., U.S. Patent No. 6,506,559; 6,511,824; 6,515,109; 6,489,127. Modification of Nucleic Acids

The invention provides methods of generating variants of the nucleic acids of the invention, e.g., those encoding a tryptophan-processing enzyme. These methods can be repeated or used in various combinations to generate tryptophan-processing enzymes having an altered or different activity or an altered or different stability from that of a tryptophan-processing enzyme encoded by the template nucleic acid. These methods also can be repeated or used in various combinations, e.g., to generate variations in gene/ message expression, message translation or message stability. In another aspect, the genetic composition of a cell is altered by, e.g., modification of a homologous gene ex vivo, followed by its reinsertion into the cell.

A nucleic acid of the invention can be altered by any means. For example, random or stochastic methods, or, non-stochastic, or "directed evolution," methods, see, e.g., U.S. Patent No. 6,361,974. Methods for random mutation of genes are well known in the art, see, e.g., U.S. Patent No. 5,830,696. For example, mutagens can be used to randomly mutate a gene. Mutagens include, e.g., ultraviolet light or gamma irradiation, or a chemical mutagen, e.g., mitomycin, nitrous acid, photoactivated psoralens, alone or in combination, to induce DNA breaks amenable to repair by recombination. Other chemical mutagens include, for example, sodium bisulfite, nitrous acid, hydroxylamine, hydrazine or formic acid. Other mutagens are analogues of nucleotide precursors, e.g., nitrosoguanidine, 5-bromouracil, 2-aminopurine, or acridine. These agents can be added to a PCR reaction in place of the nucleotide precursor thereby mutating the sequence. Intercalating agents such as proflavine, acriflavine, quinacrine and the like can also be used.

Any technique in molecular biology can be used, e.g., random PCR mutagenesis, see, e.g., Rice (1992) Proc. Natl. Acad. Sci. USA 89:5467-5471; or, combinatorial multiple cassette mutagenesis, see, e.g., Crameri (1995) Biotechniques 18:194-196. Alternatively, nucleic acids, e.g., genes, can be reassembled after random, or "stochastic," fragmentation, see, e.g., U.S. Patent Nos. 6,291,242; 6,287,862; 6,287,861; 5,955,358; 5,830,721; 5,824,514; 5,811,238; 5,605,793. In alternative aspects, modifications, additions or deletions are introduced by error-prone PCR, shuffling, oligonucleotide-directed mutagenesis, assembly PCR, sexual PCR mutagenesis, in vivo mutagenesis, cassette mutagenesis, recursive ensemble mutagenesis, exponential ensemble mutagenesis, site-specific mutagenesis, gene reassembly, Gene Site Saturation

Mutagenesis (GSSM), synthetic ligation reassembly (SLR), recombination, recursive sequence recombination, phosphothioate-modified DNA mutagenesis, uracil-containing template mutagenesis, gapped duplex mutagenesis, point mismatch repair mutagenesis, repair-deficient host strain mutagenesis, chemical mutagenesis, radiogenic mutagenesis, deletion mutagenesis, restriction-selection mutagenesis, restriction-purification mutagenesis, artificial gene synthesis, ensemble mutagenesis, chimeric nucleic acid multimer creation, and/or a combination of these and other methods.

The following publications describe a variety of recursive recombination procedures and/or methods which can be incorporated into the methods of the invention: Stemmer (1999) "Molecular breeding of viruses for targeting and other clinical properties" Tumor Targeting 4:1-4; Ness (1999) Nature Biotechnology 17:893-896; Chang (1999) "Evolution of a cytokine using DNA family shuffling" Nature Biotechnology 17:793-797; Minshull (1999) "Protein evolution by molecular breeding" Current Opinion in Chemical Biology 3:284-290; Christians (1999) "Directed evolution of thymidine kinase for AZT phosphorylation using DNA family shuffling" Nature Biotechnology 17:259-264; Crameri (1998) "DNA shuffling of a family of genes from diverse species accelerates directed evolution" Nature 391:288-291; Crameri (1997) "Molecular evolution of an arsenate detoxification pathway by DNA shuffling," Nature Biotechnology 15:436-438; Zhang (1997) "Directed evolution of an effective fucosidase from a galactosidase by DNA shuffling and screening" Proc. Natl. Acad. Sci. USA 94:4504-4509; Patten et al. (1997) "Applications of DNA Shuffling to Pharmaceuticals and Vaccines" Current Opinion in Biotechnology 8:724-733; Crameri et al. (1996) "Construction and evolution of antibody-phage libraries by DNA shuffling" Nature Medicine 2:100-103; Gates et al. (1996) "Affinity selective isolation of ligands from peptide libraries through display on a lac repressor "headpiece dimer'" Journal of Molecular Biology 255:373-386; Stemmer (1996) "Sexual PCR and Assembly PCR" In: The Encyclopedia of Molecular Biology. VCH Publishers, New York, pp.447-457; Crameri and Stemmer (1995) "Combinatorial multiple cassette mutagenesis creates all the permutations of mutant and wildtype cassettes" BioTechniques 18:194-195; Stemmer et al. (1995) "Single-step assembly of a gene and entire plasmid form large numbers of oligodeoxyribonucleotides" Gene, 164:49-53; Stemmer (1995) "The Evolution of Molecular Computation" Science 270: 1510; Stemmer (1995) "Searching Sequence Space" Bio/Technology 13:549-553; Stemmer (1994) "Rapid evolution of a protein in vitro by DNA shuffling" Nature 370:389-391; and Stemmer (1994) "DNA shuffling by random fragmentation and reassembly: In vitro recombination for molecular evolution." Proc. Natl. Acad. Sci. USA 91:10747-10751.

Mutational methods of generating diversity include, for example, site- directed mutagenesis (Ling et al. (1997) "Approaches to DNA mutagenesis: an overview" Anal Biochem. 254(2): 157-178; Dale et al. (1996) "Oligonucleotide-directed random mutagenesis using the phosphorothioate method" Methods MoI. Biol. 57:369-374; Smith

(1985) "In vitro mutagenesis" Ann. Rev. Genet. 19:423-462; Botstein & Shortle (1985) "Strategies and applications of in vitro mutagenesis" Science 229:1193-1201; Carter

(1986) "Site-directed mutagenesis" Biochem. J. 237:1-7; and Kunkel (1987) "The efficiency of oligonucleotide directed mutagenesis" in Nucleic Acids & Molecular

Biology (Eckstein, F. and Lilley, D. M. J. eds., Springer Verlag, Berlin)); mutagenesis using uracil containing templates (Kunkel (1985) "Rapid and efficient site-specific mutagenesis without phenotypic selection" Proc. Natl. Acad. Sci. USA 82:488-492; Kunkel et al. (1987) "Rapid and efficient site-specific mutagenesis without phenotypic selection" Methods in Enzymol. 154, 367-382; and Bass et al. (1988) "Mutant Trp repressors with new DNA-binding specificities" Science 242:240-245); oligonucleotide- directed mutagenesis (Methods in Enzymol. 100: 468-500 (1983); Methods in Enzymol. 154: 329-350 (1987); Zoller (1982) "Oligonucleotide-directed mutagenesis using M13- derived vectors: an efficient and general procedure for the production of point mutations in any DNA fragment" Nucleic Acids Res. 10:6487-6500; Zoller & Smith (1983)

"Oligonucleotide-directed mutagenesis of DNA fragments cloned into Ml 3 vectors" Methods in Enzymol. 100:468-500; and Zoller (1987) Oligonucleotide-directed mutagenesis: a simple method using two oligonucleotide primers and a single-stranded DNA template" Methods in Enzymol. 154:329-350); phosphorothioate-modified DNA mutagenesis (Taylor (1985) "The use of phosphorothioate-modified DNA in restriction enzyme reactions to prepare nicked DNA" Nucl. Acids Res. 13: 8749-8764; Taylor (1985) "The rapid generation of oligonucleotide-directed mutations at high frequency using phosphorothioate-modified DNA" Nucl. Acids Res. 13: 8765-8787 (1985); Nakamaye (1986) "Inhibition of restriction endonuclease Nci I cleavage by phosphorothioate groups and its application to oligonucleotide-directed mutagenesis"

Nucl. Acids Res. 14: 9679-9698; Sayers (1988) "Y-T Exonucleases in phosphorothioate- based oligonucleotide-directed mutagenesis" Nucl. Acids Res. 16:791-802; and Sayers et al. (1988) "Strand specific cleavage of phosphorothioate-containing DNA by reaction with restriction endonucleases in the presence of ethidium bromide" Nucl. Acids Res. 16: 803-814); mutagenesis using gapped duplex DNA (Kramer et al. (1984) "The gapped duplex DNA approach to oligonucleotide-directed mutation construction" Nucl. Acids Res. 12: 9441-9456; Kramer & Fritz (1987) Methods in Enzymol. "Oligonucleotide- directed construction of mutations via gapped duplex DNA" 154:350-367; Kramer (1988) "Improved enzymatic in vitro reactions in the gapped duplex DNA approach to oligonucleotide-directed construction of mutations" Nucl. Acids Res. 16: 7207; and Fritz (1988) "Oligonucleotide-directed construction of mutations: a gapped duplex DNA procedure without enzymatic reactions in vitro" Nucl. Acids Res. 16: 6987-6999).

Additional protocols that can be used to practice the invention include point mismatch repair (Kramer (1984) "Point Mismatch Repair" Cell 38:879-887), mutagenesis using repair-deficient host strains (Carter et al. (1985) "Improved oligonucleotide site-directed mutagenesis using M13 vectors" Nucl. Acids Res. 13: 4431- 4443; and Carter (1987) "Improved oligonucleotide-directed mutagenesis using M13 vectors" Methods in Enzymol. 154: 382-403), deletion mutagenesis (Eghtedarzadeh (1986) "Use of oligonucleotides to generate large deletions" Nucl. Acids Res. 14: 5115), restriction-selection and restriction-selection and restriction-purification (Wells et al. (1986) "Importance of hydrogen-bond formation in stabilizing the transition state of subtilisin" Phil. Trans. R. Soc. Lond. A 317: 415-423), mutagenesis by total gene synthesis (Nambiar et al. (1984) "Total synthesis and cloning of a gene coding for the ribonuclease S protein" Science 223: 1299-1301; Sakamar and Khorana (1988) "Total synthesis and expression of a gene for the a-subunit of bovine rod outer segment guanine nucleotide-binding protein (transducin)" Nucl. Acids Res. 14: 6361-6372; Wells et al. (1985) "Cassette mutagenesis: an efficient method for generation of multiple mutations at defined sites" Gene 34:315-323; and Grundstrom et al. (1985) "Oligonucleotide-directed mutagenesis by microscale ^λ shot-gun' gene synthesis" Nucl. Acids Res. 13: 3305-3316), double-strand break repair (Mandecki (1986); Arnold (1993) "Protein engineering for unusual environments" Current Opinion in Biotechnology 4:450-455. "Oligonucleotide- directed double-strand break repair in plasmids of Escherichia coli: a method for site- specific mutagenesis" Proc. Natl. Acad. Sci. USA, 83:7177-7181). Additional details on many of the above methods can be found in Methods in Enzymology Volume 154, which also describes useful controls for trouble-shooting problems with various mutagenesis methods.

Protocols that can be used to practice the invention are described, e.g., in

U.S. Patent Nos. 5,605,793 to Stemmer (Feb. 25, 1997), "Methods for In Vitro Recombination;" U.S. Pat. No. 5,811,238 to Stemmer et al. (Sep. 22, 1998) "Methods for Generating Polynucleotides having Desired Characteristics by Iterative Selection and Recombination;" U.S. Pat. No. 5,830,721 to Stemmer et al. (Nov. 3, 1998), "DNA Mutagenesis by Random Fragmentation and Reassembly;" U.S. Pat. No. 5,834,252 to Stemmer, et al. (Nov. 10, 1998) "End-Complementary Polymerase Reaction;" U.S. Pat. No. 5,837,458 to Minshull, et al. (Nov. 17, 1998), "Methods and Compositions for Cellular and Metabolic Engineering;" WO 95/22625, Stemmer and Crameri, "Mutagenesis by Random Fragmentation and Reassembly;" WO 96/33207 by Stemmer and Lipschutz "End Complementary Polymerase Chain Reaction;" WO 97/20078 by Stemmer and Crameri "Methods for Generating Polynucleotides having Desired

Characteristics by Iterative Selection and Recombination;" WO 97/35966 by Minshull and Stemmer, "Methods and Compositions for Cellular and Metabolic Engineering;" WO 99/41402 by Punnonen et al. "Targeting of Genetic Vaccine Vectors;" WO 99/41383 by Punnonen et al. "Antigen Library Immunization;" WO 99/41369 by Punnonen et al. "Genetic Vaccine Vector Engineering;" WO 99/41368 by Punnonen et al. "Optimization of Immunomodulatory Properties of Genetic Vaccines;" EP 752008 by Stemmer and Crameri, "DNA Mutagenesis by Random Fragmentation and Reassembly;" EP 0932670 by Stemmer "Evolving Cellular DNA Uptake by Recursive Sequence Recombination;" WO 99/23107 by Stemmer et al., "Modification of Virus Tropism and Host Range by Viral Genome Shuffling;" WO 99/21979 by Apt et al., "Human Papillomavirus Vectors;" WO 98/31837 by del Cardayre et al. "Evolution of Whole Cells and Organisms by Recursive Sequence Recombination;" WO 98/27230 by Patten and Stemmer, "Methods and Compositions for Polypeptide Engineering;" WO 98/27230 by Stemmer et al., "Methods for Optimization of Gene Therapy by Recursive Sequence Shuffling and Selection," WO 00/00632, "Methods for Generating Highly Diverse Libraries," WO

00/09679, "Methods for Obtaining in Vitro Recombined Polynucleotide Sequence Banks and Resulting Sequences," WO 98/42832 by Arnold et al., "Recombination of Polynucleotide Sequences Using Random or Defined Primers," WO 99/29902 by Arnold et al., "Method for Creating Polynucleotide and Polypeptide Sequences," WO 98/41653 by Vind, "An in Vitro Method for Construction of a DNA Library," WO 98/41622 by Borchert et al., "Method for Constructing a Library Using DNA Shuffling," and WO 98/42727 by Pati and Zarling, "Sequence Alterations using Homologous Recombination." Protocols that can be used to practice the invention (providing details regarding various diversity generating methods) are described, e.g., in U.S. Patent application serial no. (USSN) 09/407,800, "SHUFFLING OF CODON ALTERED GENES" by Patten et al. filed Sep. 28, 1999; "EVOLUTION OF WHOLE CELLS AND ORGANISMS BY RECURSIVE SEQUENCE RECOMBINATION" by del Cardayre et al., United States Patent No. 6,379,964; "OLIGONUCLEOTIDE MEDIATED NUCLEIC ACID RECOMBINATION" by Crameri et al., United States Patent Nos. 6,319,714;

6,368,861; 6,376,246; 6,423,542; 6,426,224 and PCT/USOO/01203; "USE OF CODON- VARIED OLIGONUCLEOTIDE SYNTHESIS FOR SYNTHETIC SHUFFLING" by Welch et al., United States Patent No. 6,436,675; "METHODS FOR MAKING CHARACTER STRINGS, POLYNUCLEOTIDES & POLYPEPTIDES HAVING DESIRED CHARACTERISTICS" by Selifonov et al., filed Jan. 18, 2000,

(PCT/USOO/01202) and, e.g. "METHODS FOR MAKING CHARACTER STRINGS, POLYNUCLEOTIDES & POLYPEPTIDES HAVING DESIRED CHARACTERISTICS" by Selifonov et al., filed M. 18, 2000 (U.S. Ser. No. 09/618,579); "METHODS OF POPULATING DATA STRUCTURES FOR USE IN EVOLUTIONARY SIMULATIONS" by Selifonov and Stemmer, filed Jan. 18, 2000 (PCT/USOO/01138); and "SINGLE-STRANDED NUCLEIC ACID TEMPLATE- MEDIATED RECOMBINATION AND NUCLEIC ACID FRAGMENT ISOLATION" by Affholter, filed Sep. 6, 2000 (U.S. Ser. No. 09/656,549); and United States Patent Nos. 6,177,263; 6,153,410. Non-stochastic, or "directed evolution," methods include, e.g., saturation mutagenesis, such as Gene Site Saturation Mutagenesis (GSSM), synthetic ligation reassembly (SLR), or a combination thereof are used to modify the nucleic acids of the invention to generate tryptophan-processing enzymes with new or altered properties (e.g., activity under highly acidic or alkaline conditions, high or low temperatures, and the like). Polypeptides encoded by the modified nucleic acids can be screened for an activity before testing for glucan hydrolysis or other activity. Any testing modality or protocol can be used, e.g., using a capillary array platform. See, e.g., U.S. Patent Nos. 6,361,974; 6,280,926; 5,939,250.

Saturation mutagenesis, or, GSSM In one aspect, codon primers containing a degenerate N,N,G/T sequence are used to introduce point mutations into a polynucleotide, e.g., a tryptophan-processing enzyme or an antibody of the invention, so as to generate a set of progeny polypeptides in which a full range of single amino acid substitutions is represented at each amino acid position, e.g., an amino acid residue in an enzyme active site or ligand binding site targeted to be modified. These oligonucleotides can comprise a contiguous first homologous sequence, a degenerate N,N,G/T sequence, and, optionally, a second homologous sequence. The downstream progeny translational products from the use of such oligonucleotides include all possible amino acid changes at each amino acid site along the polypeptide, because the degeneracy of the N,N,G/T sequence includes codons for all 20 amino acids. In one aspect, one such degenerate oligonucleotide (comprised of, e.g., one degenerate N,N,G/T cassette) is used for subjecting each original codon in a parental polynucleotide template to a full range of codon substitutions. In another aspect, at least two degenerate cassettes are used - either in the same oligonucleotide or not, for subjecting at least two original codons in a parental polynucleotide template to a full range of codon substitutions. For example, more than one N₃N, G/T sequence can be contained in one oligonucleotide to introduce amino acid mutations at more than one site. This plurality of N,N,G/T sequences can be directly contiguous, or separated by one or more additional nucleotide sequence(s). In another aspect, oligonucleotides serviceable for introducing additions and deletions can be used either alone or in combination with the codons containing an N,N,G/T sequence, to introduce any combination or permutation of ammo acid additions, deletions, and/or substitutions.

In one aspect, simultaneous mutagenesis of two or more contiguous amino acid positions is done using an oligonucleotide that contains contiguous N,N,G/T triplets, i.e. a degenerate (N,N,G/T)n sequence. In another aspect, degenerate cassettes having less degeneracy than the N,N,G/T sequence are used. For example, it may be desirable in some instances to use (e.g. in an oligonucleotide) a degenerate triplet sequence comprised of only one N, where said N can be in the first second or third position of the triplet. Any other bases including any combinations and permutations thereof can be used in the remaining two positions of the triplet. Alternatively, it may be desirable in some instances to use (e.g. in an oligo) a degenerate N,N,N triplet sequence.

In one aspect, use of degenerate triplets (e.g., N,N,G/T triplets) allows for systematic and easy generation of a full range of possible natural amino acids (for a total of 20 amino acids) into each and every amino acid position in a polypeptide (in alternative aspects, the methods also include generation of less than all possible substitutions per amino acid residue, or codon, position). For example, for a 100 amino acid polypeptide, 2000 distinct species (i.e. 20 possible amino acids per position X 100 amino acid positions) can be generated. Through the use of an oligonucleotide or set of oligonucleotides containing a degenerate N,N,G/T triplet, 32 individual sequences can code for all 20 possible natural amino acids. Thus, in a reaction vessel in which a parental polynucleotide sequence is subjected to saturation mutagenesis using at least one such oligonucleotide, there are generated 32 distinct progeny polynucleotides encoding 20 distinct polypeptides. In contrast, the use of a non-degenerate oligonucleotide in site- directed mutagenesis leads to only one progeny polypeptide product per reaction vessel. Nondegenerate oligonucleotides can optionally be used in combination with degenerate primers disclosed; for example, nondegenerate oligonucleotides can be used to generate specific point mutations in a working polynucleotide. This provides one means to generate specific silent point mutations, point mutations leading to corresponding amino acid changes, and point mutations that cause the generation of stop codons and the corresponding expression of polypeptide fragments.

In one aspect, each saturation mutagenesis reaction vessel contains polynucleotides encoding at least 20 progeny polypeptide (e.g., tryptophan-processing enzymes) molecules such that all 20 natural amino acids are represented at the one specific amino acid position corresponding to the codon position mutagenized in the parental polynucleotide (other aspects use less than all 20 natural combinations). The 32- fold degenerate progeny polypeptides generated from each saturation mutagenesis reaction vessel can be subjected to clonal amplification (e.g. cloned into a suitable host, e.g., E. coli host, using, e.g., an expression vector) and subjected to expression screening. When an individual progeny polypeptide is identified by screening to display a favorable change in property (when compared to the parental polypeptide, such as increased glucan hydrolysis activity under alkaline or acidic conditions), it can be sequenced to identify the correspondingly favorable amino acid substitution contained therein. In one aspect, upon mutagenizing each and every amino acid position in a parental polypeptide using saturation mutagenesis as disclosed herein, favorable amino acid changes may be identified at more than one amino acid position. One or more new progeny molecules can be generated that contain a combination of all or part of these favorable amino acid substitutions. For example, if 2 specific favorable amino acid changes are identified in each of 3 amino acid positions in a polypeptide, the permutations include 3 possibilities at each position (no change from the original amino acid, and each of two favorable changes) and 3 positions. Thus, there are 3 x 3 x 3 or 27 total possibilities, including 7 that were previously examined - 6 single point mutations

(i.e. 2 at each of three positions) and no change at any position. In yet another aspect, site-saturation mutagenesis can be used together with shuffling, chinierization, recombination and other mutagenizing processes, along with screening. This invention provides for the use of any mutagenizing process(es), including saturation mutagenesis, in an iterative manner. In one exemplification, the iterative use of any mutagenizing process(es) is used in combination with screening. The invention also provides for the use of proprietary codon primers (containing a degenerate N,N,N sequence) to introduce point mutations into a polynucleotide, so as to generate a set of progeny polypeptides in which a full range of single amino acid substitutions is represented at each amino acid position (Gene Site Saturation Mutagenesis (GSSM)). The oligos used are comprised contiguously of a first homologous sequence, a degenerate N,N,N sequence and in one aspect but not necessarily a second homologous sequence. The downstream progeny translational products from the use of such oligos include all possible amino acid changes at each amino acid site along the polypeptide, because the degeneracy of the N,N,N sequence includes codons for all 20 amino acids.

In one aspect, one such degenerate oligo (comprised of one degenerate N,N,N cassette) is used for subjecting each original codon in a parental polynucleotide template to a full range of codon substitutions. In another aspect, at least two degenerate N,N,N cassettes are used - either in the same oligo or not, for subjecting at least two original codons in a parental polynucleotide template to a full range of codon substitutions. Thus, more than one N,N,N sequence can be contained in one oligo to introduce amino acid mutations at more than one site. This plurality of N,N,N sequences can be directly contiguous, or separated by one or more additional nucleotide sequence(s). In another aspect, oligos serviceable for introducing additions and deletions can be used either alone or in combination with the codons containing an N,N,N sequence, to introduce any combination or permutation of amino acid additions, deletions and/or substitutions.

In a particular exemplification, it is possible to simultaneously mutagenize two or more contiguous amino acid positions using an oligo that contains contiguous N₃N₅N triplets, i.e. a degenerate (N₅N₅N)_n sequence. ^•

In another aspect, the present invention provides for the use of degenerate cassettes having less degeneracy than the N₅N₉N sequence. For example, it may be desirable in some instances to use (e.g. in an oligo) a degenerate triplet sequence comprised of only one N, where the N can be in the first second or third position of the triplet. Any other bases including any combinations and permutations thereof can be used in the remaining two positions of the triplet. Alternatively, it may be desirable in some instances to use {e.g., in an oligo) a degenerate N₅N₃N triplet sequence, N₅N₅GAT, or an N₃N, G/C triplet sequence. It is appreciated, however, that the use of a degenerate triplet (such as

N₉N₅GAT or an N₅N₅ G/C triplet sequence) as disclosed in the instant invention is advantageous for several reasons. In one aspect, this invention provides a means to systematically and fairly easily generate the substitution of the full range of possible amino acids (for a total of 20 amino acids) into each and every amino acid position in a polypeptide. Thus, for a 100 amino acid polypeptide, the invention provides a way to systematically and fairly easily generate 2000 distinct species {i.e., 20 possible amino acids per position times 100 amino acid positions). It is appreciated that there is provided, through the use of an oligo containing a degenerate N₅N₅GAT or anN,N, G/C triplet sequence, 32 individual sequences that code for 20 possible amino acids. Thus, in a reaction vessel in which a parental polynucleotide sequence is subjected to saturation mutagenesis using one such oligo, there are generated 32 distinct progeny polynucleotides encoding 20 distinct polypeptides. In contrast, the use of a non-degenerate oligo in site- directed mutagenesis leads to only one progeny polypeptide product per reaction vessel. This invention also provides for the use of nondegenerate oligos, which can optionally be used in combination with degenerate primers disclosed. It is appreciated that in some situations, it is advantageous to use nondegenerate oligos to generate specific point mutations in a working polynucleotide. This provides a means to generate specific silent point mutations, point mutations leading to corresponding amino acid changes and point mutations that cause the generation of stop codons and the corresponding expression of polypeptide fragments.

Thus, in one aspect of this invention, each saturation mutagenesis reaction vessel contains polynucleotides encoding at least 20 progeny polypeptide molecules such that all 20 amino acids are represented at the one specific amino acid position corresponding to the codon position mutagenized in the parental polynucleotide. The 32- fold degenerate progeny polypeptides generated from each saturation mutagenesis reaction vessel can be subjected to clonal amplification {e.g., cloned into a suitable E. coli host using an expression vector) and subjected to expression screening. When an individual progeny polypeptide is identified by screening to display a favorable change in property (when compared to the parental polypeptide), it can be sequenced to identify the correspondingly favorable amino acid substitution contained therein.

It is appreciated that upon mutagenizing each and every amino acid position in a parental polypeptide using saturation mutagenesis as disclosed herein, favorable amino acid changes may be identified at more than one amino acid position.

One or more new progeny molecules can be generated that contain a combination of all or part of these favorable amino acid substitutions. For example, if 2 specific favorable amino acid changes are identified in each of 3 amino acid positions in a polypeptide, the permutations include 3 possibilities at each position (no change from the original amino acid and each of two favorable changes) and 3 positions. Thus, there are 3 x 3 x 3 or 27 total possibilities, including 7 that were previously examined - 6 single point mutations (i.e., 2 at each of three positions) and no change at any position.

Thus, in a non-limiting exemplification, this invention provides for the use of saturation mutagenesis in combination with additional mutagenization processes, such as process where two or more related polynucleotides are introduced into a suitable host cell such that a hybrid polynucleotide is generated by recombination and reductive reassortment.

In addition to performing mutagenesis along the entire sequence of a gene, the instant invention provides that mutagenesis can be use to replace each of any number of bases in a polynucleotide sequence, wherein the number of bases to be mutagenized is in one aspect every integer from 15 to 100,000. Thus, instead of mutagenizing every position along a molecule, one can subject every or a discrete number of bases (in one aspect a subset totaling from 15 to 100,000) to mutagenesis. In one aspect, a separate nucleotide is used for mutagenizing each position or group of positions along a polynucleotide sequence. A group of 3 positions to be mutagenized may be a codon. The mutations can be introduced using a mutagenic primer, containing a heterologous cassette, also referred to as a mutagenic cassette. Exemplary cassettes can have from 1 to 500 bases. Each nucleotide position in such heterologous cassettes be N, A, C, G, T, AJC, AJG, AJT, C/G, C/T, G/T, C/G/T, AJGIT, AJCIT, A/C/G, or E, where E is any base that is not A, C, G, or T (E can be referred to as a designer oligo).

In a general sense, saturation mutagenesis is comprised of mutagenizing a complete set of mutagenic cassettes (wherein each cassette is in one aspect about 1-500 bases in length) in defined polynucleotide sequence to be mutagenized (wherein the sequence to be mutagenized is in one aspect from about 15 to 100,000 bases in length). Thus, a group of mutations (ranging from 1 to 100 mutations) is introduced into each cassette to be mutagenized. A grouping of mutations to be introduced into one cassette can be different or the same from a second grouping of mutations to be introduced into a second cassette during the application of one round of saturation mutagenesis. Such groupings are exemplified by deletions, additions, groupings of particular codons and groupings of particular nucleotide cassettes.

Defined sequences to be mutagenized include a whole gene, pathway, cDNA, an entire open reading frame (ORF) and entire promoter, enhancer, repressor/transactivator, origin of replication, intron, operator, or any polynucleotide functional group. Generally, a "defined sequences" for this purpose may be any polynucleotide that a 15 base-polynucleotide sequence and polynucleotide sequences of lengths between 15 bases and 15,000 bases (this invention specifically names every integer in between). Considerations in choosing groupings of codons include types of amino acids encoded by a degenerate mutagenic cassette. In one exemplification a grouping of mutations that can be introduced into a mutagem^'c cassette, this invention specifically provides for degenerate codon substitutions (using degenerate oligos) that code for 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 and 20 amino acids at each position and a library of polypeptides encoded thereby. Synthetic Ligation Reassembly (SLR)

The invention provides a non-stochastic gene modification system termed "synthetic ligation reassembly," or simply "SLR," a "directed evolution process," to generate polypeptides, e.g., tryptophan-processing enzymes or antibodies of the invention, with new or altered properties. SLR is a method of ligating oligonucleotide fragments together non- stochastically. This method differs from stochastic oligonucleotide shuffling in that the nucleic acid building blocks are not shuffled, concatenated or chimerized randomly, but rather are assembled non-stochastically. See, e.g., U.S. Patent Application Serial No. (USSN) 09/332,835 entitled "Synthetic Ligation Reassembly in Directed Evolution" and filed on June 14, 1999 ("USSN 09/332,835"). In one aspect, SLR comprises the following steps: (a) providing a template polynucleotide, wherein the template polynucleotide comprises sequence encoding a homologous gene; (b) providing a plurality of building block polynucleotides, wherein the building block polynucleotides are designed to cross-over reassemble with the template polynucleotide at a predetermined sequence, and a building block polynucleotide comprises a sequence that is a variant of the homologous gene and a sequence homologous to the template polynucleotide flanking the variant sequence; (c) combining a building block polynucleotide with a template polynucleotide such that the building block polynucleotide cross-over reassembles with the template polynucleotide to generate polynucleotides comprising homologous gene sequence variations.

SLR does not depend on the presence of high levels of homology between polynucleotides to be rearranged. Thus, this method can be used to non-stochastically generate libraries (or sets) of progeny molecules comprised of over 10¹⁰⁰ different chimeras. SLR can be used to generate libraries comprised of over io¹⁰⁰⁰ different progeny chimeras. Thus, aspects of the present invention include non-stochastic methods of producing a set of finalized chimeric nucleic acid molecule shaving an overall assembly order that is chosen by design. This method includes the steps of generating by design a plurality of specific nucleic acid building blocks having serviceable mutually compatible ligatable ends, and assembling these nucleic acid building blocks, such that a designed overall assembly order is achieved.

The mutually compatible ligatable ends of the nucleic acid building blocks to be assembled are considered to be "serviceable" for this type of ordered assembly if they enable the building blocks to be coupled in predetermined orders. Thus, the overall assembly order in which the nucleic acid building blocks can be coupled is specified by the design of the ligatable ends. If more than one assembly step is to be used, then the overall assembly order in which the nucleic acid building blocks can be coupled is also specified by the sequential order of the assembly step(s). In one aspect, the annealed building pieces are treated with an enzyme, such as a ligase (e.g. T4 DNA ligase), to achieve covalent bonding of the building pieces.

In one aspect, the design of the oligonucleotide building blocks is obtained by analyzing a set of progenitor nucleic acid sequence templates that serve as a basis for producing a progeny set of finalized chimeric polynucleotides. These parental oligonucleotide templates thus serve as a source of sequence information that aids in the design of the nucleic acid building blocks that are to be mutagenized, e.g., chimerized or shuffled. In one aspect of this method, the sequences of a plurality of parental nucleic acid templates are aligned in order to select one or more demarcation points. The demarcation points can be located at an area of homology, and are comprised of one or more nucleotides. These demarcation points are in one aspect shared by at least two of the progenitor templates. The demarcation points can thereby be used to delineate the boundaries of oligonucleotide building blocks to be generated in order to rearrange the parental polynucleotides. The demarcation points identified and selected in the progenitor molecules serve as potential chimerization points in the assembly of the final chimeric progeny molecules. A demarcation point can be an area of homology (comprised of at least one homologous nucleotide base) shared by at least two parental polynucleotide sequences. Alternatively, a demarcation point can be an area of homology that is shared by at least half of the parental polynucleotide sequences, or, it can be an area of homology that is shared by at least two thirds of the parental polynucleotide sequences. Even more in one aspect a serviceable demarcation points is an area of homology that is shared by at least three fourths of the parental polynucleotide sequences, or, it can be shared by at almost all of the parental polynucleotide sequences. In one aspect, a demarcation point is an area of homology that is shared by all of the parental polynucleotide sequences.

In one aspect, a ligation reassembly process is performed exhaustively in order to generate an exhaustive library of progeny chimeric polynucleotides. In other words, all possible ordered combinations of the nucleic acid building blocks are represented in the set of finalized chimeric nucleic acid molecules. At the same time, in another aspect, the assembly order (i.e. the order of assembly of each building block in the 5' to 3 sequence of each finalized chimeric nucleic acid) in each combination is by design (or non-stochastic) as described above. Because of the non-stochastic nature of this invention, the possibility of unwanted side products is greatly reduced.

In another aspect, the ligation reassembly method is performed systematically. For example, the method is performed in order to generate a systematically compartmentalized library of progeny molecules, with compartments that can be screened systematically, e.g. one by one. In other words this invention provides that, through the selective and judicious use of specific nucleic acid building blocks, coupled with the selective and judicious use of sequentially stepped assembly reactions, a design can be achieved where specific sets of progeny products are made in each of several reaction vessels. This allows a systematic examination and screening procedure to be performed. Thus, these methods allow a potentially very large number of progeny molecules to be examined systematically in smaller groups. Because of its ability to perform chimerizations in a manner that is highly flexible yet exhaustive and systematic as well, particularly when there is a low level of homology among the progenitor molecules, these methods provide for the generation of a library (or set) comprised of a large number of progeny molecules. Because of the non-stochastic nature of the instant ligation reassembly invention, the progeny molecules generated in one aspect comprise a library of finalized chimeric nucleic acid molecules having an overall assembly order that is chosen by design. The saturation mutagenesis and optimized directed evolution methods also can be used to generate different progeny molecular species. It is appreciated that the invention provides freedom of choice and control regarding the selection of demarcation points, the size and number of the nucleic acid building blocks, and the size and design of the couplings. It is appreciated, furthermore, that the requirement for intermolecular homology is highly relaxed for the operability of this invention. In fact, demarcation points can even be chosen in areas of little or no intermolecular homology. For example, because of codon wobble, i.e. the degeneracy of codons, nucleotide substitutions can be introduced into nucleic acid building blocks without altering the amino acid originally encoded in the corresponding progenitor template. Alternatively, a codon can be altered such that the coding for an originally amino acid is altered. This invention provides that such substitutions can be introduced into the nucleic acid building block in order to increase the incidence of intermolecular homologous demarcation points and thus to allow an increased number of couplings to be achieved among the building blocks, which in turn allows a greater number of progeny chimeric molecules to be generated.

In one aspect, the present invention provides a non-stochastic method termed synthetic gene reassembly, that is somewhat related to stochastic shuffling, save that the nucleic acid building blocks are not shuffled or concatenated or chimerized randomly, but rather are assembled non-stochastically.

The synthetic gene reassembly method does not depend on the presence of a high level of homology between polynucleotides to be shuffled. The invention can be used to non-stochastically generate libraries (or sets) of progeny molecules comprised of over 10¹⁰⁰ different chimeras. Conceivably, synthetic gene reassembly can even be used to generate libraries comprised of over 1O¹⁰⁰⁰ different progeny chimeras.

Thus, in one aspect, the invention provides a non-stochastic method of producing a set of finalized chimeric nucleic acid molecules having an overall assembly order that is chosen by design, which method is comprised of the steps of generating by design a plurality of specific nucleic acid building blocks having serviceable mutually compatible ligatable ends and assembling these nucleic acid building blocks, such that a designed overall assembly order is achieved.

The mutually compatible ligatable ends of the nucleic acid building blocks to be assembled are considered to be "serviceable" for this type of ordered assembly if they enable the building blocks to be coupled in predetermined orders. Thus, in one aspect, the overall assembly order in which the nucleic acid building blocks can be coupled is specified by the design of the ligatable ends and, if more than one assembly step is to be used, then the overall assembly order in which the nucleic acid building blocks can be coupled is also specified by the sequential order of the assembly step(s). In a one aspect of the invention, the annealed building pieces are treated with an enzyme, such as a ligase (e.g., T4 DNA ligase) to achieve covalent bonding of the building pieces. In a another aspect, the design of nucleic acid building blocks is obtained upon analysis of the sequences of a set of progenitor nucleic acid templates that serve as a basis for producing a progeny set of finalized chimeric nucleic acid molecules. These progenitor nucleic acid templates thus serve as a source of sequence information that aids in the design of the nucleic acid building blocks that are to be mutagenized, i.e. chimerized or shuffled.

In one exemplification, the invention provides for the chimerization of a family of related genes and their encoded family of related products. In a particular ^■ exemplification, the encoded products are enzymes. The tryptophan-processing enzymes of the present invention can be mutagenized in accordance with the methods described herein.

Thus according to one aspect of the invention, the sequences of a plurality of progenitor nucleic acid templates (e.g., polynucleotides of the invention) are aligned in order to select one or more demarcation points, which demarcation points can be located at an area of homology. The demarcation points can be used to delineate the boundaries of nucleic acid building blocks to be generated. Thus, the demarcation points identified and selected in the progenitor molecules serve as potential chimerization points in the assembly of the progeny molecules. Typically a serviceable demarcation point is an area of homology

(comprised of at least one homologous nucleotide base) shared by at least two progenitor templates, but the demarcation point can be an area of homology that is shared by at least half of the progenitor templates, at least two thirds of the progenitor templates, at least three fourths of the progenitor templates and in one aspect at almost all of the progenitor templates. Even more in one aspect still a serviceable demarcation point is an area of homology that is shared by all of the progenitor templates.

In a one aspect, the gene reassembly process is performed exhaustively in order to generate an exhaustive library. In other words, all possible ordered combinations of the nucleic acid building blocks are represented in the set of finalized chimeric nucleic acid molecules. At the same time, the assembly order (i.e. the order of assembly of each building block in the 5' to 3 sequence of each finalized chimeric nucleic acid) in each combination is by design (or non-stochastic). Because of the non-stochastic nature of the method, the possibility of unwanted side products is greatly reduced. In another aspect, the method provides that the gene reassembly process is performed systematically, for example to generate a systematically compartmentalized library, with compartments that can be screened systematically, e.g., one by one. In other words the invention provides that, through the selective and judicious use of specific nucleic acid building blocks, coupled with the selective and judicious use of sequentially stepped assembly reactions, an experimental design can be achieved where specific sets of progeny products are made in each of several reaction vessels. This allows a systematic examination and screening procedure to be performed. Thus, it allows a potentially very large number of progeny molecules to be examined systematically in smaller groups. Because of its ability to perform chimerizations in a manner that is highly flexible yet exhaustive and systematic as well, particularly when there is a low level of homology among the progenitor molecules, the instant invention provides for the generation of a library (or set) comprised of a large number of progeny molecules. Because of the non-stochastic nature of the instant gene reassembly invention, the progeny molecules generated in one aspect comprise a library of finalized chimeric nucleic acid molecules having an overall assembly order that is chosen by design. In a particularly aspect, such a generated library is comprised of greater than 10³ to greater than 1O¹⁰⁰⁰ different progeny molecular species.

In one aspect, a set of finalized chimeric nucleic acid molecules, produced as described is comprised of a polynucleotide encoding a polypeptide. According to one aspect, this polynucleotide is a gene, which may be a man-made gene. According to another aspect, this polynucleotide is a gene pathway, which may be a man-made gene pathway. The invention provides that one or more man-made genes generated by the invention may be incorporated into a man-made gene pathway, such as pathway operable in a eukaryotic organism (including a plant).

In another exemplification, the synthetic nature of the step in which the building blocks are generated allows the design and introduction of nucleotides (e.g., one or more nucleotides, which may be, for example, codons or introns or regulatory sequences) that can later be optionally removed in an in vitro process (e.g., by mutagenesis) or in an in vivo process (e.g., by utilizing the gene splicing ability of a host organism). It is appreciated that in many instances the introduction of these nucleotides may also be desirable for many other reasons in addition to the potential benefit of creating a serviceable demarcation point.

Thus, according to another aspect, the invention provides that a nucleic acid building block can be used to introduce an intron. Thus, the invention provides that functional introns may be introduced into a man-made gene of the invention. The invention also provides that functional introns may be introduced into a man-made gene pathway of the invention. Accordingly, the invention provides for the generation of a chimeric polynucleotide that is a man-made gene containing one (or more) artificially introduced intron(s).

Accordingly, the invention also provides for the generation of a chimeric polynucleotide that is a man-made gene pathway containing one (or more) artificially introduced intron(s). In one aspect, the artificially introduced intron(s) are functional in one or more host cells for gene splicing much in the way that naturally-occurring introns serve functionally in gene splicing. The invention provides a process of producing man- made intron-containing polynucleotides to be introduced into host organisms for recombination and/or splicing. A man-made gene produced using the invention can also serve as a substrate for recombination with another nucleic acid. Likewise, a man-made gene pathway produced using the invention can also serve as a substrate for recombination with another nucleic acid. In one aspect, the recombination is facilitated by, or occurs at, areas of homology between the man-made, intron-containing gene and a nucleic acid, which serves as a recombination partner. In one aspect, the recombination partner may also be a nucleic acid generated by the invention, including a man-made gene or a man- made gene pathway. Recombination may be facilitated by or may occur at areas of homology that exist at the one (or more) artificially introduced intron(s) in the man-made gene.

Ill The synthetic gene reassembly method of the invention utilizes a plurality of nucleic acid building blocks, each of which in one aspect has two ligatable ends. The two ligatable ends on each nucleic acid building block may be two blunt ends {i.e. each having an overhang of zero nucleotides), or in one aspect one blunt end and one overhang, or more in one aspect still two overhangs.

A useful overhang for this purpose may be a 3' overhang or a 5' overhang. Thus, a nucleic acid building block may have a 3' overhang or alternatively a 5' overhang or alternatively two 3' overhangs or alternatively two 5' overhangs. The overall order in which the nucleic acid building blocks are assembled to form a finalized chimeric nucleic acid molecule is determined by purposeful experimental design and is not random.

In one aspect, a nucleic acid building block is generated by chemical synthesis of two single-stranded nucleic acids (also referred to as single-stranded oligos) and contacting them so as to allow them to anneal to form a double-stranded nucleic acid building block. A doublσ-stranded nucleic acid building block can be of variable size. The sizes of these building blocks can be small or large. Exemplary sizes for building block range from 1 base pair (not including any overhangs) to 100,000 base pairs (not including any overhangs). Other exemplary size ranges are also provided, which have lower limits of from 1 bp to 10,000 bp (including every integer value in between) and upper limits of from 2 bp to 100, 000 bp (including every integer value in between).

Many methods exist by which a double-stranded nucleic acid building block can be generated that is serviceable for the invention; and these are known in the art and can be readily performed by the skilled artisan.

According to one aspect, a double-stranded nucleic acid building block is generated by first generating two single stranded nucleic acids and allowing them to anneal to form a double-stranded nucleic acid building block. The two strands of a double-stranded nucleic acid building block may be complementary at every nucleotide apart from any that form an overhang; thus containing no mismatches, apart from any overhang(s). According to another aspect, the two strands of a double-stranded nucleic acid building block are complementary at fewer than every nucleotide apart from any that form an overhang. Thus, according to this aspect, a double-stranded nucleic acid building block can be used to introduce codon degeneracy. In one aspect the codon degeneracy is introduced using the site-saturation mutagenesis described herein, using one or more

N₅N₉GAT cassettes or alternatively using one or more N₉N₅N cassettes. The in vivo recombination method of the invention can be performed blindly on a pool of unknown hybrids or alleles of a specific polynucleotide or sequence. However, it is not necessary to know the actual DNA or RNA sequence of the specific polynucleotide. The approach of using recombination within a mixed population of genes can be useful for the generation of any useful proteins, for example, interleukin I, antibodies, tPA and growth hormone. This approach may be used to generate proteins having altered specificity or activity. The approach may also be useful for the generation of hybrid nucleic acid sequences, for example, promoter regions, introns, exons, enhancer sequences, 31 untranslated regions or 51 untranslated regions of genes. Thus this approach may be used to generate genes having increased rates of expression. This approach may also be useful in the study of repetitive DNA sequences. Finally, this approach may be useful to mutate ribozymes or aptamers.

In one aspect the invention described herein is directed to the use of repeated cycles of reductive reassortment, recombination and selection which allow for the directed molecular evolution of highly complex linear sequences, such as DNA, RNA or proteins thorough recombination.

Optimized Directed Evolution System

The invention provides a non-stochastic gene modification system termed "optimized directed evolution system" to generate polypeptides, e.g., tryptophan- processing enzymes or antibodies of the invention, with new or altered properties. Optimized directed evolution is directed to the use of repeated cycles of reductive reassortment, recombination and selection that allow for the directed molecular evolution of nucleic acids through recombination. Optimized directed evolution allows generation of a large population of evolved chimeric sequences, wherein the generated population is significantly enriched for sequences that have a predetermined number of crossover events.

A crossover event is a point in a chimeric sequence where a shift in sequence occurs from one parental variant to another parental variant. Such a point is normally at the juncture of where oligonucleotides from two parents are ligated together to form a single sequence. This method allows calculation of the correct concentrations of oligonucleotide sequences so that the final chimeric population of sequences is enriched for the chosen number of crossover events. This provides more control over choosing chimeric variants having a predetermined number of crossover events.

In addition, this method provides a convenient means for exploring a tremendous amount of the possible protein variant space in comparison to other systems. Previously, if one generated, for example, 10¹³ chimeric molecules during a reaction, it would be extremely difficult to test such a high number of chimeric variants for a particular activity. Moreover, a significant portion of the progeny population would have a very high number of crossover events which resulted in proteins that were less likely to have increased levels of a particular activity. By using these methods, the population of chimerics molecules can be enriched for those variants that have a particular number of crossover events. Thus, although one can still generate 10¹³ chimeric molecules during a reaction, each of the molecules chosen for further analysis most likely has, for example, only three crossover events. Because the resulting progeny population can be skewed to have a predetermined number of crossover events, the boundaries on the functional variety between the chimeric molecules is reduced. This provides a more manageable number of variables when calculating which oligonucleotide from the original parental polynucleotides might be responsible for affecting a particular trait.

One method for creating a chimeric progeny polynucleotide sequence is to create oligonucleotides corresponding to fragments or portions of each parental sequence. Each oligonucleotide in one aspect includes a unique region of overlap so that mixing the oligonucleotides together results in a new variant that has each oligonucleotide fragment assembled in the correct order. Additional information can also be found, e.g., in USSN 09/332,835; U.S. Patent No. 6,361,974.

The number of oligonucleotides generated for each parental variant bears a relationship to the total number of resulting crossovers in the chimeric molecule that is ultimately created. For example, three parental nucleotide sequence variants might be provided to undergo a ligation reaction in order to find a chimeric variant having, for example, greater activity at high temperature. As one example, a set of 50 oligonucleotide sequences can be generated corresponding to each portions of each parental variant. Accordingly, during the ligation reassembly process there could be up to 50 crossover events within each of the chimeric sequences. The probability that each of the generated chimeric polynucleotides will contain oligonucleotides from each parental variant in alternating order is very low. If each oligonucleotide fragment is present in the ligation reaction in the same molar quantity it is likely that in some positions oligonucleotides from the same parental polynucleotide will ligate next to one another and thus not result in a crossover event. If the concentration of each oligonucleotide from each parent is kept constant during any ligation step in this example, there is a 1/3 chance (assuming 3 parents) that an oligonucleotide from the same parental variant will ligate within the chimeric sequence and produce no crossover.

Accordingly, a probability density function (PDF) can be determined to predict the population of crossover events that are likely to occur during each step in a ligation reaction given a set number of parental variants, a number of oligonucleotides corresponding to each variant, and the concentrations of each variant during each step in the ligation reaction. The statistics and mathematics behind determining the PDF is described below. By utilizing these methods, one can calculate such a probability density function, and thus enrich the chimeric progeny population for a predetermined number of crossover events resulting from a particular ligation reaction. Moreover, a target number of crossover events can be predetermined, and the system then programmed to calculate the starting quantities of each parental oligonucleotide during each step in the ligation reaction to result in a probability density function that centers on the predetermined number of crossover events. These methods are directed to the use of repeated cycles of reductive reassortment, recombination and selection that allow for the directed molecular evolution of a nucleic acid encoding a polypeptide through recombination. This system allows generation of a large population of evolved chimeric sequences, wherein the generated population is significantly enriched for sequences that have a predetermined number of crossover events. A crossover event is a point in a chimeric sequence where a shift in sequence occurs from one parental variant to another parental variant. Such a point is normally at the juncture of where oligonucleotides from two parents are ligated together to form a single sequence. The method allows calculation of the correct concentrations of oligonucleotide sequences so that the final chimeric population of sequences is enriched for the chosen number of crossover events. This provides more control over choosing chimeric variants having a predetermined number of crossover events. In addition, these methods provide a convenient means for exploring a tremendous amount of the possible protein variant space in comparison to other systems. By using the methods described herein, the population of chimerics molecules can be enriched for those variants that have a particular number of crossover events. Thus, although one can still generate 10¹³ chimeric molecules during a reaction, each of the molecules chosen for further analysis most likely has, for example, only three crossover events. Because the resulting progeny population can be skewed to have a predetermined number of crossover events, the boundaries on the functional variety between the chimeric molecules is reduced. This provides a more manageable number of variables when calculating which oligonucleotide from the original parental polynucleotides might be responsible for affecting a particular trait.

In one aspect, the method creates a chimeric progeny polynucleotide sequence by creating oligonucleotides corresponding to fragments or portions of each parental sequence. Each oligonucleotide in one aspect includes a unique region of overlap so that mixing the oligonucleotides together results in a new variant that has each oligonucleotide fragment assembled in the correct order. See also USSN 09/332,835.

Determining Crossover Events

Aspects of the invention include a system and software that receive a desired crossover probability density function (PDF), the number of parent genes to be reassembled, and the number of fragments in the reassembly as inputs. The output of this program is a "fragment PDF" that can be used to determine a recipe for producing reassembled genes, and the estimated crossover PDF of those genes. The processing described herein is in one aspect performed in MATLAB™ (The Mathworks, Natick, Massachusetts) a programming language and development environment for technical computing.

Iterative Processes

In practicing the invention, these processes can be iteratively repeated. For example, a nucleic acid (or, the nucleic acid) responsible for an altered or new tryptophan-processing enzyme phenotype is identified, re-isolated, again modified, re- tested for activity. This process can be iteratively repeated until a desired phenotype is engineered. For example, an entire biochemical anabolic or catabolic pathway can be engineered into a cell, including, e.g., tryptophan-processing enzyme activity.

Similarly, if it is determined that a particular oligonucleotide has no affect at all on the desired trait (e.g., a new tryptophan-processing enzyme phenotype), it can be removed as a variable by synthesizing larger parental oligonucleotides that include the sequence to be removed. Since incorporating the sequence within a larger sequence prevents any crossover events, there will no longer be any variation of this sequence in the progeny polynucleotides. This iterative practice of determining which oligonucleotides are most related to the desired trait, and which are unrelated, allows more efficient exploration all of the possible protein variants that might be provide a particular trait or activity.

In vivo shuffling In vivo shuffling of molecules is use in methods of the invention that provide variants of polypeptides of the invention, e.g., antibodies, tryptophan-processing enzymes, and the like. In vivo shuffling can be performed utilizing the natural property of cells to recombine multimers. While recombination in vivo has provided the major natural route to molecular diversity, genetic recombination remains a relatively complex process that involves 1) the recognition of homologies; 2) strand cleavage, strand invasion, and metabolic steps leading to the production of recombinant chiasma; and finally 3) the resolution of chiasma into discrete recombined molecules. The formation of the chiasma requires the recognition of homologous sequences.

In another aspect, the invention includes a method for producing a hybrid polynucleotide from at least a first polynucleotide and a second polynucleotide. The invention can be used to produce a hybrid polynucleotide by introducing at least a first polynucleotide and a second polynucleotide (e.g., one, or both, being an exemplary tryptophan-degrading enzyme-encoding sequence of the invention) which share at least one region of partial sequence homology into a suitable host cell. The regions of partial sequence homology promote processes which result in sequence reorganization producing a hybrid polynucleotide. The term "hybrid polynucleotide", as used herein, is any nucleotide sequence which results from the method of the present invention and contains sequence from at least two original polynucleotide sequences. Such hybrid polynucleotides can result from intermolecular recombination events which promote sequence integration between DNA molecules. In addition, such hybrid polynucleotides can result from intramolecular reductive reassortment processes which utilize repeated sequences to alter a nucleotide sequence within a DNA molecule.

In vivo reassortment is focused on "inter-molecular" processes collectively referred to as "recombination" which in bacteria, is generally viewed as a "RecA- dependent" phenomenon. The invention can rely on recombination processes of a host cell to recombine and re-assort sequences, or the cells' ability to mediate reductive processes to decrease the complexity of quasi-repeated sequences in the cell by deletion. This process of "reductive reassortment" occurs by an "intra-molecular", RecA- iαdependent process.

Therefore, in another aspect of the invention, novel polynucleotides can be generated by the process of reductive reassortment. The method involves the generation of constructs containing consecutive sequences (original encoding sequences), their insertion into an appropriate vector and their subsequent introduction into an appropriate host cell. The reassortment of the individual molecular identities occurs by combinatorial processes between the consecutive sequences in the construct possessing regions of homology, or between quasi-repeated units. The reassortment process recombines and/or reduces the complexity and extent of the repeated sequences and results in the production of novel molecular species. Various treatments may be applied to enhance the rate of reassortment. These could include treatment with ultra-violet light, or DNA damaging chemicals and/or the use of host cell lines displaying enhanced levels of "genetic instability". Thus the reassortment process may involve homologous recombination or the natural property of quasi-repeated sequences to direct their own evolution.

Repeated or "quasi-repeated" sequences play a role in genetic instability. In the present invention, "quasi-repeats" are repeats that are not restricted to their original unit structure. Quasi-repeated units can be presented as an array of sequences in a construct; consecutive units of similar sequences. Once ligated, the junctions between the consecutive sequences become essentially invisible and the quasi-repetitive nature of the resulting construct is now continuous at the molecular level. The deletion process the cell performs to reduce the complexity of the resulting construct operates between the quasi- repeated sequences. The quasi-repeated units provide a practically limitless repertoire of templates upon which slippage events can occur. The constructs containing the quasi- repeats thus effectively provide sufficient molecular elasticity that deletion (and potentially insertion) events can occur virtually anywhere within the quasi-repetitive units.

When the quasi-repeated sequences are all ligated in the same orientation, for instance head to tail or vice versa, the cell cannot distinguish individual units. Consequently, the reductive process can occur throughout the sequences. In contrast, when for example, the units are presented head to head, rather than head to tail, the inversion delineates the endpoints of the adjacent unit so that deletion formation will favor the loss of discrete units. Thus, it is preferable with the present method that the sequences are in the same orientation. Random orientation of quasi-repeated sequences will result in the loss of reassortment efficiency, while consistent orientation of the sequences will offer the highest efficiency. However, while having fewer of the contiguous sequences in the same orientation decreases the efficiency, it may still provide sufficient elasticity for the effective recovery of novel molecules. Constructs can be made with the quasi-repeated sequences in the same orientation to allow higher efficiency.

Sequences can be assembled in a head to tail orientation using any of a variety of methods, including the following: a) Primers that include a poly-A head and poly-T tail which when made single- stranded would provide orientation can be utilized. This is accomplished by having the first few bases of the primers made from RNA and hence easily removed RNaseH. b) Primers that include unique restriction cleavage sites can be utilized. Multiple sites, a battery of unique sequences and repeated synthesis and ligation steps would be required. c) The inner few bases of the primer could be thiolated and an exonuclease used to produce properly tailed molecules.

The recovery of the re-assorted sequences relies on the identification of cloning vectors with a reduced repetitive index (RI). The re-assorted encoding sequences can then be recovered by amplification. The products are re-cloned and expressed. The recovery of cloning vectors with reduced RI can be affected by:

1) The use of vectors only stably maintained when the construct is reduced in complexity.

2) The physical recovery of shortened vectors by physical procedures. In this case, the cloning vector would be recovered using standard plasmid isolation procedures and size fractionated on either an agarose gel, or column with a low molecular weight cut off utilizing standard procedures.

3) The recovery of vectors containing interrupted genes which can be selected when insert size decreases. 4) The use of direct selection techniques with an expression vector and the appropriate selection.

Encoding sequences (for example, genes) from related organisms may demonstrate a high degree of homology and encode quite diverse protein products. These types of sequences are particularly useful in the present invention as quasi-repeats. However, while the examples illustrated below demonstrate the reassortment of nearly identical original encoding sequences (quasi-repeats), this process is not limited to such nearly identical repeats. The following example demonstrates a method of the invention. Encoding nucleic acid sequences (quasi-repeats) derived from three (3) unique species are described. Each sequence encodes a protein with a distinct set of properties. Each of the sequences differs by a single or a few base pairs at a unique position in the sequence. The quasi-repeated sequences are separately or collectively amplified and ligated into random assemblies such that all possible permutations and combinations are available in the population of ligated molecules. The number of quasi-repeat units can be controlled by the assembly conditions. The average number of quasi-repeated units in a construct is defined as the repetitive index (RI).

Once formed, the constructs may, or may not be size fractionated on an agarose gel according to published protocols, inserted into a cloning vector and transfected into an appropriate host cell. The cells are then propagated and "reductive reassortment" is effected. The rate of the reductive reassortment process may be stimulated by the introduction of DNA damage if desired. Whether the reduction in RI is mediated by deletion formation between repeated sequences by an "intra-molecular" mechanism, or mediated by recombination-like events through "inter-molecular" mechanisms is immaterial. The end result is a reassortment of the molecules into all possible combinations.

Optionally, the method comprises the additional step of screening the library members of the shuffled pool to identify individual shuffled library members having the ability to bind or otherwise interact, or catalyze a particular reaction (e.g., such as catalytic domain of an enzyme) with a predetermined macromolecule, such as for example a proteinaceous receptor, an oligosaccharide, virion, or other predetermined compound or structure.

The polypeptides that are identified from such libraries can be used for therapeutic, diagnostic, research and related purposes (e.g., catalysts, solutes for increasing osmolality of an aqueous solution and the like) and/or can be subjected to one or more additional cycles of shuffling and/or selection.

In another aspect, it is envisioned that prior to or during recombination or reassortment, polynucleotides generated by the method of the invention can be subjected to agents or processes which promote the introduction of mutations into the original polynucleotides. The introduction of such mutations would increase the diversity of resulting hybrid polynucleotides and polypeptides encoded therefrom. The agents or processes which promote mutagenesis can include, but are not limited to: (+)-CC-1065, or a synthetic analog such as (+)-CC-1065-(N3-Adenine (See Sun and Hurley, (1992); an N-acetylated or deacetylated 4'-fluro-4-aminobiphenyl adduct capable of inhibiting DNA synthesis (See , for example, van de Poll et al. (1992)); or a N-acetylated or deacetylated 4-aminobiphenyl adduct capable of inhibiting DNA synthesis (See also, van de Poll et al. (1992), pp. 751-758); trivalent chromium, a trivalent chromium salt, a polycyclic aromatic hydrocarbon (PAH) DNA adduct capable of inhibiting DNA replication, such as 7-bromomethyl-benz[fl]anthracene ("BMA"), tris(2,3-dibromopropyl)phosphate ("Tris- BP"), l,2-dibromo-3-chloropropane ("DBCP"), 2-bromoacrolein (2BA), benzo[α]pyrene- 7,8-dihydrodiol-9-10-epoxide ("BPDE"), a ρlatinum(II) halogen salt, N-hydroxy-2- amino-3-methylimidazo[4,5_:/]-quinolme ("N-hydroxy-IQ") and N-hydroxy-2-amino-l- methyl-6-phenylimidazo[4,5-/|-pyridine ("N-hydroxy-PhIP"). Exemplary means for slowing or halting PCR amplification consist of UV light (+)-CC-1065 and (+)-CC-1065- (N3 -Adenine). Particularly encompassed means are DNA adducts or polynucleotides comprising the DNA adducts from the polynucleotides or polynucleotides pool, which can be released or removed by a process including heating the solution comprising the polynucleotides prior to further processing.

In another aspect the invention is directed to a method of producing recombinant proteins having biological activity by treating a sample comprising double- stranded template polynucleotides encoding a wild-type protein under conditions according to the invention which provide for the production of hybrid or re-assorted polynucleotides.

Producing sequence variants

The invention also provides additional methods for making sequence variants of the nucleic acid (e.g., tryptophan-processing enzyme) sequences of the invention. The invention also provides additional methods for isolating tryptophan- processing enzymes using the nucleic acids and polypeptides of the invention. In one aspect, the invention provides for variants of a tryptophan-processing enzyme coding sequence (e.g., a gene, cDNA or message) of the invention, which can be altered by any means, including, e.g., random or stochastic methods, or, non-stochastic, or "directed evolution," methods, as described above.

The isolated variants may be naturally occurring. Variant can also be created in vitro. Variants may be created using genetic engineering techniques such as site directed mutagenesis, random chemical mutagenesis, Exonuclease in deletion procedures, and standard cloning techniques. Alternatively, such variants, fragments, analogs, or derivatives may be created using chemical synthesis or modification procedures. Other methods of making variants are also familiar to those skilled in the art. These include procedures in which nucleic acid sequences obtained from natural isolates are modified to generate nucleic acids which encode polypeptides having characteristics which enhance their value in industrial or laboratory applications. In such procedures, a large number of variant sequences having one or more nucleotide differences with respect to the sequence obtained from the natural isolate are generated and characterized. These nucleotide differences can result in amino acid changes with respect to the polypeptides encoded by the nucleic acids from the natural isolates.

For example, variants may be created using error prone PCR. In error prone PCR, PCR is performed under conditions where the copying fidelity of the DNA polymerase is low, such that a high rate of point mutations is obtained along the entire length of the PCR product. Error prone PCR is described, e.g., in Leung (1989) Technique 1:11-15) and Caldwell (1992) PCR Methods Applic. 2:28-33. Briefly, in such procedures, nucleic acids to be mutagenized are mixed with PCR primers, reaction buffer, MgCl₂, MnCl₂, Taq polymerase and an appropriate concentration of dNTPs for achieving a high rate of point mutation along the entire length of the PCR product. For example, the reaction may be performed using 20 fmoles of nucleic acid to be mutagenized, 30 pmole of each PCR primer, a reaction buffer comprising 5OmM KCl, 1OmM Tris HCl (pH 8.3) and 0.01% gelatin, 7mM MgC12, 0.5mM MnCl₂, 5 units of Taq polymerase, 0.2mM dGTP, 0.2mM dATP, ImM dCTP, and ImM dTTP. PCR may be performed for 30 cycles of 94°C for 1 min, 45°C for 1 min, and 72⁰C for 1 min. However, it will be appreciated that these parameters may be varied as appropriate. The mutagenized nucleic acids are cloned into an appropriate vector and the activities of the polypeptides encoded by the mutagenized nucleic acids are evaluated.

Variants may also be created using oligonucleotide directed mutagenesis to generate site-specific mutations in any cloned DNA of interest. Oligonucleotide mutagenesis is described, e.g., in Reidhaar-Olson (1988) Science 241:53-57. Briefly, in such procedures a plurality of double stranded oligonucleotides bearing one or more mutations to be introduced into the cloned DNA are synthesized and inserted into the cloned DNA to be mutagenized. Clones containing the mutagenized DNA are recovered and the activities of the polypeptides they encode are assessed. Another method for generating variants is assembly PCR. Assembly PCR involves the assembly of a PCR product from a mixture of small DNA fragments. A large number of different PCR reactions occur in parallel in the same vial, with the products of one reaction priming the products of another reaction. Assembly PCR is described in, e.g., U.S. Patent No. 5,965,408. Still another method of generating variants is sexual PCR mutagenesis. In sexual PCR mutagenesis, forced homologous recombination occurs between DNA molecules of different but highly related DNA sequence in vitro, as a result of random fragmentation of the DNA molecule based on sequence homology, followed by fixation of the crossover by primer extension in a PCR reaction. Sexual PCR mutagenesis is described, e.g., in Stemmer (1994) Proc. Natl. Acad. Sci. USA 91:10747-10751. Briefly, in such procedures a plurality of nucleic acids to be recombined are digested with DNase to generate fragments having an average size of 50-200 nucleotides. Fragments of the desired average size are purified and resuspended in a PCR mixture. PCR is conducted under conditions which facilitate recombination between the nucleic acid fragments. For example, PCR may be performed by resuspending the purified fragments at a concentration of 10-30ng/μl in a solution of 0.2mM of each dNTP, 2.2mM MgCl₂, 5OmM KCL, 1OmM Tris HCl, pH 9.0, and 0.1% Triton X-100. 2.5 units of Taq polymerase per 100:1 of reaction mixture is added and PCR is performed using the following regime: 94⁰C for 60 seconds, 94°C for 30 seconds, 50-55⁰C for 30 seconds, 72°C for 30 seconds (30-45 times) and 72°C for 5 minutes. However, it will be appreciated that these parameters may be varied as appropriate. In some aspects, oligonucleotides may be included in the PCR reactions. In other aspects, the Klenow fragment of DNA polymerase I may be used in a first set of PCR reactions and Taq polymerase may be used in a subsequent set of PCR reactions. Recombinant sequences are isolated and the_^ activities of the polypeptides they encode are assessed.

Variants may also be created by in vivo mutagenesis. In some aspects, random mutations in a sequence of interest are generated by propagating the sequence of interest in a bacterial strain, such as an E. coli strain, which carries mutations in one or more of the DNA repair pathways. Such "mutator" strains have a higher random mutation rate than that of a wild-type parent. Propagating the DNA in one of these strains will eventually generate random mutations within the DNA. Mutator strains suitable for use for in vivo mutagenesis are described in PCT Publication No. WO 91/16427, published October 31, 1991, entitled "Methods for Phenotype Creation from Multiple Gene Populations".

Variants may also be generated using cassette mutagenesis. In cassette mutagenesis a small region of a double stranded DNA molecule is replaced with a synthetic oligonucleotide "cassette" that differs from the native sequence. The oligonucleotide often contains completely and/or partially randomized native sequence. Recursive ensemble mutagenesis may also be used to generate variants.

Recursive ensemble mutagenesis is an algorithm for protein engineering (protein mutagenesis) developed to produce diverse populations of phenotypically related mutants whose members differ in amino acid sequence. This method uses a feedback mechanism to control successive rounds of combinatorial cassette mutagenesis. Recursive ensemble mutagenesis is described, e.g., in Arkin (1992) Proc. Natl. Acad. Sci. USA 89:7811-7815.

In some aspects, variants are created using exponential ensemble mutagenesis. Exponential ensemble mutagenesis is a process for generating combinatorial libraries with a high percentage of unique and functional mutants, wherein small groups of residues are randomized in parallel to identify, at each altered position, amino acids which lead to functional proteins. Exponential ensemble mutagenesis is described, e.g., in Delegrave (1993) Biotechnology Res. 11:1548-1552. Random and site-directed mutagenesis are described, e.g., in Arnold (1993) Current Opinion in Biotechnology 4:450-455.

In some aspects, the variants are created using shuffling procedures wherein portions of a plurality of nucleic acids which encode distinct polypeptides are fused together to create chimeric nucleic acid sequences which encode chimeric polypeptides as described in U.S. Patent No. 5,965,408, filed July 9, 1996, entitled, "Method of DNA Reassembly by Interrupting Synthesis" and U.S. Patent No. 5,939,250, filed May 22, 1996, entitled, "Production of Enzymes Having Desired Activities by Mutagenesis.

The variants of the polypeptides of the invention may be variants in which one or more of the amino acid residues of the polypeptides of the sequences of the invention are substituted with a conserved or non-conserved amino acid residue (in one aspect a conserved amino acid residue) and such substituted amino acid residue may or may not be one encoded by the genetic code.

Conservative substitutions are those that substitute a given amino acid in a polypeptide by another amino acid of like characteristics. Typically seen as conservative substitutions are the following replacements: replacements of an aliphatic amino acid such as Alanine, Valine, Leucine and Isoleucine with another aliphatic amino acid; replacement of a Serine with a Threonine or vice versa; replacement of an acidic residue such as Aspartic acid and Glutamic acid with another acidic residue; replacement of a residue bearing an amide group, such as Asparagine and Glutamine, with another residue bearing an amide group; exchange of a basic residue such as Lysine and Arginine with another basic residue; and replacement of an aromatic residue such as Phenylalanine,

Tyrosine with another aromatic residue.

Other variants are those in which one or more of the amino acid residues of a polypeptide of the invention includes a substituent group. Still other variants are those in which the polypeptide is associated with another compound, such as a compound to increase the half-life of the polypeptide (for example, polyethylene glycol).

Additional variants are those in which additional amino acids are fused to the polypeptide, such as a leader sequence, a secretory sequence, a proprotein sequence or a sequence which facilitates purification, enrichment, or stabilization of the polypeptide. In some aspects, the fragments, derivatives and analogs retain the same biological function or activity as the polypeptides of the invention. In other aspects, the fragment, derivative, or analog includes a proprotein, such that the fragment, derivative, or analog can be activated by cleavage of the proprotein portion to produce an active polypeptide.

Optimizing codons to achieve high levels of protein expression in host cells

The invention provides methods for modifying tryptophan-degrading enzyme-encoding nucleic acids to modify codon usage. In one aspect, the invention provides methods for modifying codons in a nucleic acid encoding a tryptophan- processing enzyme to increase or decrease its expression in a host cell. The invention also provides nucleic acids encoding a tryptophan-processing enzyme modified to increase its expression in a host cell, tryptophan-processing enzyme so modified, and methods of making the modified tryptophan-processing enzymes. The method comprises identifying a "non-preferred" or a "less preferred" codon in tryptophan-degrading enzyme-encoding nucleic acid and replacing one or more of these non- preferred or less preferred codons with a "preferred codon" encoding the same amino acid as the replaced codon and at least one non- preferred or less preferred codon in the nucleic acid has been replaced by a preferred codon encoding the same amnio acid. A preferred codon is a codon over-represented in coding sequences in genes in the host cell and a non- preferred or less preferred codon is a codon under-represented in coding sequences in genes in the host cell.

Host cells for expressing the nucleic acids, expression cassettes and vectors of the invention include bacteria, yeast, fungi, plant cells, insect cells and mammalian cells. Thus, the invention provides methods for optimizing codon usage in all of these cells, codon-altered nucleic acids and polypeptides made by the codon-altered nucleic acids. Exemplary host cells include gram negative bacteria, such as Escherichia coli; gram positive bacteria, such as Streptomyces sp., Lactobacillus gasseri, Lactococcus lactis, Lactococcus cremoris, Bacillus subtilis, Bacillus cereus. Exemplary host cells also include eukaryotic organisms, e.g., various yeast, such as Saccharomyces sp., including Saccharomyces cerevisiae, Schizosaccharomycespom.be, Pichiapastoris, and Kluyveromyces lactis, Hansenula polymorpha, Aspergillus niger, and mammalian cells and cell lines and insect cells and cell lines. Thus, the invention also includes nucleic acids and polypeptides optimized for expression in these organisms and species. For example, the codons of a nucleic acid encoding a tryptophan- processing enzyme isolated from a bacterial cell are modified such that the nucleic acid is optimally expressed in a bacterial cell different from the bacteria from which the tryptophan-processing enzyme was derived, a yeast, a fungi, a plant cell, an insect cell or a mammalian cell. Methods for optimizing codons are well known in the art, see, e.g.,

U.S. Patent No. 5,795,737; Baca (2000) Int. J. Parasitol. 30:113-118; Hale (1998) Protein Expr. Purif. 12:185-188; Narum (2001) Infect. Immun. 69:7250-7253. See also Narum (2001) Infect. Immun. 69:7250-7253, describing optimizing codons in mouse systems; Outchkourov (2002) Protein Expr. Purif. 24:18-24, describing optimizing codons hi yeast; Feng (2000) Biochemistry 39:15399-15409, describing optimizing codons inis. coli;

Humphreys (2000) Protein Expr. Purif. 20:252-264, describing optimizing codon usage that affects secretion hi E. coli. Transgenic non-human animals

The invention provides transgenic non-human animals comprising a nucleic acid, a polypeptide (e.g., a tryptophan-processing enzyme), an expression cassette or vector or a transfected or transformed cell of the invention. The invention also provides methods of making and using these transgenic non-human animals.

The transgenic non-human animals can be, e.g., goats, rabbits, sheep, pigs (including all swine, hogs and related animals), cows, rats and mice, comprising the nucleic acids of the invention. These animals can be used, e.g., as in vivo models to study tryptophan-processing enzyme activity, or, as models to screen for agents that change the tryptophan-processing enzyme activity in vivo. The coding sequences for the polypeptides to be expressed in the transgenic non-human animals can be designed to be constitutive, or, under the control of tissue-specific, developmental-specific or inducible transcriptional regulatory factors. Transgenic non-human animals can be designed and generated using any method known in the art; see, e.g., U.S. Patent Nos. 6,211,428; 6,187,992; 6,156,952; 6,118,044; 6,111,166; 6,107,541; 5,959,171; 5,922,854; 5,892,070; 5,880,327; 5,891,698; 5,639,940; 5,573,933; 5,387,742; 5,087,571, describing making and using transformed cells and eggs and transgenic mice, rats, rabbits, sheep, pigs and cows. See also, e.g., Pollock (1999) J. Immunol. Methods 231 : 147-157, describing the production of recombinant proteins in the milk of transgenic dairy animals; Baguisi (1999) Nat. Biotechnol. 17:456-461, demonstrating the production of transgenic goats. U.S. Patent No. 6,211,428, describes making and using transgenic non-human mammals which express in their brains a nucleic acid construct comprising a DNA sequence. U.S. Patent No. 5,387,742, describes injecting cloned recombinant or synthetic DNA sequences into fertilized mouse eggs, implanting the injected eggs in pseudo-pregnant females, and growing to term transgenic mice. U.S. Patent No. 6,187,992, describes making and using a transgenic mouse.

"Knockout animals" can also be used to practice the methods of the invention. For example, in one aspect, the transgenic or modified animals of the invention comprise a "knockout animal," e.g., a "knockout mouse," engineered not to express an endogenous gene, which is replaced with a gene expressing a tryptophan- processing enzyme of the invention, or, a fusion protein comprising a tryptophan- processing enzyme of the invention. Transgenic Plants and Seeds

The invention provides transgenic plants and seeds comprising a nucleic acid, a polypeptide (e.g., a tryptophan-processing enzyme), an expression cassette or vector or a transfected or transformed cell of the invention. The invention also provides plant products, e.g., oils, seeds, leaves, extracts and the like, comprising a nucleic acid and/or a polypeptide (e.g., a tryptophan-processing enzyme) of the invention. The transgenic plant can be dicotyledonous (a dicot) or monocotyledonous (a monocot). The invention also provides methods of making and using these transgenic plants and seeds. The transgenic plant or plant cell expressing a polypeptide of the present invention may be constructed in accordance with any method known in the art. See, for example, U.S. Patent No. 6,309,872.

Nucleic acids and expression constructs of the invention can be introduced into a plant cell by any means. For example, nucleic acids or expression constructs can be introduced into the genome of a desired plant host, or, the nucleic acids or expression constructs can be episomes. Introduction into the genome of a desired plant can be such that the host's tryptophan-processing enzyme production is regulated by endogenous transcriptional or translational control elements. The invention also provides "knockout plants" where insertion of gene sequence by, e.g., homologous recombination, has disrupted the expression of the endogenous gene. Means to generate "knockout" plants are well-known in the art, see, e.g., Strepp (1998) Proc Natl. Acad. Sci. USA 95:4368- 4373; Miao (1995) Plant J 7:359-365. See discussion on transgenic plants, below.

The nucleic acids of the invention can be used to confer desired traits on essentially any plant, e.g., on starch-producing plants, such as potato, wheat, rice, barley, and the like. Nucleic acids of the invention can be used to manipulate metabolic pathways of a plant in order to optimize or alter host' s expression of tryptophan- processing enzyme. The can change tryptophan-processing enzyme activity in a plant. Alternatively, a tryptophan-processing enzyme of the invention can be used in production of a transgenic plant to produce a compound not naturally produced by that plant. This can lower production costs or create a novel product. In one aspect, the first step in production of a transgenic plant involves making an expression construct for expression in a plant cell. These techniques are well known in the art. They can include selecting and cloning a promoter, a coding sequence for facilitating efficient binding of ribosomes to mRNA and selecting the appropriate gene terminator sequences. One exemplary constitutive promoter is CaMV35S, from the cauliflower mosaic virus, which generally results in a high degree of expression in plants. Other promoters are more specific and respond to cues in the plant's internal or external environment. An exemplary light-inducible promoter is the promoter from the cab gene, encoding the major chlorophyll a^ binding protein. In one aspect, the nucleic acid is modified to achieve greater expression in a plant cell. For example, a sequence of the invention is likely to have a higher percentage of A-T nucleotide pairs compared to that seen in a plant, some of which prefer G-C nucleotide pairs. Therefore, A-T nucleotides in the coding sequence can be substituted with G-C nucleotides without significantly changing the amino acid sequence to enhance production of the gene product in plant cells.

Selectable marker gene can be added to the gene construct in order to identify plant cells or tissues that have successfully integrated the transgene. This may be necessary because achieving incorporation and expression of genes in plant cells is a rare event, occurring in just a few percent of the targeted tissues or cells. Selectable marker genes encode proteins that provide resistance to agents that are normally toxic to plants, such as antibiotics or herbicides. Only plant cells that have integrated the selectable marker gene will survive when grown on a medium containing the appropriate antibiotic or herbicide. As for other inserted genes, marker genes also require promoter and termination sequences for proper function. In one aspect, making transgenic plants or seeds comprises incorporating sequences of the invention and, optionally, marker genes into a target expression construct (e.g., a plasmid), along with positioning of the promoter and the terminator sequences. This can involve transferring the modified gene into the plant through a suitable method. For example, a construct may be introduced directly into the genomic DNA of the plant cell using techniques such as electroporation and microinjection of plant cell protoplasts, or the constructs can be introduced directly to plant tissue using ballistic methods, such as DNA particle bombardment. For example, see, e.g., Christou (1997) Plant MoI. Biol. 35:197-203; Pawlowski (1996) MoI. Biotechnol. 6:17-30; Klein (1987) Nature 327:70-73; Takumi (1997) Genes Genet. Syst. 72:63-69, discussing use of particle bombardment to introduce transgenes into wheat; and Adam (1997) supra, for use of particle bombardment to introduce YACs into plant cells. For example, Rinehart (1997) supra, used particle bombardment to generate transgenic cotton plants. Apparatus for accelerating particles is described U.S. Pat. No. 5,015,580; and, the commercially available BioRad (Biolistics) PDS-2000 particle acceleration instrument; see also, John, U.S. Patent No. 5,608,148; and Ellis, U.S. Patent No. 5, 681,730, describing particle- mediated transformation of gymnosperms.

In one aspect, protoplasts can be immobilized and injected with a nucleic acids, e.g., an expression construct. Although plant regeneration from protoplasts is not easy with cereals, plant regeneration is possible in legumes using somatic embryogenesis from protoplast derived callus. Organized tissues can be transformed with naked DNA using gene gun technique, where DNA is coated on tungsten microprojectiles, shot 1/lOOth the size of cells, which carry the DNA deep into cells and organelles. Transformed tissue is then induced to regenerate, usually by somatic embryogenesis. This technique has been successful in several cereal species including maize and rice.

Nucleic acids, e.g., expression constructs, can also be introduced in to plant cells using recombinant viruses. Plant cells can be transformed using viral vectors, such as, e.g., tobacco mosaic virus derived vectors (Rouwendal (1997) Plant MoI. Biol. 33:989-999), see Porta (1996) "Use of viral replicons for the expression of genes in plants," MoI. Biotechnol. 5:209-221.

Alternatively, nucleic acids, e.g., an expression construct, can be combined with suitable T-DNA flanking regions and introduced into a conventional Agrobacteήum tumefaciens host vector. The virulence functions of the Agrobacterium tumefaciens host will direct the insertion of the construct and adjacent marker into the plant cell DNA when the cell is infected by the bacteria. Agrobacterium tumefaciens-mediated transformation techniques, including disarming and use of binary vectors, are well described in the scientific literature. See, e.g., Horsch (1984) Science 233:496-498; Fraley (1983) Proc. Nαtl. Acαd. ScL USA 80:4803 (1983); Gene Transfer to Plants, Potrykus, ed. (Springer- Verlag, Berlin 1995). The DNA in an A. tumefaciens cell is contained in the bacterial chromosome as well as in another structure known as a Ti

(tumor-inducing) plasmid. The Ti plasmid contains a stretch of DNA termed T-DNA (~20 kb long) that is transferred to the plant cell in the infection process and a series of vir (virulence) genes that direct the infection process. A. tumefaciens can only infect a plant through wounds: when a plant root or stem is wounded it gives off certain chemical signals, in response to which, the vir genes of A. tumefaciens become activated and direct a series of events necessary for the transfer of the T-DNA from the Ti plasmid to the plant's chromosome. The T-DNA then enters the plant cell through the wound. One speculation is that the T-DNA waits until the plant DNA is being replicated or transcribed, then inserts itself into the exposed plant DNA. In order to use A. tumefaciens as a transgene vector, the tumor-inducing section of T-DNA have to be removed, while retaining the T-DNA border regions and the vir genes. The transgene is then inserted between the T-DNA border regions, where it is transferred to the plant cell and becomes integrated into the plant's chromosomes. The invention provides for the transformation of monocotyledonous plants using the nucleic acids of the invention, including important cereals, see Hiei (1997) Plant MoI. Biol. 35:205-218. See also, e.g., Horsch, Science (1984) 233:496; Fraley (1983) Proc. Natl. Acad. Sci USA 80:4803; Thykjaer (1997) supra; Park (1996) Plant MoI. Biol. 32:1135-1148, discussing T-DNA integration into genomic DNA. See also D'Halluin, U.S. Patent No. 5,712,135, describing a process for the stable integration of a DNA comprising a gene that is functional in a cell of a cereal, or other monocotyledonous plant.

In one aspect, the third step can involve selection and regeneration of whole plants capable of transmitting the incorporated target gene to the next generation. Such regeneration techniques rely on manipulation of certain phytohormones in a tissue culture growth medium, typically relying on a biocide and/or herbicide marker that has been introduced together with the desired nucleotide sequences. Plant regeneration from cultured protoplasts is described in Evans et al, Protoplasts Isolation and Culture, Handbook of Plant Cell Culture, pp. 124-176, MacMillilan Publishing Company, New York, 1983; and Binding, Regeneration of Plants, Plant Protoplasts, pp. 21-73, CRC

Press, Boca Raton, 1985. Regeneration can also be obtained from plant callus, explants, organs, or parts thereof. Such regeneration techniques are described generally in Klee (1987) Ann. Rev. of Plant Phys. 38:467-486. To obtain whole plants from transgenic tissues such as immature embryos, they can be grown under controlled environmental conditions in a series of media containing nutrients and hormones, a process known as tissue culture. Once whole plants are generated and produce seed, evaluation of the progeny begins.

After the expression cassette is stably incorporated in transgenic plants, it can be introduced into other plants by sexual crossing. Any of a number of standard breeding techniques can be used, depending upon the species to be crossed. Since transgenic expression of the nucleic acids of the invention leads to phenotypic changes, plants comprising the recombinant nucleic acids of the invention can be sexually crossed with a second plant to obtain a final product. Thus, the seed of the invention can be derived from a cross between two transgenic plants of the invention, or a cross between a plant of the invention and another plant. The desired effects (e.g., expression of the polypeptides of the invention to produce a plant in which flowering behavior is altered) can be enhanced when both parental plants express the polypeptides (e.g., a tryptophan- processing enzyme) of the invention. The desired effects can be passed to future plant generations by standard propagation means.

The nucleic acids and polypeptides of the invention are expressed in or inserted in any plant or seed. Transgenic plants of the invention can be dicotyledonous or monocotyledonous. Examples of monocot transgenic plants of the invention are grasses, such as meadow grass (blue grass, Pod), forage grass such as festuca, lolium, temperate grass, such as Agrostis, and cereals, e.g., wheat, oats, rye, barley, rice, sorghum, and maize (corn). Examples of dicot transgenic plants of the invention are tobacco, legumes, such as lupins, potato, sugar beet, pea, bean and soybean, and cruciferous plants (family Brassicaceae), such as cauliflower, rape seed, and the closely related model organism Arabidopsis thaliana. Thus, the transgenic plants and seeds of the invention include a broad range of plants, including, but not limited to, species from the genera Anacardhim, Arachis, Asparagus, Atropa, Avena, Brassica, Citrus, Citrullus, Capsicum, Carthamus, Cocos, Coffea, Cucumis, Cucurbita, Daucus, Elaeis, Fragaria, Glycine, Gossypium, Helianthus, Heterocallis, Hordeum, Hyoscyamus, Lactuca, Linum, Lolium, Lupinus, Lycopersicon, Malus, Manihot, Majorana, Medicago, Nicotiana, Olea, Oryza, Panieum, Pannisetum, Persea, Phaseolus, Pistachio, Pisum, Pyrus, Prunus, Raphanus, Ricinus, Secale, Senecio, Sinapis, Solatium, Sorghum, Tlieobromus, Trigonella, Triticum, Vicia, Vitis, Vigna, and Zea.

In alternative embodiments, the nucleic acids of the invention are expressed in plants which contain fiber cells, including, e.g., cotton, silk cotton tree (Kapok, Ceiba pentandra), desert willow, creosote bush, winterfat, balsa, ramie, kenaf, hemp, roselle, jute, sisal abaca and flax. In alternative embodiments, the transgenic plants of the invention can be members of the genus Gossypium, including members of any Gossypium species, such as G. arbor eum;. G. herbaceum, G. barbadense, and G. hirsutum. The invention also provides for transgenic plants to be used for producing large amounts of the polypeptides (e.g., a tryptophan-processing enzyme or antibody) of the invention. For example, see Palmgren (1997) Trends Genet. 13:348; Chong (1997) Transgenic Res. 6:289-296 (producing human milk protein beta-casein in transgenic potato plants using an auxin-inducible, bidirectional mannopine synthase (masl',2¹) promoter with Agrobacterium tumefaciens-mediated leaf disc transformation methods).

Using known procedures, one of skill can screen for plants of the invention by detecting the increase or decrease of transgene mRNA or protein in transgenic plants. Means for detecting and quantitation of mRNAs or proteins are well known in the art.

Polypeptides and peptides

In one aspect, the invention provides isolated or recombinant polypeptides having a sequence identity (e.g., at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more, or complete (100%) sequence identity, or homology) to an exemplary sequence of the invention, e.g., proteins having a sequence as set forth in SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68 or SEQ ID NO:70). The percent sequence identity can be over the full length of the polypeptide, or, the identity can be over a region of at least about 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700 or more residues.

In one aspect, a polypeptide or peptide of the invention has tryptophan- processing activity. As used herein, the terms "tryptophan-processing" and "tryptophan- degrading" encompass any polypeptide or enzymes capable of catalyzing a tryptophan- processing, tryptophan-degrading or tryptophan-modifying activity, including, e.g., the exemplary polypeptides having a sequence as set forth in SEQ ID NO:6 (encoded by, e.g., SEQ ID NO:5), and SEQ ID NO: 10 (encoded by, e.g., SEQ ID NO:9), which are tryptophanases, which are 1 amino acid different from each other; and, SEQ ID NO:4

(encoded by, e.g., SEQ ID NO:3) which is a tryptophan decarboxylase; and SEQ ID NO:8 (encoded by, e.g., SEQ ID NO:7) which is a tyrosine phenol lyase - very similar to tryptophanase; there are only 3 amino acids differentiating these 2 enzyme classes. The terms "tryptophan-processing" and "tryptophan-degrading" encompass any polypeptide or enzyme having tryptophanase, tryptophan decarboxylase, tryptophan dioxygenase, tryptophan transaminase activity, tryptophan side chain oxidase and/or tyrosine phenol lyase activity. For example, see Figure 8, illustrating alternative routes of tryptophan processing used by the compositions (e.g., enzymes) and methods of the invention.

Polypeptides of the invention can also be shorter than the full length of exemplary polypeptides. In alternative aspects, the invention provides polypeptides (peptides, fragments) ranging in size between about 5 and the full length of a polypeptide, e.g., an enzyme, such as a tryptophan-processing enzyme; exemplary sizes being of about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 100, 125, 150, 175,

200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, or more residues, e.g., contiguous residues of an exemplary tryptophan-processing enzyme of the invention. Peptides of the invention (e.g., a subsequence of an exemplary polypeptide of the invention) can be useful as, e.g., labeling probes, antigens, toleragens, motifs, tryptophan-processing enzyme active sites (e.g., "catalytic domains"), signal sequences and/or prepro domains.

In alternative aspects, polypeptides of the invention having tryptophan- processing activity are members of a genus of polypeptides sharing specific structural elements, e.g., amino acid residues, that correlate with tryptophan-processing activity, e.g., catalysis of the tryptophan ring, e.g., as a tryptophanase, tryptophan aminotransferase, tryptophan decarboxylase, tryptophan dioxygenase, and/or tyrosine phenol lyase. These shared structural elements can be used for the routine generation of tryptophan-processing variants. These shared structural elements of tryptophan- processing enzymes of the invention can be used as guidance for the routine generation of tryptophan-processing enzymes variants within the scope of the genus of polypeptides of the invention.

Additionally, the crystal (three-dimensional) structure of tryptophanases and tyrosine phenol lyases have been analyzed, e.g., see Isupov (1998) "Crystal structure of tryptophanase" J. MoI. Biol. 276(3):603-623; Dementieva (1994) "Crystallization and preliminary X-ray investigation of holotryptophanases from Escherichia coli and Proteus vulgaris," J MoI Biol. 235(2):783-786; Antson (1993) "Three-dimensional structure of tyrosine phenol-lyase," Biochemistry 32(16):4195-4206; Demidkina (1988) "Crystallization and crystal data on tyrosine phenol-lyase," FEBS Lett. 1988 May 23;232(2):381-382, illustrating specific structural elements as guidance for the routine generation of tryptophanase variants. Polypeptides and peptides of the invention can be isolated from natural sources, be synthetic, or be recombinantly generated polypeptides. Peptides and proteins can be recombinantly expressed in vitro or in vivo. The peptides and polypeptides of the invention can be made and isolated using any method known in the art. Polypeptide and peptides of the invention can also be synthesized, whole or in part, using chemical methods well known in the art. See e.g., Caruthers (1980) Nucleic Acids Res. Symp. Ser. 215-223; Horn (1980) Nucleic Acids Res. Symp. Ser. 225-232; Banga, A.K., Therapeutic Peptides and Proteins, Formulation, Processing and Delivery Systems (1995) Technomic Publishing Co., Lancaster, PA. For example, peptide synthesis can be performed using various solid-phase techniques (see e.g., Roberge (1995) Science 269:202; Merrifield (1997) Methods Enzymol. 289:3-13) and automated synthesis maybe achieved, e.g., using the ABI 43 IA Peptide Synthesizer (Perkin Elmer) in accordance with the instructions provided by the manufacturer.

The peptides and polypeptides of the invention can also be glycosylated. The glycosylation can be added post-translationally either chemically or by cellular biosynthetic mechanisms, wherein the later incorporates the use of known glycosylation motifs, which can be native to the sequence or can be added as a peptide or added in the nucleic acid coding sequence. The glycosylation can be O-linked or N-linked.

The peptides and polypeptides of the invention, as defined above, include all "mimetic" and "peptidomimetic" forms. The terms "mimetic" and "peptidomimetic" refer to a synthetic chemical compound which has substantially the same structural and/or functional characteristics of the polypeptides of the invention. The mimetic can be either entirely composed of synthetic, non-natural analogues of amino acids, or, is a chimeric molecule of partly natural peptide amino acids and partly non-natural analogs of amino acids. The mimetic can also incorporate any amount of natural amino acid conservative substitutions as long as such substitutions also do not substantially alter the mimetic 's structure and/or activity. As with polypeptides of the invention which are conservative variants or members of a genus of polypeptides of the invention (e.g., having about 50% or more sequence identity to an exemplary sequence of the invention), routine experimentation will determine whether a mimetic is within the scope of the invention, i.e., that its structure and/or function is not substantially altered. Thus, in one aspect, a mimetic composition is within the scope of the invention if it has a tryptophan-processing enzymes activity. Polypeptide mimetic compositions of the invention can contain any combination of non-natural structural components. In alternative aspect, mimetic compositions of the invention include one or all of the following three structural groups: a) residue linkage groups other than the natural amide bond ("peptide bond") linkages; b) non-natural residues in place of naturally occurring amino acid residues; or c) residues which induce secondary structural mimicry, i.e., to induce or stabilize a secondary structure, e.g., a beta turn, gamma turn, beta sheet, alpha helix conformation, and the like. For example, a polypeptide of the invention can be characterized as a mimetic when all or some of its residues are joined by chemical means other than natural peptide bonds. Individual peptidomimetic residues can be j oined by peptide bonds, other chemical bonds or coupling means, such as, e.g., glutaraldehyde, N-hydroxysuccinimide esters, bifunctional maleimides, N,N'-dicyclohexylcarbodiimide (DCC) or N₃N'- diisopropylcarbodiimide (DIC). Linking groups that can be an alternative to the traditional amide bond ("peptide bond") linkages include, e.g., ketomethylene (e.g., - C(=O)-CH₂- for -C(=O)-NH-), aminomethylene (CH₂-NH), ethylene, olefin (CH=CH), ether (CH₂-O), thioether (CH₂-S), tetrazole (CN₄-), thiazole, retroamide, thioamide, or ester (see, e.g., Spatola (1983) in Chemistry and Biochemistry of Amino Acids, Peptides and Proteins, Vol. 7, pp 267-357, "Peptide Backbone Modifications," Marcell Dekker, NY). A polypeptide of the invention can also be characterized as a mimetic by containing all or some non-natural residues in place of naturally occurring amino acid residues. Non-natural residues are well described in the scientific and patent literature; a few exemplary non-natural compositions useful as mimetics of natural amino acid residues and guidelines are described below. Mimetics of aromatic amino acids can be generated by replacing by, e.g., D- or L- naphylalanine; D- or L- phenylglycine; D- or L- 2 thieneylalanine; D- or L-I, -2, 3-, or 4- pyreneylalanine; D- or L-3 thieneylalanine; D- or L-(2-pyridinyl)-alanine; D- or L-(3-pyridinyl)-alanine; D- or L-(2-pyrazinyl)-alanine; D- or L-(4-isopropyl)-phenylglycine; D-(trifluoromethyl)-phenylglycine; D- (trifluoromethyl)-phenylalanine; D-p-fluoro-phenylalanine; D- or L-p- biphenylphenylalanine; D- or L-p-methoxy-biphenylphenylalanine; D- or L-2- indole(alkyl)alanines; and, D- or L-alkylainines, where alkyl can be substituted or unsubstituted methyl, ethyl, propyl, hexyl, butyl, pentyl, isopropyl, iso-butyl, sec-isotyl, iso-pentyl, or a non-acidic amino acids. Aromatic rings of a non-natural amino acid include, e.g., thiazolyl, thiophenyl, pyrazolyl, benzimidazolyl, naphthyl, furanyl, pyrrolyl, and pyridyl aromatic rings.

Mimetics of acidic amino acids can be generated by substitution by, e.g., non-carboxylate amino acids while maintaining a negative charge; (phosphono)alanine; sulfated threonine. Carboxyl side groups (e.g., aspartyl or glutamyl) can also be selectively modified by reaction with carbodiimides (R' -N-C-N-R') such as, e.g., 1- cyclohexyl-3(2-morpholinyl-(4-ethyl) carbodiimide or l-ethyl-3(4-azonia- 4,4- dimetholpentyl) carbodiimide. Aspartyl or glutamyl can also be converted to asparaginyl and glutaminyl residues by reaction with ammonium ions. Mimetics of basic amino acids can be generated by substitution with, e.g., (in addition to lysine and arginine) the amino acids ornithine, citrulline, or (guanidino)-acetic acid, or (guanidino)alkyl-acetic acid, where alkyl is defined above. Nitrile derivative (e.g., containing the CN-moiety in place of COOH) can be substituted for asparagine or glutamine. Asparaginyl and glutaminyl residues can be deaminated to the corresponding aspartyl or glutamyl residues. Arginine residue mimetics can be generated by reacting arginyl with, e.g., one or more conventional reagents, including, e.g., phenylglyoxal, 2,3-butanedione, 1,2-cyclo- hexanedione, or ninhydrin, in one aspect under alkaline conditions. Tyrosine residue mimetics can be generated by reacting tyrosyl with, e.g., aromatic diazonium compounds or tetranitromethane. N-acetylimidizol and tetranitromethane can be used to form O- acetyl tyrosyl species and 3-nitro derivatives, respectively. Cysteine residue mimetics can be generated by reacting cysteinyl residues with, e.g., alpha-haloacetates such as 2- chloroacetic acid or chloroacetamide and corresponding amines; to give carboxymethyl or carboxyamidomethyl derivatives. Cysteine residue mimetics can also be generated by reacting cysteinyl residues with, e.g., bromo-trifluoroacetone, alpha-bromo-beta-(5- imidozoyl) propionic acid; chloroacetyl phosphate, N-alkylmaleimides, 3-nitro-2-pyridyl disulfide; methyl 2-pyridyl disulfide; p-chloromercuribenzoate; 2-chloromercuri-4 nitrophenol; or, chloro-7-nitrobenzo-oxa-l,3-diazole. Lysine mimetics can be generated (and amino terminal residues can be altered) by reacting lysinyl with, e.g., succinic or other carboxylic acid anhydrides. Lysine and other alpha-amino-containing residue mimetics can also be generated by reaction with imidoesters, such as methyl picolinimidate, pyridoxal phosphate, pyridoxal, chloroborohydride, trmitro- benzenesulfonic acid, O-methylisourea, 2,4, pentanedione, and transamidase-catalyzed reactions with glyoxylate. Mimetics of methionine can be generated by reaction with, e.g., methionine sulfoxide. Mimetics of proline include, e.g., pipecolic acid, thiazolidine carboxylic acid, 3- or 4- hydroxy proline, dehydroproline, 3- or 4-methylproline, or 3,3,- dimethylproline. Histidine residue mimetics can be generated by reacting histidyl with, e.g., diethylprocarbonate or para-bromophenacyl bromide. Other mimetics include, e.g., those generated by hydroxylation of proline and lysine; phosphorylation of the hydroxyl groups of seryl or threonyl residues; methylation of the alpha-amino groups of lysine, arginine and histidine; acetylation of the N-terminal amine; methylation of main chain amide residues or substitution with N-methyl amino acids; or amidation of C-terminal carboxyl groups.

A residue, e.g., an amino acid, of a polypeptide of the invention can also be replaced by an amino acid (or peptidomimetic residue) of the opposite chirality. Thus, any amino acid naturally occurring in the L-configuration (which can also be referred to as the R or S, depending upon the structure of the chemical entity) can be replaced with the amino acid of the same chemical structural type or a peptidomimetic, but of the opposite chirality, referred to as the D- amino acid, but also can be referred to as the R- or S- form.

The invention also provides methods for modifying the polypeptides of the invention by either natural processes, such as post-translational processing (e.g., phosphorylation, acylation, etc), or by chemical modification techniques, and the resulting modified polypeptides. Modifications can occur anywhere in the polypeptide, including the peptide backbone, the amino acid side-chains and the amino or carboxyl termini. It will be appreciated that the same type of modification may be present in the same or varying degrees at several sites in a given polypeptide. Also a given polypeptide may have many types of modifications. Modifications include acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of a phosphatidylinositol, cross-linking cyclization, disulfide bond formation, demethylation, formation of covalent cross-links, formation of cysteine, formation of pyroglutamate, formylation, gamma- carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristolyation, oxidation, pegylation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, and transfer-RNA mediated addition of amino acids to protein such as arginylation. See, e.g., Creighton, T.E., Proteins - Structure and Molecular Properties 2nd Ed., W.H. Freeman and Company, New York (1993); Posttranslational Covalent Modification of Proteins, B.C. Johnson, Ed., Academic Press, New York, pp. 1-12 (1983).

Solid-phase chemical peptide synthesis methods can also be used to synthesize the polypeptide or fragments of the invention. Such method have been known in the art since the early 1960's (Merrifield, R. B., J. Am. Chem. Soc, 85:2149-2154,

1963) (See also Stewart, J. M. and Young, J. D., Solid Phase Peptide Synthesis, 2nd Ed., Pierce Chemical Co., Rockford, 111., pp. 11-12)) and have recently been employed in commercially available laboratory peptide design and synthesis kits (Cambridge Research Biochemicals). Such commercially available laboratory kits have generally utilized the teachings of H. M. Geysen et al, Proc. Natl. Acad. ScL, USA, 81 :3998 (1984) and provide for synthesizing peptides upon the tips of a multitude of "rods" or "pins" all of which are connected to a single plate. When such a system is utilized, a plate of rods or pins is inverted and inserted into a second plate of corresponding wells or reservoirs, which contain solutions for attaching or anchoring an appropriate amino acid to the pin's or rod's tips. By repeating such a process step, i.e., inverting and inserting the rod's and pin's tips into appropriate solutions, amino acids are built into desired peptides. In addition, a number of available FMOC peptide synthesis systems are available. For example, assembly of a polypeptide or fragment can be carried out on a solid support using an Applied Biosystems, Inc. Model 431 A™ automated peptide synthesizer. Such equipment provides ready access to the peptides of the invention, either by direct synthesis or by synthesis of a series of fragments that can be coupled using other known techniques.

The polypeptides of the invention include tryptophan-processing enzymes in an active or inactive form. For example, the polypeptides of the invention include proproteins before "maturation" or processing of prepro sequences, e.g., by a proprotein- processing enzyme, such as a proprotein convertase to generate an "active" mature protein. The polypeptides of the invention include tryptophan-processing enzymes inactive for other reasons, e.g., before "activation" by a post-translational processing event, e.g., an endo- or exo-peptidase or proteinase action, a phosphorylation event, an amidation, a glycosylation or a sulfation, a dimerization event, and the like. The polypeptides of the invention include all active forms, including active subsequences, e.g., catalytic domains or active sites, of the enzyme.

The invention includes immobilized tryptophan-processing enzymes, anti- tryptophan-processing enzyme antibodies and fragments thereof. The invention provides methods for inhibiting tryptophan-processing enzyme activity, e.g., using dominant negative mutants or anti-tryptophan-processing enzyme antibodies of the invention. The invention includes heterocomplexes, e.g., fusion proteins, heterodimers, etc., comprising the tryptophan-processing enzymes of the invention.

Polypeptides of the invention can have a tryptophan-processing enzyme activity under various conditions, e.g., extremes in pH and/or temperature, oxidizing agents, and the like. The invention provides methods leading to alternative tryptophan- processing enzyme preparations with different catalytic efficiencies and stabilities, e.g., towards temperature, oxidizing agents and changing wash conditions. In one aspect, tryptophan-processing enzyme variants can be produced using techniques of site-directed mutagenesis and/or random mutagenesis. In one aspect, directed evolution can be used to produce a great variety of tryptophan-processing enzyme variants with alternative specificities and stability.

The proteins of the invention are also useful as research reagents to identify tryptophan-processing enzyme modulators, e.g., activators or inhibitors of tryptophan-processing enzyme activity. Briefly, test samples (compounds, broths, extracts, and the like) are added to tryptophan-processing enzyme assays to determine their ability to inhibit substrate cleavage. Inhibitors identified in this way can be used in industry and research to reduce or prevent undesired proteolysis. As with tryptophan- processing enzymes, inhibitors can be combined to increase the spectrum of activity. The enzymes of the invention are also useful as research reagents to digest proteins or in protein sequencing. For example, the tryptophan-processing enzymes may be used to break polypeptides into smaller fragments for sequencing using, e.g. an automated sequencer.

The invention also provides methods of discovering new tryptophan- processing enzymes using the nucleic acids, polypeptides and antibodies of the invention. In one aspect, phagemid libraries are screened for expression-based discovery of tryptophan-processing enzymes. In another aspect, lambda phage libraries are screened for expression-based discovery of tryptophan-processing enzymes. Screening of the phage or phagemid libraries can allow the detection of toxic clones; improved access to substrate; reduced need for engineering a host, by-passing the potential for any bias resulting from mass excision of the library; and, faster growth at low clone densities. Screening of phage or phagemid libraries can be in liquid phase or in solid phase. In one aspect, the invention provides screening in liquid phase. This gives a greater flexibility in assay conditions; additional substrate flexibility; higher sensitivity for weak clones; and ease of automation over solid phase screening.

The invention provides screening methods using the proteins and nucleic acids of the invention and robotic automation to enable the execution of many thousands of biocatalytic reactions and screening assays in a short period of time, e.g., per day, as well as ensuring a high level of accuracy and reproducibility (see discussion of arrays, below). As a result, a library of derivative compounds can be produced in a matter of weeks. For further teachings on modification of molecules, including small molecules, see PCT/US94/09174. In one aspect, polypeptides or fragments of the invention may be obtained through biochemical enrichment or purification procedures. The sequence of potentially homologous polypeptides or fragments may be determined by tryptophan-processing enzyme assays (see, e.g., Example 1, below), gel electrophoresis and/or microsequencing. The sequence of the prospective polypeptide or fragment of the invention can be compared to an exemplary polypeptide of the invention, or a fragment, e.g., comprising at least about 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 or more consecutive amino acids thereof using any of the programs described above.

Another aspect of the invention is an assay for identifying fragments or variants of the invention, which retain the enzymatic function of the polypeptides of the invention. For example the fragments or variants of said polypeptides, may be used to catalyze biochemical reactions (e.g., production of a nootkatoήe from a valencene), which indicate that the fragment or variant retains the enzymatic activity of a polypeptide of the invention.

An exemplary assay for determining if fragments of variants retain the enzymatic activity of the polypeptides of the invention includes the steps of: contacting the polypeptide fragment or variant with a substrate molecule under conditions which allow the polypeptide fragment or variant to function and detecting either a decrease in the level of substrate or an increase in the level of the specific reaction product of the reaction between the polypeptide and substrate. The present invention exploits the unique catalytic properties of enzymes.

Whereas the use of biocatalysts (i.e., purified or crude enzymes, non-living or living cells) in chemical transformations normally requires the identification of a particular biocatalyst that reacts with a specific starting compound, the present invention uses selected biocatalysts and reaction conditions that are specific for functional groups that axe present in many starting compounds, such as small molecules. Each biocatalyst is specific for one functional group, or several related functional groups and can react with many starting compounds containing this functional group.

The biocatalytic reactions produce a population of derivatives from a single starting compound. These derivatives can be subjected to another round of biocatalytic reactions to produce a second population of derivative compounds. Thousands of variations of the original small molecule or compound can be produced with each iteration of biocatalytic derivatization.

Enzymes react at specific sites of a starting compound without affecting the rest of the molecule, a process which is very difficult to achieve using traditional chemical methods. This high degree of biocatalytic specificity provides the means to identify a single active compound within the library. The library is characterized by the series of biocatalytic reactions used to produce it, a so called "biosynthetic history". Screening the library for biological activities and tracing the biosynthetic history identifies the specific reaction sequence producing the active compound. The reaction sequence is repeated and the structure of the synthesized compound determined. This mode of identification, unlike other synthesis and screening approaches, does not require immobilization technologies and compounds can be synthesized and tested free in solution using virtually any type of screening assay. It is important to note, that the high degree of specificity of enzyme reactions on functional groups allows for the "tracking" of specific enzymatic reactions that make up the biocatalytically produced library.

Many of the procedural steps are performed using robotic automation enabling the execution of many thousands of biocatalytic reactions and screening assays per day as well as ensuring a high level of accuracy and reproducibility. As a result, a library of derivative compounds can be produced in a matter of weeks which would take years to produce using current chemical methods.

In a particular aspect, the invention provides a method for modifying small molecules, comprising contacting a polypeptide encoded by a polynucleotide described herein or enzymatically active fragments thereof with a small molecule to produce a modified small molecule. A library of modified small molecules is tested to determine if a modified small molecule is present within the library which exhibits a desired activity. A specific biocatalytic reaction which produces the modified small molecule of desired activity is identified by systematically eliminating each of the biocatalytic reactions used to produce a portion of the library and then testing the small molecules produced in the portion of the library for the presence or absence of the modified small molecule with the desired activity. The specific biocatalytic reactions which produce the modified small molecule of desired activity is optionally repeated. The biocatalytic reactions are conducted with a group of biocatalysts that react with distinct structural moieties found within the structure of a small molecule, each biocatalyst is specific for one structural moiety or a group of related structural moieties; and each biocatalyst reacts with many different small molecules which contain the distinct structural moiety.

Tryptophan-processing enzyme signal sequences, prepro and catalytic domains The invention provides tryptophan-processing enzyme signal sequences (e.g., signal peptides (SPs)), prepro domains and catalytic domains (CDs). The SPs, prepro domains and/or CDs of the invention can be isolated or recombinant peptides or can be part of a fusion protein, e.g., as a heterologous domain in a chimeric protein. The invention provides nucleic acids encoding these catalytic domains (CDs), prepro domains and signal sequences (SPs, e.g., a peptide having a sequence comprising/ consisting of amino terminal residues of a polypeptide of the invention).

The invention provides isolated or recombinant signal sequences (e.g., signal peptides) consisting of or comprising a sequence as set forth in residues 1 to 14, 1 to 15, 1 to 16, 1 to 17, 1 to 18, 1 to 19, 1 to 20, 1 to 21, 1 to 22, 1 to 23, 1 to 24, 1 to 25, 1 to 26, 1 to 27, 1 to 28, 1 to 28, 1 to 30, 1 to 31, 1 to 32, 1 to 33, 1 to 34, 1 to 35, 1 to 36, 1 to 37, 1 to 38, 1 to 40, 1 to 41, 1 to 42, 1 to 43, 1 to 44, 1 to 45, 1 to 46, or 1 to 47, or more,, of a polypeptide of the invention, e.g., SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO: 10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO: 18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68 or SEQ ID NO:70. In one aspect, the invention provides signal sequences comprising the first 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 61, 68, 69, 70 or more amino terminal residues of a polypeptide of the invention. Methods for identifying "prepro" domain sequences and signal sequences are well known in the art, see, e.g., Van de Ven (1993) Crit. Rev. Oncog. 4(2):115-136. For example, to identify a prepro sequence, the protein is purified from the extracellular space and the N-terminal protein sequence is determined and compared to the unprocessed form.

The invention includes polypeptides with or without a signal sequence and/or a prepro sequence. The invention includes polypeptides with heterologous signal sequences and/or prepro sequences. The prepro sequence (including a sequence of the invention used as a heterologous prepro domain) can be located on the amino terminal or the carboxy terminal end of the protein. The invention also includes isolated or recombinant signal sequences, prepro sequences and catalytic domains (e.g., "active sites") comprising sequences of the invention. The polypeptide comprising a signal sequence of the invention can be a tryptophan-processing enzyme of the invention or another tryptophan-processing enzyme or another enzyme or other polypeptide. The tryptophan-processing enzyme signal sequences (SPs) and/or prepro sequences of the invention can be isolated peptides, or, sequences joined to another tryptophan-processing enzyme or a non-tryptophan-processing polypeptide, e.g., as a fusion (chimeric) protein. In one aspect, the invention provides polypeptides comprising tryptophan-processing enzyme signal sequences of the invention. In one aspect, polypeptides comprising tryptophan-processing enzyme signal sequences SPs and/or prepro of the invention comprise sequences heterologous to a tryptophan-processing enzyme of the invention (e.g., a fusion protein comprising an SP and/or prepro of the invention and sequences from another tryptophan-processing enzyme or a non- tryptophan-processing protein). In one aspect, the invention provides tryptophan- processing enzymes of the invention with heterologous SPs and/or prepro sequences, e.g., sequences with a yeast signal sequence. A tryptophan-processing enzyme of the invention can comprise a heterologous SP and/or prepro in a vector, e.g., a pPIC series vector (Invitrogen, Carlsbad, CA).

In one aspect, SPs and/or prepro sequences of the invention are identified following identification of novel tryptophan-processing polypeptides. The pathways by which proteins are sorted and transported to their proper cellular location are often referred to as protein targeting pathways. One of the most important elements in all of these targeting systems is a short amino acid sequence at the amino terminus of a newly synthesized polypeptide called the signal sequence. This signal sequence directs a protein to its appropriate location in the cell and is removed during transport or when the protein reaches its final destination. Most lysosomal, membrane, or secreted proteins have an amino-terminal signal sequence that marks them for translocation into the lumen of the endoplasmic reticulum. The signal sequences can vary in length from about 10 to 65, or more, amino acid residues. Various methods of recognition of signal sequences are known to those of skill in the art. For example, in one aspect, novel tryptophan- processing enzyme signal peptides are identified by a method referred to as SignalP. SignalP uses a combined neural network which recognizes both signal peptides and their cleavage sites. (Nielsen (1997) "Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites." Protein Engineering 10: 1-6.

It should be understood that in some aspects tryptophan-processing enzymes of the invention may not have SPs and/or prepro sequences, or "domains." In one aspect, the invention provides the tryptophan-processing enzymes of the invention lacking all or part of an SP and/or a prepro domain. In one aspect, the invention provides a nucleic acid sequence encoding a signal sequence (SP) and/or prepro from one tryptophan-processing enzyme operably linked to a nucleic acid sequence of a different tryptophan-processing enzyme or, optionally, a signal sequence (SPs) and/or prepro domain from a non- tryptophan-processing protein may be desired.

The invention also provides isolated or recombinant polypeptides comprising signal sequences (SPs), prepro domain and/or catalytic domains (CDs) of the invention and heterologous sequences. The heterologous sequences are sequences not naturally associated (e.g., to a tryptophan-processing enzyme) with an SP, prepro domain and/or CD. The sequence to which the SP, prepro domain and/or CD are not naturally associated can be on the SP's, prepro domain and/or CD's amino terminal end, carboxy terminal end, and/or on both ends of the SP and/or CD. In one aspect, the invention provides an isolated or recombinant polypeptide comprising (or consisting of) a polypeptide comprising a signal sequence (SP), prepro domain and/or catalytic domain (CD) of the invention with the proviso that it is not associated with any sequence to which it is naturally associated (e.g., a tryptophan-processing enzyme sequence). Similarly in one aspect, the invention provides isolated or recombinant nucleic acids encoding these polypeptides. Thus, in one aspect, the isolated or recombinant nucleic acid of the invention comprises coding sequence for a signal sequence (SP), prepro domain and/or catalytic domain (CD) of the invention and a heterologous sequence (i.e., a sequence not naturally associated with the a signal sequence (SP), prepro domain and/or catalytic domain (CD) of the invention). The heterologous sequence can be on the 3' terminal end, 5' terminal end, and/or on both ends of the SP, prepro domain and/or CD coding sequence.

Hybrid (chimeric) tryptophan-processing enzymes and peptide libraries In one aspect, the invention provides hybrid tryptophan-processing enzymes and fusion proteins, including peptide libraries, comprising sequences of the invention. The peptide libraries of the invention can be used to isolate peptide modulators (e.g., activators or inhibitors) of targets, such as tryptophan-processing enzyme substrates, receptors, enzymes. The peptide libraries of the invention can be used to identify formal binding partners of targets, such as ligands, e.g., cytokines, hormones and the like. In one aspect, the invention provides chimeric proteins comprising a signal sequence (SP), prepro domain and/or catalytic domain (CD) of the invention or a combination thereof and a heterologous sequence (see above).

In one aspect, the fusion proteins of the invention (e.g., the peptide moiety) are conformationally stabilized (relative to linear peptides) to allow a higher binding affinity for targets. The invention provides fusions of tryptophan-processing enzymes of the invention and other peptides, including known and random peptides. They can be fused in such a manner that the structure of the tryptophan-processing enzymes is not significantly perturbed and the peptide is metabolically or structurally conformationally stabilized. This allows the creation of a peptide library that is easily monitored both for its presence within cells and its quantity.

Amino acid sequence variants of the invention can be characterized by a predetermined nature of the variation, a feature that sets them apart from a naturally occurring form, e.g., an allelic or interspecies variation of a tryptophan-processing enzyme sequence. In one aspect, the variants of the invention exhibit the same qualitative biological activity as the naturally occurring analogue. Alternatively, the variants can be selected for having modified characteristics. In one aspect, while the site or region for introducing an amino acid sequence variation is predetermined, the mutation per se need not be predetermined. For example, in order to optimize the performance of a mutation at a given site, random mutagenesis may be conducted at the target codon or region and the expressed tryptophan-processing enzyme variants screened for the optimal combination of desired activity. Techniques for making substitution mutations at predetermined sites in DNA having a known sequence are well known, as discussed herein for example, Ml 3 primer mutagenesis and PCR mutagenesis. Screening of the mutants can be done using, e.g., assays of glucan hydrolysis. In alternative aspects, amino acid substitutions can be single residues; insertions can be on the order of from about 1 to 20 amino acids, although considerably larger insertions can be done. Deletions can range from about 1 to about 20, 30, 40, 50, 60, 70 residues or more. To obtain a final derivative with the optimal properties, substitutions, deletions, insertions or any combination thereof may be used. Generally, these changes are done on a few amino acids to minimize the alteration of the molecule. However, larger changes may be tolerated in certain circumstances. The invention provides tryptophan-processing enzymes where the structure of the polypeptide backbone, the secondary or the tertiary structure, e.g., an alpha-helical or beta-sheet structure, has been modified.¹In one aspect, the charge or hydrophobicity has been modified. In one aspect, the bulk of a side chain has been modified. Substantial changes in function or immunological identity are made by selecting substitutions that are less conservative. For example, substitutions can be made which more significantly affect: the structure of the polypeptide backbone in the area of the alteration, for example a alpha-helical or a beta-sheet structure; a charge or a hydrophobic site of the molecule, which can be at an active site; or a side chain. The invention provides substitutions in polypeptide of the invention where (a) a hydropbilic residues, e.g. seryl or threonyl, is substituted for (or by) a hydrophobic residue, e.g. leucyl, isoleucyl, phenylalanyl, valyl or alanyl; (b) a cysteine or proline is substituted for (or by) any other residue; (c) a residue having an electropositive side chain, e.g. lysyl, arginyl, or histidyl, is substituted for (or by) an electronegative residue, e.g. glutamyl or aspartyl; or (d) a residue having a bulky side chain, e.g. phenylalanine, is substituted for (or by) one not having a side chain, e.g. glycine. The variants can exhibit the same qualitative biological activity (i.e., a tryptophan-processing enzyme activity) although variants can be selected to modify the characteristics of the tryptophan-processing enzymes as needed.

In one aspect, tryptophan-processing enzymes of the invention comprise epitopes or purification tags, signal sequences or other fusion sequences, etc. In one aspect, the tryptophan-processing enzymes of the invention can be fused to a random peptide to form a fusion polypeptide. By "fused" or "operably linked" herein is meant that the random peptide and the tryptophan-processing enzyme are linked together, in such a manner as to minimize the disruption to the stability of the tryptophan-processing enzyme structure, e.g., it retains tryptophan-processing enzyme activity. The fusion polypeptide (or fusion polynucleotide encoding the fusion polypeptide) can comprise further components as well, including multiple peptides at multiple loops.

In one aspect, the peptides and nucleic acids encoding them are ^' randomized, either fully randomized or they are biased in their randomization, e.g. in nucleotide/residue frequency generally or per position. "Randomized" means that each nucleic acid and peptide consists of essentially random nucleotides and amino acids, respectively. In one aspect, the nucleic acids which give rise to the peptides can be chemically synthesized, and thus may incorporate any nucleotide at any position. Thus, when the nucleic acids are expressed to form peptides, any amino acid residue may be incorporated at any position. The synthetic process can be designed to generate randomized nucleic acids, to allow the formation of all or most of the possible combinations over the length of the nucleic acid, thus forming a library of randomized nucleic acids. The library can provide a sufficiently structurally diverse population of randomized expression products to affect a probabilistically sufficient range of cellular responses to provide one or more cells exhibiting a desired response. Thus, the invention provides an interaction library large enough so that at least one of its members will have a structure that gives it affinity for some molecule, protein, or other factor.

In one aspect, a tryptophan-processing enzyme of the invention is a multidomain enzyme that comprises a signal peptide, a carbohydrate binding module, a tryptophan-processing enzyme catalytic domain, a linker and/or another catalytic domain.

The invention provides a means for generating chimeric polypeptides which may encode biologically active hybrid polypeptides {e.g., hybrid tryptophan- processing enzymes). In one aspect, the original polynucleotides encode biologically active polypeptides. The method of the invention produces new hybrid polypeptides by utilizing cellular processes which integrate the sequence of the original polynucleotides such that the resulting hybrid polynucleotide encodes a polypeptide demonstrating activities derived from the original biologically active polypeptides. For example, the original polynucleotides may encode a particular enzyme from different microorganisms. An enzyme encoded by a first polynucleotide from one organism or variant may, for example, function effectively under a particular environmental condition, e.g. high salinity. An enzyme encoded by a second polynucleotide from a different organism or variant may function effectively under a different environmental condition, such as extremely high temperatures. A hybrid polynucleotide containing sequences from the first and second original polynucleotides may encode an enzyme which exhibits characteristics of both enzymes encoded by the original polynucleotides. Thus, the enzyme encoded by the hybrid polynucleotide may function effectively under environmental conditions shared by each of the enzymes encoded by the first and second polynucleotides, e.g., high salinity and extreme temperatures. A hybrid polypeptide resulting from the method of the invention may exhibit specialized enzyme activity not displayed in the original enzymes. For example, following recombination and/or reductive reassortment of polynucleotides encoding tryptophan-processing enzymes, the resulting hybrid polypeptide encoded by a hybrid polynucleotide can be screened for specialized non-tryptophan-processing enzyme activities, e.g., hydrolase, peptidase, phosphorylase, etc., activities, obtained from each of the original enzymes. Thus, for example, the hybrid polypeptide may be screened to ascertain those chemical functionalities which distinguish the hybrid polypeptide from the original parent polypeptides, such as the temperature, pH or salt concentration at which the hybrid polypeptide functions. In one aspect, the invention relates to a method for producing a biologically active hybrid polypeptide and screening such a polypeptide for enhanced activity by:

1) introducing at least a first polynucleotide in operable linkage and a second polynucleotide in operable linkage, the at least first polynucleotide and second polynucleotide sharing at least one region of partial sequence homology, into a suitable host cell;

2) growing the host cell under conditions which promote sequence reorganization resulting in a hybrid polynucleotide in operable linkage;

3) expressing a hybrid polypeptide encoded by the hybrid polynucleotide; 4) screening the hybrid polypeptide under conditions which promote identification of enhanced biological activity; and 5) isolating the a polynucleotide encoding the hybrid polypeptide.

Isolating and discovering trvptophan-processing enzymes

The invention provides methods for isolating and discovering tryptophan- processing enzymes and the nucleic acids that encode them. Polynucleotides or enzymes may be isolated from individual organisms ("isolates"), collections of organisms that have been grown in defined media ("enrichment cultures"), or, uncultivated organisms ("environmental samples"). The organisms can be isolated by, e.g., in vivo biopanning (see discussion, below). The use of a culture-independent approach to derive polynucleotides encoding novel bioactivities from environmental samples is most preferable since it allows one to access untapped resources of biodiversity. Polynucleotides or enzymes also can be isolated from any one of numerous skatole- degrading bacteria, which can be isolated from composting pig wastes, including aerobic and facultative anaerobic gram-positive cocci, aerobic gram-positive endospore-forming rods and several species of anaerobes (e.g. Clostridia). In addition to whole cells, polynucleotides or enzymes also can be isolated from crude enzyme preparations derived from cultures of these bacteria. Screening for compounds that inhibit the formation of skatole or degrade skatole can also use crude enzyme preparations derived from cultures of these bacteria.

"Environmental libraries" are generated from environmental samples and represent the collective genomes of naturally occurring organisms archived in cloning vectors that can be propagated in suitable prokaryotic hosts. Because the cloned DNA is initially extracted directly from environmental samples, the libraries are not limited to the small fraction of prokaryotes that can be grown in pure culture. Additionally, a normalization of the environmental DNA present in these samples could allow more equal representation of the DNA from all of the species present in the original sample. This can dramatically increase the efficiency of finding interesting genes from minor constituents of the sample which may be under-represented by several orders of magnitude compared to the dominant species.

For example, gene libraries generated from one or more uncultivated microorganisms are screened for an activity of interest. Potential pathways encoding bioactive molecules of interest are first captured in prokaryotic cells in the form of gene expression libraries. Polynucleotides encoding activities of interest are isolated from such libraries and introduced into a host cell. The host cell is grown under conditions which promote recombination and/or reductive reassortment creating potentially active biomolecules with novel or enhanced activities.

In vivo biopanning may be performed utilizing a FACS-based and non- optical (e.g., magnetic) based machines. Complex gene libraries are constructed with vectors which contain elements which stabilize transcribed RNA. For example, the inclusion of sequences which result in secondary structures such as hairpins which are designed to flank the transcribed regions of the RNA would serve to enhance their stability, thus increasing their half life within the cell. The probe molecules used in the biopanning process consist of oligonucleotides labeled with reporter molecules that only fluoresce upon binding of the probe to a target molecule. These probes are introduced into the recombinant cells from the library using one of several transformation methods. The probe molecules bind to the transcribed target mRNA resulting in DNA/KNA heteroduplex molecules. Binding of the probe to a target will yield a fluorescent signal which is detected and sorted by the FACS machine during the screening process.

Additionally, subcloning may be performed to further isolate sequences of interest. In subcloning, a portion of DNA is amplified, digested, generally by restriction enzymes, to cut out the desired sequence, the desired sequence is ligated into a recipient vector and is amplified. At each step in subcloning, the portion is examined for the activity of interest, in order to ensure that DNA that encodes the structural protein has not been excluded. The insert may be purified at any step of the subcloning, for example, by gel electrophoresis prior to ligation into a vector or where cells containing the recipient vector and cells not containing the recipient vector are placed on selective media containing, for example, an antibiotic, which will kill the cells not containing the recipient vector. Specific methods of subcloning cDNA inserts into vectors are well-known in the art (Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd Ed_^, Cold Spring Harbor Laboratory Press (1989)). In another aspect, the enzymes of the invention are subclones. Such subclones may differ from the parent clone by, for example, length, a mutation, a tag or a label.

In one aspect, the signal sequences of the invention are identified following identification of novel tryptophan-processing polypeptides. The pathways by which proteins are sorted and transported to their proper cellular location are often referred to as protein targeting pathways. One of the most important elements in all of these targeting systems is a short amino acid sequence at the amino terminus of a newly synthesized polypeptide called the signal sequence. This signal sequence directs a protein to its appropriate location in the cell and is removed during transport or when the protein reaches its final destination. Most lysosomal, membrane, or secreted proteins have an amino-terminal signal sequence that marks them for translocation into the lumen of the endoplasmic reticulum. More than 100 signal sequences for proteins in this group have been determined. The sequences vary in length from 13 to 36 amino acid residues. Various methods of recognition of signal sequences are known to those of skill in the art. In one aspect, the peptides are identified by a method referred to as SignalP. SignalP uses a combined neural network which recognizes both signal peptides and their cleavage sites. See, e.g., Nielsen (1997) "Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites." Protein Engineering, vol. 10, no. 1, p. 1- 6. It should be understood that some of the tryptophan-processing enzymes of the invention may or may not contain signal sequences. It may be desirable to include a 5 nucleic acid sequence encoding a signal sequence from one tryptophan-processing enzyme operably linked to a nucleic acid sequence of a different tryptophan-processing enzyme or, optionally, a signal sequence from a non-tryptophan-processing protein may be desired.

The microorganisms from which the polynucleotide may be discovered, o isolated or prepared include prokaryotic microorganisms, such as Eubacteria and

Archaebacteria and lower eukaryotic microorganisms such as fungi, some algae and protozoa. Polynucleotides may be discovered, isolated or prepared from environmental samples in which case the nucleic acid may be recovered without culturing of an organism or recovered from one or more cultured organisms. In one aspect, such 5 microorganisms may be extremophiles, such as hyperthermophiles, psychrophiles, psychrotrophs, halophiles, barophiles and acidophiles. Polynucleotides encoding enzymes isolated from extremophilic microorganisms can be used. Such enzymes may function at temperatures above 100⁰C in terrestrial hot springs and deep sea thermal vents, at temperatures below O⁰C in arctic waters, in the saturated salt environment of the 0 Dead Sea, at pH values around 0 in coal deposits and geothermal sulfur-rich springs, or at pH values greater than 11 in sewage sludge. For example, several esterases and lipases cloned and expressed from extremophilic organisms show high activity throughout a wide range of temperatures and pHs.

Polynucleotides selected and isolated as hereinabove described are 5 introduced into a suitable host cell. A suitable host cell is any cell which is capable of promoting recombination and/or reductive reassortment. The selected polynucleotides are in one aspect already in a vector which includes appropriate control sequences. The host cell can be a higher eukaryotic cell, such as a mammalian cell, or a lower eukaryotic cell, such as a yeast cell, or in one aspect, the host cell can be a prokaryotic cell, such as a 0 bacterial cell. Introduction of the construct into the host cell can be effected by calcium phosphate transfection, DEAE-Dextran mediated transfection, or electroporation (Davis et al, 19S6). '

As representative examples of appropriate hosts, there may be mentioned: bacterial cells, such as E. coli, Streptomyces, Salmonella typhimurium; fungal cells, such as yeast; insect cells such as Drosophila S2 and Spodoptera Sβ>; animal cells such as CHO, COS or Bowes melanoma; adenoviruses; and plant cells. The selection of an appropriate host is deemed to be within the scope of those skilled in the art from the teachings herein. With particular references to various mammalian cell culture systems that can be employed to express recombinant protein, examples of mammalian expression systems include the COS-7 lines of monkey kidney fibroblasts, described in "SV40- transformed simian cells support the replication of early SV40 mutants" (Gluzman, 1981) and other cell lines capable of expressing a compatible vector, for example, the C 127, 3T3, CHO, HeLa and BHK cell lines. Mammalian expression vectors will comprise an origin of replication, a suitable promoter and enhancer and also any necessary ribosome binding sites, polyadenylation site, splice donor and acceptor sites, transcriptional termination sequences and 5' flanking nontranscribed sequences. DNA sequences derived from the SV40 splice and polyadenylation sites may be used to provide the required nontranscribed genetic elements.

In another aspect, it is envisioned the method of the present invention can be used to generate novel polynucleotides encoding biochemical pathways from one or more operons or gene clusters or portions thereof. For example, bacteria and many eukaryotes have a coordinated mechanism for regulating genes whose products are involved in related processes. The genes are clustered, in structures referred to as "gene clusters," on a single chromosome and are transcribed together under the control of a single regulatory sequence, including a single promoter which initiates transcription of the entire cluster. Thus, a gene cluster is a group of adjacent genes that are either identical or related, usually as to their function. An example of a biochemical pathway encoded by gene clusters are polyketides.

Gene cluster DNA can be isolated from different organisms and ligated into vectors, particularly vectors containing expression regulatory sequences which can control and regulate the production of a detectable protein or protein-related array activity from the ligated gene clusters. Use of vectors which have an exceptionally large capacity for exogenous DNA introduction are particularly appropriate for use with such gene clusters and are described by way of example herein to include the f-factor (or fertility factor) of E. coli. This f-factor of E. coli is a plasmid which affects high-frequency transfer of itself during conjugation and is ideal to achieve and stably propagate large

DNA fragments, such as gene clusters from mixed microbial samples. One aspect is to use cloning vectors, referred to as "fosmids" or bacterial artificial chromosome (BAC) vectors. These are derived from E. coli f-factor which is able to stably integrate large segments of genomic DNA. When integrated with DNA from a mixed uncultured environmental sample, this makes it possible to achieve large genomic fragments in the form of a stable "environmental DNA library." Another type of vector for use in the present invention is a cosmid vector. Cosmid vectors were originally designed to clone and propagate large segments of genomic DNA. Cloning into cosmid vectors is described in detail in Sambrook et al, Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory Press (1989). Once ligated into an appropriate vector, two or more vectors containing different polyketide synthase gene clusters can be introduced into a suitable host cell. Regions of partial sequence homology shared by the gene clusters will promote processes which result in sequence reorganization resulting in a hybrid gene cluster. The novel hybrid gene cluster can then be screened for enhanced activities not found in the original gene clusters. Methods for screening for various enzyme activities are known to those of skill in the art and are discussed throughout the present specification, see, e.g., Example 1, below. Such methods may be employed when isolating the polypeptides and polynucleotides of the invention.

In one aspect, the invention provides methods for discovering and isolating tryptophan-processing or skatole-degrading enzymes, or compounds to modify the activity of these enzymes, using a whole cell approach. A variety of samples can be used, including enrichments of animal excrement, fecal samples from animals, e.g., cattle, swine, hogs, pigs and related animals. Putative clones encoding tryptophan-processing or skatole-degrading enzymes from genomic DNA library can be screened. Enzymes can be screened for removal of the precursor to skatole, tryptophan, or for direct skatole- degrading activity. In one aspect, the best whole cell candidates give 20% disappearance of skatole in 48 hours. More effective disappearance may be required for a viable product candidate.

Whole Cell Approach In the whole cell approach, samples from enrichment experiments and fecal and colonic (caecal) samples from animals, e.g., swine (including hogs, pigs, boars) are used to isolate bacteria that degrade skatole. Samples are plated and isolated colonies re-grown in media, e.g., liquid media, and evaluated for skatole degrading activity. In one aspect, enrichment samples that have been shown to degrade skatole are plated on skatole containing minimal and rich media and colonies will be isolated. The isolated colonies are evaluated for their ability to degrade skatole. In one aspect, at least 5 colonies will be picked for each sample for testing. In one aspect, for strain isolation, two new sets of samples are evaluated for their ability to degrade skatole as isolate bacteria: (1) excrement samples from several varieties of swine and (2) swine intestinal material. These samples are used for plating on skatole media under anaerobic conditions. In one aspect, at least 5 isolated colonies for each individual sample will be re-grown and evaluated for skatole degrading potential in liquid media.

In one aspect, a combination of top performing culture isolates for skatole degrading activity are evaluated. Since culture strains have been shown to degrade skatole, combinations of different culture strains can generate synergy in the degradation of skatole. In one aspect, a set of experiments including 5 top performing culture strains in different combinations will be assessed.

In the whole cell approach, screens for isolated bacteria were developed to assess skatole disappearance activity in minimal media. These studies validated the concept that feed affects microbial populations in the pig intestines. Particular attention was paid to ensuring that skatole was the only carbon source. At least 5 colonies for each environmental sample were chosen for experiments. Colonies were picked based on differing colony morphologies with the goal to isolate as many different bacteria as possible. Skatole disappearance was determined for samples versus controls with autoclaved material or no inoculum added.

LAB combinations: o From the top performing strains that have been screened from plant and intestinal isolates, a selection of the top performers was chosen for synergy studies. o Combinations were tested in a cell free extract. o LAB strains alone in 0.00025% skatole (physiological concentration) were previously shown to give a maximum of 15-20% skatole disappearance in

24 hr as a cell free extract. o In two separate experiments, 5 LAB strains as cell free extracts in combination resulted in 70% disappearance of skatole in 48h (see table below). Table 1. % skatole disappearance of crude cell lysates from LAB combinations. Assays performed twice.

• Screening of Environmental Samples: o Samples from various animal excrement samples were used to generate enrichments grown in the presence of skatole. Enrichments were transferred to fresh media containing skatole generating secondary enrichments. Depending on growth of the samples, they were transferred additional times up to a quaternary enrichment. o In some cases bacteria were isolated by laser sorting. Laser sorted samples were followed for growth or a period of several weeks resulting in no real hits. o Direct plating and testing of isolated colonies from the environmental enrichment samples produced a maximum of 20% skatole disappearance over 48h.

• Swine samples were plated and isolated colonies tested for skatole disappearance. o For the samples, a variety of colony morphologies were observed, o Two of the samples were submitted for RFLP analysis.

^■ This work demonstrated that for fecal material from two different genera of pigs, 4 main genera of bacteria were contained in the sample.

^■ This work validates the concept that feed affects microbial populations in the pig intestines. o No skatole disappearance was observed.

In one aspect, moderate high throughput assays are used for detection of skatole, e.g., involving GC, LC-MS or reverse phase HPLC methods. Optimization based on a screening target (whole cells or enzymes) may be required. Isolates from cell cultures (LABs) can be screened initially for organisms that can degrade skatole. Cell culture (e.g., LAB) strains can be inoculated in MRS medium and grown under anaerobic conditions (strain dependent). After overnight growth, cells can be transferred into fresh medium and skatole can be added at time of inoculation (final concentration 0.01-0.03%, to mimic physiological conditions). Same volume of methanol can be added into control samples. In one aspect, whenever possible, cultures are incubated anaerobically (strain dependent). Samples can be removed at different time points (e.g. 0, 24 and 48 hours). Skatole concentration can be determined at each time point and monitored over time.

In one aspect, cell-free extracts are prepared from total broth of cell cultures (e.g., LABs). Skatole is added and its concentration in reaction mixtures determined at different time points. In one aspect, environmental samples are screened. When applicable, enrichment methods are used to select for organisms that can degrade skatole. If skatole-degrading organisms discovered in environmental samples are considered for further characterization, their phylogenetic classification can be determined in order to eliminate pathogenic strains (e.g. ribosomal RNA profiling can be conducted). Resistance to gastric juice can be evaluated in simulated gastric assay under laboratory conditions in order to identify organisms that could survive passage through stomach and reach colon. However, because gastric stability can be substantially improved by formulations, organisms that efficiently degrade skatole, but may not show sufficient gastric stability in this preliminary screen, can be eliminated from further characterization, or further modified to have desired characteristics.

In one aspect, skatole-degrading organisms found in cell culture (e.g., LAB) collections or in environmental samples are be fractionated and enzymes responsible for activity on skatole identified. Alternatively, gene libraries are constructed from environmental samples or skatole-degrading isolates and screened for (1) enzymes that can degrade skatole or its precursors or (2) for cells that can grow in the presence of skatole (e.g. skatole is toxic to E. coli). Alternatively, sequence-based discovery of skatole-degrading enzymes is done.

In one aspect, optimization of assays developed to screen whole cells is done to screen for skatole degrading enzymes. Any high throughput (HTP) screen is likely to monitor the conversion of skatole to a specific product. Therefore, these screens may not be the best general method for discovering any type of skatole degrading enzymes.

Skatole degradation (e.g. BC, I3A) or modification (e.g. IAA, indole, tryptophan) products can be characterized in samples where decrease in skatole concentration was observed. In one aspect, if no degradation or modification products could be detected, possible absorption of skatole is investigated. In one aspect, cells or enzymes are incubated with skatole precursors (e.g., IAA) and the formation of tryptophan monitored. When identified, these cells or enzymes are used with compositions of the invention or in methods of the invention to remove skatole precursors in gut and to complement skatole degrading activities. In one aspect, skatole-degrading organisms or enzymes are evaluated for their ability to degrade tryptophan. In one aspect, formulations (e.g., encapsulation) are used to improve gastric stability of skatole-degrading organisms or enzymes.

In one aspect, initial probiotic characterization is conducted under laboratory conditions (e.g. cell growth in the presence of prebiotics /FOS/, gastric stability of cells or enzymes after encapsulation).

In one aspect, selected skatole-degrading organisms are evaluated in vitro in a pig gut model under simulated physiological conditions for (1) gastric stability (e.g. acid resistance), (2) growth in the presence of prebiotics and eventually (3) the ability to colonize pig gut. Gut colonization may provide extended benefits, but because of a short half-life of skatole in fat, it may not be necessary.

In one aspect, skatole-degradation activity of candidates originally selected in the in vitro or in vivo models are optimized. For that purpose, several factors can be evaluated simultaneously, including effect of various (1) prebiotics, (2) inhibitors of enzymes involved in skatole formation (e.g. BC, BA), (3) combination of different strains in co-culture, and (4) different probiotic doses.

In one aspect, skatole-degrading enzymes are characterized are varying temperatures and pH. The activities of the skatole-degrading enzymes can be optimized by evolution technologies (e.g. GSSM evolution). If skatole-degrading enzymes can be evaluated in an in vitro model as well. In one aspect, skatole-degrading organisms or enzymes are used as feed additives, and thermal stability under pelleting conditions is determined. For example, in one aspect, an enzyme of the invention is active after, or during, exposure to 85⁰C for up to 5 minutes. Encapsulation may be required to improve stability. In alternative aspects, polypeptides of the invention (e.g., tryptophan-modifying or skatole-degrading enzymes, antibodies) or organisms are sprayed on feed after pelleting, added to or sprayed on food, or supplied as a liquid, e.g., in drinking water. In one aspect, meat technology laboratories are used for evaluation of skatole content in fat (e.g. meat sensory quality). In one aspect, consistency of performance of candidates selected in small-scale animal trials is further analyzed in large groups of animals (e.g. skatole content in fat will be evaluated). Product candidates can be identified for scale up and manufacturing.

If all skatole produced in colon would be absorbed by intestinal mucosa and accumulated in fat, 100-fold reduction in skatole concentration may be required to eliminate boar taint completely (from 26 μg/g in colon to 0.25 μg/g in fat). However, under physiological conditions, numerous additional factors should be considered, including: (1) skatole excretion in faeces; (2) absorption in colon; (3) degradation in liver;

(4) short half-life in fat; (5) opportunity to boost probiotic effect with prebiotics; (6) optimization of probiotic dose (number of organisms (cfu)/g feed; in one aspect probiotics are dosed at 10¹⁰ cfu/g, which is a 10-fold higher cell density than in bacterial culture);

(7) in one aspect a combination of different skatole-degrading organisms in co-cultures is used to achieve synergetic effects; (8) extended benefits of gut colonizing probiotic strains due to their persistence in colon.

In one aspect, skatole degradation potential of organisms identified in original laboratory screen are optimized in in vitro or in vivo models in order to identify product candidates which could in vivo reduce skatole concentration in fat to acceptable levels.

In one aspect, gastric stability of selected candidates is significantly improved by encapsulation (the invention provides encapsulated compositions comprising polypeptides of the invention). Numerous coating materials are available to enhance delivery of functional material into colon, including some which can be activated for release of material based on change in pH conditions (e.g. in colon vs. stomach).

In one aspect, different stabilization and formulation methods (e.g. freeze- drying, vitrification, encapsulation) are used to improve heat tolerance of cells or enzymes. In one aspect, these methods are evaluated in order to enhance survival of selected candidates during pelleting.

In one aspect, the invention provides a moderate throughput assay to monitor degradation of skatole and identify organisms that can degrade or modify skatole in whole cells or in cell-free extracts by at least 10% under laboratory conditions. In one aspect, gastric stability of selected candidates (raw, unformulated materials) is evaluated under laboratory conditions. In one aspect, phylogenetic classification of selected organisms is determined and these isolates are characterized with respect to GRAS status and requirements for future regulatory approval. In one aspect, the invention provides organisms (e.g., cells) or enzymes that can degrade or modify skatole by at least 50% in a pig gut model under optimized in vitro conditions.

In one aspect, the invention provides compositions that can degrade or modify skatole in vivo in small groups of male pigs and reduce its content in fat to a level below 0.25 μg/g. In one aspect, the invention provides compositions that can consistently reduce skatole content in fat to a level below 0.25 μg/g in large groups of male pigs under different dietary regimes.

Enzyme Approach An alternative aspect provides an enzyme approach (versus a "whole cell" approach) for discovering and isolating tryptophan-processing or skatole-degrading enzymes focused on tryptophanase, tryptophan decarboxylase, tryptophan dioxygenase, tryptophan transaminase activity and/or tyrosine phenol lyase enzymes, or compounds that modify the activity of these enzymes. An enzyme approach can also involve identifying enzymes capable of degrading skatole and/or tryptophan.

• Tryptophanase o Subcloned E. coli tryptophanase and developed assays to measure activity. o Identified tryptophanases from sequence archive and have initiated subcloning and expression studies.

Pseudomonas XA produces an enzyme, tryptophan side chain oxidase (TSCO), which is known to oxidize skatole. In one aspect, Pseudomonas XA is grown and the enzyme in a crude lysate tested for its ability to degrade skatole. Active enzymes are purified and sequenced in order to clone the gene. The invention provides an enzyme that is capable of removing tryptophan in the gut, e.g., the small and/or large intestines, thus also reducing the levels of or removing skatole in the body, e.g., in fat.

In one aspect, the invention provides a method comprising lactic acid bacterial (LAB) competition with Lactobacillus sp. Strain 11201. The assay identifies bacteria that reduce Lactobacillus sp. Strain 11201 colonization by competitive exclusion or growth inhibition. As discussed above, the invention also provides assays that identify lactic acid bacterial (LAB) that degrade skatole, including identifying and isolating bacteria able to colonize a hindgut (e.g., a colon) and convert skatole to indole, or, convert skatole to any compound that cannot be absorbed by the gut. Indole can be assayed qualitatively or quantitatively. High or moderate throughput assays can be used.

In one aspect, the invention provides a method comprising assaying for skatole derivatives that are not problematic, e.g., non-toxic, acceptable pallatability, no regulatory issues, etc. High or moderate throughput assays can be used.

Genetic approach

An alternative aspect provides an enzyme approach (versus an "enzyme" or "whole cell" approach) for discovering and isolating tryptophan-processing or skatole- degrading enzymes focused on tryptophanase, tryptophan decarboxylase, tryptophan dioxygenase, tryptophan transaminase activity and/or tyrosine phenol lyase enzymes, or compounds that modify the activity of these enzymes.

In one aspect, genomic DNA libraries were screened using skatole as a bactericidal compound. Recombinant E. coli that were skatole resistant were isolated. The hits from this screening were evaluated. These clones can be assayed using skatole as substrate. It can be determined if these enzymes convert skatole to another product or if they only sequester skatole, allowing E. coli to grow in the original experiment.

The invention provides additional alternative approaches for discovering and isolating tryptophan-processing or skatole-degrading enzymes, including using a skatole binding protein or an antibody (large quantities of antibody may be needed), and screening for inhibitors of skatole production, in addition to screening for promoters of tryptophan (skatole precursor) degradation. In one aspect, the assay of the invention screens for inhibitors of skatole production using small molecules as test compounds.

In one aspect, the methods of the invention comprise microencapsulation of individual bacteria from enrichments to assess the ability of the individual bacteria to inhibit or slow the production of skatole (e.g., "tryptophan-processing" activity) or to degrade skatole. Isolated bacteria may be more likely to grow than bacteria in a consortium. Clarified intestinal fluid can be used as a media source for the encapsulated bacteria and tryptophan-processing or skatole degrading activity can be assessed, e.g., in microtiter well plates (such as 96 well plates). Indole-3-acetonitrile (I3A) is a precursor to indole acetic acid (IAA). IAA is an inhibitor of skatole production. A nitrilase converts BA to IAA in plant cells while in bacteria IAA is thought to be generated from indolepyruvate. Although it is energetically unfavorable to ran a reverse nitrilase reaction generating BA from IAA, other enzymes may be capable of this reaction. Thus, the invention provides compositions and methods comprising use of enzymes that increase IAA, which, as an inhibitor of skatole production, would decrease the amount of skatole.

On the assumption that oxygen is present in the pig colon and Pseudomonas XA produces a skatole-degrading activity, a TSCO is cloned. The purified protein can be sequenced using mass spectrometry techniques. The protein sequence can be used to create degenerate oligonucleotide probes to obtain a full-length gene.

The invention also provides screening for tryptophanases that operate at high pH. In one aspect, if an isolated tryptophanase is active under alkaline conditions, it can be further modified to be active only under alkaline conditions, e.g., using GSSM evolution.

Animal models

The invention also provides methods for discovering and isolating tryptophan-processing or skatole-degrading enzymes, or compounds to modify the activity of these enzymes, using animal models in animal trials. In one aspect, screening assays focus on direct addition of the enzyme to the hindgut, e.g., colon, large intestine, rumen and/or caecum of a cannulated animal, such as a pig (see discussion Example 6, below). Attention is paid to the growth of the pigs versus control pigs with no enzyme fed, as well as skatole levels in the fat, e.g., back fat, of these pigs after slaughter. In one aspect, the invention provides in vivo tests to evaluate the impact of added enzyme on skatole accumulation after introduction to a hindgut via an ileo-cecal cannula. For example, the invention provides for in vivo tests using pigs fitted with an ileal cannula that will allow direct introduction of enzyme and/or substrate into the large intestine, thereby by-passing the major sites of absorption in the pig. This protocol can provide proof of concept that feeding of any particular enzyme will reduce skatole production. See discussion Example 6, below.

Screening Methodologies and "On-line" Monitoring Devices

In practicing the methods of the invention, a variety of apparatus and methodologies can be used to in conjunction with the polypeptides and nucleic acids of the invention, e.g., to screen polypeptides for tryptophan-processing enzyme activity (e.g., assays such as hydrolysis of tryptophan), to screen compounds as potential modulators, e.g., activators or inhibitors, of a tryptophan-processing enzyme activity, for antibodies that bind to a polypeptide of the invention, for nucleic acids that hybridize to a nucleic acid of the invention, to screen for cells expressing a polypeptide of the invention and the like. In addition to the array formats described in detail below for screening samples, alternative formats can also be used to practice the methods of the invention. Such formats include, for example, mass spectrometers, chromatographs, e.g., high- throughput HPLC and other forms of liquid chromatography, and smaller formats, such as 1536-well plates, 384-well plates and so on. High throughput screening apparatus can be adapted and used to practice the methods of the invention, see, e.g., U.S. Patent Application No. 20020001809.

Capillary Arrays Nucleic acids or polypeptides of the invention can be immobilized to or applied to an array, e.g., a capillary array, e.g., GIGAMATRIX™. Arrays can be used to screen for or monitor libraries of compositions (e.g., small molecules, antibodies, nucleic acids, etc.) for their ability to bind to or modulate the activity of a nucleic acid or a polypeptide of the invention. Arrays can be used to screen polypeptides to determine if they have the requisite activity to be within the scope of the invention, e.g., having tryptophanase activity, ability to bind to skatole, and the like. Capillary array screenings also can be done under various conditions, e.g., conditions that are similar to an animal's digestive tract, e.g., a colon, rumen, caecum, intestine and the like.

Capillary arrays that can be used to practice the invention include arrays such as the GIGAMATRIX™, Diversa Corporation, San Diego, CA, as described, e.g., in U.S. Patent Nos. 6,764,818, 6,798,520, 6,918,738; U.S. Patent Application Pubs. 2005- 0046833, and 2005-0118707; Lafferty (2004) "GigaMatrix: An Ultra High-Throughput Tool for Accessing Biodiversity," J. American Laboratory Assoc. (9) 200-208); and arrays described in, e.g., U.S. Patent Application Pub. No. 20020080350 Al; WO 0231203 A; WO 0244336 A, which provide an alternative apparatus for holding and screening samples. An exemplary protocol for GIGAMATRIX™ screening for tryptophanases is set forth in Example 4, below.

In one aspect, the capillary array includes a plurality of capillaries formed into an array of adjacent capillaries, wherein each capillary comprises at least one wall defining a lumen for retaining a sample. The lumen may be cylindrical, square, hexagonal or any other geometric shape so long as the walls form a lumen for retention of a liquid or sample. The capillaries of the capillary array can be held together in close proximity to form a planar structure. The capillaries can be bound together, by being fused (e.g., where the capillaries are made of glass), glued, bonded, or clamped side-by- side. Additionally, the capillary array can include interstitial material disposed between adjacent capillaries in the array, thereby forming a solid planar device containing a plurality of through-holes. A capillary array can be formed of any number of individual capillaries, for example, a range from 100 to 4,000,000 capillaries. Further, a capillary array having about 100,000 or more individual capillaries can be formed into the standard size and shape of a MICROTITER® plate for fitment into standard laboratory equipment. The lumens are filled manually or automatically using either capillary action or microinjection using a thin needle. Samples of interest may subsequently be removed from individual capillaries for further analysis or characterization. For example, a thin, needle-like probe is positioned in fluid communication with a selected capillary to either add or withdraw material from the lumen.

In a single-pot screening assay, the assay components are mixed yielding a solution of interest, prior to insertion into the capillary array. The lumen is filled by capillary action when at least a portion of the array is immersed into a solution of interest. Chemical or biological reactions and/or activity in each capillary are monitored for detectable events. A detectable event is often referred to as a "hit", which can usually be distinguished from "non-hit" producing capillaries by optical detection. Thus, capillary arrays allow for massively parallel detection of "hits".

In a multi-pot screening assay, a polypeptide or nucleic acid, e.g., a ligand, can be introduced into a first component, which is introduced into at least a portion of a capillary of a capillary array. An air bubble can then be introduced into the capillary behind the first component. A second component can then be introduced into the capillary, wherein the second component is separated from the first component by the air bubble. The first and second components can then be mixed by applying hydrostatic pressure to both sides of the capillary array to collapse the bubble. The capillary array is then monitored for a detectable event resulting from reaction or non-reaction of the two components. In a binding screening assay, a sample of interest can be introduced as a first liquid labeled with a detectable particle into a capillary of a capillary array, wherein the lumen of the capillary is coated with a binding material for binding the detectable particle to the lumen. The first liquid may then be removed from the capillary tube, wherein the bound detectable particle is maintained within the capillary, and a second liquid may be introduced into the capillary tube. The capillary is then monitored for a detectable event resulting from reaction or non-reaction of the particle with the second liquid.

Arrays, or "Biochips" Nucleic acids or polypeptides of the invention can be immobilized to or applied to an array. Arrays can be used to screen for or monitor libraries of compositions (e.g., small molecules, antibodies, nucleic acids, etc.) for their ability to bind to or modulate the activity of a nucleic acid or a polypeptide of the invention. For example, in one aspect of the invention, a monitored parameter is transcript expression of a tryptophan-processing enzyme gene. One or more, or, all the transcripts of a cell can be measured by hybridization of a sample comprising transcripts of the cell, or, nucleic acids representative of or complementary to transcripts of a cell, by hybridization to immobilized nucleic acids on an array, or "biocbip." By using an "array" of nucleic acids on a microchip, some or all of the transcripts of a cell can be simultaneously quantified. Alternatively, arrays comprising genomic nucleic acid can also be used to determine the genotype of a newly engineered strain made by the methods of the invention. Polypeptide arrays" can also be used to simultaneously quantify a plurality of proteins. The present invention can be practiced with any known "array," also referred to as a "microarray" or "nucleic acid array" or "polypeptide array" or "antibody array" or "biocbip," or variation thereof. Arrays are genetically a plurality of "spots" or "target elements," each target element comprising a defined amount of one or more biological molecules, e.g., oligonucleotides, immobilized onto a defined area of a substrate surface for specific binding to a sample molecule, e.g., mRNA transcripts.

In practicing the methods of the invention, any known array and/or method of making and using arrays can be incorporated in whole or in part, or variations thereof, as described, for example, in U.S. Patent Nos. 6,277,628; 6,277,489; 6,261,776; 6,258,606; 6,054,270; 6,048,695; 6,045,996; 6,022,963; 6,013,440; 5,965,452; 5,959,098; 5,856,174; 5,830,645; 5,770,456; 5,632,957; 5,556,752; 5,143,854; 5,807,522; 5,800,992; 5,744,305; 5,700,637; 5,556,752; 5,434,049; see also, e.g., WO 99/51773; WO 99/09217; WO 97/46313; WO 96/17958; see also, e.g., Johnston (1998) Curr. Biol. 8:R171-R174; Schummer (1997) Biotechniques 23:1087-1092; Kern (1997) Biotechniques 23:120-124; Solinas-Toldo (1997) Genes, Chromosomes & Cancer 20:399-407; Bowtell (1999) Nature Genetics Supp. 21 :25-32. See also published U.S. patent applications Nos. 20010018642; 20010019827; 20010016322; 20010014449; 20010014448; 20010012537; 20010008765.

Antibodies and Antibodv-based screening methods

The invention provides isolated or recombinant antibodies that specifically bind to a tryptophan-processing enzyme of the invention. These antibodies can be used to isolate, identity or quantify the tryptophan-processing enzymes of the invention or related polypeptides (see Example 7, below). These antibodies can be used to isolate other polypeptides within the scope the invention or other related tryptophan-processing enzymes. The antibodies can be designed to bind to an active site of a tryptophan- processing enzyme. Thus, the invention provides methods of inhibiting tryptophan- processing enzymes using the antibodies of the invention (see discussion above regarding applications for anti-tryptophan-processing enzyme compositions of the invention).

The invention provides fragments of the enzymes of the invention, including immunogenic fragments of a polypeptide of the invention. The invention provides compositions comprising a polypeptide or peptide of the invention and adjuvants or carriers and the like.

The invention also provides methods for removing skatole from the digestive tract, e.g., colon, of an animal (including rumen, caecum and colon of monogastric animals), e.g., swine, pig and related animals, using anti-skatole antibodies. Monoclonal antibodies against skatole have been described in the literature, see, e.g., Tuomola (2000) J. Immunol. Methods 240: 111 -124, and the invention provides compositions and methods comprising the administration of polyclonal or monoclonal anti-skatole antibodies to remove skatole.

The term "antibody" includes a peptide or polypeptide derived from, modeled after or substantially encoded by an immunoglobulin gene or immunoglobulin genes, or fragments thereof, capable of specifically binding an antigen or epitope, see, e.g. Fundamental Immunology, Third Edition, W.E. Paul, ed., Raven Press, N. Y. (1993); Wilson (1994) J. Immunol. Methods 175:267-273; Yarmush (1992) J. Biochem. Biophys. Methods 25:85-97. The term antibody includes antigen-binding portions, i.e., "antigen binding sites," (e.g., fragments, subsequences, complementarity determining regions (CDRs)) that retain capacity to bind antigen, including (i) a Fab fragment, a monovalent fragment consisting of the VL, VH, CL and CHl domains; (ii) a F(ab')2 fragment, a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region; (iii) a Fd fragment consisting of the VH and CHl domains; (iv) a Fv fragment consisting of the VL and VH domains of a single arm of an antibody, (v) a dAb fragment (Ward et al., (1989) Nature 341:544-546), which consists of a VH domain; and (vi) an isolated complementarity determining region (CDR). Single chain antibodies are also included by reference in the term "antibody."

The antibodies can be used in immunoprecipitation, staining, immunoaffmity columns, and the like. If desired, nucleic acid sequences encoding for specific antigens can be generated by immunization followed by isolation of polypeptide or nucleic acid, amplification or cloning and immobilization of polypeptide onto an array of the invention. Alternatively, the methods of the invention can be used to modify the structure of an antibody produced by a cell to be modified, e.g., an antibody's affinity can be increased or decreased. Furthermore, the ability to make or modify antibodies can be a phenotype engineered into a cell by the methods of the invention.

Methods of immunization, producing and isolating antibodies (polyclonal and monoclonal) are known to those of skill in the art and described in the scientific and patent literature, see, e.g., Coligan, CURRENT PROTOCOLS IN IMMUNOLOGY, Wiley/Greene, NY (1991); Stites (eds.) BASIC AND CLINICAL IMMUNOLOGY (7th ed.) Lange Medical Publications, Los Altos, CA ("Stites"); Goding, MONOCLONAL ANTIBODIES: PRINCIPLES AND PRACTICE (2d ed.) Academic Press, New York, NY (1986); Kohler (1975) Nature 256:495; Harlow (1988) ANTIBODIES, A

LABORATORY MANUAL, Cold Spring Harbor Publications, New York. Antibodies also can be generated in vitro, e.g., using recombinant antibody binding site expressing phage display libraries, in addition to the traditional in vivo methods using animals. See, e.g., Hoogenboom (1997) Trends Biotechnol. 15:62-70; Katz (1997) Annu. Rev. Biophys. Biomol. Struct. 26:27-45.

The polypeptides of the invention or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof, may also be used to generate antibodies which bind specifically to the polypeptides or fragments. The resulting antibodies may be used in immunoaffmity chromatography procedures to isolate or purify the polypeptide or to determine whether the polypeptide is present in a biological sample. In such procedures, a protein preparation, such as an extract, or a biological sample is contacted with an antibody capable of specifically binding to one of the polypeptides of the invention, or fragments comprising at least 5, 10, 15, 20, 25, 30,

35, 40, 50, 75, 100, or 150 consecutive amino acids thereof. In immunoaffinity procedures, the antibody is attached to a solid support, such as a bead or other column matrix. The protein preparation is placed in contact with the antibody under conditions in which the antibody specifically binds to one of the polypeptides of the invention, or fragment thereof. After a wash to remove non- specifically bound proteins, the specifically bound polypeptides are eluted.

The ability of proteins in a biological sample to bind to the antibody may be determined using any of a variety of procedures familiar to those skilled in the art. For example, binding may be determined by labeling the antibody with a detectable label such as a fluorescent agent, an enzymatic label, or a radioisotope. Alternatively, binding of the antibody to the sample may be detected using a secondary antibody having such a detectable label thereon. Particular assays include ELISA assays, sandwich assays, radioimmunoassays and Western Blots.

Polyclonal antibodies generated against the polypeptides of the invention, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof can be obtained by direct inj ection of the polypeptides into an animal or by administering the polypeptides to an animal, for example, a nonhuman. The antibody so obtained can bind the polypeptide itself. In this manner, even a sequence encoding only a fragment of the polypeptide can be used to generate antibodies which may bind to the whole native polypeptide. Such antibodies can then be used to isolate the polypeptide from cells expressing that polypeptide.

For preparation of monoclonal antibodies, any technique which provides antibodies produced by continuous cell line cultures can be used. Examples include the hybridoma technique (Kohler and Milstein, Nature, 256:495-497, 1975), the trioma technique, the human B-cell hybridoma technique (Kozbor et al, Immunology Today 4:72, 1983) and the EBV-hybridorna technique (Cole, et al. , 1985, in Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96).

Techniques described for the production of single chain antibodies (U.S. Patent No. 4,946,778) can be adapted to produce single chain antibodies to the polypeptides of the invention, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof. Alternatively, transgenic mice may be used to express humanized antibodies to these polypeptides or fragments thereof.

Antibodies generated against the polypeptides of the invention, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof may be used in screening for similar polypeptides from other organisms and samples. In such techniques, polypeptides from the organism are contacted with the antibody and those polypeptides which specifically bind the antibody are detected. Any of the procedures described above may be used to detect antibody binding. One such screening assay is described in "Methods for Measuring Cellulase Activities", Methods in Enzymology, VoI 160, pp. 87-116.

Kits

The invention provides kits comprising the compositions, e.g., nucleic acids, expression cassettes, vectors, cells, transgenic seeds or plants or plant parts, polypeptides (e.g., a tryptophan-processing enzyme) and/or antibodies of the invention. The kits also can contain instructional material teaching the methodologies and industrial uses of the invention, as described herein.

Whole cell engineering and measuring metabolic parameters

The methods of the invention provide whole cell evolution, or whole cell engineering, of a cell to develop a new cell strain having a new phenotype, e.g., a new or modified tryptophan-processing enzyme activity, by modifying the genetic composition of the cell. The genetic composition can be modified by addition to the cell of a nucleic acid of the invention, e.g., a coding sequence for an enzyme of the invention. See, e.g., WO0229032; WO0196551.

To detect the new phenotype, at least one metabolic parameter of a modified cell is monitored in the cell in a "real time" or "on-line" time frame. In one aspect, a plurality of cells, such as a cell culture, is monitored in "real time" or "on-line." In one aspect, a plurality of metabolic parameters is monitored in "real time" or "on-line." Metabolic parameters can be monitored using the tryptophan-processing enzymes of the invention. Metabolic flux analysis (MFA) is based on a known biochemistry framework. A linearly independent metabolic matrix is constructed based on the law of mass conservation and on the pseudo-steady state hypothesis (PSSH) on the intracellular metabolites. In practicing the methods of the invention, metabolic networks are established, including the: • identity of all pathway substrates, products and intermediary metabolites

• identity of all the chemical reactions interconverting the pathway metabolites, the stoichiometry of the pathway reactions,

• identity of all the enzymes catalyzing the reactions, the enzyme reaction kinetics, • the regulatory interactions between pathway components, e.g. allosteric interactions, enzyme-enzyme interactions etc,

• intracellular compartmentalization of enzymes or any other supramolecular organization of the enzymes, and, ^» the presence of any concentration gradients of metabolites, enzymes or effector molecules or diffusion barriers to their movement.

Once the metabolic network for a given strain is built, mathematic presentation by matrix notion can be introduced to estimate the intracellular metabolic fluxes if the on-line metabolome data is available. Metabolic phenotype relies on the changes of the whole metabolic network within a cell. Metabolic phenotype relies on the change of pathway utilization with respect to environmental conditions, genetic regulation, developmental state and the genotype, etc. In one aspect of the methods of the invention, after the on-line MFA calculation, the dynamic behavior of the cells, their phenotype and other properties are analyzed by investigating the pathway utilization. For example, if the glucose supply is increased and the oxygen decreased during the yeast fermentation, the utilization of respiratory pathways will be reduced and/or stopped, and the utilization of the fermentative pathways will dominate. Control of physiological state of cell cultures will become possible after the pathway analysis. The methods of the invention can help determine how to manipulate the fermentation by determining how to change the substrate supply, temperature, use of inducers, etc. to control the physiological state of cells to move along desirable direction. In practicing the methods of the invention, the MFA results can also be compared with transcriptome and proteome data to design experiments and protocols for metabolic engineering or gene shuffling, etc.

In practicing the methods of the invention, any modified or new phenotype can be conferred and detected, including new or improved characteristics in the cell. Any aspect of metabolism or growth can be mom^'tored.

Monitoring expression of an mRNA transcript

In one aspect of the invention, the engineered phenotype comprises increasing or decreasing the expression of an mRNA transcript (e.g., a tryptophan- processing enzyme message) or generating new (e.g., tryptophan-processing enzyme) transcripts in a cell. This increased or decreased expression can be traced by testing for the presence of a tryptophan-processing enzyme of the invention or by tryptophan- processing enzyme activity assays. mRNA transcripts, or messages, also can be detected and quantified by any method known in the art, including, e.g., Northern blots, quantitative amplification reactions, hybridization to arrays, and the like. Quantitative amplification reactions include, e.g., quantitative PCR, including, e.g., quantitative reverse transcription polymerase chain reaction, or RT-PCR; quantitative real time RT- PCR, or "real-time kinetic RT-PCR" (see, e.g., Kreuzer (2001) Br. J. Haematol. 114:313- 318; Xia (2001) Transplantation 72:907-914).

In one aspect of the invention, the engineered phenotype is generated by knocking out expression of a homologous gene. The gene's coding sequence or one or more transcriptional control elements can be knocked out, e.g., promoters or enhancers. Thus, the expression of a transcript can be completely ablated or only decreased.

In one aspect of the invention, the engineered phenotype comprises increasing the expression of a homologous gene. This can be effected by knocking out of a negative control element, including a transcriptional regulatory element acting in cis- or trans- , or, mutagenizing a positive control element. One or more, or, all the transcripts of a cell can be measured by hybridization of a sample comprising transcripts of the cell, or, nucleic acids representative of or complementary to transcripts of a cell, by hybridization to immobilized nucleic acids on an array.

Monitoring expression of a polypeptides, peptides and amino acids

In one aspect of the invention, the engineered phenotype comprises increasing or decreasing the expression of a polypeptide (e.g., a tryptophan-processing enzyme) or generating new polypeptides in a cell. This increased or decreased expression can be traced by determining the amount of tryptophan-processing enzyme present or by tryptophan-processing enzyme activity assays. Polypeptides, peptides and amino acids also can be detected and quantified by any method known in the art, including, e.g., nuclear magnetic resonance (NMR), spectrophotometry, radiography (protein radiolabeling), electrophoresis, capillary electrophoresis, high performance liquid chromatography (HPLC), thin layer chromatography (TLC), hyperdiffusion chromatography, various immunological methods, e.g. immunoprecipitation, immunodiffusion, immuno-electrophoresis, radioimmunoassays (RIAs), enzyme-linked immunosorbent assays (ELISAs), immuno-fluorescent assays, gel electrophoresis (e.g., SDS-PAGE), staining with antibodies, fluorescent activated cell sorter (FACS), pyrolysis mass spectrometry, Fourier-Transform Infrared Spectrometry, Raman spectrometry, GC- MS, and LC-Electrospray and cap-LC-tandem-electrospray mass spectrometries, and the like. Novel bioactivities can also be screened using methods, or variations thereof, described in U.S. Patent No. 6,057,103. Furthermore, as discussed below in detail, one or more, or, all the polypeptides of a cell can be measured using a protein array.

Applications: Industrial, Animal Husbandry, Medical The invention provides methods and compositions for decreasing the amount of skatole absorbed from the digestive tract of an animal, or decreasing the amount of skatole in the digestive tract of an animal, or decreasing the amount of skatole in the fat of an animal, comprising feeding or otherwise administering to the animal an effective amount of at least one polypeptide having a tryptophanase activity. The invention provides methods and compositions for decreasing the amount of skatole absorbed from the digestive tract of an animal comprising feeding or otherwise administering at least one skatole-binding composition to the animal, wherein optionally the skatole-binding composition comprises at least one hydrophobic polypeptide. In one aspect, polypeptides of the invention are used to practice the invention. In one aspect, tryptophanase activity comprises having tryptophan-processing or skatole-degrading enzyme activity. In one aspect, tryptophanase activity comprises catalyzing the modification (e.g., the hydrolysis) of tryptophan, e.g., to inhibit the formation of skatole, or, to modify skatole and prevent its absorption from the gut. The enzymes of the invention can be highly selective catalysts. The invention provides methods using enzymes of the invention in the food and feed industries, e.g., in methods for making food and feed products and food and feed additives. In one aspect, the invention provides processes using enzymes of the invention in the medical industry, e.g., to make pharmaceuticals.

The enzymes of the invention can catalyze reactions with exquisite stereo-, regio- and chemo- selectivities. The tryptophan-processing enzymes of the invention can be engineered to function in various solvents, operate at extreme pHs (for example, high pHs and low pHs) extreme temperatures (for example, high temperatures and low temperatures), extreme salinity levels (for example, high salinity and low salinity) and catalyze reactions with compounds that are structurally unrelated to their natural, physiological substrates.

Animal feeds, foods, and food or feed additives

The invention provides compositions and methods for treating animal feeds, and treating foods, and making food and feed additives, using tryptophan- processing enzymes of the invention, and/or the antibodies of the invention. The invention provides animal feeds, foods, and additives comprising tryptophan-processing enzymes of the invention, antibodies of the invention and/or skatole-binding compounds (e.g., hydrophobic compounds). The animal can be any farm animal or any animal raised for its meat, e.g., a pig, goat, cattle, sheep, horse and the like.

These compositions can be formulated in a variety of forms, e.g., as liquids, sprays, aerosols, powders, food, feed pellets, tablets or as capsules, such as encapsulated forms. In one aspect, a formulation of the invention (e.g., an encapsulated form) only releases a tryptophan-processing (tryptophan-degrading) enzyme, or only releases an active form of the enzyme, in the hindgut (e.g., rumen, caecum and colon of monogastric animals).

The animal feed additive of the invention may be a granulated enzyme product that may readily be-mixed with feed components. Alternatively, feed additives of the invention can form a component of a pre-mix. The granulated enzyme product of the invention may be coated or uncoated. The particle size of the enzyme granulates can be compatible with that of feed and pre-mix components. This provides a safe and convenient mean of incorporating enzymes into feeds. Alternatively, the animal feed additive of the invention may be a stabilized liquid composition. This may be an aqueous or oil-based slurry. See, e.g., U.S. Patent No. 6,245,546. An enzyme of the invention can be formulated, e.g., encapsulated, using any methodology, e.g., an enzyme can be encapsulated in sol-gel matrices prepared with a combination of alkyl-alkoxysilane precursors of different chain-lengths, as described, e.g., by Vidinha (2005) J. Biotechnol. 2005 Aug 8 (Epub); or a phyllosilicate sol-gel matrix, as described, e.g., by Hsu (2000) Biotechnol. Appl. Biochem. 31:179-183; or sol- gel-derived hybrid silica nanocomposites containing polysaccharides, as described, e.g., by Shchipunov (2004) J. Biochem. Biophys. Methods. 58:25-38; or using amphiphilic, hyperbranched polymers obtained by modification of hyperbranched aliphatic polyesters with succinic anhydride and glycidyl methacrylate to form nanoparticles in aqueous solution, as described, e.g., by Zou (2005) Macromol Biosci. 5:662-668; or simple alginate encapsulation, as described, e.g., by Oca-Cossio (2005) J. Mater. Sci. Mater Med. 6:521-524.

Alternatively, an enzyme can be spray-dried onto a particle, e.g., a particle, such as a pellet, that is fed to an animal or person as a food, feed or food or feed additive; see e.g., U.S. Patent No. 6,924,133, describing a process for preparing enzyme-containing particles, where the process comprises spray drying a fermentation broth comprising an enzyme onto a particle.

In one aspect, an enzyme of the invention can be formulated for delivery to the gut of an animal, or formulated as a food or feed additive, in the form of a transgenic cell, e.g., a transgenic plant cell, microbial cell and the like. For example, a nucleic acid encoding a tryptophan-processing enzyme is inserted into a cell (see discussion, above, regarding transgenic plant and animal cells, and transformed cells), and the cell is fed to the animal or human as a food, feed or food or feed additive.

Tryptophan-processing enzymes of the invention, in the modification of animal feed or a food, can process the food or feed either in vitro (by modifying components of the feed or food) or in vivo. In one aspect, polypeptides (including formulations) of the invention are added to animal feed or food compositions containing high amounts of tryptophan.

In one aspect, tryptophan-processing enzymes of the invention are engineered to ensure stability in feed, stability in the presence of the feed premix and stability through the process of feed pelleting and manufacture, e.g., engineered to be thermostable or thermotolerant, e.g., stable or tolerant to temperatures in excess of 85⁰C, 9O⁰C, 95°C, 96°C, 97⁰C, 98⁰C or 99⁰C, as discussed above. For example, a tryptophan- processing enzyme used in a formulation of the invention can be engineered to retain a tryptophan-processing activity under conditions comprising a temperature range of between about 37⁰C to about 95°C; between about 55°C to about 85⁰C, between about 70⁰C to about 95°C, or, between about 9O⁰C to about 95°C, 96⁰C, 97°C, 98°C or 99⁰C. In one aspect, an enzyme of the invention is added in combination with another enzyme, e.g., beta-galactosidases, catalases, laccases, cellulases, endoglycosidases, endo-beta-l,4-laccases, amyloglucosidases, glucose isomerases, glycosyltransferases, lipases, phospholipases, lipooxygenases, beta-laccases, endo-beta- l,3(4)-laccases, cutinases, peroxidases, amylases, glucoamylases, pectinases, reductases, oxidases, decarboxylases, phenoloxidases, ligninases, pullulanases, arabinanases, hemicellulases, mannanases, xylolaccases, xylanases, pectin acetyl esterases, rhamnogalacturonan acetyl esterases, proteases, peptidases, proteinases, polygalacturonases, rhamnogalacturonases, galactanases, pectin lyases, transglutaminases, pectin methylesterases, cellobiohydrolases and/or transglutaminases. These enzyme digestion products are more digestible by the animal. Thus, tryptophan- processing enzymes of the invention can contribute to the available energy of the feed or food. Also, by contributing to the degradation of tryptophan-containing material, a tryptophan-processing enzyme of the invention can improve the digestibility and uptake of carbohydrate and non-carbohydrate feed or food constituents such as protein, fat and minerals. In another aspect, tryptophan-processing enzyme of the invention can be supplied by expressing the enzymes directly in transgenic feed crops (as, e.g., transgenic plants, seeds and the like), such as grains, cereals, corn, soy bean, rape seed, lupin and the like. As discussed above, the invention provides transgenic plants, plant parts and plant cells comprising a nucleic acid sequence encoding a polypeptide of the invention. In one aspect, the nucleic acid is expressed such that the tryptophan-processing enzyme of the invention is produced in recoverable quantities. The tryptophan-processing enzyme can be recovered from any plant or plant part. Alternatively, the plant or plant part containing the recombinant polypeptide can be used as such for improving the quality of a food or feed, e.g., improving nutritional value, palatability, etc. The enzyme delivery matrix of the invention is in the form of discrete plural particles, pellets or granules. By "granules" is meant particles that are compressed or compacted, such as by a pelletizing, extrusion, or similar compacting to remove water from the matrix. Such compression or compacting of the particles also promotes intraparticle cohesion of the particles. For example, the granules can be prepared by pelletizing the grain-based substrate in a pellet mill. The pellets prepared thereby are ground or crumbled to a granule size suitable for use as an adjuvant in animal feed. Since the matrix is itself approved for use in animal feed, it can be used as a diluent for delivery of enzymes in animal feed.

The tryptophan-processing enzyme contained in the invention enzyme delivery matrix and methods is in one aspect a thermostable tryptophan-processing enzyme, as described herein, so as to resist inactivation of the tryptophan-processing enzyme during manufacture where elevated temperatures and/or steam may be employed to prepare the palletized enzyme delivery matrix. During digestion of feed containing the invention enzyme delivery matrix, aqueous digestive fluids will cause release of the active enzyme. Other types of thermostable enzymes and nutritional supplements that are thermostable can also be incorporated in the delivery matrix for release under any type of aqueous conditions.

A coating can be applied to the invention enzyme matrix particles for many different purposes, such as to add a flavor or nutrition supplement to animal feed, to delay release of animal feed supplements and enzymes in gastric conditions, and the like. Or, the coating may be applied to achieve a functional goal, for example, whenever it is desirable to slow release of the enzyme from the matrix particles or to control the conditions under which the enzyme will be released. The composition of the coating material can be such that it is selectively broken down by an agent to which it is susceptible (such as heat, acid or base, enzymes or other chemicals). Alternatively, two or more coatings susceptible to different such breakdown agents may be consecutively applied to the matrix particles.

The invention is also directed towards a process for preparing an enzyme- releasing matrix. In accordance with the invention, the process comprises providing discrete plural particles of a grain-based substrate in a particle size suitable for use as an enzyme-releasing matrix, wherein the particles comprise a tryptophan-processing enzyme encoded by an amino acid sequence of the invention. In one aspect, the process includes compacting or compressing the particles of enzyme-releasing matrix into granules, which most in one aspect is accomplished by pelletizing. The mold inhibitor and cohesiveness agent, when used, can be added at any suitable time, and in one aspect are mixed with the grain-based substrate in the desired proportions prior to pelletizing of the grain-based substrate. Moisture content in the pellet mill feed in one aspect is in the ranges set forth above with respect to the moisture content in the finished product, and in one aspect is about 14-15%. In one aspect, moisture is added to the feedstock in the form of an aqueous preparation of the enzyme to bring the feedstock to this moisture content. The temperature in the pellet mill in one aspect is brought to about 82°C with steam. The pellet mill may be operated under any conditions that impart sufficient work to the feedstock to provide pellets. The pelleting process itself is a cost-effective process for removing water from the enzyme-containing composition.

The compositions and methods of the invention can be practiced in conjunction with various nutritional and environmental factors that can reduce intestinal levels of skatole, including, e.g., (1) manipulation of gut microflora by supplementing feed with prebiotics and/or antibiotics, (2) low fiber diet (low energy and low purine diet), (3) restricting feed for 48 hours and withholding feed for 12 hours before slaughter, (4) increasing consumption of water, and/or (5) keeping animals (e.g., pigs) clean. Half-life of skatole in fat is only 10 hours, and because of such rapid clearing, treatments to reduce intestinal levels of skatole may need to be conducted only shortly before slaughter (e.g., one week). The compositions and methods of the invention can be practiced in conjunction with administration of prebiotics, which are high molecular weight sugars, e.g., fructo-oligosaccharides (FOS); galacto-oligosaccharides (GOS), GRAS (Generally Recognized As Safe) material. These prebiotics can be metabolized by some probiotic lactic acid bacteria (LAB). They are non-digestible by the majority of intestinal microbes. In an in vitro study, addition of 0.5% to 1.5% FOS to faecal slurries, containing pig intestinal bacteria and supplemented with L-tryptophan, resulted in significant decrease in skatole formation and the medium pH. In vivo, addition of FOS was shown to (1) enrich for endogenous probiotic organisms (e.g. Bifidobacteria), (2) decrease pH, and (3) reduce skatole formation in the colon. It was proposed that due to enrichment in Bifidobacteria by prebiotics and subsequent increase in protein synthesis, lesser amount of tryptophan would be available for degradation to skatole. In addition, recent literature evidence revealed that supplementation of feed with prebiotics (e.g. inulin) for 7 days resulted in 56% decrease in skatole concentration in pig fat tissue. Therefore, the invention provides compositions and methods comprising use of probiotic bacteria and/or probiotics (e.g., fructo-oligosaccharides (FOS); galacto-oligosaccharides (GOS)), in the reduction or elimination of skatole precursors (e.g. tryptophan) and in reduction of its accumulation in animal digestive tracts (e.g., pig colon) and fat.

Treating foods and food processing The tryptophan-processing enzymes of the invention have numerous applications in food processing industry. The invention provides methods for hydrolyzing tryptophan-comprising compositions, including, e.g., a plant cell, a bacterial cell, a yeast cell, an insect cell, or an animal cell, or any plant or plant part, or any food or feed, a waste product and the like. The invention provides feeds or foods comprising a tryptophan-processing enzyme the invention, e.g., a feed, a liquid, e.g., a beverage (such as a fruit juice or a beer), a bread or a dough or a bread product, or a beverage precursor (e.g., a wort).

The food treatment processes of the invention can also include the use of any combination of other enzymes such as other tryptophanases or tyrosine decarboxylases, laccases, catalases, laccases, cellulases, endoglycosidases, endo-beta-1,4- laccases, amyloglucosidases, glucose isomerases, glycosyltransferases, lipases, phospholipases, lipooxygenases, beta-laccases, endo-beta-l,3(4)-laccases, cutinases, peroxidases, amylases, glucoamylases, pectinases, reductases, oxidases, decarboxylases, phenoloxidases, ligninases, pullulanases, arabinanases, hemicellulases, mannanases, xylolaccases, xylanases, pectin acetyl esterases, rhamnogalacturonan acetyl esterases, proteases, peptidases, proteinases, polygalacturonases, rhamnogalacturonases, galactanases, pectin lyases, transglutaminases, pectin methylesterases, cellobiohydrolases and/or transglutaminases.

Waste treatment

The tryptophan-processing enzymes of the invention can be used in a variety of other industrial applications, e.g., in waste treatment (in addition to, e.g., biomass conversion to fuels). For example, in one aspect, the invention provides a solid waste digestion process using tryptophan-processing enzymes of the invention. The methods can comprise reducing the mass and volume of substantially untreated solid waste. Solid waste can be treated with an enzymatic digestive process in the presence of an enzymatic solution (including tryptophan-processing enzymes of the invention) at a controlled temperature. This results in a reaction without appreciable bacterial fermentation from added microorganisms. The solid waste is converted into a liquefied waste and any residual solid waste. The resulting liquefied waste can be separated from said any residual solidified waste. See e.g., U.S. Patent No. 5,709,796.

In one aspect, the compositions and methods of the invention are used for odor removal or odor reduction in animal waste lagoons, e.g., on swine farms, and other animal waste management systems.

The waste treatment processes of the invention can include the use of any combination of other enzymes such as other tryptophan-processing enzymes, catalases, laccases, cellulases, endoglycosidases, endo-beta-l,4-laccases, amyloglucosidases, glucose isomerases, glycosyltransferases, lipases, phospholipases, lipooxygenases, beta- laccases, endo-beta-l,3(4)-laccases, cutinases, peroxidases, amylases, glucoamylases, pectinases, reductases, oxidases, decarboxylases, phenoloxidases, ligninases, pullulanases, phytases, arabinanases, hemicellulases, mannanases, xylolaccases, xylanases, pectin acetyl esterases, rhamnogalacturonan acetyl esterases, proteases, peptidases, proteinases, polygalacturonases, rhamnogalacturonases, galactanases, pectin lyases, transglutaminases, pectin methylesterases, cellobiohydrolases and/or transglutaminases. The following examples are offered to illustrate, but not to limit the claimed invention.

EXAMPLES Example 1 : Exemplary trvptophanase (trpase) screening assays

In one aspect, the invention provides a polypeptides having tryptophanase (trpase) activity, which in one aspect includes the ability to catalyze the β-elimination of tryptophan. In one aspect, this results in three products: indole, ammonia and pyruvate. In one aspect, a polypeptide of the invention can also catalyze the reverse reaction (indole, ammonia and pyruvate to tryptophan, particularly in conditions comprising a relatively high concentration of ammonia and pyruvate).

This example described two exemplary methods to analyze the effects of tryptophanase on FAA, and tryptophanyl di-, and tri- peptides, and, in some aspects, to determine if a polypeptide has tryptophanase (trpase) activity and is within the scope of the invention.

Method for derivatizing primary amines

1-Naphthyl isocyanate (NIC, sigma cat # 170518) reacts with FAA, peptide, and ammonia to produce naphthyl derivatives. See Figure 5 A. The derivatization products can be separated with HPLC (ZORBAX XDB-C8 column (Bodman Industries, Aston, PA) and visualized at 290nm.

Tryptophanase (SEQ ID NO:2) activities on ten essential amino acids - Phenylalanine, Valine, Tryptophan, Threonine, Isoleucine, Methionine, Leucine, Lysine, Arginine, Histidine - and non-essential FAA serine, were tested. The reaction products were derivatized with NIC and analyzed using HPLC. For the derivatization reaction, 2mM NH₄Cl was used as positive control. Tryptophanase (SEQ ID NO:2; encoded by, e.g., SEQ ID NO: 1) is a publicly known tryptophanase from E. coli (Genbank accession nos. NC_002695 REGION: 4677439.4678854 for the DNA sequence and NP_312672 for the protein sequence).

As illustrated in Figure 5B, there was no detectable derivatized NIC-NH₃ peak on essential amino acid reactions except tryptophan. The results show the tryptophanase (SEQ ID NO:2; encoded by, e.g., SEQ ID NO:1) did not cross-react with other essential amino acids. HPLC- fluorescence length detector (FLD) method for tryptophanase assay

HPLC-FLD method can be used to measure the enzymatically liberated indole, see, e.g., Krstulovic (1979) "Rapid assay for tryptophanase using reversed phase high performance liquid chromatography," J Chromatogr. 176(2): 217-224. Tryptophan and Tryptophanyl di- and tri- peptides were incubated with a purified Trpase (SEQ ID NO:2) at 37⁰C, pH 8 for 3hr. The reaction mixes were labeled as AA-AA+ase. Peptides without Trpase were also incubated as negative control, labeled as AA-AA. The reaction products were analyzed using HPLC (ZORBAX XDB-C8 column) with fluorescence length detector (FLD). HPLC was performed at ImI per min with 60% methanol and 40% water. FLD excitation is 285nm and emission is 320nm.

The results, illustrated in Figures 6A and 6B, and Figure 7, demonstrate that Trpase digested Tryptophan and produced indole. There was no indole detected from tryptophanase digested di-peptides, even for the Trp-Trp dipeptide (Figures 6A and 6B). Trpase activities on tri-peptides were also tested (Figure 7). Gly-Trp-Gly and Leu-Trp- Leu had low solubility in water, but the initial peptide signals from HPLC were good enough for evaluating the reaction products. There was no indole peak produced from those tri-peptide reactions.

Tripeptide Lys-Trp-Lys had low fluorescence signal while Trpase digested products had good fluorescence. Mass spectrometry (MS) analysis showed that lysine was the major product after Trpase treatment. These experiments demonstrated that Trpase (SEQ ID NO:2; encoded by, e.g., SEQ ID NO:1) had peptidase activity specifically on Lys-Trp bond, since Trpase had no effect on Trp-lys dipeptide. The fluorescence after Trpase treatment most likely came from Trp-Lys dipeptide.

Example 2: Exemplary screening assays The following example described an exemplary assay of the invention, which can be used to determine if a nucleic acid or polypeptide sequence is within the scope of the invention. In one aspect, lactic acid bacteria (LAB) isolates were screened. Screening of intestinal isolates: Whole cells and cell-free extracts were prepared from intestinal lactic acid bacteria (LAB) isolates and screened for skatole degradation by GC/FID assay. For primary screening, 4 experiments were performed in duplicate. 17 preliminary hits were found and subjected to secondary screening. For that purpose 3 experiments were performed in triplicate and 10 hits were confirmed. Skatole degradation activities are shown in Table 2. Most active isolate degraded 15+/-4% skatole in cell-free extracts (1-007-0-0-28). Two strains (1-007-0-0-25 and -65) degraded skatole in both whole cells and cell-free extracts.

Table 2. Skatole degradation by intestinal LAB isolates.

5 Summary of screening efforts: Total of 295 lactic acid bacteria (LAB) strains were screened by GC/FID for skatole degradation, 259 plant and 36 intestinal isolates. 22 hits were confirmed, 12 of plant and 10 of intestinal origin. Most active plant isolates degraded 19% skatole in whole cells (+1-2%, 1-049-0-0-2792) and 16% in cell- free extracts (+/-5%, 1-049-0-0-149) during 48h incubation at 37⁰C (Table 2). Most o active intestinal isolate degraded 15% skatole in cell-free extract (+/-4%, 1-007-0-028).

Two intestinal isolates showed degradation both in whole cells and in cell-free extracts (I- 007-0-0-25 and 1-007-0-0-65). Significant difference in hit rate was found between plant and intestinal isolates (5% vs. 28%). Intestinal strains are more likely to be exposed to skatole in GI tract and as such could be more accustomed to its degradation. 5 Characterization of 22 LAB hits: Selected strains were further characterized by the following means: (1) Spontaneous skatole resistant mutants were isolated by propagation of cells in the presence of increased amounts of skatole (0.02- 0.12%, MRS media); (2) Growth requirement for tryptophan (Tip) and (3) the ability to use skatole as carbon source were determined (OD_6O0 were measured and compared in 0 minimal media with and without Trp or skatole added). Results are summarized in Table 3 (strains #1-12 are plant and #13-22 are intestinal isolates). Table 3. Characterization of LAB hits.

See below; Growth on skatole was 10-fold lower than with glucose as carbon source (24h incubation).

²p, b; Resistance to designated amounts of skatole was determined on plate or in broth. Spontaneous mutants were isolated for all lactic acid bacteria (LAB) bits.

Nine of 22 mutants were resistant to 0.12% skatole (amount 12-fold higher than what is used in skatole degradation assay and 480-fold higher than physiological concentration of skatole in pig colon; 8/9 strains are intestinal isolates). Thirteen of 22 strains listed in Table 3 showed Trp growth requirement (7/13 very strong; 5/7 are intestinal isolates). Four of 22 strains utilized skatole as carbon source (3/4 are intestinal isolates). Skatole resistant mutants of these 4 strains showed stronger growth on skatole compared to the corresponding wild type (wt) isolates (the difference was most significant (3 -fold) for isolate 1-049-0-0-2792 in the presence of 0.02% skatole in minimal media). Skatole degrading activities of LAB hits and corresponding mutants will be evaluated next in the presence of physiological concentration of skatole (40-fold lower than used in in vitro assays). Of 22 characterized LAB hits, 2 intestinal isolates could be the most promising candidates for further development (1-007-0-0-122 and 1-007-0-0-61). These two strains degrade 10-15% skatole in cell-free extracts, have strong Trp growth requirement and may utilize skatole as carbon source. Skatole degrading activities were compared for 7 of 22 spontaneous lactic acid bacteria (LAB) mutants and the corresponding wt strains (1-049-0-0-149, -173, -294, -148, -181, 1-007-0-0-122 and -65). Whole cells and cell-free extracts were prepared and incubated with 0.01% skatole at 37⁰C for 48h (GCMD assay was used for skatole detection). No significant difference in skatole degrading activity was found between wt and mutant strains.

To determine how much skatole could partition into cultured cells, 4 lactic acid bacteria (LAB) mutants and the corresponding wild type (wt) strains (1-049-0-0-122 and 1-007-0-065, both resistant to 0.12% skatole; 1-049-0-0-168 and -3362, both resistant to 0.06% skatole) were incubated with 0.01% skatole. Samples were removed at 0 hour (h) and 24 h and culture supernatants were separated from cells and filtered. Cells were disrupted with glass beads to separate soluble and insoluble fractions (cytosol from cell walls and membranes). Amount of skatole present in each fraction was analyzed by GC/FID. At 0 h, skatole remained in supernatant fractions in all mutants and wt isolates (no skatole could be detected in soluble or insoluble fractions). At 24 h, although most of skatole remained in supernatant fractions, 13-17% was also detected in soluble and 3-5% in insoluble fractions. There was no significant difference between mutants and wt isolates or between mutants resistant to 0.06% or 0.12 % skatole (experiment was performed in triplicate). These data suggest that very little amount of skatole could be accessible for degradation inside LAB cytoplasm or cell wall in whole cells and that skatole-degrading enzymes (or cell-free extracts) should be supplied to enhance degradation.

Environmental enrichments

Enrichment experiments with environmental samples can include obligate anaerobes (OAN) or facultative anaerobes (FAN). The enrichment experiment can comprise primary (1°), secondary (2°), tertiary (3°) and quaternary (4°) enrichment screening steps. In one aspect, samples are transferred into fresh media with 0.03% skatole for continuing rounds of enrichment.

In alternative aspect, organisms from 3° and 4° enriched samples are enriched by plating (e.g., on minimal media with skatole as carbon source) and/or by laser sorting (e.g., in broth with skatole as carbon source). Single colonies can be isolated and analyzed under microscope. In one experiment, all isolated single colonies were Gram- positive rods of different sizes and shapes. These can be inoculated in minimal media to confirm growth on skatole. They can be subjected to 16S rRNA analysis to determine phylogenetic classification of isolated organisms. 3° and 4° enrichment can further comprise additional plating and laser sorting.

Small insert genomic libraries

10 small insert genomic libraries were constructed and screened. These are genomic clones (l-7.5kb inserts) that showed stronger growth in LB+0.02% skatole (MIC for E. coli library host) compared to vector control. Data were obtained for 12 hits identified in 6 different libraries (1-4.5 kb inserts). All were found to encode GaIE (UDP- glucose-4 epimerase). This enzyme is involved not only in galactose metabolism, but also in biosynthesis of lipo-polysaccharide (LPS) component of cell membranes (based on the literature, partitioning of skatole into membrane lipids causes its' toxicity). In addition to GaIE, genes encoding proteins involved in tolerance to toluene were also detected in some of sequenced hits. Therefore, it appears that skatole resistant E. coli mutants, not clones encoding skatole-degrading enzymes, were recovered when libraries were screened based on E. coli survival on LB+0.02% skatole. To counteract this problem, more stringent library screening method is needed.

Alternative approaches

In addition to whole cells and enzymes, the invention provides alternative approaches to eliminate skatole from gut contents; for example, application of skatole binding proteins as feed additives. Skatole binding by serum albumin was evaluated in an in vitro assay (in in vivo situation, albumin binds skatole after absorption into blood and transports it into liver). Skatole was used at physiological concentration (2.4 μg/ml) and incubated with 0%, 0.1%, 0.5%, 1% and 2% of albumin (BSA, fatty-acid free) for 0-60 min at 37⁰C (physiological concentration of albumin in pig serum is about 3.4%). Samples were removed at 0 min and 60 min and unbound skatole was separated from the mixture using size-exclusion columns (10 kD cutoff, MW of albumin is 60 kD) and

Montage Albumin Deplete Kit (Millipore, Billerica, MA), with columns that selectively bind albumin. Amount of unbound (eluted) skatole was determined by GC/FID (5-methyl indol was used as internal standard). Concentration dependent binding of skatole to albumin was observed at 0 min and at 60 min (binding increased with increase in albumin concentration). No loss of skatole (which could happen due to nonspecific binding to columns) was obtained in negative control (assay mixture without albumin). As additional control, serum γ-globulin was used instead of albumin in the above described assay. Similar results were obtained except that γ-globulin bound less skatole compared to albumin (exclusion columns were used to separate bound and unbound material). Results described above suggest that skatole could be efficiently sequestered by binding to hydrophobic proteins applied at low concentrations. Thus, the invention provides methods for removing skatole from rumen, caecum and colon of monogastric animals, e.g., pig colon, using proteins which specifically bind skatole. The invention also provides methods for removing skatole from pig colon using albumin (which can sequester other hydrophobic molecules) and anti-skatole antibodies. Example 3: Exemplary GIGAMATRIX™ Screening Assays for Trvptophanases The following example described an exemplary GIGAMATRIX™ screening assay of the invention, which can be used to determine if a nucleic acid or polypeptide sequence is within the scope of the invention. Excised Escherichia coli environmental libraries (see U.S. Patent Nos.

5,958,672; 6,004,788, 6,168,919, 6,280,926, 6,528,249, 6,528,249, 6,566,050, 6,656,677, 6,677,115, and 6,849,395; Int'l Pub. WO 2005/012550) were mixed with kanamycin (50 ug/mL final concentration) and serine AMC-carbamate (0.1 mg/mL). This mixture was loaded into 400,000 well GIGAMATRIX™ plates (see U.S. Patent Nos. 6,764,818, 6,798,520, 6,918,738; U.S. Patent Pubs. 2005-0046833, and 2005-0118707; Lafferty (2004) "GigaMatrix: An Ultra High-Throughput Tool for Accessing Biodiversity," Journal of the American Laboratory Association (9) 200-208). The plates were incubated overnight at 37⁰C, then hits were visualized using a 7-hydroxy-4-methylcoumarin (4- methylumbelliferone) filter (excitation 365nm, emission 450nm), and recovered as previously described (Lafferty).

Recovered cultures were tested for indole production in the presence of tryptophan, then plated onto solid medium. Individual colonies were tested for indole production from tryptophan. Positive hits were sequenced to determine the genetic material responsible for the indole positive signal.

Example 4: Exemplary Tryptophanase Activity Assay

The following example described an exemplary tryptophanase screening assay of the invention, which can be used to determine if a nucleic acid or polypeptide sequence is within the scope of the invention. Assay conditions uL

100 mM potassium phosphate pH 7.5 80

10 mM tryptophan 10

Enzyme 10

Take timepoints of 10 uL and pipet into 90 uL of 0.2 M HCl to quench reaction

Add 100 uL of indole spot reagent

Standard curve Standards are 0.2, 0.15, 0.1, 0.05, 0.02 & 0.01 in water

Add 100 uL of each standard plus 100 uL of indole spot reagent

Read plate at 630 nm Indole spot reagent

Sample run: 96-well plate format:

A B C D

E F G

H

[continued]

RAW DATA - sample run

##BLOCKS= 1

Plate: Plate#1 1.3 PlateFormat Endpoint Absorbance Raw put cursor here Temp (' O) 1 2 3 4 5

37.1 0 .2339 0.1722 0.1304 0.1211 0.0849

0 .4954 0.4532 0.3422 0.2517 0.2036 0.6975 0.4311 0.3644 0.2857 0.2592

0.5555 0.6865 0.5725 0.403 0.3356

0.5586 0.6621 0.6237 0.417 0.3698

0.5952 0.615 0.6125 0.4356 0.3774

1.2451 1.0644 0.8132 0.4958 0.2675

[Continued]

FALSE 1 6 7 8 9 10 11 12

0.0699 0.1274 0.0951 0.0721 0.0722 0.0649 0.0583 0.1688 0.2018 0.0611 0.0831 0.1031 0.0763 0.0702 0.1939 0.2556 0.0634 0.1112 0.1294 0.0921 0.0943 0.2742 0.3049 0.0836 0.1244 0.1711 0.1008 0.1103 0.3348 0.3627 0.1169 0.2139 0.197 0.14 0.1233 0.3306 0.3304 0.1252 0.1999 0.2045 0.1413 0.132 0.1659 1.2811 1.0859 0.8603 0.5413 0.2913 0.0769 0.1659 1.2811 1.0859 0.8603 0.5413 0.2913 0.0769

STD Protein sample name SLOPE DF SLOPE U/ML mg/ml SEQ ID NO:44 E1 0.401464 0.00176581 4 5.879003 12.01435 48.3 SEQ ID NO:44 E2 0.726064 0.00294867 8 5.879003 40.12471 38.9 SEQ ID NO:44 E3 0.891481 0.00329819 16 5.879003 89.76189 48.3 SEQ ID NO:46 E4 0.909254 0.00208162 4 5.879003 14.16307 38.9 SEQ ID NO:46 E5 0.91851 0.00194048 8 5.879003 26.40551 48.3 SEQ ID NO:46 E6 0.941568 0.00179219 16 5.879003 48.77535 38.9 SEQ ID NO:44 E7 0.889817 0.00147333 4 5.879003 10.02437 48.3 SEQ ID NO:44 E8 0.457723 0.000322 8 5.879003 4.381695 38.9 SEQ ID NO:44 E9 0.877668 0.00099486 16 5.879003 27.07553 48.3 SEQ ID NO:46 E10 0.974827 0.000938 4 5.879003 6.382034 38.9 SEQ ID NO:46 E11 0.943914 0.0005541 8 5.879003 7.539989 48.3 SEQ ID NO:46 E12 0.98018 0.0005179 16 5.879003 14.09504 38.9

indole mM 0.2 0.15 0.1 0.05 0.02 0.01

STD AVERAGE 1.2631 1.07515 0.83675 0 .51855 0.2794 0.1214

STDEV 0.02078 0.012413 0.0271932 0. 026269 0.013741 0.051384

SEM 0.01039 0.006207 0.0135966 0. 013135 0.00687 0.025692

Example 5: Activity of Exemplary Tryptophanases of the Invention in Cecal and Intestinal Fluids

The following example describes the results of experiments demonstrating activity of an exemplary tryptophanases of the invention in both hindgut (e.g., cecal) and intestinal fluids. In one aspect, exemplary polypeptides having a sequence as set forth in SEQ ID NO:40 (encoded by, e.g., SEQ ID NO:39) and SEQ ID NO:44 (encoded by, e.g., SEQ ID NO:43) were tested. The assays described herein can also be used to determine if a polypeptide is within the scope of the invention. The invention provides enzymes, and methods of using them, for degrading skatole or its precursors in the hindgut of an animal, e.g., a pig colon, and reduce skatole accumulation in fat. The invention provides enzymes, and methods of using them, to control a boar taint problem and to improve efficiency of pig production and the flavor of cooked pork meat

The polypeptide having a sequence as set forth in SEQ ID NO:44 (encoded by, e.g., SEQ ID NO:43) was tested for its ability to produce indole from tryptophan in the presence of cecal fluid. A fermentation sample representing SEQ ID NO: 44 was used to assay activity. The graph illustrated in Figure 9 indicates that the enzyme can convert all available tryptophan to indole in about 2.5 h versus a buffer control which achieves the same level of activity in less than 30 minutes. Figure 9 illustrates data from an activity assay for tryptophanase in cecal fluid (CF).

In general tryptophanases not as active in cecal fluid as in potassium phosphate buffer (pH 7.5). Data obtained from the tested exemplary tryptophanases having a sequence as set forth in SEQ ID NO:48 (encoded, e.g., by SEQ ID NO:47) and SEQ ID NO:40 (encoded, e.g., by SEQ ID NO:39) shows that enzymes, including a subset of polypeptides of the invention, can fall into two main groups: enzymes stable in the presence of simulated gastric fluid (SGF) and those stable in the presence of simulated intestinal fluid (SIF). For the most part, each group is not stable in the corresponding condition. Figure 38 shows data from assays under SGF or SIF conditions which indicates the two groups. In Figure 38, data demonstrating the stability of candidate tryptophanases after treatment in SGF and SIF is shown. Enzymes were evaluated in separate experiments. Residual activity was measured using 1 mM S-p-nitrophenyl cysteine (SPPC) in 50 mM potassium phosphate buffer pH 7.5. Residual activity was determined as % activity remaining based on a t=0 timepoint and after subtracting background activity from a negative control (vector (no insert) in same host cells).

SEQ ID NO:48 and SEQ ID NO:40 were the most stable in SGF and SIF treatments respectively. Sequence analysis of these two enzymes indicates they do belong to distinct phylogenetic groups. The SEQ ID NO:48 has a large number of lysine or arginine residues relative to the SEQ ID NO:40 suggesting that it is sensitive to proteolysis by trypsin. Pepsin, found in SGF, preferentially cleaves at Phe, Tyr, Trp and Leu in position Pl or Pl'. Chymotrypsin, found in SIF, preferentially cleaves at Phe, Tyr,

Trp in position Pl . Since these two enzymes cleave mainly the same amino acid and pepsin is less specific, it is reasonable to assume an enzyme stable in the presence of pepsin would also be stable in the presence of chymotrypsin.

Stability tests were performed on SEQ ID NO:48 and SEQ ID NO:40. Figure 39A (panel on the left) shows the purified SEQ ID NO:48 in SGF and Figure 39B (panel on the right) shows a partially purified SEQ ID NO:40 in SIF. SEQ ID NO:48 was mixed with 50 U of pepsin and incubated at 37⁰C. Samples were taken at 0, 5, 10, 30 & 120 minutes and loaded onto an SDS-PAGE gel. SEQ ID NO:40 (20 uL) was mixed with 0.5 ug trypsin and incubated at 37⁰C. Samples were taken at 0, 5, 10, 30 and 120 minutes and loaded onto an SDS-PAGE gel. An arrow indicates the position of SEQ ID NO:40 on the gel. Lane "s" represents a protein standard

In one aspect, the invention provides a modified, or an "improved" SEQ ID NO:48 stability in SIF by removing one, several or all trypsin cleavage sites in SEQ ID NO:48 not in common with SEQ ID NO:40. In one aspect, the invention encompasses modified versions of all enzymes of the invention (including SEQ ID NO: 48 and SEQ ID NO:40) wherein at least one, several, or all protease cleavage sites have been

"engineered" out. For example, the invention provides for enzymes of the invention wherein one, several or all pepsin, trypsin and/or chymotrypsin cleavage sites have been "engineered" out. The invention also provides methods for making modified, or an "improved" tryptophanases using, for example, GSSM or any other technology. In one aspect, SEQ ID NO:48 and SEQ ID NO:40 are further evolved for improved protease

(e.g., pepsin, trypsin and/or chymotrypsin) stability. The invention provides a screen to effectively measure modified enzyme activity over the wild type protein; any tryptophanase activity assay can be used, e.g., as described herein. The screen(s) of the invention include thermotolerance, SGF and SIF components. Evolved biomolecules can be assessed for their specific activity levels.

Polypeptides of the invention were tested in simulated gastric and intestinal stability assays, and, as illustrated in Figure 40, at least four enzymes were identified that retained significant activity under simulated gastric and intestinal conditions: polypeptides having sequences as set forth in SEQ ID NO:48 (encoded by, e.g., SEQ ID NO:47); SEQ ID NO:28 (encoded by, e.g., SEQ ID NO:27); SEQ ID NO:44 (encoded by, e.g., SEQ ID NO:43); SEQ ID NO:2 (encoded by, e.g., SEQ ID NO: 1). Specific activity of tryptophanases was determined at pH 7.5 and 37 ⁰C. Based on the results obtained from in vitro stability tests simulating gastric and intestinal phases of digestion, at least these four exemplary tryptophanases have the potential to degrade 2 gram (g) free tryptophan per day in the colon when administered in feed at a dose of 1.5 g per day.

Figure 40 illustrates the results of stability studies of exemplary tryptophanases after treatment in simulated gastric fluid and simulated intestinal fluid. Enzymes were evaluated in separate experiments. Residual activity was measured using 1 mM S-p-nitrophenyl cysteine (SPPC) in 50 mM potassium phosphate buffer pH 7.5. Residual activity was determined as % activity remaining based on a t=0 timepoint and after subtracting background activity from a negative control (vector (no insert) in same host cells). Green circles indicate clones chosen for in vitro colon simulation experiments. SGF: enzymes were incubated in potassium phosphate buffer (final pH=2.6) + 50 μg/mL pepsin (50 U/mL) for 30 minutes at 37°C. SIF: enzymes were incubated in 10 mg/mLpancreatin (pH 6.3) for 60 minutes at 37⁰C.

Table 1, below, summarizes predicted activity of exemplary tryptophanases based on % residual activity and specific activity. It is assumed that 1500 mg of enzyme will be produced based on COGs and 2 g of tryptophan is produced per day in the pig. Specific activity was measured using 100 μg/mL tryptophan in 50 mM potassium phosphate buffer pH 7.5. Specific activity is indicated as U/mg where a Unit is the amount of enzyme required to degrade 1 μmole of tryptophan in 1 minute at pH 7.5 and 37 ⁰C. Table 1

##: theoretical amount of tryptophan (g) degraded in the colon (per day)

Tryptophanase characterization was carried out using in vitro gastric and intestinal simulations, as noted above. The criteria for validation in this model are: reproducibility, evidence of skatole production, ability to quantify skatole, impact of added tryptophan on skatole level, and responsiveness to tryptophanase addition. In one aspect, in vitro assays of the invention are performed in a sequential fashion with quadruplicate samples for each enzyme tested. Assay is designed to measure starting activity as well as activity at various times during the assay to track enzyme performance. Volume in the assay can be increased to allow for timepoints. For SIF, pH is adjusted with 1 M NaOH to a final pH of 7.5 (step 6, below) and timepornt aliquots from assay are mixed with a protease inhibitor cocktail to quench protease activity. The activity of samples is measured using S-4-nitrophenyl cysteine as substrate and % remaining activity remaining is calculated based on activity of time zero sample versus final timepoint sample according to the formula below. % activity remaining= 100-((x-y)/x*100) Where x is the activity at time zero and y is the activity after SIF treatment.

Simulated Gastric Fluid (SGF) 30 uL KH₂PO₄ pH 2.6 20 uL enzyme lysate 50 U/mL pepsin IPX Simulated Intestinal Fluid (SIF)

100 mg/mL pancreatin 40 mg/mL bile salts 50O mM KH₂PO₄ pH 7.5

Exemplary Assay of the invention 1. prewarm SGF to 37 ⁰C

2. add enzyme lysate

3. remove time zero sample for assay

4. incubate at 37 C for 2 hours

5. remove sample for assay 6. add a total of 5 uL of 1 M NaOH over a period of 3 minutes to gradually increase pH

7. add SIF to achieve a Ix concentration

8. remove sample for assay

9. incubate 37⁰C for 2 h 10. remove sample for assay

11. Assay all samples and determine residual activity Example 6: In vitro and In vivo Tests to Assess Efficacy of Enzymes

The invention provides assays for screening tryptophanases using in vitro and in vivo tests to assess efficacy in reducing microbially-produced skatole in animal hindguts, e.g., in pigs; and these in vitro and in vivo can be used to determine if an enzyme is within the scope of the invention. Enzyme for use in these tests can be produced using bacteria, e.g., an E. coli, as a host. Enzymes can be supplied either in lyophilized form or as a liquid formulation. Enzyme produced in a food grade production host will not be necessary until after animal trials have been completed.

In vitro tests In one aspect, in vitro tests assess an enzyme's responsiveness to tryptophan in a laboratory simulation of the pig colon. An assay - an in vitro model - was developed which simulates bacterial fermentation in the swine colon. The fermentation product portfolio seemed authentic and corresponded to that measured in live animals. Accumulation of skatole and indole was directly proportional to the initial concentration of tryptophan, demonstrating that the use of tryptophanase for skatole reduction is a viable concept. Tryptophanase having a sequence as set forth in SEQ ID NO:48 failed to reduce skatole accumulation in the simulation model; E. coli lysate increased skatole concentration irrespective of its tryptophanase activity. Most likely this is due to additional protein provided with the lysate. Several characteristics of the colon environment were detrimental to the activity of the tested tryptophanase; SEQ ID NO:48 had too high pH optimum, it was sensitive to low redox potential, it was inhibited by the end product indole, and, unknown factors in digesta extract (possibly proteases) killed the activity of the enzyme. Tryptophanases can be ranked for the critical characteristics and included in a simulation assay to reveal the parameters most critical for that particular enzyme action in a particular hindgut (e.g., colon) environment.

The invention provides a test system which simulates bacterial fermentation in the colon of pigs. The basic idea was to feed boar colonic microflora with the soluble fraction of the digesta from the colon of boars. The usage of authentic digesta as a source of substrate is important since it is not possible to artificially compose a medium that would even roughly mimic nutritional environment bacteria meet in the colon. Likewise, it would not be possible to use a defined inoculum that would even roughly mimic the structure of bacterial community present in the colon and directly or indirectly participate in the metabolic process leading to skatole production.

Simulation medium. The major part of the simulation medium was derived from domestic boars. At a local slaughterhouse boars were slaughtered and intestines instantly removed. Digesta from mid colon was recovered and packed in airtight glass jars. In anaerobic clove box, digesta from several boars was pooled and mixed 1:1 with an anaerobic buffer pH 7.0 (K₂HPO₄, 2.99g; NH₄H₂PO₄, 2.23g; MgSO₄ X 7H₂O, 122mg;

NaOH, 33mg; Na₂Sx9H₂0, 128mg; cysteine, 128mg; ad.l liter H₂O). After thorough mixing, the suspension was centrifuged for 15 minutes at 47,500 x g and the supernatant recovered in anaerobic clove box to be used as medium in the simulations. Aliquots of the medium were dispensed in 10-ml serum bottles for the simulations.

Inoculum. Digesta from the distal colon of boars was recovered and packed in airtight glass jars in the slaughterhouse. In anaerobic clove box, digesta from several boars was pooled, diluted 1 : 1 in an anaerobic buffer (see above), and forced through a 0.4 mm metal mesh to remove large feed particles. The sieved digesta was directly weighed in individual simulation vessels to be used as an inoculum in simulations.

In some studies Clostridium scatologenes was used as part of the inoculum. In such cases the bacterium was precultured and mixed with the digesta inoculum prior to onset of simulation so that the density of C. scatologenes was 10% of that of the total bacteria. Bacterial densities were determined by flow cytometry essentially as described previously, e.g., by Apajalahti (2002) Appl Environ Microbiol.

68:4986-4995.

Simulation protocol. Simulations were carried out in 10-ml serum bottles equipped with gas tight butyl rubber stoppers. Depending on the experiment different test compounds were added as indicated in descriptions of different experiments. In a 5-ml simulation the additions were as follows:

• Medium, 3.5 ml

• Tryptophan solution, 0.2 ml (alternatively anaerobic H₂O) • Anaerobic enzyme solution, 0.5 ml (alternatively anaerobic H₂O or

(exemplary) enzyme lysate); final enzyme level 0.08U/ml

• Inoculum, 0.8 g (alternatively 0.8 ml of anaerobic buffer)

Simulation was started by inoculation, then sealing the bottles and transferring them from anaerobic clove box to 37°C incubator room, where they were gently shaken till the end of the simulation. Simulation time was from 0 to 3 days as indicated in the results of each individual experiment. All incubations and analysis were done in 2 to 5 replicates.

Measured parameters. Gas production was measured at various time points during the incubation. At the end of the incubation pH was measured and samples taken 5 for the analysis of indole and skatole. Indole and skatole were analyzed by gas chromatography using internal standard method essentially as described by Jensen & Jensen (1994) J. Chromatogr. B. Biomed. Appl. 655:275-280.

Enzyme assays. Assays studying the role of various simulation parameters on enzyme activity we carried out in 100 mM potassium phosphate buffer mixed with o mineral medium for anaerobic bacteria and other components as described in results.

Results

Demonstration of in v/vo-type of tryptophan conversion to indole and skatole in the simulation model for swine colon:

Time course of tryptophan fermentation: In live swine skatole and indole 5 begin to accumulate gradually in the intestine towards the distal colon. In fact, their residual concentrations are insignificant in compartments proximal to mid colon. For the simulation it would be important to know which length of incubation should be used in the model to make it ideal for the testing of inhibitors of skatole formation. Therefore, we initially analyzed fermentation parameters from various time points between 0 and 68 0 hours. Results illustrated in Figure 11 indicate that indole formation was rapid.

Maximum residual concentration of indole, 0.4 mM, was found after 15 hour incubation. In molar basis this corresponds to one third of the added 1.2 mM tryptophan, the precursor of indole. In prolonged incubation indole concentration slowly decreased suggesting that it was only a transient metabolite and becomes converted further by 5 intestinal bacteria.

Unlike indole, skatole appeared to accumulate and its concentration increased in prolonged incubation. Accordingly, the maximum residual concentration of skatole was measured after 68 hour incubation (as illustrated by the data shown in Figure- 12). The maximum concentration of skatole was 0.3 mM corresponding to about one 0 fourth of the added tryptophan.

The results of indole and skatole analysis indicated that at least ~ 60% (0.4 mM + 0.3 mM) of the added tryptophan was routed to pathways leading to indole and skatole, assuming that no indole is converted to skatole. In reality this percentage is likely to be bigger due to the fact that only residual concentration of indole, not the total flow, can be measured. If we simply sum up the residual concentrations of indole and skatole at different time points we end up in a time course illustrated in Figure 13. At any given time point the maximum sum of indole and skatole is ~ 0.6 mM which is likely to be less than the total sum of indole and skatole produced in 68 hours. In addition to conversion products of tryptophan, we also followed pH and the total gas production during the simulation. After slight increase during the first 15 hours, pH gradually decreased during the 68 hours of incubation, as illustrated in Figure 14. In fact, pH evolution appeared to follow the residual concentration of indole, which indicates concomitant ammonia (base) release from tryptophan. The fact that pH gradually decreased indicates acid formation which may be from bacterial digestion of complex fibrous substrates present in colon digesta used as a substrate.

Gas production is a general indicator of bacterial metabolism including saccharolytic and putrefactive fermentations. Analysis of the total gas production revealed that there was a major activity during the first 15 hours accounting for 60% of the total gas production occurring during the entire time of incubation. However, the fermentation remained active for two more days, as illustrated in Figure 15.

Effect of tryptophan concentration on indole and skatole production: The simulation model used here is designed for screening of enzymes which reduce the production of skatole by reducing the concentration of its precursor, tryptophan (and can be used to determine if an enzyme is within the scope of the invention). Tryptophanase enzymes convert tryptophan to indole, which is not a precursor of skatole production. Since a model for tryptophanase screening is valid only if the concentration of free tryptophan directly affects the yield of skatole, we determined the dependence of colon fermentation on the concentration of added tryptophan. In this 68 hour simulation we used tryptophan concentrations from 0 to 6 mM. When no exogenous tryptophan was added the resulting concentration of indole and skatole at 68 hours was less than 0.05 mM. At low concentrations of tryptophan, 0.048 and 0.25 mM, the concentration of skatole after 68 hour incubation was higher than the concentration of indole, as illustrated in Figure 16 and Figure 17. However, when higher concentrations of exogenous tryptophan were used, indole accumulation exceeded that of skatole. This is most likely due to the fact that low level of indole is a rapidly converted transient metabolite of tryptophan metabolism, which does not accumulate. In contrast, skatole is an accumulating dead end metabolite of tryptophan metabolism (Figures 16 and

17). The overall yield of indole + skatole from tryptophan depended on the concentration of the latter so that slightly more than 50% of the added tryptophan was converted to the indole derivatives when 1.2 and 6 mM tryptophan was used, whereas the apparent yield was 80 and 200 % at 0.25 and 0.048 mM added tryptophan, respectively, as illustrated in Figure 18. This is most likely due to the effect of endogenous tryptophan, the role of which becomes significant when the concentration of added tryptophan is low.

The lowest levels of added of tryptophan appeared to decrease pH slightly probably indicating stimulation of general bacterial activity through improved availability tryptophan for biosynthesis. However, excess tryptophan added in the colon fermentation appeared to lead to significant amino acid fermentation, which releases ammonia. This was apparent from the measured pH which increased almost by one unit with the highest level of tryptophan used, as illustrated in Figure 19.

Total gas production measured at different tryptophan levels followed almost exactly the response observed for pH; the highest level of tryptophan stimulated gas production by more than 20%, as illustrated in Figure 20. The results obtained in the simulation studies with growing levels of tryptophan showed clearly that indole and skatole production in the colon of swine is highly dependent on the availability of tryptophan. Figures 21 to 23 show correlations between the level of added tryptophan and the residual concentration of indole, skatole and the sum of the two after the 68 hour simulation, respectively. In each case the concentration of added tryptophan explained more than 99% of the final metabolite concentration (Figures 21 to 23). The outcome of this study demonstrates that if the microbial system in the colon can be modified to reduce skatole production, the concept based on tryptophan removal is an excellent one.

Activity of tryptophanase SEQ ID NO:48 in colon simulation: The results reported above demonstrated that an enzyme capable of reducing the concentration of free tryptophan in the colon also can reduce the concentration of skatole. In the next study we tested the effect of an exemplary tryptophanase SEQ ID NO:48 of the invention on colon fermentation and microbial conversion of tryptophan to indole and skatole. While the invention is not limited by any particular mechanism of action, this enzyme converts tryptophan to indole, pyruvate and ammonia and when doing so prevents the accumulation of skatole.

In this study, two different concentrations of tryptophan, 0.5 and 1.2 mM were used. Simulations with each concentration of tryptophan were run for 44 hours in the presence and absence of tryptophanase SEQ ID NO:48. Furthermore, SEQ ID NO:48 was added in the simulation vessel either 3 hours before inoculation, at inoculation or 20 hours after inoculation. This was done to demonstrate that the added enzyme actually competes with the microflora for free tryptophan. The later the enzyme would be added, the more tryptophan there would be available for the skatole producing bacteria. Theoretically, the dose of tryptophanase used, 0.4 units per 5 ml, should completely convert the added 0.5 and 1.2 mM tryptophan to end products in 6.25 and 15 minutes, respectively. If uninhibited the enzyme added 3 hours before inoculation should have removed all free tryptophan before the addition of the competing skatole producing bacteria. The concentration of added tryptophan had little or no effect on the total gas production in the simulation vessels. This suggests that the general activity of the colon microbial community changed little when the concentration of tryptophan increased from 0.5 to 1.2 mM, as illustrated in Figures 24A, 24B, and 24C. The addition of enzyme caused significant, about a 40%, increase in the total gas production. This stimulatory effect was similar with all the used enzyme addition regimens, from 3 hours before inoculation to 20 hours after (Figures 24A to 24C). This remarkable stimulatory effect might be due to the specific enzyme activity, additional substrates provided with the enzyme preparation or some indirect stimulatory effect.

Although the concentration of added tryptophan had no effect on the total gas production it significantly affected the concentration of produced indole and skatole, see Figures 25A, 25B, 25C; and, 26A, 26B, 26C and 27A, 27B and 27C. The results of the present simulation were thus consistent with those of the simulation illustrated in Figures 16 to 18. Also the addition of the exemplary enzyme SEQ ID NO:48 affected production indole and skatole. However, unlike anticipated from the assumed mode of action of the enzyme, both indole and skatole concentrations were elevated.

Theoretically, indole concentration should have increased since it is a product of tryptophanase activity. In contrast, skatole concentration should have decreased since skatole producing bacteria are using the same substrate, tryptophan, as the added enzyme. The skatole increasing effect was independent of the time of tryptophanase addition (see Figures 26A to 26C). This suggests that added enzyme had failed to catalyze any significant conversion of tryptophan, which at the same time would have reduced substrate availability for the skatole producing bacteria.

The results obtained raised several questions concerning the characteristics of the enzyme used. It had been earlier shown that the enzyme was active and converted tryptophan to indole in the buffer in the absence of reductant, colon extract and inoculum. However, under the conditions mimicking swine colon with all the mentioned elements present no positive enzyme effect was found after 44-hour simulation. Instead, SEQ ID NO:48 increased the total yield of skatole. To see whether the effect of the tryptophanase on skatole production was connected to the specific activity of the enzyme or whether it was caused by addition of protein in general, we tested also the effect of the host which had been used for the production of SEQ ID NO:48. Lysate of the production host had been produced similarly to that of the actual enzyme production strain. Therefore, the lysate of the enzyme-producing host should well represent the background activities and nutrients present in the production host.

The results obtained showed that during the first hours of simulation the active tryptophanase stimulated indole production as it theoretically should. After 3 hours of simulation the residual concentration of indole in the presence of the host lysate was 0.05 mM, but when the tryptophanase was added the concentration of indole exceeded 0.1 mM, as illustrated in Figure 28 and Figure 29. However, after 24 hours this specific tryptophanase effect was attenuated rather than enhanced as one would expect if the enzyme had been active. During the first 3 hours of simulation the production of skatole appeared to be suppressed in vessels with the lysate of enzyme production strain whether or not the active tryptophanase was present. However, in prolonged incubation the effect of lysate was opposite; the amendment increased the yield of skatole by more than 0.05 mM. The presence of additional reductant (Figure 29) had little or no effect on the production of indole and skatole.

The results obtained from studies with the production strain of E. coli indicated that the stimulatory effect of SEQ ID NO:48 on indole and skatole yield was not specifically resulting from the tryptophanase activity but rather from unspecific protein amendment or enzyme activities of the host strain. Yet, it appeared that the tryptophanase was active during the first hours of incubation resulting in elevated level of indole.

Factors potentially inhibiting the activity of tryptophanase SEQ ID NO:48 in the swine colon and the simulation model: The results indicated that while the tryptophanase SEQ ID NO:48 readily converted tryptophan to indole in the buffer system, it failed to function in the colon simulation. We, therefore, designed a series of experiments to reveal the parameters which inhibited the enzyme activity in the system mimicking the colon of swine. The parameters tested included pH (higher in the assay buffer), redox potential (higher in the assay buffer), an end product indole (initially lower in the assay buffer), and soluble digesta components (absent in the assay buffer).

Effect of pH on the activity of SEQ ID NO:48: The assay used for tryptophanase activity assessment is using a potassium phosphate buffer at pH 7.5. This is clearly higher than typical pH in the colon. Therefore, we wanted test how steeply the reduction of pH would reduce the enzyme activity. In this study the yield of indole was used as a measure of enzyme activity and it was measured after 3 and 24 hours of incubation at 37°C. After three hours of incubation the decrease of pH from 7.5 to 6.5 led to 25% reduction of indole yield and after 24 hours of incubation the corresponding reduction was 35%. When the pH was reduced from 7.5 to 5.5 the corresponding decrease in enzyme activities after 3 and 24 hours of incubation was about 65 and 75%, respectively, as illustrated in Figure 30.

The practical meaning of the pH effect may be significant, when taking into account that the inhibitory effect of lower pH became more significant when the time of incubation increased. The pH of the swine colon is typically between 6 and 7 and at its lowest in the proximal colon. According to the results obtained it is possible that pH effect alone may lead to 50% reduction of enzyme activity from that assayed under the ideal conditions.

Effect of redox potential on the activity of SEQ ID NO:48: Many of the components used in the simulation potentially reduce redox potential of the simulation medium. Low redox potential is a prerequisite for the growth of many fastidious anaerobes and, therefore, elementary if we wish to mimic bacterial fermentations taking place in the colon, where redox may be lower than - 350 mV. To achieve redox potential prevailing in the colon we use a mixture of reducing compounds occurring also in the natural anaerobic ecosystems (cysteine and NaS). When adding such reductants in anaerobic buffer we observed 30 and 40% reduction in indole production activity by SEQ ID NO:48 after 3 and 24h incubation, respectively, see Figures 31 and 32). The addition of reductant led to more than 300 mV decrease in redox potential, see Figure 35.

We also found that colon extract and E. coli lysate alone decreased redox potential by 150 to 250 mV (see Figure 35). In case of colon extract this is due to the presence of reducing compounds produced by anaerobic bacteria in the colon, whereas in case of the bacterial lysates the effect was likely to be based on many reducing enzymes (dehydrogenases etc) present in the gently lysed bacteria. Potential inhibitory effect of low redox potential generated by lysates cannot be shown by the experimental arrangement used, since indole was only produced in the presence of SEQ ID NO:48. However, colon extract, which reduced redox potential, reduced also indole producing activity of SEQ ID NO:48 (see Figure 33). The extent to which activity was reduced was comparable to that of the added chemical reductant (see Figures 32 and 33). When the chemical reductant was added together with the colon extract the enzyme activity was inhibited by 65% (Figure 34). This combination of medium components dropped redox potential to that prevailing under typical methanogenic conditions, -370 mV (Figure 35).

The negative effect of redox potential on the activity of the tested tryptophanase SEQ ID NO:48 appeared to be even more significant than that of the pH discussed above. Indeed, the inhibition by these two mechanisms combined may exceed 90% when compared to the conditions ideal for the enzyme.

Effect of indole on the activity of SEQ ID NO:48: Indole is one of the end products of tryptophan conversion by tryptophanase SEQ ID NO:48 and as such a potential inhibitor of the enzyme activity. There are also other end products of the tryptophanase activity, pyruvate and ammonia, but they are likely to be very short lived in the microbial community of the swine colon. Further conversion of indole takes place by the colon microflora, but so slowly that in practice it accumulates. In this study the target was to test how the concentration of indole affects the activity of SEQ ID NO:48. In the experimental arrangement we had two different starting concentrations of tryptophan, 1.2 and 5.0 mM, which were provided as a substrate for

SEQ ID NO:48 in the presence and absence of 0.4 mM indole. We found that within the first 3 hours the pre-existing indole inhibited the further production of indole by more than 80% when the tryptophan concentration was 1.2 mM and by 50% when the initial tryptophan concentration was 5 mM (Figure 36). After 24 hours the corresponding inhibitions were 60% for the 1.2 mM initial concentration of tryptophan and 35% for 5 mM tryptophan.

The concentration of indole added in the reaction mixture is realistic in the colon of swine. Therefore, the degree of end product inhibition measured here for indole is most likely not far off from what would occur in the colon of swine. In the colon simulation the maximum levels of indole produced from 1.2 mM and 5 mM tryptophan were 0.4 mM and 2 mM, respectively. It is worth noting that in the colon simulation the inhibition becomes significant only when indole starts to accumulate, the initial concentration of indole being lower than 0.4 mM. Effect of soluble digesta components on SEQ ID NO:48 activity: The effect of redox potential and reducing compounds on the tryptophanase activity was discussed above. The results showed that colon extract was one of the components that lowered redox potential and inhibited enzyme activity. In addition to the redox lowering effect digesta components may also affect tryptophanase activity by other mechanisms.

The impact of digesta extract was studied by measuring indole production rate of the exemplary tryptophanase SEQ ID NO:48 in the presence of increasing proportions of the extract. The results showed that the inhibitory effect of digesta extract on indole production was growing when the reaction time was expanded from 45 min to 24 hours, as illustrated in Figure 37. After 24 hours of incubation 60% digesta extract inhibited indole production activity by 30%, whereas the corresponding inhibition after 3 hours of incubation was only 12% (Figure 37).

The results suggest that there is something in digesta that destroys tryptophanase activity in prolonged incubation. According to the experiments done here it is not possible to identify the factor(s) responsible for the inhibition. One possible scenario is that the enzyme is gradually digested by proteases present in swine digesta. The practical importance of this inactivation depends on the digesta transition rate and the ideal site for the tryptophanase activity in the swine intestine. From these data, it seems likely that the enzyme should function in the colon rather than in the small intestine and, therefore, should remain active preferable for 24 hours.

The basic idea for these in vitro colon simulation assays is to feed boar colonic microflora with the soluble fraction of the digesta from the distal small intestine of boars. The usage of boar digesta is important since those animals would have an established colonic microflora which actively produces skatole and/or indole, provided that tryptophan is available.

Skatole, indole and tryptophan analysis in digesta matrix: In one aspect of the in vitro colon simulation assay, indole and skatole is be extracted from digesta matrix with an organic solvent, and the concentration of both substances determined by a gas chromatographic method. Tryptophan analyses can be by HPLC, or a high-throughput method for tryptophan concentration determinations.

Development and specifications of fermentation medium constructed from the ileal digesta of pigs: The contents of the last 3 meters of the distal small intestine are recovered from several pigs and transported on ice to our laboratory. The small intestinal digesta of individual pigs is pooled and processed through a number of extractions and centrifugations, and the final supernatant used as a basis for the growth medium for the colonic microbes. The medium is prepared in excess and frozen in aliquots for later use. The batch of medium, once prepared will last for an entire project.

The extract used for the medium preparation can be analyzed for several compounds for the possible need to build specifications for scientific or regulatory use. Medium can be analyzed for:

• Skatole (ileal background)

• Indole (ileal background)

• Reducing sugars (indicates efficiency of animal absorption) • D,L-lactic acid (indicates occurred ileal fermentation)

• Tryptophan (indicates potential for skatole formation)

Alternatively, the medium can be analyzed for any compound of interest. Arrangements for regular slaughtering of boars to access fresh colon digesta: Digesta from the mid colon of boars can be used as an inoculum in fermentations. Digesta can be collected from newly slaughtered boars, transferred to laboratory under anaerobic conditions, and, the fermentation started within 3 hours from digesta recovery. This procedure requires good consensus with a slaughterhouse allowing regular access to live boars, and, application of required licenses from an ethical committee. The following parameters can be measured from individual inocula:

• dry matter content

• microbial community profiles (%G+C)

• total bacterial density

• skatole • indole

These analyses can illustrate the structure and function of the microbial community used as inoculum each time. It is important to characterize the used inocula due to the fact that inoculum for each fermentation batch comes from different boar individual, and, therefore, is the only factor changing between fermentations. The data can be used afterwards to explain possible deviations observed between recurrent fermentations.

Optimization of the colon simulation for skatole production: It is essential for enzyme/ product testing in the future that the simulation system produces skatole. If the inoculum contains skatole it is obvious that simulation vessels should have skatole producing bacteria. However, occasionally transfer from live animal to glass vessel affects the competition between different bacterial groups. Accordingly, indole producers may out-compete skatole producers, in which case conditions must be modified to favor skatole production. The effect of tryptophan amendment to the medium can be tested. Furthermore, the effect of enrichment of the inoculum with skatole producing bacteria such as Clostridium scatologenes can be tested. In one aspect, the invention provides a simulation system producing constant level of skatole, similar to that found in the colon of live boars. Achieving this may require an import of exogenous skatole producers and substrates/cofactors.

Testing of the repeatability of the simulation: To work for product testing, simulation must have a low coefficient of variation (CV). As a part of this work, the CV of the system can be determined, which can be used to determine the number of replicates needed for the desired detection limit in actual product screening. Skatole concentration, indole concentration and gas production can be used as parameters for CV determination. Gas production is a measure for overall metabolic activity of the bacterial community in the simulation system. It seem likely that due to the changing source (and composition) of the fresh inocula used in recurrent fermentations, there will be batch to batch variation in the parameters mentioned. Thus, vessel to vessel variation in individual simulations can be determined and minimized. Furthermore, the batch to batch effect of the inoculum can be determined by running the optimized simulation with inoculum from (three) different boars. In the product testing phase two treatments can be used, which will be present in every simulation. These can be used to normalize the effect of each inoculum.

Testing of enzyme candidates: To test the viability of selected enzymes on skatole reduction, their effect on skatole and indole production in this model system of the invention is tested. The selected enzymes can be tested at two levels. The number of replicate vessels will be chosen so that < 5% effects on the fermentation parameters would be detected at α = 0.05.

In vivo tests

In one aspect, in vivo tests focus on evaluating the impact of added enzyme on skatole accumulation after introduction via an ileo-cecal cannula. One set of in vivo tests uses pigs fitted with an ileal cannula that will allow direct introduction of enzyme and/or substrate into the large intestine, thereby by-passing the major sites of absorption in the pig. This protocol can provide proof of concept that feeding of any particular enzyme will reduce skatole production. The overall goal of these in vivo assays is to provide proof of concept for using any particular enzyme (e.g., an enzyme of the invention) to control skatole production in the hindgut of a pig as a means to limit tissue accumulation, e.g., in intact male pigs. The objective of these in vivo assays is two-fold. First, it can be determined if infusion of free tryptophan into the hind gut results in a detectable increase in fecal skatole concentration that would be indicative of greater production. Secondly, the present in vivo assay can determine if infusion of any particular tryptophanase into a hind gut results in a decrease in skatole production due to conversion of tryptophan to indole (rather than the gut microorganism-driven conversion of tryptophan to skatole). These tests can be performed on a small scale, but depending on results, may also include directly feeding the enzyme to pigs then segmenting the gastrointestinal tract in order to evaluate stability of the enzyme. To support these tests, candidate enzymes can be produced in shake flasks or small scale fermentors; if necessary, production can be scaled up to generate enough enzyme for a trial. Pigs can be fed a special diet to ensure that skatole is produced by all animals. Attention will be paid to the growth of the pigs versus control pigs with no enzyme fed, as well as to skatole levels in the back fat of these pigs in biopsies during the experiment and after slaughter. If small scale studies are successful, then large scale animal trials can be conducted. Three tryptophanases along with a negative control (empty vector in same host) have been produced for a cannulated boar animal trial. Fermentation work entails assessment of production host candidates and production of material (1 kg) needed for animal studies. For animal studies, a diet for reliable production of skatole in pigs can be used, since only 10% of intact male boars produce skatole in high (> 0.125 ppm) levels. Introduction of tryptophan via the cannula may be an effective way to achieve reliable skatole production in pigs. This alternative strategy can focus on animals (e.g., pigs, barrows) which are immediately available. In one exemplary study, four barrows are cannulated and varying amounts of tryptophan added. Once reliable amounts of skatole are produced, enzyme can then be added via an ileocecal cannula. Direct addition of enzyme via a cannula will bypass the stomach and small intestine and test proof of concept of the product (any particular enzyme); adding a tryptophanase will decrease tryptophan levels and a decrease in tryptophan will lead to lower levels of skatole in the back fat of a pig. Methods: This protocol will be reviewed by the University of Georgia Institutional Animal Care and Use Committee. Four littermate, castrated, male pigs weighing approximately 70 kg will be identified from the UGA swine herd and transported to the University of Georgia College of Veterinary Medicine. Ileal cannulas will be placed in these pigs under general anesthesia by the Large Animal Medicine

Department. The pigs are of PIC genetics and typical of commercial hogs produced in the United States. After recovery from surgery, pigs will be transported to the Large Animal Research Unit of the Animal and Dairy Science department. Pigs will be housed individually and allowed ad libitum access to feed and water. The standard UGA grower pig diet will be fed as the control. It is expected that these pigs can be used in multiple experiments with various combinations of enzyme and substrate.

As an alternative to the cannulated pig studies, enzyme can be directly fed to pigs. To test in vivo enzyme stability, candidate tryptophanases can be directly fed to the pigs over several days, after which the pigs will be slaughtered and residual tryptophanase activity assayed, e.g., as described herein. Gastric and intestinal stability can be assessed as well as performance of enzymes in reducing skatole levels. Pigs are slaughtered and skatole levels and residual enzyme measured. Due to the predicted lower cost of such experiments, both the number of pigs and the variables tested can be increased. Pigs used in the study will not enter the food chain and will be destroyed after the completion of experiments.

Diet study for reliable skatole production. A study to understand how diet affects skatole levels was performed in collaboration with the University of Georgia Dept. of Animal and Dairy Science. Two test diets, alfalfa and wheat/canola, and one control diet, corn/soy, were chosen for the study. The two test diets had high tryptophan levels, but low tryptophan digestibility meaning that more tryptophan should theoretically make it to the colon. However, the results shown in Figure 10 indicate that the corn soy diet gave higher levels of skatole. The hypothesis to explain these results is that the Corn/Soy diet has less fiber than the test diets and high fiber is a factor in low observed skatole levels based on previous studies. As noted above, one study focuses on direct addition of the enzyme to the cecum of pigs via an ileo-cecal cannula. Pigs can be fed a special diet to ensure that skatole is produced by all animals. Attention is paid to the growth of the pigs versus control pigs with no enzyme fed, as well as to skatole levels in the back fat of these pigs in biopsies during the experiment and after slaughter. In one aspect, a formulation comprising a tryptophanase (e.g., an enzyme of the invention) is delivered either daily, every two day or every three days to entire male pigs prior to slaughter. In one aspect, the enzyme (e.g., as a formulation) is provided and delivered by one of a number of different routes either, in feed, as a feed additive, in the drinking water, as a daily oral supplement, as a drench, as a slow release bolus, or as a rectal pessary. The supplement can be provided in addition to the normal daily diet of the pigs. The supplement would be given for a period from a maximum of two months prior to slaughter to the day before slaughter. All male pigs would receive the supplement or for groups of mixed sex all pigs could receive the supplement. The pigs would receive the recommended dose of tryptophanase in one of these forms.

In one aspect, as a result of receiving tryptophanase in one of these forms, at the time of slaughter the level of skatole in the back fat of entire male pigs may be reduced to a level of less than 0.25 ug/g of fat. The results of the treatment would be meat with improved organoleptic characteristics from entire male pigs without the need for castration.

Example 7: Expression and Activity Studies of Exemplary Tryptophanases of the Invention

The following example describes the results of studies demonstrating activity of an exemplary tryptophanases of the invention. Expression and robust assay of exemplary tryptophanases were assessed.

Exemplary tryptophanase-encoding nucleic acids of the invention were expressed in E. coli. Table 1, below, lists exemplary tryptophanases of the invention that perfoπned well in the robust in vitro digestion assay (described below). A test was run to determine thermotolerance of exemplary enzymes with 1 enzyme having good stability at 88°C. as noted in Table 1 , below.

Antibodies were generated against the E. coli tryptophanase and shown to cross-react with two exemplary tryptophanases of the invention. This antibody is used in methods of the invention for detection of tryptophanases in both in vitro and in vivo systems, e.g., in one aspect, based on immunoprecipitation to concentrate residual tryptophanase for activity assays. Exemplary tryptophanases of the invention can be purified for antibody production.

Table 1, below, lists data from expression and robust assays of exemplary tryptophanases. As noted in Table 1, below, three subclones were active and tested in the robust in vitro digestion test. One subclone SEQ ID NO:48 (encoded, e.g., by SEQ ID NO:47) showed significant stability in the assay.

Tryptophanase % survival s.d.

SEQ ID NO:48 15.85 4.14

(encoded, e.g., by SEQ ID NO:47)

SEQ ID NO:32 7.94 2.83

(encoded, e.g., by SEQ ID NO:31)

SEQ ID NO:26 0.24 0.15

(encoded, e.g., by SEQ ID NO:25)

SEQ ID NO:52 0.45 0.4

(encoded, e.g., by SEQ ID NO:51)

Evaluation of expression of exemplary tryptophanases of the invention in Pichia was assessed. Secretion of a glycosylated tryptophanase may lead to an enzyme with increased gut stability. A method for detecting tryptophanase activity was developed using E. coli and then used to assay expression in Pichia. The method is based on the ability of tryptophanase to produce indole from tryptophan and its subsequent detection. Nucleic acid subclones encoding exemplary tryptophanases of the invention were subcloned into an appropriate Pichia expression vector containing an alpha factor to ensure secretion. Pichia subclones representing 2 tryptophanases corresponding to SEQ ID NO:48 and SEQ ID NO: 12 (encoded, e.g., by SEQ ID NO: 11) were assessed. Integrants were picked and patched onto YPM media containing 100 ug/mL tryptophan. After overnight growth, plates were flooded with an indole spot reagent and the ability of clones to produce indole was observed as compared to positive (E. coli w/ same vector) and negative (Pichia w/ vector no insert) controls. No indole production was observed for experimental samples or negative controls, but seen in positive controls. In the indole spot tests of tryptophanases expressed in Pichia, negative controls (vector no insert) and positive controls (wild type E. coli) were used. Pichia transformants with the E. coli tryptophanase subcloned into a Pichia expression vector were plated onto media containing 100 ug/mL tryptophan. Plates were flooded with an indole detection reagent. Production of a bluish color indicated the presence of indole while a white color in negative control indicated no indole produced.

Thermotolerance of tryptophanases of the invention was evaluated. In some applications and aspects of the invention, enzymes will need to have a degree of thermotolerance in order to survive a formulation, e.g., a pelleting, process. An initial assessment of thermostability was performed at 88⁰C. Results, as shown in Figure 41, indicate that one candidate tryptophanase, SEQ ID NO:48, retains significant activity after 4 minutes incubation at 88 ⁰C.

Figure 41 shows data from thermostability analysis studies of exemplary tryptophanases. Enzymes were heated at 88⁰C for 4 minutes. Timepoints were taken and immediately mixed with buffer at room temperature to allow proteins to refold. After all timepoints were taken, recovered enzyme in buffer was preheated at 37 ⁰C for 3 minutes. A 1Ox substrate was added to final concentration of Ix to start the reaction. The graph of Figure 41 indicates relative enzyme rates at each timepoint. A Western analysis using anti-i?. coli tryptophanase antibody was also performed. Identification of antibodies specific for tryptophanase may be important for development of assays to quantitate in vitro or in vivo stability of enzymes, e.g., enzyme fed to an animal, e.g., a pig. Purified E. coli tryptophanase was used to generate polyclonal antibodies which were tested against all candidate tryptophanases in western blots. Serum was diluted 30,000 fold and used in western blot analysis, as shown in Figure 42.

Figure 42 is an illustration of Western analysis of exemplary tryptophanases of the invention. Samples included SEQ ID NO:48 (encoded, e.g., by SEQ ID NO:47) *, SEQ ID NO:2 (encoded, e.g., by SEQ ID NO:1), SEQ ID NO:40 (encoded, e.g., by SEQ ID NO:39)*, negative control (empty vector), SEQ ID NO:42 (encoded, e.g., by SEQ ID NO:41), Wild type E. coli strain, SEQ ID NO: 12 (encoded, e.g., by SEQ ID NO: H)* and SEQ ID NO: 14 (encoded, e.g., by SEQ ID NO: 13)*. An anti-i?. coli tryptophanase antibody was used to detect protein. A "*" indicates that the enzyme is an exemplary tryptophanase of the invention. The invention also provides methods for detection of tryptophanases in vivo. This method detects tryptophanases using immunoprecipitation. In one alternative aspect, in addition to using antibodies specific of one or more enzymes of the invention, the E. coli anti-tryptophanase antibody is used, as discussed below.

The invention provides a protocol for detecting tryptophanases in vivo using, e.g., antibodies of the invention, as illustrated in Figure 43. This assay can be used to determine residual activity of candidate tryptophanases when fed to pigs. After feeding, pigs are slaughtered and gut contents segmented. Residual tryptophanase is then be determined after protein is captured using specific antibodies (e.g., antibodies of the invention). Ability to stabilize samples to decrease further proteolysis may be critical to accurately assessing enzyme performance.

In one aspect, exemplary enzymes of the invention are purified for antibody production. Proteins are partially purified using a combination of heat treatment, ammonium sulfate precipitation and hydrophobic interaction chromatography.

Example 8: Tryptophan-degrading enzymes of the invention retain activity after passage through the upper gastrointestinal system

The following example describes the results of assays of the invention that can demonstrate activity of a tryptophan-degrading enzyme (e.g., an exemplary tryptophanase of the invention) after passage through the upper gastrointestinal system of an animal. In one aspect, these studies demonstrate that a tryptophan-degrading enzyme of the invention retains sufficient activity after passage through the upper gastrointestinal system to reduce theoretical physiological concentrations of free tryptophan in the colon by at least 90% under in vitro conditions similar to the pig colon. Enzymes are evaluated for their specific activity and their stability in relevant in vitro gastrointestinal simulations, as described herein. Enzymes with the potential to transit through the upper gastrointestinal tract of the pig and retain sufficient activity to degrade at least 90% of the theoretical daily level of free tryptophan in the colon are identified. In these exemplary assays of the invention, specific performance targets for enzymes are:

• Maximum starting dose for demonstrating potential to degrade free tryptophan under colon conditions is set at 1500 mg tryptophanase (i.e.: 1OX the dose of 150 mg/day set for the feed additive product). Conservative estimates of expression levels and fermentation costs were used to set a maximum dose that could be delivered cost effectively.

• Theoretical daily level of free tryptophan to be degraded in the colon was estimated to be 2 grams (g). Sources of tryptophan in the colon are unabsorbed tryptophan from the feed and tryptophan originating from endogenous secretions.

The following exemplary assays of the invention can be used to evaluate exemplary enzymes of the invention, and to determine if a polypeptide is within the scope of the invention:

• In one aspect, tryptophanase stability is first tested in separate assays to calculate the theoretical amounts of each tryptophanase that would be expected to be degraded during passage through the upper GI. Stability of enzymes was tested under SGF (simulated gastric fluid) conditions (30 min at 37⁰C and pH 2.6 with 50 U/ml pepsin) and SIF (simulated intestinal fluid) conditions (60 min at 37⁰C and pH 6.3 with 10 mg/ml pancreatin). Several of the tryptophanases displayed appreciable stability in the two assays, enabling them to be ranked by SGF survival (Table I, below, Column A), SIF survival (Table I, below, Column B) or a combination of the two.

• In one aspect, sequential tests are also performed in order to present the best enzymes with a more robust test of their stability. This more robust test consisted of incubation under SGF conditions (pH 3.1 and 50 U/mL pepsin for 30 min. at

37⁰C) followed immediately by incubation under SIF conditions (10 mg/rnL pancreatin, pH shifted to 6.3 for 1 hour at 37⁰C). Multiple enzymes were still active after testing under these more stringent conditions (Table I, Column C).

• In one aspect, the specific activity of each enzyme on tryptophan was measured under simulated colon conditions (37⁰C and pH 7.5 with 100 ug/ml tryptophan). 1 unit is the amount of enzyme required to convert 1 μmole of tryptophan, to indole, pyruvate and ammonia in 1 minute. Assays were performed in quadruplicate. (Table I, Column D)

• In one aspect, the % survival through the SGF/SIF sequential assay and the specific activity were used to estimate the amount of tryptophan that could be degraded in 24 hrs when a pig was fed a 1.5 g enzyme dose (Table I, Column E). From these calculations, three enzymes (SEQ ID NO:48 (encoded, e.g., by SEQ ID NO:47), SEQ ID NO:2 (encoded, e.g., by SEQ ID NO:1), and SEQ ID NO:28 (encoded, e.g., by SEQ ID NO:27)) have the potential to degrade >100% of the targeted 2g of free tryptophan (Table I, Column F).

Table I: Stability and activity of Tryptophanase enzymes

(A) (B) (C) (D) (E) (F)

Enzyme

% % Specific Tryptophan

Survival Survival % Survival Activity Degraded % Target in SGF in SIF in SGF/SIF (U/g) (g) Achieved

SEQ ID NO:44 48.4 10.3 0.12±0.05 1400±l 0.5 25%

(encoded, e.g., by SEQ ID NO:43)

SEQ ID NO:46 3.73±1.91 ND ND

(encoded, e.g., by SEQ ID NO:45)

SEQ ID NO:6₂ 1.01±0.2 ND ND

(encoded, e.g., by SEQ ID Nθ:61)

SEQ ID NO:48 75.9 30.4 2.46±0.11 990±ll 7.12 356%

(encoded, e.g., by SEQ ID NO:47)

SEQ ID NO:2 45 1.3 0.59±0.37 1532±4 2.32 116%

(encoded, e.g., by SEQ ID Nθ:l) SEQ ID NO:24 o±o ND ND

(encoded, e.g., by SEQ ID NO:23)

SEQ ID NO:38 0.25±0.05 ND ND

(encoded, e.g., by SEQ ID NO:37)

SEQ ID NO:30 0.25±0.06 1324±7 0.96 48%

(encoded, e.g., by SEQ ID NO:29)

SEQ ID NO:36 0.53±0.36 ND ND

(encoded, e.g., by SEQ ID NO:35)

SEQ ID NO:28 27 81.7 0.57±0.09 1533±5 2.54 127%

(encoded, e.g., by SEQ ID NO:27)

SEQ IDNO:42 4.51±0.57 ND ND

(encoded, e.g., by SEQ ID N0:41)

Based on data from the separate in vitro SGF and SIF experiments, as discussed above, and the more robust sequential SGF/SIF experiments, also discussed above, tryptophanases of the invention have been demonstrated to have the potential to transit through the upper gastrointestinal tract of the pig when administered as a feed additive and retain sufficient activity to degrade two grams (2 g) tryptophan when they reach the colon. Conservative estimates of enzyme cost were used to calculate maximum dose. Enzyme performance can be dramatically improved through routine variation and screening of alternative formulations, random or rational mutagenesis of enzyme sequences and/or expression optimization.

A range of enzymes of the invention was discovered to display a range of stabilities in SGF and SIF. Correlation between sequence, structure and stability of these sequences identifies potential mutations to dramatically further increase enzyme stability. More stringent in vitro tests can be performed to test the limits of these exemplary polypeptides or any enzyme. However, there is always a question of the relevance and predictability of in vitro assays in relation to actual performance observed in the target animal. The intent of these assays of the invention is to provide an routine methodology to identify tryptophanases that have the potential to deliver sufficient activity to the colon to meet the performance required of a feed additive product, and to provide the means to rank the enzymes for further studies. The data presented here demonstrate the potential of exemplary enzymes of the invention.

A number of aspects of the invention have been described. Nevertheless, it will be understood that various modifications may be made without departing from the spirit and scope of the invention. Accordingly, other aspects are within the scope of the following claims.

Claims

WHAT IS CLAIMED IS:

1. An isolated or recombinant nucleic acid comprising a nucleic acid sequence having at least 50% sequence identity to SEQ ID NO: 1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO: 13, SEQ ID NO: 15,

5 SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67 o or SEQ ID NO:69, over a region of at least about 100 residues, wherein the nucleic acid encodes at least one polypeptide having a tryptophan-processing enzyme activity.

2. The isolated or recombinant nucleic acid of claim 1, wherein the sequence identity is at least about 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 5 60%, 61%, 62%, 63% 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more, or 100% sequence identity.

0 3. The isolated or recombinant nucleic acid of claim 1 , wherein the sequence identity is over a region of at least about 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150 or more residues, or the full length of a gene or a transcript.

5 4. The isolated or recombinant nucleic acid of claim 1, wherein the nucleic acid sequence comprises a sequence as set forth in SEQ ID NO: 1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31, SEQ ID NO:33, SEQ ID 0 NO:35, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67 or SEQ ID NO:69. 5. The isolated or recombinant nucleic acid of claim 1, wherein the nucleic acid sequence encodes a polypeptide having a sequence as set forth in SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO: 10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO.16, SEQ IDNO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ IDNO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68 or SEQ ID NO:70.

6. The isolated or recombinant nucleic acid of claim 1, wherein the sequence identities are determined by analysis with a sequence comparison algorithm or by a visual inspection.

7. The isolated or recombinant nucleic acid of claim 6, wherein the sequence comparison algorithm is a BLAST version 2.2.2 algorithm where a filtering setting is set to blastall -p blastp -d "nr pataa" -F F, and all other options are set to default.

8. The isolated or recombinant nucleic acid of claim 1 , wherein the tryptophan-processing enzyme activity comprises tryptophanase activity.

9. The isolated or recombinant nucleic acid of claim 1, wherein the tryptophan-processing enzyme activity comprises catalyzing the β-elimination of tryptophan.

10. The isolated or recombinant nucleic acid of claim 1, wherein the tryptophan-processing enzyme activity comprises tryptophan transaminase activity.

11. The isolated or recombinant nucleic acid of claim 1 , wherein the tryptophan-processing enzyme activity comprises catalyzing the oxidation or amination of tryptophan. 12. The isolated or recombinant nucleic acid of claim 1 , wherein the tryptophan-processing enzyme activity comprises tryptophan decarboxylase or tryptophan dioxygenase activity.

13. The isolated or recombinant nucleic acid of claim 11 , wherein the tryptophan-processing enzyme activity comprises tyrosine phenol lyase activity.

14. The isolated or recombinant nucleic acid of claim 1 , wherein the tryptophan-processing enzyme activity is thermostable or thermotolerant.

15. The isolated or recombinant nucleic acid of claim 14, wherein the polypeptide retains enzyme activity under conditions comprising a temperature range of between about 37⁰C to about 95⁰C, or between about 55°C to about 85°C, or between about 70⁰C to about 75°C, or between about 70⁰C to about 95⁰C, or between about 9O⁰C to about 95°C, or, the polypeptide retains enzyme activity after exposure to a temperature in the range from greater than 37⁰C to about 95⁰C, from greater than 55⁰C to about 85⁰C, or between about 70⁰C to about 75⁰C₃ or from greater than 90⁰C to about 95°C.

16. An isolated or recombinant nucleic acid encoding a polypeptide having a tryptophan-processing enzyme activity, wherein the nucleic acid comprises a sequence that hybridizes under stringent conditions to a nucleic acid comprising SEQ ID NO: 1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO: 15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67 or SEQ ID NO:69, and the nucleic acid encodes a polypeptide having tryptophan-processing enzyme activity.

17. The isolated or recombinant nucleic acid of claim 16, wherein the nucleic acid is at least about 50, 75, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000 or more residues in length or the full length of the gene or transcript. 18. The isolated or recombinant nucleic acid of claim 16, wherein the stringent conditions include a wash step comprising a wash in 0.2X SSC at a temperature of about 65⁰C for about 15 minutes.

19. A nucleic acid probe for identifying a nucleic acid encoding a polypeptide with a tryptophan-processing enzyme activity, wherein the probe comprises at least about 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500 or more consecutive bases of a sequence as set forth in claim 1, wherein the probe identifies the nucleic acid by binding or hybridization.

20. The nucleic acid probe of claim 19, wherein the probe comprises an oligonucleotide comprising at least about 10 to 50, about 20 to 60, about 30 to 70, about 40 to 80, about 60 to 100, or about 50 to 150 consecutive bases.

21. A nucleic acid probe for identifying a nucleic acid encoding a polypeptide having a tryptophan-processing enzyme activity, wherein the probe comprises a nucleic acid comprising at least about 10 consecutive residues of a nucleic acid sequence having at least 50% sequence identity to SEQ ID NO: 1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67 or SEQ ID NO:69, wherein the sequence identities are determined by analysis with a sequence comparison algorithm or by visual inspection.

22. The nucleic acid probe of claim 21, wherein the probe comprises an oligonucleotide comprising at least about 10 to 50, about 20 to 60, about 30 to 70, about 40 to 80, about 60 to 100, or about 50 to 150 consecutive bases.

23. An amplification primer pair for amplifying a nucleic acid encoding a polypeptide having a tryptophan-processing enzyme activity, wherein the primer pair is capable of amplifying a nucleic acid comprising a sequence as set forth in claim 1 or claim 16, or a subsequence thereof.

24. The amplification primer pair of claim 23, wherein a member of the amplification primer pair comprises an oligonucleotide comprising at least about 10 to 50 consecutive bases of the sequence, or, about 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40 or more consecutive bases of the sequence.

25. An amplification primer pair, wherein the amplification primer pair comprises a first member having a sequence as set forth by about the first (the 5') 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 42, 33, 34, 35 or more residues of SEQ ID NO: 1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO.63, SEQ ID NO:65, SEQ ID NO:67 or SEQ ID NO:69, and a second member having a sequence as set forth by about the first (the 5') 12, 13, 14, 15, 16, 17,

18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 42, 33, 34, 35 or more residues of the complementary strand of the first member.

26. A tryptophan-degrading enzyme-encoding nucleic acid generated by amplification of a polynucleotide using an amplification primer pair as set forth in claim 23 or claim 25.

27. The tryptophan-degrading enzyme-encoding nucleic acid of claim 26, wherein the amplification is by polymerase chain reaction (PCR).

28. The tryptophan-degrading enzyme-encoding nucleic acid of claim 26, wherein the nucleic acid generated by amplification of a gene library. 29. The tryptophan-degrading enzyme-encoding nucleic acid of claim 28, wherein the gene library is an environmental library.

30. An isolated or recombinant polypeptide having tryptophan- processing enzyme activity encoded by a nucleic acid as set forth in claim 26.

31. A method of amplifying a nucleic acid encoding a polypeptide having a tryptophan-processing enzyme activity comprising amplification of a template nucleic acid with an amplification primer pair capable of amplifying a nucleic acid sequence as set forth in claim 1 or claim 16, or a subsequence thereof.

32. An expression cassette comprising a nucleic acid comprising a sequence as set forth in claim 1 or claim 16.

33. A vector comprising a nucleic acid comprising a sequence as set forth in claim 1 or claim 16.

34. A cloning vehicle comprising a nucleic acid comprising a sequence as set forth in claim 1 or claim 16, wherein the cloning vehicle comprises a viral vector, a plasmid, a phage, a phagemid, a cosmid, a fosmid, a bacteriophage or an artificial chromosome.

35. The cloning vehicle of claim 34, wherein the viral vector comprises an adenovirus vector, a retroviral vector or an adeno-associated viral vector.

36. A bacterial artificial chromosome (BAC), a bacteriophage Pl- derived vector (PAC), a yeast artificial chromosome (YAC) or a mammalian artificial chromosome (MAC) comprising a sequence as set forth in claim 1 or claim 16.

37. A transformed cell comprising a nucleic acid comprising a sequence as set forth in claim 1 or claim 16.

38. A transformed cell comprising an expression cassette as set forth in claim 32. 39. The transformed cell of claim 38, wherein the cell is a bacterial cell, a mammalian cell, a fungal cell, a yeast cell, an insect cell or a plant cell.

40. A transgenic non-human animal comprising a sequence as set forth in claim 1 or claim 16.

41. The transgenic non-human animal of claim 40, wherein the animal is a mouse, a goat, a rabbit, a sheep, a pig, a cow or a rat.

42. A transgenic plant comprising a sequence as set forth in claim 1 or claim 16.

43. The transgenic plant of claim 42, wherein the plant is a corn plant, a sorghum plant, a potato plant, a tomato plant, a wheat plant, an oilseed plant, a rapeseed plant, a soybean plant, a rice plant, a barley plant, a grass, or a tobacco plant.

44. A transgenic seed comprising a sequence as set forth in claim 1 or claim 16.

45. The transgenic seed of claim 44, wherein the seed is a corn seed, a wheat kernel, an oilseed, a rapeseed, a soybean seed, a palm kernel, a sunflower seed, a sesame seed, a rice, a barley, a peanut or a tobacco plant seed.

46. An antisense oligonucleotide comprising a nucleic acid sequence complementary to or capable of hybridizing under stringent conditions to a sequence as set forth in claim 1 or claim 16, or a subsequence thereof.

47. The antisense oligonucleotide of claim 46, wherein the antisense oligonucleotide is between about 10 to 50, about 20 to 60, about 30 to 70, about 40 to 80, or about 60 to 100 bases in length.

48. A method of inhibiting the translation of a tryptophan-processing enzyme message in a cell comprising administering to the cell or expressing in the cell an antisense oligonucleotide comprising a nucleic acid sequence complementary to or capable of hybridizing under stringent conditions to a sequence as set forth in claim 1 or claim 16.

5 49. A double-stranded inhibitory RNA (RNAi) molecule comprising a subsequence of a sequence as set forth in claim 1 or claim 16.

50. The double-stranded inhibitory RNA (RNAi) molecule of claim 49, wherein the RNAi is about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more duplex o nucleotides in length.

51. A method of inhibiting the expression of a tryptophan-processing enzyme in a cell comprising administering to the cell or expressing in the cell a double- stranded inhibitory RNA (lRNA), wherein the RNA comprises a subsequence of a 5 sequence as set forth in claim 1 or claim 16.

52. An isolated or recombinant polypeptide (i) having at least 50% sequence identity to SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID 0 NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68 or SEQ ID 5 NO:70, over a region of at least about 100 residues, wherein the sequence identities are determined by analysis with a sequence comparison algorithm or by a visual inspection, or, (ii) encoded by a nucleic acid having at least 50% sequence identity to a sequence as set forth in SEQ ID NO: 1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO: 13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO: 19, SEQ 0 ID NO:21, SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID

NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67 or SEQ ID NO:69, over a region of at least about 100 residues, or encoded by a nucleic acid capable of hybridizing under stringent conditions to a sequence as set forth in SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:?, SEQ ID NO:9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO:17, SEQ ID NO: 19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31₃ SEQ ID NO:33, SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67 or SEQ ID NO:69.

53. The isolated or recombinant polypeptide of claim 52, wherein the sequence identity is over a region of at least about at least about 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more, or is 100% sequence identity.

54. The isolated or recombinant polypeptide of claim 52, wherein the sequence identity is over a region of at least about 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050 or more residues, or the full length of an enzyme.

55.. The isolated or recombinant polypeptide of claim 52, wherein the polypeptide has a sequence as set forth in SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO: 18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68 or SEQ IDNO:70.

56. The isolated or recombinant polypeptide of claim 52, wherein the polypeptide has a tryptophan-processing enzyme activity. 57. The isolated or recombinant polypeptide of claim 56, wherein the tryptophan-processing enzyme activity comprises tryptophanase activity.

5 58. The isolated or recombinant polypeptide of claim 56, wherein the tryptophan-processing enzyme activity comprises catalyzing the β-elimination of tryptophan.

59. The isolated or recombinant polypeptide of claim 56, wherein the o tryptophan-processing enzyme activity comprises tryptophan transaminase activity.

60. The isolated or recombinant polypeptide of claim 56, wherein the tryptophan-processing enzyme activity comprises catalyzing the oxidation or animation of tryptophan. 5

61. The isolated or recombinant polypeptide of claim 68, wherein the tryptophan-processing enzyme activity comprises tryptophan decarboxylase or tryptophan dioxygenase activity.

0 62. The isolated or recombinant polypeptide of claim 56, wherein the tryptophan-processing enzyme activity comprises tyrosine phenol lyase activity.

63. The isolated or recombinant polypeptide of claim 56, wherein the tryptophan-processing enzyme activity is thermostable or thermotolerant. 5

64. The isolated or recombinant polypeptide of claim 63, wherein the polypeptide retains tryptophan-processing enzyme activity under conditions comprising a temperature range of between about 1°C to about 5°C, between about 5⁰C to about 15⁰C, between about 15°C to about 25⁰C, between about 25⁰C to about 37°C, between about 0 37⁰C to about 95⁰C, between about 55⁰C to about 85⁰C, between about 7O⁰C to about 95⁰C, between about 70⁰C to about 75°C, or between about 9O⁰C to about 95⁰C, or, the polypeptide retains tryptophan-processing enzyme activity after exposure to a temperature in the range from between about I⁰C to about 5⁰C, between about 5⁰C to about 15⁰C, between about 15⁰C to about 25°C, between about 25⁰C to about 37⁰C, between about 37°C to about 95⁰C, between about 55°C to about 85°C, between about 70⁰C to about 75°C, or between about 9O⁰C to about 95°C, or more.

65. An isolated or recombinant polypeptide comprising a polypeptide as set forth in claim 52 and lacking a signal sequence or a prepro sequence.

66. An isolated or recombinant polypeptide comprising a polypeptide as set forth in claim 52 and having a heterologous signal sequence or a heterologous prepro sequence.

67. The isolated or recombinant polypeptide of claim 56, wherein the tryptophan-processing enzyme activity comprises a specific activity at about 37°C in the range from about 100 to about 1000 units per milligram of protein, from about 500 to about 750 units per milligram of protein, from about 500 to about 1200 units per milligram of protein, or from about 750 to about 1000 units per milligram of protein.

68. The isolated or recombinant polypeptide of claim 63, wherein the thermotolerance comprises retention of at least half of the specific activity of the tryptophan-processing enzyme at 37°C after being heated to an elevated temperature.

69. The isolated or recombinant polypeptide of claim 63, wherein the thermotolerance comprises retention of specific activity at 37⁰C in the range from about 500 to about 1200 units per milligram of protein after being heated to an elevated temperature.

70. The isolated or recombinant polypeptide of claim 52, wherein the polypeptide comprises at least one glycosylation site.

71. The isolated or recombinant polypeptide of claim 70, wherein the glycosylation is an N-linked glycosylation.

72. The isolated or recombinant polypeptide of claim 70, wherein the polypeptide is glycosylated after being expressed in a P. pastoris or a S. pombe. 73. The isolated or recombinant polypeptide of claim 56, wherein the polypeptide retains a tryptophan-processing enzyme activity under conditions comprising about pH 6.5, pH 6.0, pH 5.5, 5.0, pH 4.5 or 4.0.

74. The isolated or recombinant polypeptide of claim 56, wherein the polypeptide retains a tryptophan-processing enzyme activity under conditions comprising about pH 7.5, pH 8.0, pH 8.5, pH 9, pH 9.5, pH 10 or pH 10.5.

75. A protein preparation comprising a polypeptide as set forth in claim 52, wherein the protein preparation comprises a liquid, a solid or a gel.

76. A heterodimer comprising a polypeptide as set forth in claim 52 and a second domain.

77. The heterodimer of claim 76, wherein the second domain is a polypeptide and the heterodimer is a fusion protein.

78. The heterodimer of claim 76, wherein the second domain is an epitope or a tag.

79. A homodimer comprising a polypeptide as set forth in claim 52.

80. An immobilized polypeptide, wherein the polypeptide comprises a sequence as set forth in claim 52, or a subsequence thereof.

81. The immobilized polypeptide of claim 80, wherein the polypeptide is immobilized on a cell, a metal, a resin, a polymer, a ceramic, a glass, a micro electrode, a graphitic particle, a bead, a gel, a plate, an array or a capillary tube.

82. An array comprising an immobilized polypeptide as set forth in claim 52.

83. An array comprising an immobilized nucleic acid as set forth in claim 1 or claim 16. 84. An isolated or recombinant antibody that specifically binds to a polypeptide as set forth in claim 52.

85. The isolated or recombinant antibody of claim 84, wherein the antibody is a monoclonal or a polyclonal antibody.

86. A hybridoma comprising an antibody that specifically binds to a polypeptide as set forth in claim 52.

87. A method of isolating or identifying a polypeptide with a tryptophan-processing enzyme activity comprising the steps of:

(a) providing an antibody as set forth in claim 84;

(b) providing a sample comprising polypeptides; and (c) contacting the sample of step (b) with the antibody of step (a) under conditions wherein the antibody can specifically bind to the polypeptide, thereby isolating or identifying a polypeptide having a tryptophan-processing enzyme activity.

88. A method of making an anti-tryptophan-processing enzyme antibody comprising administering to a non-human animal a nucleic acid as set forth in claim 1 or claim 16 or a subsequence thereof in an amount sufficient to generate a humoral immune response, thereby making an anti-tryptophan-processing enzyme antibody.

89. A method of making an anti-tryptophan-processing enzyme antibody comprising administering to a non-human animal a polypeptide as set forth in claim 52 or a subsequence thereof in an amount sufficient to generate a humoral immune response, thereby making an anti-tryptophan-processing enzyme antibody.

90. A method of producing a recombinant polypeptide comprising the steps of: (a) providing a nucleic acid operably linked to a promoter, wherein the nucleic acid comprises a sequence as set forth in claim 1 or claim 16; and (b) expressing the nucleic acid of step (a) under conditions that allow expression of the polypeptide, thereby producing a recombinant polypeptide.

91. The method of claim 90, further comprising transforming a host 5 cell with the nucleic acid of step (a) followed by expressing the nucleic acid of step (a), thereby producing a recombinant polypeptide.

92. A method for identifying a polypeptide having a tryptophan- processing enzyme activity comprising the following steps: o (a) providing a polypeptide as set forth in claim 52;

(b) providing a tryptophan-processing enzyme substrate; and

(c) contacting the polypeptide with the substrate of step (b) and detecting a decrease in the amount of substrate or an increase in the amount of a reaction product, wherein a decrease in the amount of the substrate or an increase in the amount of the 5 reaction product detects a polypeptide having a tryptophan-processing enzyme activity.

93. A method for identifying a tryptophan-processing enzyme substrate comprising the following steps:

(a) providing a polypeptide as set forth in claim 52; 0 (b) providing a test substrate; and

(c) contacting the polypeptide of step (a) with the test substrate of step (b) and detecting a decrease in the amount of substrate or an increase in the amount of reaction product, wherein a decrease in the amount of the substrate or an increase in the amount of a reaction product identifies the test substrate as a tryptophan-processing 5 enzyme substrate.

94. A method of determining whether a test compound specifically binds to a polypeptide comprising the following steps:

(a) expressing a nucleic acid or a vector comprising the nucleic acid under 0 conditions permissive for translation of the nucleic acid to a polypeptide, wherein the nucleic acid has a sequence as set forth in claim 1 or claim 16;

(b) providing a test compound;

(c) contacting the polypeptide with the test compound; and (d) determining whether the test compound of step (b) specifically binds to the polypeptide.

95. A method of deterrnining whether a test compound specifically binds to a polypeptide comprising the following steps:

(a) providing a polypeptide as set forth in claim 52;

(b) providing a test compound;

(c) contacting the polypeptide with the test compound; and

(d) determining whether the test compound of step (b) specifically binds to the polypeptide.

96. A method for identifying a modulator of a tryptophan-processing enzyme activity comprising the following steps:

(a) providing a polypeptide as set forth in claim 56; (b) providing a test compound;

(c) contacting the polypeptide of step (a) with the test compound of step (b) and measuring an activity of the tryptophan-processing enzyme, wherein a change in the tryptophan-processing enzyme activity measured in the presence of the test compound compared to the activity in the absence of the test compound provides a determination that the test compound modulates the tryptophan-processing enzyme activity.

97. The method of claim 96, wherein the tryptophan-processing enzyme activity is measured by providing a tryptophan-processing enzyme substrate and detecting a decrease in the amount of the substrate or an increase in the amount of a reaction product, or, an increase in the amount of the substrate or a decrease in the amount of a reaction product.

98. The method of claim 97, wherein a decrease in the amount of the substrate or an increase in the amount of the reaction product with the test compound as compared to the amount of substrate or reaction product without the test compound identifies the test compound as an activator of a tryptophan-processing enzyme activity.

99. The method of claim 97, wherein an increase in the amount of the substrate or a decrease in the amount of the reaction product with the test compound as compared to the amount of substrate or reaction product without the test compound identifies the test compound as an inhibitor of a tryptophan-processing enzyme activity.

100. A computer system comprising a processor and a data storage device wherein said data storage device has stored thereon a polypeptide sequence or a nucleic acid sequence, wherein the polypeptide sequence comprises sequence as set forth in claim 52, a polypeptide encoded by a nucleic acid as set forth in claim 1 or claim 16.

101. The computer system of claim 100, further comprising a sequence comparison algorithm and a data storage device having at least one reference sequence stored thereon.

102. The computer system of claim 101, wherein the sequence comparison algorithm comprises a computer program that indicates polymorphisms.

103. The computer system of claim 100, further comprising an identifier that identifies one or more features in said sequence.

104. A computer readable medium having stored thereon a polypeptide sequence or a nucleic acid sequence, wherein the polypeptide sequence comprises a polypeptide as set forth in claim 52; a polypeptide encoded by a nucleic acid as set forth in claim 1 or claim 16.

105. A method for identifying a feature in a sequence comprising the steps of: (a) reading the sequence using a computer program which identifies one or more features in a sequence, wherein the sequence comprises a polypeptide sequence or a nucleic acid sequence, wherein the polypeptide sequence comprises a polypeptide as set forth in claim 52; a polypeptide encoded by a nucleic acid as set forth in claim 1 or claim 16; and (b) identifying one or more features in the sequence with the computer program.

106. A method for comparing a first sequence to a second sequence comprising the steps of: (a) reading the first sequence and the second sequence through use of a computer program which compares sequences, wherein the first sequence comprises a polypeptide sequence or a nucleic acid sequence, wherein the polypeptide sequence comprises a polypeptide as set forth in claim 52 or a polypeptide encoded by a nucleic acid as set forth in claim 1 or claim 16; and (b) determining differences between the first sequence and the second sequence with the computer program.

107. The method of claim 108, wherein the step of determining differences between the first sequence and the second sequence further comprises the step of identifying polymorphisms.

108. The method of claim 108, further comprising an identifier that identifies one or more features in a sequence.

109. The method of claim 108, comprising reading the first sequence using a computer program and identifying one or more features in the sequence.

110. A method for isolating or recovering a nucleic acid encoding a polypeptide with a tryptophan-processing enzyme activity from an environmental sample comprising the steps of:

(a) providing an amplification primer pair as set forth in claim 23 or claim 25; (b) isolating a nucleic acid from the environmental sample or treating the environmental sample such that nucleic acid in the sample is accessible for hybridization to the amplification primer pair; and,

(c) combining the nucleic acid of step (b) with the amplification primer pair of step (a) and amplifying nucleic acid from the environmental sample, thereby isolating or recovering a nucleic acid encoding a polypeptide with a tryptophan- processing enzyme activity from an environmental sample.

111. The method of claim 110, wherein each member of the amplification primer sequence pair comprises an oligonucleotide comprising at least about 10 to 50 consecutive bases of a sequence as set forth in SEQ ID NO: 1 , SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ IDNO:11, SEQ ID NO:13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31, SEQ ID NO:33, SEQ ID

NO:35, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67 or SEQ ID NO:69, or a subsequence thereof.

112. A method for isolating or recovering a nucleic acid encoding a polypeptide with a tryptophan-processing enzyme activity from an environmental sample comprising the steps of:

(a) providing a polynucleotide probe comprising a sequence as set forth in claim 1 or claim 16, or a subsequence thereof; (b) isolating a nucleic acid from the environmental sample or treating the environmental sample such that nucleic acid in the sample is accessible for hybridization to a polynucleotide probe of step (a);

(c) combining the isolated nucleic acid or the treated environmental sample of step (b) with the polynucleotide probe of step (a); and (d) isolating a nucleic acid that specifically hybridizes with the polynucleotide probe of step (a), thereby isolating or recovering a nucleic acid encoding a polypeptide with a tryptophan-processing enzyme activity from an environmental sample.

113. The method of claim 110 or claim 112, wherein the environmental sample comprises a water sample, a liquid sample, a soil sample, an air sample or a biological sample.

114. The method of claim 113, wherein the biological sample is derived from a bacterial cell, a protozoan cell, an insect cell, a yeast cell, a plant cell, a fungal cell or a mammalian cell.

115. A method of generating a variant of a nucleic acid encoding a polypeptide with a tryptophan-processing enzyme activity comprising the steps of:

(a) providing a template nucleic acid comprising a sequence as set forth in claim 1 or claim 16; and

(b) modifying, deleting or adding one or more nucleotides in the template sequence, or a combination thereof, to generate a variant of the template nucleic acid. 116. The method of claim 115, further comprising expressing the variant nucleic acid to generate a variant tryptophan-processing enzyme polypeptide.

117. The method of claim 115, wherein the modifications, additions or deletions are introduced by a method comprising error-prone PCR, shuffling, oligonucleotide-directed mutagenesis, assembly PCR, sexual PCR mutagenesis, in vivo mutagenesis, cassette mutagenesis, recursive ensemble mutagenesis, exponential ensemble mutagenesis, site-specific mutagenesis, gene reassembly, Gene Site Saturation Mutagenesis™ (GSSM™), synthetic ligation reassembly (SLR) and a combination thereof.

118. The method of claim 115, wherein the modifications, additions or deletions are introduced by a method comprising recombination, recursive sequence recombination, phosphothioate-modified DNA mutagenesis, uracil-containing template mutagenesis, gapped duplex mutagenesis, point mismatch repair mutagenesis, repair- deficient host strain mutagenesis, chemical mutagenesis, radiogenic mutagenesis, deletion mutagenesis, restriction-selection mutagenesis, restriction-purification mutagenesis, artificial gene synthesis, ensemble mutagenesis, chimeric nucleic acid multimer creation and a combination thereof.

119. The method of claim 115, wherein the method is iteratively repeated until a tryptophan-processing enzyme having an altered or different activity or an altered or different stability from that of a polypeptide encoded by the template nucleic acid is produced.

120. The method of claim 119, wherein the variant tryptophan- processing enzyme polypeptide is thermotolerant, and retains some activity after being exposed to an elevated temperature.

121. The method of claim 119, wherein the variant tryptophan- processing enzyme polypeptide has increased glycosylation as compared to the tryptophan-processing enzyme encoded by a template nucleic acid. 122. The method of claim 119, wherein the variant tryptophan- processing enzyme polypeptide has a tryptophan-processing enzyme activity under a high temperature, wherein the tryptophan-processing enzyme encoded by the template nucleic acid is not active under the high temperature.

123. The method of claim 115, wherein the method is iteratively repeated until a tryptophan-processing enzyme coding sequence having an altered codon usage from that of the template nucleic acid is produced.

124. The method of claim 115, wherein the method is iteratively repeated until a tryptophan-processing enzyme gene having higher or lower level of message expression or stability from that of the template nucleic acid is produced.

125. A method for modifying codons in a nucleic acid encoding a polypeptide with a tryptophan-processing enzyme activity to increase its expression in a host cell, the method comprising the following steps:

(a) providing a nucleic acid encoding a polypeptide with a tryptophan- processing enzyme activity comprising a sequence as set forth in claim 1 or claim 16; and, (b) identifying a non-preferred or a less preferred codon in the nucleic acid of step (a) and replacing it with a preferred or neutrally used codon encoding the same amino acid as the replaced codon, wherein a preferred codon is a codon over-represented in coding sequences in genes in the host cell and a non-preferred or less preferred codon is a codon under-represented in coding sequences in genes in the host cell, thereby modifying the nucleic acid to increase its expression in a host cell.

126. A method for modifying codons in a nucleic acid encoding a tryptophan-processing enzyme polypeptide, the method comprising the following steps:

(a) providing a nucleic acid encoding a polypeptide with a tryptophan- processing enzyme activity comprising a sequence as set forth in claim 1 or claim 16; and,

(b) identifying a codon in the nucleic acid of step (a) and replacing it with a different codon encoding the same amino acid as the replaced codon, thereby modifying codons in a nucleic acid encoding a tryptophan-processing enzyme. 127. A method for modifying codons in a nucleic acid encoding a tryptophan-processing enzyme polypeptide to increase its expression in a host cell, the method comprising the following steps: (a) providing a nucleic acid encoding a tryptophan-processing enzyme polypeptide comprising a sequence as set forth in claim 1 or claim 16; and,

(b) identifying a non-preferred or a less preferred codon in the nucleic acid of step (a) and replacing it with a preferred or neutrally used codon encoding the same amino acid as the replaced codon, wherein a preferred codon is a codon over-represented in coding sequences in genes in the host cell and a non-preferred or less preferred codon is a codon under-represented in coding sequences in genes in the host cell, thereby modifying the nucleic acid to increase its expression in a host cell.

128. A method for modifying a codon in a nucleic acid encoding a polypeptide having a tryptophan-processing enzyme activity to decrease its expression in a host cell, the method comprising the following steps:

(a) providing a nucleic acid encoding a tryptophan-processing enzyme polypeptide comprising a sequence as set forth in claim 1 or claim 16; and

(b) identifying at least one preferred codon in the nucleic acid of step (a) and replacing it with a non-preferred or less preferred codon encoding the same amino acid as the replaced codon, wherein a preferred codon is a codon over-represented in coding sequences in genes in a host cell and a non-preferred or less preferred codon is a codon under-represented in coding sequences in genes in the host cell, thereby modifying the nucleic acid to decrease its expression in a host cell.

129. The method of claim 128, wherein the host cell is a bacterial cell, a fungal cell, an insect cell, a yeast cell, a plant cell or a mammalian cell.

130. A method for producing a library of nucleic acids encoding a plurality of modified tryptophan-processing enzyme active sites or substrate binding sites, wherein the modified active sites or substrate binding sites are derived from a first nucleic acid comprising a sequence encoding a first active site or a first substrate binding site the method comprising the following steps: (a) providing a first nucleic acid encoding a first active site or first substrate binding site, wherein the first nucleic acid sequence comprises a sequence that hybridizes under stringent conditions to a sequence as set forth in SEQ ID NO: 1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO: 17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67 or SEQ ID NO:69, or a subsequence thereof, and the nucleic acid encodes a tryptophan-processing enzyme active site or a tryptophan-processing enzyme substrate binding site;

(b) providing a set of mutagenic oligonucleotides that encode naturally- occurring amino acid variants at a plurality of targeted codons in the first nucleic acid; and,

(c) using the set of mutagenic oligonucleotides to generate a set of active site-encoding or substrate binding site-encoding variant nucleic acids encoding a range of amino acid variations at each amino acid codon that was mutagenized, thereby producing a library of nucleic acids encoding a plurality of modified tryptophan-processing enzyme active sites or substrate binding sites.

131. The method of claim 130, comprising mutagenizing the first nucleic acid of step (a) by a method comprising an optimized directed evolution system, Gene Site Saturation Mutagenesis™ (GSSM™), or a synthetic ligation reassembly (SLR).

132. The method of claim 130, comprising mutagenizing the first nucleic acid of step (a) or variants by a method comprising error-prone PCR, shuffling, oligonucleotide-directed mutagenesis, assembly PCR, sexual PCR mutagenesis, in vivo mutagenesis, cassette mutagenesis, recursive ensemble mutagenesis, exponential ensemble mutagenesis, site-specific mutagenesis, gene reassembly, Gene Site Saturation Mutagenesis™ (GSSM™), synthetic ligation reassembly (SLR) and a combination thereof. 133. The method of claim 130, comprising mutagenizing the first nucleic acid of step (a) or variants by a method comprising recombination, recursive sequence recombination, phosphothioate-modified DNA mutagenesis, uracil-containing template mutagenesis, gapped duplex mutagenesis, point mismatch repair mutagenesis, repair-deficient host strain mutagenesis, chemical mutagenesis, radiogenic mutagenesis, deletion mutagenesis, restriction-selection mutagenesis, restriction-purification mutagenesis, artificial gene synthesis, ensemble mutagenesis, chimeric nucleic acid multimer creation and a combination thereof.

134. A method for making a small molecule comprising the following steps:

(a) providing a plurality of biosynthetic enzymes capable of synthesizing or modifying a small molecule, wherein one of the enzymes comprises a tryptophan- processing enzyme encoded by a nucleic acid comprising a sequence as set forth in claim l or claim 16;

(b) providing a substrate for at least one of the enzymes of step (a); and

(c) reacting the substrate of step (b) with the enzymes under conditions that facilitate a plurality of biocatalytic reactions to generate a small molecule by a series of biocatalytic reactions.

135. A method for modifying a small molecule comprising the following steps:

(a) providing a tryptophan-processing enzyme, wherein the enzyme comprises a polypeptide as set forth in claim 52, or a polypeptide encoded by a nucleic acid comprising a nucleic acid sequence as set forth in claim 1 or claim 16;

(b) providing a small molecule; and

(c) reacting the enzyme of step (a) with the small molecule of step (b) under conditions that facilitate an enzymatic reaction catalyzed by the tryptophan- processing enzyme, thereby modifying a small molecule by a tryptophan-processing enzyme enzymatic reaction.

136. The method of claim 135, comprising a plurality of small molecule substrates for the enzyme of step (a), thereby generating a library of modified small molecules produced by at least one enzymatic reaction catalyzed by the tryptophan- processing enzyme.

137. The method of claim 135, further comprising a plurality of

5 additional enzymes under conditions that facilitate a plurality of biocatalytic reactions by the enzymes to form a library of modified small molecules produced by the plurality of enzymatic reactions.

138. The method of claim 137, further comprising the step of testing the o library to determine if a particular modified small molecule which exhibits a desired activity is present within the library.

139. The method of claim 138, wherein the step of testing the library further comprises the steps of systematically eliminating all but one of the biocatalytic 5 reactions used to produce a portion of the plurality of the modified small molecules within the library by testing the portion of the modified small molecule for the presence or absence of the particular modified small molecule with a desired activity, and identifying at least one specific biocatalytic reaction that produces the particular modified small molecule of desired activity. 0

140. A method for determining a functional fragment of a tryptophan- processing enzyme comprising the steps of:

(a) providing a tryptophan-processing enzyme, wherein the enzyme comprises a polypeptide as set forth in claim 52, or a polypeptide encoded by a nucleic 5 acid as set forth in claim 1 or claim 16; and

(b) deleting a plurality of amino acid residues from the sequence of step (a) and testing the remaining subsequence for a tryptophan-processing enzyme activity, thereby determining a functional fragment of a tryptophan-processing enzyme.

0 141. The method of claim 140, wherein the tryptophan-processing enzyme activity is measured by providing a tryptophan-processing enzyme substrate and detecting a decrease in the amount of the substrate or an increase in the amount of a reaction product. 142. A method for whole cell engineering of new or modified phenotypes by using real-time metabolic flux analysis, the method comprising the following steps:

(a) making a modified cell by modifying the genetic composition of a cell, 5 wherein the genetic composition is modified by addition to the cell of a nucleic acid comprising a sequence as set forth in claim 1 or claim 16;

(b) culturitig the modified cell to generate a plurality of modified cells;

(c) measuring at least one metabolic parameter of the cell by monitoring the cell culture of step (b) in real time; and, o (d) analyzing the data of step (c) to determine if the measured parameter differs from a comparable measurement in an unmodified cell under similar conditions, thereby identifying an engineered phenotype in the cell using real-time metabolic flux analysis.

5 143. The method of claim 142, wherein the genetic composition of the cell is modified by a method comprising deletion of a sequence or modification of a sequence in the cell, or, knocking out the expression of a gene.

144. The method of claim 143, further comprising selecting a cell 0 comprising a newly engineered phenotype.

145. The method of claim 144, further comprising culturing the selected cell, thereby generating a new cell strain comprising a newly engineered phenotype.

5 146. An isolated or recombinant signal sequence (signal peptide) consisting of a sequence as set forth in residues 1 to 14, 1 to 15, 1 to 16, 1 to 17, 1 to 18, 1 to 19, 1 to 20, 1 to 21, 1 to 22, 1 to 23, 1 to 24, 1 to 25, 1 to 26, 1 to 27, 1 to 28, 1 to 28, 1 to 30, 1 to 31, 1 to 32, 1 to 33, 1 to 34, 1 to 35, 1 to 36, 1 to 37, 1 to 38, 1 to 40, 1 to 41, 1 to 42, 1 to 43, 1 to 44, 1 to 45, 1 to 46, or 1 to 47, of SEQ ID NO:2, SEQ ID NO:4, SEQ 0 ID NO:6, SEQ ID NO:8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID

NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68 or SEQ ID NO:70.

147. A cliimeric polypeptide comprising at least a first domain comprising signal peptide (SP) having a sequence as set forth in claim 146, and at least a second domain comprising a heterologous polypeptide or peptide, wherein the heterologous polypeptide or peptide is not naturally associated with the signal peptide (SP).

148. The chimeric polypeptide of claim 147, wherein the heterologous polypeptide or peptide is not a tryptophan-processing enzyme.

149. The chimeric polypeptide of claim 147, wherein the heterologous polypeptide or peptide is amino terminal to, carboxy terminal to or on both ends of the signal peptide (SP) or a tryptophan-processing enzyme catalytic domain (CD).

150. An isolated or recombinant nucleic acid encoding a chimeric polypeptide, wherein the chimeric polypeptide comprises at least a first domain comprising signal peptide (SP) having a sequence as set forth in claim 146, and at least a second domain comprising a heterologous polypeptide or peptide, wherein the heterologous polypeptide or peptide is not naturally associated with the signal peptide (SP).

151. A method of increasing thermotolerance or thermostability of a tryptophan-processing enzyme polypeptide, the method comprising glycosylating a tryptophan-processing enzyme, wherein the polypeptide comprises at least thirty contiguous amino acids of a polypeptide as set forth in claim 52, or a polypeptide encoded by a nucleic acid as set forth in claim 1 or claim 16, thereby increasing the thermotolerance or thermostability of the tryptophan-processing enzyme.

152. A method for overexpressing a recombinant tryptophan-processing enzyme in a cell comprising expressing a vector comprising a nucleic acid sequence as set forth in claim 1 or claim 16, wherein overexpression is effected by use of a high activity promoter, a dicistronic vector or by gene amplification of the vector. 153. A method of making a transgenic plant comprising the following steps:

(a) introducing a heterologous nucleic acid sequence into the cell, wherein the heterologous nucleic sequence comprises a sequence as set forth in claim 1 or claim

16, thereby producing a transformed plant cell;

(b) producing a transgenic plant from the transformed cell.

154. The method as set forth in claim 153, wherein the step (a) further comprises introducing the heterologous nucleic acid sequence by electroporation or microinjection of plant cell protoplasts.

155. The method as set forth in claim 154, wherein the step (a) comprises introducing the heterologous nucleic acid sequence directly to plant tissue by DNA particle bombardment or by using an Agrohacterium tumefaciens host.

156. A method of expressing a heterologous nucleic acid sequence in a plant cell comprising the following steps:

(a) transforming the plant cell with a heterologous nucleic acid sequence operably linked to a promoter, wherein the heterologous nucleic sequence comprises a sequence as set forth in claim 1 or claim 16;

(b) growing the plant under conditions wherein the heterologous nucleic acids sequence is expressed in the plant cell.

157. A method for decreasing the amount of tryptophan in a composition comprising the following steps:

(a) providing a polypeptide having a tryptophan-processing enzyme activity as set forth in claim 52, or a polypeptide encoded by a nucleic acid as set forth in claim 1 or claim 16; (b) providing a composition comprising tryptophan; and

(c) contacting the polypeptide of step (a) with the composition of step (b) under conditions wherein the tryptophan-processing enzyme hydrolyzes, breaks up or otherwise processes the tryptophan in the composition. 158. The method as set forth in claim 173, wherein the composition comprises an animal food or feed.

159. A method of decreasing the amount of tryptophan in the digestive 5 tract of an animal comprising feeding or otherwise administering at least one polypeptide as set forth in claim 52 to the animal.

160. A method of decreasing the amount of skatole in the digestive tract of an animal comprising feeding or otherwise administering at least one polypeptide as o set forth in claim 52 to the animal.

161. A method of decreasing the amount of skatole in the fat of an animal comprising feeding or otherwise administering at least one polypeptide as set forth in claim 52 to the animal. 5

162. The method of claim 161, wherein the animal comprises a pig, a goat or a sheep.

163. A drink or beverage comprising at least one polypeptide as set 0 forth in claim 52.

164. The method of claim 163, wherein the drink or beverage is a food or feed supplement.

5 165. A food, a feed or a nutritional supplement comprising a polypeptide as set forth in claim 52.

166. A method for utilizing a tryptophan-processing enzyme as a nutritional supplement in an animal diet, the method comprising: 0 preparing a nutritional supplement containing a tryptophan-processing enzyme comprising at least thirty contiguous amino acids of a polypeptide as set forth in claim 52, wherein the enzyme has tryptophan-processing activity; and administering the nutritional supplement to the animal. 167. The method of claim 166, wherein the animal is a human.

168. The method of claim 166, wherein the animal is a ruminant or a monogastric animal.

5

169. The method of claim 166, wherein the animal is a pig, a boar, a hog or a swine.

170. The method of claim 166, wherein the tryptophan-processing o enzyme is prepared by expression of a polynucleotide encoding the tryptophan-processing enzyme in an organism selected from the group consisting of a bacterium, a yeast, a plant, an insect, a fungus and an animal.

171. The method of claim 170, wherein the organism is selected from 5 the group consisting of a S. pombe, S. cerevisiae, Pichiapastoris, E. coli, Streptomyces sp., Bacillus sp. and Lactobacillus sp.

172. An edible enzyme delivery matrix comprising a thermostable recombinant tryptophan-processing enzyme having a sequence as set forth in claim 56. 0

173. A method for delivering a tryptophan-processing enzyme supplement to an animal, the method comprising: preparing an edible enzyme delivery matrix in the form of pellets comprising a granulate edible carrier and a thermostable recombinant tryptophan- 5 processing enzyme having a sequence as set forth in claim 56, wherein the pellets readily disperse the tryptophan-processing enzyme contained therein into aqueous media, and administering the edible enzyme delivery matrix to the animal.

174. The method of claim 173, wherein the granulate edible carrier 0 comprises a carrier selected from the group consisting of a grain germ, a grain germ that is spent of oil, a hay, an alfalfa, a timothy, a soy hull, a sunflower seed meal and a wheat midd. 175. The method of claim 173, wherein the granulate edible carrier comprises grain germ that is spent of oil.

176. The method of claim 173, wherein the tryptophan-processing enzyme is glycosylated to provide thermostability at pelletizing conditions.

177. The method of claim 173, wherein the delivery matrix is formed by pelletizing a mixture comprising a grain germ and a tryptophan-processing enzyme.

178. The method of claim 173, wherein the pelletizing conditions include application of steam.

179. The method of claim 173, wherein the pelletizing conditions comprise application of a temperature in excess of about 80⁰C for about 5 minutes and the enzyme retains a specific activity of at least 350 to about 900 units per milligram of enzyme.

180. An isolated or recombinant nucleic acid comprising a sequence encoding a polypeptide having a tryptophan-processing enzyme activity and a signal sequence, wherein the nucleic acid comprises a sequence as set forth in claim 1.

181. The isolated or recombinant nucleic acid of claim 180, wherein the signal sequence is derived from another tryptophan-processing enzyme or a non- tryptophan-processing enzyme.

182. An isolated or recombinant nucleic acid comprising a sequence encoding a polypeptide having a tryptophan-processing enzyme activity, wherein the sequence does not contain a signal sequence and the nucleic acid comprises a sequence as set forth in claim 1.

183. A pharmaceutical or dietary supplement composition comprising a polypeptide having a tryptophanase activity. 184. The pharmaceutical or dietary supplement composition of claim 183 formulated as an edible delivery agent or an orally deliverable formulation.

185. The pharmaceutical or dietary supplement composition of claim 184, wherein the formulation comprises a feed, a food, a liquid, an elixir, an aerosol, a spray, a powder, a tablet, a pill, a capsule, a gel, a geltab, a nanosuspension, a nanoparticle, a microgel or a suppository.

186. The pharmaceutical or dietary supplement composition of claim 183, wherein the polypeptide having a tryptophanase activity comprises a polypeptide having a sequence as set forth in claim 52.

187. A method for delivering a tryptophan-processing enzyme supplement to an animal, the method comprising: (a) providing a cell that recombinantly generates a polypeptide having a tryptophanase activity, or a formulation of the recombinantly generated polypeptide; and

(b) administering the cell or the recombinantly generated polypeptide to the animal.

188. The method as claim 187, wherein the cell is a plant cell, a bacterial cell, a yeast cell, an insect cell or an animal cell.

189. The method of claim 188, wherein the cell is selected from the group consisting of a Schizosaccharomyces sp., Saccharomyces sp., Pichia Sp., Escherichia sp., Streptomyces sp., Bacillus sp. and Lactobacillus sp., and optionally the cell is Saccharomyces pombe, Saccharomyces cerevisiae, Pichia pastoris, Escherichia coli, or Bacillus cereus.

190. The method as claim 187, wherein the recombinantly generated polypeptide is a polypeptide as set forth in claim 56.

191. A method for decreasing the amount of skatole in the meat or fat of an animal, the method comprising: (a) providing a cell that recombinantly generates a polypeptide having tryptophanase activity, and

5

192. The method of claim 191, wherein the administered cell recombinantly generates a polypeptide as set forth in claim 56.

193. The method of claim 191, wherein the administered cell comprises o at least one microorganism.

194. The method of claim 193, wherein the administered cell at least one member of a Schizosaccharomyces sp., a Saccharomyces sp., a Pichia sp., a Escherichia sp., a Streptomyces sp., a Bacillus sp. or a Lactobacillus sp. 5

195. The method of claim 193, wherein the animal is a pig, a swine, a boar or a hog, and the method is effective in controlling boar taint and optionally improves the efficiency of animal production and the flavor of cooked pork meat derived from the animal. 0

196. A method for identifying an inhibitor of skatole production comprising the following steps:

(a) providing a polypeptide as set forth in claim 56;

(b) providing a test compound; 5 (c) providing an in vitro or in vivo test system comprising tryptophan as a substrate, wherein the in vitro or in vivo test system can synthesize skatole; and

(c) contacting the polypeptide of step (a) and the test compound of step (b) with the in vitro or in vivo test system and measuring the amount of skatole synthesized, wherein a decrease in the amount of skatole synthesized measured in the presence of the 0 test compound compared to the amount of skatole synthesized in the absence of the test compound provides a determination that the test compound is an inhibitor of skatole production. 197. The method of claim 196, wherein the test compound comprises a small molecule.

198. The method of claim 196, wherein the in vitro or in vivo test 5 system comprises a cell.

199. A method of decreasing the amount of skatole absorbed from the digestive tract of an animal comprising feeding or otherwise administering at least one skatole-binding composition to the animal, wherein optionally the skatole-binding o composition comprises at least one hydrophobic polypeptide.

200. A method of decreasing the amount of skatole absorbed from the digestive tract of an animal comprising feeding or otherwise administering to the animal an effective amount of at least one polypeptide having a tryptophanase activity. 5

201. A method of decreasing the amount of skatole in the digestive tract of an animal comprising feeding or otherwise administering to the animal an effective amount of at least one polypeptide having a tryptophanase activity.

0 202. A method of decreasing the amount of skatole in the fat of an animal comprising feeding or otherwise administering to the animal an effective amount of at least one polypeptide having a tryptophanase activity.

203. The method of claim 200, claim 201 or claim 202, wherein the at 5 least one polypeptide having a tryptophanase activity comprises a polypeptide as set forth in claim 56.

204. The method of any one of claims 200 to 203, wherein the at least one polypeptide having a tryptophanase activity is formulated such that it retains activity 0 in the digestive tract of the animal, wherein optionally the digestive tract of the animal comprises a rumen, caecum or colon of the animal. 205. The method of claim 204, wherein the at least one polypeptide having a tryptophanase activity is formulated such that it is substantially more active in a rumen, caecum or colon of the animal than in the intestine of the animal.

5 206. A method of decreasing the amount of skatole absorbed from the digestive tract of an animal comprising feeding or otherwise administering to the animal an effective amount of at least one polypeptide having a skatole-degrading activity.

207. A method of decreasing the amount of skatole absorbed from the o digestive tract of an animal comprising feeding or otherwise administering to the animal an effective amount of at least one polypeptide having skatole-binding activity.

208. The method of claim 207, wherein the at least one polypeptide having skatole-binding activity comprises a skatole binding antibody (anti-skatole 5 antibody).

209. A method of decreasing the amount of skatole absorbed from the digestive tract of an animal comprising feeding or otherwise administering at least one polypeptide as set forth in claim 56 and at least one anti-skatole antibody to the animal. 0

210. A method of decreasing the amount of skatole in the fat of an animal comprising feeding or otherwise administering at least one skatole-binding hydrophobic polypeptide to the animal.

5 211. A method of decreasing the amount of skatole in the fat of an animal comprising feeding or otherwise administering at least one polypeptide as set forth in claim 56 and at least one skatole-binding hydrophobic polypeptide to the animal.

212. A method of decreasing the amount of skatole in the fat of an 0 animal comprising feeding or otherwise administering at least one polypeptide as set forth in claim 56 and at least one anti-skatole antibody to the animal.

213. A method of decreasing the amount of skatole absorbed from the digestive tract of an animal comprising feeding or otherwise administering at least one polypeptide as set forth in claim 56 and indole-3-carbinol (I3C) or indole-3-acetonytril (I3A).

214. A method of decreasing the amount of skatole in the fat of an animal comprising feeding or otherwise administering at least one polypeptide as set forth in claim 56 and indole-3-carbinol (I3C) or indole-3-acetonytril (I3A).

215. A method of decreasing the amount of skatole absorbed from the digestive tract of an animal comprising feeding or otherwise administering at least one polypeptide as set forth in claim 56 and a probiotic or a probiotic bacteria.

216. A method of decreasing the amount of skatole in the fat of an animal comprising feeding or otherwise administering at least one polypeptide as set forth in claim 56 and a probiotic or a probiotic bacteria.

217. A method of decreasing the amount of skatole absorbed from the digestive tract of an animal comprising feeding or otherwise administering at least one polypeptide as set forth in claim 56 and an enzyme that can modify or degrade a skatole precursor.

218. A method of decreasing the amount of skatole in the fat of an animal comprising feeding or otherwise administering at least one polypeptide as set forth in claim 56 and an enzyme that can modify or degrade a skatole precursor.

219. The method of claim 217 or claim 218, wherein the skatole precursor is indolacetate or indolepyruvate.

220. The method of any one of claims 199 to 219, wherein the animal is a monogastric animal, and optionally the monogastric animal is a pig, swine or hog.

221. A composition comprising a formulation of a tryptophanase, wherein the formulation causes the tryptophanase to be only active, or substantially more active, in a rumen, caecum or colon of an animal, as compared to its activity in the intestine of the animal. 222. The composition of claim 221 , wherein the formulation comprises an encapsulated formulation of at least one tryptophanase,

223. The composition of claim 221 , wherein the formulation comprises a feed, a food, a liquid, an elixir, an aerosol, a spray, a powder, a tablet, a pill, a capsule, a gel, a geltab, a nanosuspension, a nanoparticle, a microgel or a suppository.

224. The composition of claim 221 , wherein the formulation comprises at least one polypeptide as set forth in claim 56.

225. The composition of claim 221, the formulation further comprising an enzyme that can modify or degrade a skatole precursor, a probiotic, a probiotic bacteria, an indole-3-carbinol (I3C) or indole-3-acetonytril (I3A), anti-skatole antibody or a skatole-binding polypeptide or a combination thereof.

226. The method of any one of claims 221 to 225, wherein the animal is a monogastric animal, and optionally the monogastric animal is a pig, boar, swine or hog.

227. A food or feed comprising (a) at least one polypeptide having a tryptophanase activity; (b) an enzyme that can modify or degrade a skatole precursor, a probiotic, a probiotic bacteria, an indole-3-carbinol (I3C) or an indole-3-acetonytril (I3A), an anti-skatole antibody or a skatole-binding polypeptide; or (c) a combination thereof.

228. The food or feed of claim 227, wherein the food or feed is formulated as a liquid, an elixir, an aerosol, a spray, a powder, a tablet, a pill, a capsule, a gel, a geltab, a nanosuspension, a nanoparticle, a microgel or a suppository.

229. The food or feed of claim 227, wherein the at least one polypeptide having a tryptophanase activity comprises at least one polypeptide as set forth in claim

56.

230. An isolated or recombinant polypeptide having a tryptophanase activity comprising a sequence as set forth in claim 56 and wherein at least one protease cleavage site sequence has been modified such that the protease no longer cleaves the polypeptide at that modified sequence.

231. The isolated or recombinant polypeptide of claim 230, wherein at least two, several or all protease cleavage sites have been modified such that the protease no longer cleaves the polypeptide at that modified sequence, wherein optionally the protease is a cathepsin B, an aminopeptidase, a serine protease, an aspartyl protease, a pepsin, a trypsin or a chymotrypsin.

232. A method for making a tryptophanase resistant to protease digestion comprising

(a) providing a polypeptide having tryptophanase activity comprising a sequence as set forth in claim 56;

(b) identifying at least one protease cleavage site in the sequence of the polypeptide of (a); and

(c) modifying at least one protease cleavage site in the sequence of the polypeptide of (a) such that the protease no longer cleaves the polypeptide at that at least one modified sequence.

233. The method of claim 232, wherein the protease comprises a cathepsin B, an aminopeptidase, a serine protease, an aspartyl protease, a pepsin, a trypsin or a chymotrypsin.