AU721534B2 - Fungal lichenase and coding sequences - Google Patents

Description

4 WO 98/14595 PCT/US97/17811 FUNGAL LICHENASE AND CODING SEQUENCES STATEMENT REGARDING FEDERAL RESEARCH SUPPORT This invention was made, at least in part, with funding from the United States Department of Energy. Accordingly, the United States Government has certain rights in this invention.

BACKGROUND OF THE INVENTION The present invention relates to polysaccharide-degrading enzymes, especially to the enzymes, in particular, to a lichenase enzyme which is capable of degrading (1,3-1,4)-3-glucans and sequences encoding lichenase enzymes.

Hemicellulose (non-cellulosic polysaccharides including glucans, mannans and xylan) is the major constituents of plant cell walls. The mixed-linked 1,3-1,4-0-glucans form the major part of cell walls of cereals like oat and barley. /-Glucans consist of glucose units jointed by 0-1,4 and 0-1,3 linkages, and include lichenan and barley 0-glucan. -Glucan accounts for up to 70% of the cell wall in barley endosperm (Guliga and Brant, 1986).

Endo- 1,3-1,4-/-D-glucanohydrolase (1,3-1,4-3-glucanase, lichenase) cleaves 3-1,4 linkages adjacent to 3-1,3 in glucans yielding chiefly cellobiosyltriose and cellotriosyltetraose (Fleming and Kawami, 1977; Anderson and Stone, 1975). 0-Glucanase is especially interesting to the brewing industry because 0-glucans cause problems in filtration processes (Godfrey, 1983). 0-glucanase also has application in the poultryindustry; it has been added to broiler chick feedstuffs to improve digestibility (White et al., 1983). (-Glucanases have been cloned from several Bacillus species, including Bacillus subtilis (Murphy et al., 1984), B. amyloliquefaciens (Hofemeister et al., 1986), B.

macerans (Borriss et al 1990), B. licheniformis (Lloberas et al., 1991), B. brevis (Louw et al., 1991), B. polymyxa (Gosalbes et al., 1991), and from other genera, including Clostridium thermocellum (Schimming et al., 1992; Zverlov et al., 1992), Fibrobacter succinogenes (Teather and Erfle, 1990), Ruminococcus flavefaciens (Flint et al., 1993), Rhizobium meliloti (Berker et al., 1993, and Cellvibrio mixtus (Sakellaris et al., 1993). A cDNA clone encoding barley 0-glucanase has been isolated and sequenced from germinating barley (Fincher et al., 1986).

Unlike endo-1,4-0-D-cellulases which are widely distributed in various organisms, 1,3-1,4-8- D-glucanases are known to be produced only by plants and certain bacteria (Borriss et al., 1990; Fincher et al., 1986). No fungal 1,3-1,4-0-glucanases which lack the ability to degrade f-(1,4)-glucans are believed to have been discovered prior to the present invention.

Obligately anaerobic fungi are part of the natural microflora of the alimentary tract of many herbivorous mammals (Orpin and Joblin, 1988). Since the first strictly anaerobic and filamentous fungus Neocallimastixfrontallis-was isolated in 1975 from the rumen of a sheep (Orpin, 1975), at least thirteen different anaerobic fungi have been isolated from ruminant and nonruminant herbivores (Chen et al., 1995a). Anaerobic fungi are divided into two groups based on morphology. One is WO 98/14595 PCT/US97/17811 monocentric, and it includes Neocallimastix (Orpin, 1975), Caecomyces (Wubah and Fuller, 1991), and Piromyces species (Barr et al., (1989) Can. J. Botany 67:2815-2824); the other is polycentric and it contains Orpinomyces (Barr et al., (1989) supra), Anaeromyces (Breton et al., 1990), and Ruminomyces (Ho and Bauchop, 1990). The anaerobic fungi produce a variety of enzymes that degrade plant materials ingested by the host animals (Borneman et al., 1989). The physical association with the lignocellulosic tissues of plant fragments, and the ability to penetrate and weaken the plant tissue in vivo (Akin et al., 1983) suggest that the fungi are involved in degradation of digesture and that they play an important role in the rumen ecosystem. Several cellulases and xylanases have been cloned and sequenced from both monocentric Neocallimastix patriciarum (Gilbert et al., 1992; Zhou et al., 1994; Black et al., (1994) Biochem.J. 299:381-387; Denman et al., (1996) Appl. Envir. Microbiol. 62:1889- 1896; Piromyces sp. (Fanutti et al., 1995) and polycentric Orpinomyces PC-2. A mannanase was cloned and sequenced from Piromyces sp. (Fanutti et al., 1995).

SUMMARY OF THE INVENTION The present invention provides a substantially purified lichenase. As used herein, a lichenase is an enzyme which hydrolyzes the B-1,4-glucan bonds adjacent to B-1,3-linked glucan bonds, but does not cleave B-1,4-linked glucans. Substrates for lichenase include, without limitation, lichenan and barley B-glucan. As specifically exemplified, the lichenase is selected from the group consisting of that naturally produced by Orpinomyces PC2 (SEQ ID NO:2, amino acids 1 to 216) and that recombinantly produced, for example, in Escherichia coli (SEQ ID NO:2, amino acids -8 to 216). The complete amino acid sequence of the exemplified lichenase, including the signal sequence, is given in SEQ ID NO:2, amino acids -29 to 216.

It is a further object of the invention to provide a nucleotide sequence encoding a mature lichenase enzyme from Orpinomyces, where that sequence has at least about 80% sequence identity with the exemplified coding sequence (nucleotides 210 to 860 of SEQ ID NO:1) and encodes a lichenase enzyme having the same enzymatic specificity as the exemplified lichenase. Additional objects of the invention are nucleotide sequences which encode a lichenase enzyme of the disclosed specificity and having an amino acid sequence as given in SEQ ID NO:2, amino acid 1 to amino acid 216 or as given in SEQ ID NO:2, from amino acid -8 to amino acid 216 or as given in SEQ ID NO:2 from -29 to 216, for a lichenase with signal sequence. Variations from the specifically exemplified sequence are permitted, to the extent that the functionality of the enzyme is not changed.

Specifically exemplified embodiments of the Orpinomyces PC2 coding sequences for a mature natural lichenase is as given in SEQ ID NO:1, nucleotides 210-860; for the recombinantly expressed lichenase, SEQ ID NO:1, nucleotides 186-860, and for the complete coding sequence including the signal peptide, SEQ ID NO:2, nucleotides 123-860, and sequences with at least about 70% homology to the recited Sequences. Synonymous codings are within the scope of the present invention, and are WO 98/14595 PCT/US97/17811 well within the grasp of the ordinary skilled artisan without the expense of undue experimentation, given the teachings of the present disclosure taken with what is well known to the art.

It is a further object of the present invention to provide non-naturally occurring recombinant DNA molecules which direct the expression of a lichenase protein of the present invention. Where expression and secretion is desired, the complete coding sequence (SEQ ID NO: 1, nucleotides 123-860) is operably linked downstream of promoter sequences appropriate to the recombinant host cell in which expression is desired. If it is preferred that the expressed lichenase protein be intracellular, then the coding sequence for lichenase (either as given in SEQ ID NO:1, nucleotides 186-860 or as given in SEQ ID NO:1, nucleotides 210-860) is joined immediately downstream of a translation start signal (ATG) and operably linked downstream of a promoter appropriate to the host cell of choice.

Recombinant cells which express lichenase, also an object of the present invention, are cultured under conditions suitable for the expression of the lichenase coding sequence. Where an inducible promoter is used to control the expression of the lichenase coding sequence, the skilled artisan understands that it is desirable or essential, depending on the inducible promoter, to add the cognate inducer to the culture to effect gene expression. Substitution of alternative signal peptide coding sequences is also within the skill of the skilled artisan.

A further object of the present invention is to provide a method for the expression of a lichenase protein of the present invention. This method includes the step of producing a non-naturally occurring recombinant DNA molecule as described hereinabove, with the lichenase coding sequence operably linked to transcriptional and translational control sequences suitable for the host cell of choice, said combination being incorporated within a vector plasmid or virus suitable for the chosen host cell, introducing that recombinant DNA molecule into the host cell to produce a recombinant host cell, and culturing the recombinant host cells under conditions suitable for expression of the lichenase coding sequence. Substantially pure lichenase can be purified from cell-free medium of such cultures using the methods provided herein.

It is a further object of the present invention to provide a substantially pure lichenase, said lichenase having the ability to cleave B-1,4 glucan bonds adjacent to 8-1,3 glucan bonds, but having no hydrolytic activity for f-1,4 glucans. As specifically exemplified, the lichenase expressed by Orpinomyces PC2 has an extracellular (secreted) enzyme having a molecular weight of about 26 kDa, while the recombinant enzyme expressed and secreted by Escherichia coli has an apparent molecular weight of about 27 kDa. The lichenase of the present invention has no apparent activity when assayed with carboxymethylcellulose as substrate.

WO 98/14595 PCT/US97/17811 BRIEF DESCRIPTION OF THE DRAWINGS Figure 1 shows protein staining patterns for crude enzyme sample (lane 1) and purified enzyme (lane 2) and the lichenase activity patterns for the crude enzyme sample (lane 3) and purified enzyme (lane 4) using lichenase as the substrate.

Figure 2 is a photograph of crude (lane 2) and purified recombinant lichenase (lane 3) from the extracellular medium of the E. coli culture producing the lichenase. Lane 1 contains the low molecular weight standards.

Figure 3 shows the effects of pH on the activity of the Orpinomyces lichenase. Maximal activity on the curve is defined as 100%.

Figure 4 illustrates the pH stability of the Orpinomyces lichenase.

Figure 5 shows the effect of temperature on Orpinomyces lichenase activity. Maximal activity is defined as 100%.

Figure 6 shows thermostability profiles for Orpinomyces lichenase at selected temperatures.

Figure 7 is a photograph of a thin layer chromatogram of the products of barley 0-glucan and lichenan incubated with Orpinomyces lichenase.

Figure 8A shows the protein staining profile for low molecular weight standards (lane 1), crude recombinant E. coli cell extract (lane purified recombinant LICA (lane supernatant from Orpinomyces PC2 grown on CBG (lane 4) and supernatant from Neocallimastix EB188 grown on CBG (lane Figure 8B is a lichenan zymogram and Figure 8C is a CMC cellulose zymogram. Lanes are as in Figure 8A.

DETAILED DESCRIPTION OF THE INVENTION As used herein, lichenase is used synonymously with endo-o-(1-3,1-4)-D-glucanase; the enzyme code assigned to enzymes having this activity is EC 3.2.1.73.

The gene and cDNA encoding the lichenase of the present invention is called licA. As specifically exemplified, the mature licA gene product (LICA) has an amino acid sequence as given in SEQ ID NO:2, amino acids 1-216 as expressed in Orpinomyces PC2, or a functionally equivalent amino acid sequence, for example, as given in SEQ ID NO: 2, amino acids -8 to 216, or -29 to 216.

Also encompassed by the present invention are lichenases with about 70% amino acid sequence identity to any of the foregoing sequences. These functionally equivalent sequences differ in the proteolytic cleavage site for the removal of the signal peptide.

The lichenase of the present invention is distinguished from prior art lichenases from rumen bacteria in that there are no repeated oligopeptide sequence motifs in the present lichenase. Without wishing to be bound by theory, it is proposed that the lack of the repeated motifs contributes to the efficient expression and secretion, with functionally correct signal peptide processing in the Escherichia coli recombinant host cells.

WO 98/14595 PCT/US97/17811 The lichenase proteins of the present invention is useful for treatment of animal graincontaining feeds to improve nutrient availability and for treatment of grain barley or wheat) in the brewing and fermentation industries to increase carbon substrate availability and to maximize production of desired products. The lichenase coding sequences of the present invention are useful to direct the recombinant expression (in Orpinomyces or in other host cells, including, but not limited to, Escherichia coli, Bacillus subtilis, Aspergillus nidulans, Aspergillus niger, Saccharomyces cerevisiae, and Pichia pastoris).

A cDNA expression library in ZAPII using mRNA isolated from Orpinomyces sp. strain PC-2 cells cultivated with Avicel and oat spelt xylan as carbon source was screened for clones with 3glucanase activity on lichenan plates. Initially, 15 positive plaques were identified after screening 2x10 4 plaques from the library. Eight of them were randomly choose for further enrichment and purification. The remaining lichenase-positive clones were not further studied. After secondary screening, the recombinant lambda clones were converted to pBluescript clones. Then these eight clones were tested for CMCase (carboxymethylcellulose-degrading activity) and lichenase activities after culturing them in LB-ampicillin medium. Three of them showed only lichenase activity without detectable CMCase activity; these clones contain the licA coding sequence. Four of them exhibited both lichenase and CMCase activities, and these later were further confirmed as cellulase- positive clones.

Analysis of the lichenase producer clones by restriction mapping revealed that they had similar restriction patterns (inserts of 0.9, 1.0, and 1.7 kbp, respectively). Sequencing of both ends of the inserts showed that they were transcripts from the same gene (licA) differing in length at their 3' ends.

The complete nucleotide sequence of licA derived from pLIC6 (1.0 kbp) was determined (Table 4, SEQ ID NO:1). The whole sequence was 971 bp with a G-C content of 28%, and it contained an open reading frame (ORF) encoding a polypeptide of 245 amino acids with a calculated M, value of 27,929 (See SEQ ID NO: A typical 18-mer poly(A) tail was found at its 3' end. The putative start codon (ATG) for licA was identified because there were stop codons in all three reading frames preceding the ORF, there was no ATG codon upstream of the identified ORF, and a typical signal peptide occurred at the N-terminus of the ORF. In addition, zymogram analysis and N-terminal sequencing of the purified LICA enzyme from the recombinant E. coli supernatant and partially purified native enzyme from Orpinomyces PC-2 further confirmed this assignment. Only one potential N-glycosylation site (Asn4-Gly-Ser 6 was present near the N-terminus of the mature enzyme; the enzyme may not be glycosylated.

The G+C content of the ORF of licA was 35.5 while that of the 5' and 3' non-coding sequences was extremely low The codon usage for licA was similar to that observed for other Orpinomyces PC-2 cellulase and xylanase genes. 21 codons were not utilized, and there was a marked preference for a T in the third position (53 of all codons contained T in the third position).

WO 98/14595 PCT/US97/17811 mRNAs of anaerobic fungi do not contain a typical E. coli Shine-Dalgarno-like sequence for translation initiation. However, presumably the sequence AGA, 10 bp upstream of the ATG start codon, acts as a weak ribosome-binding sequence in E. coli. This sequence was also found in a xylanase gene (xynA) from N. patriciarum (Gilbert et al., 1992).

The deduced amino acid sequence of the protein LICA was compared with other protein sequences in the SWISS PROT and GP data banks. A number of 0-glucanases from mesophilic and thermophilic bacteria, including anaerobic rumen bacteria, with some identity to LICA were found.

Greater than 50% identity was found with 0-glucanases from certain Bacillus strains, Clostridium thermocellum, and the carboxy-terminal lichenase domain of the xylD gene of the anaerobic rumen bacterium R. flavefaciens. LICA has 30.6% amino acid identity with f-glucanase from Fibrobacter succinogenes (Table In contrast, limited sequence homology was found upon comparison with barley f-glucanase.

Some of the homologous sequences were aligned with LICA sequence (Table This alignment revealed that the similarity between these 0-glucanases is stronger in the central and Cterminal parts of the proteins. The motif DEIDI (SEQ ID NO:6), which is located in the active site cleft in lichenase from Bacillus licheniformisformis (Juncosa et al., 1994), was conserved in the LICA sequence (133-137 position). According to the classification of Henrissat and Bairoch (1993), LICA should be placed in Glycosyl Hydrolase Family 16, which includes most bacterial lichenases.

In order to study the expression and the distribution of the f-glucanase synthesized in E. coli harboring pLIC6, extracellular, periplasmic and cellular fractions were isolated according to the method described by Cornelis et al. (1982). A major part of the total activity was found in the extracellular fraction, with significant periplasmic activity. These two fractions contained greater than 90% of the expressed enzyme activity in E. coli. /-Galactosidase and alkaline phosphatase were used as cytoplasmic and periplasmic markers, respectively. Additionally, the secreted enzyme encoded by clone pLIC6 was visualized by the zymogram technique involving renaturation of enzyme activity following separation by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (Fig. The results show that a strong polypeptide band detected at 27 kDa exhibited only lichenase but not CMCase activity.

Taken with results for the N-terminal sequence of the mature protein, these results indicate that the export mechanism of E. coli accepts export signals from the anaerobic fungus Orpinomyces lichenase, correctly processes the protein and transports it to the periplasmic space. Similar results have been reported for expression of bacterial extracellular lichenase genes cloned in E. coli (Lloberas, 1991; Borriss et al. 1990). By contrast, the xylanase, the cellulase and the mannanase from the fungus N. partricerum expressed in E. coli were found predominantly in cell-free extracts, indicating that these enzymes were not effectively secreted by E. coli (Gilbert et al, 1992; Zhou et al., 1994, Fanutti et al., 1995).

WO 98/14595 PCT/US97/17811 A summary of the purification of the recombinant LICA from the supernatant of the E. coli culture is given in Table 2. The enzyme was purified about 24-fold, with a yield of about 43.5%.

Based on calculations of the specific lichenase activity of the purified LICA and the recovery of the enzyme, the recombinant LICA protein constituted about 4% of the secreted protein in the recombinant E. coli culture. Considering that E. coli XL1 is not considered a superb expression host for recombinant proteins, the surprisingly large amount of recombinant LICA detected in the culture supernatant indicates that the signal sequence of LICA is very effectively processed in E. coli. Using a similar purification strategy and zymogram analysis to monitor lichenase, the native lichenase from the supernatant of Orpinomyces PC-2 culture was also partially purified.

Analysis of the amino acid sequence of the N-terminus of the recombinant LICA isolated from the supernatant of E. coli culture indicated that the recombinant protein is processed in E. coli, with a 21-amino acid signal sequence being removed to give a mature active enzyme of 224 amino acids (22 N-terminal residues if the LICA exactly matched the deduced protein sequence). The presumptive 21-amino-acid signal sequence deduced from the DNA sequence contains all of the features normally associated with a signal sequence for secretion (Von Heijne, 1988), including a positively charged lysine terminal n region and a strongly hydrophobic h region from amino acid residues -18 through -6 (10 out of 13 are hydrophobic; amino acid positions are given relative to the first residue of the mature peptide). The c region of the signal peptide conforms to the rule", with small, uncharged threonine and alanine residue at positions -3 and -1 relative to the cleavage site, which is typical for a peptide cleaved by signal peptidase I in E. coli.

The partially purified native lichenase from supernatant of Orpinomyces PC-2 culture was subjected to N-terminal sequence analysis. The enzyme had a M, of 26,000 and an N-terminal sequence of GTAWNGLHDVMD, (SEQ ID NO:3) which, with the exception of one amino acid, matched the corresponding amino acid sequence deduced from the DNA sequence. Thus, a 29-amino acid signal sequence was removed to give a natural mature enzyme of 216 amino acids (Table 4).

These results indicate that there are differences in the substrate specificities of the prokaryotic E. coli and eukaryotic (anaerobic fungus) signal peptidases. Normally, proline is conspicuously absent from 3 to +1 regions of prokaryotic signal peptides, but it is not usual to have proline at the corresponding region of eukaryotic signal peptide (Von Heijne, 1986). Another reason for the lichenase N-terminal signal sequence being processed differently may come from "the Charge-Block Effect". A region encompassing the first 10-20 resides of the mature protein is also critical for the initiation of membrane translocation in E. coli (Anderson and von Heijne, 1991). This region normally contains few positively charged amino acids; hence, the introduction of only one or two extra positively charged amino acids can dramatically affect secretion (Li et al., 1988). With much higher numbers of_charged residues, a similar blocking effect can be observed in eukaryotic secreted proteins (Kohara et al., 1991). The first 20 amino acid residues of the mature recombinant lichenase contain only one positively charged amino acid (histidine); this makes the processed enzyme effectively secreted. If the cleavage site of WO 98/14595 PCT/US97/17811 the lichenase processed in E. coli was the same as in the fungus, the mature recombinant lichenase would be difficult to export from E. coli, simply because the N-terminal region of the mature chain carries too many positively charged amino acids (3 out of 20 animo acid residues).

The purified recombinant lichenase appeared as single band with an apparent molecular mass of 27 kDa on SDS-PAGE (Fig. which is consistent with the deduced molecular mass of the mature LICA (25.7 kDa) after removal of a signal peptide of 21 animo acid residues. The lichenase activity of the enzyme was measured from pH 4.2 to 8.6 using lichenan as substrate. A typical pH profile was obtained (Fig. with a broad pH optimum from pH 5.8-6.2, with approximately 80% of maximum activity at pH 5.4 and pH 7.0. The enzyme was stable for at least 24 h between pH 3.4 and 9.8 at 4 0 C (Fig. The lichenase activity was measured in 50 mM sodium citrate at pH 6.0 from 30 to 65 0

C.

Maximum activity was observed at 45°C (Fig. The enzyme exhibited at least 70% of its optimal activity over the range 35-55 0 C, and its activity decreased rapidly above 55 0 C. Thermal stability was investigated by incubating the enzyme, up to 24 h, at different temperatures (Fig. Almost no activity loss was observed at 40 0 C with incubation in the above buffer for 24 h. 72% and 59% of the enzyme activity was retained after 24 h incubation at 45 0 C and 50°C, respectively. Inactivation occurred at 55°C with only 30% of the enzyme activity remaining after lh.

The enzymatic activities of the recombinant lichenase were assayed using lichenan, barley-#glucan, laminarin, pachyman, CMC, acid swollen cellulose, puslutan and other polysaccharides and glycosides as substrates and analyzed by the dinitrosalicylic acid (DNS) method. The enzyme was specific for polysaccharides with mixed 1,3-1,4-13-D-linkages (lichenan and barley 0-glucan) and did not hydrolyze the other substrates tested (Table K, and V ,values at 40°C were obtained from Lineweaver-Burk plots. Km values of the enzyme towards lichenan and barley-P-glucan were 0.75% and 0.91% and V. values were 3,786 and 5,314 U/mg protein, respectively.

The nature of products formed during the action of the purified recombinant lichenase on lichenan and barley-S-glucan was studied using silica gel thin layer chromatography (TLC, Fig. 7).

In extended incubation with both substrates, the reactions proceeded to apparent completion. With lichenan as substrate, the major product was a triose which was migrated on TLC just slightly ahead of cellotriose, and was considered to be 3 -O-9-cellobiosyl-D-glucose (Huber and Nevin, 1977; Erfle et al., 1988). Minor products included pentose (3-O-0-cellotetraosyl-D-glucose) and tetraose (3-0-8cellotriosyl-D-glucose) which migrated on TLC a little ahead of cellopentose and cellotriose. An additional minor component was a biose (laminobiose), which migrated ahead of cellobiose. Barley 3-glucan treated in the same manner gave distinctly different profiles which reflected the structural differences between lichenan and barley f3-glucan (Buliga et al., 1986). The major products from barley P-glucan hydrolysis were triose and tetrose. The products from both substrates were similar with those described for the lichenases from B. subtilis (Huber and Nevin, 1977) and R. succinogenes (Erfle et al., 1988). From these results, the recombinant lichenase appears similar to other 1,3-1,4-3- WO 98/14595 PCT/US97/17811 D-glucanases in its general pattern of action, with a cleavage site which is a 0-1,4 glucopyranosidic linkage of a 3-O-substituted -D-glucopyranose unit (Buliga et al., 1986).

Lichenase and cellulase activities were detected using zymogram technology with an overlay containing lichenan or CMC, respectively. A clear strong band of lichenase activity was observed at approximately 27 kDa for the cell extract of the recombinant E. coli, the purified recombinant LICA, and the supernatant of Orpinomyces PC-2 culture. No activity was observed at this molecular weight when CMC was used as substrate, indicating that the LICA is specific for lichenan (Fig. 8).

Additionally, the results revealed that the licA gene product was actively synthesized and secreted into medium of the Orpinomyces PC-2 culture. There were multiple faint high molecular mass bands in both Orpinomyces PC-2 and Neocallimastex EB188 culture supematant, which reflects cellulases having some ability to hydrolyze lichenan. No equivalent lichenase activity band corresponding to the Orpinomyces PC-2 lichenase was detected in the monocentric anaerobic fungus Neocallimastix EB188 sample. Thus, Neocallimastix EB188 appears to lack a lichenase gene.

1,3-1,4-3-D-Glucanases cleave 1,4-fl-glycosidic linkages that are adjacent to 1,3-0glycosidic linkages in mixed-linked glucans, which comprise an important component of plant hemicellulose. The present 1,3-1,4-3-D-glucanase (lichenase) does not cleave the 0-1,4 glycosidic bonds in carboxymethylcellulose. To date, 1,3-1,4-fl-D-glucanase has been found only in certain bacterial strains and in plants. This is believed to be the first report that describes the primary structure and properties of a typical (-1,3-1,4-D-glucanase from a fungus.

Most hydrolytic enzymes (particularly xylanases or cellulases) cloned from anaerobic fungi have a protein docking domain containing 2-3 repeated motifs of 30-40 amino acids each. The repeated peptide sequences are highly homologous to each other regardless of monocentric or polycentric origins. The repeated domains are not involved in catalysis or cellulose binding, but in formation of multienzyme complexes similar to the cellulosomes of anaerobic bacteria (Felex and Ljungdahl, 1993).

Orpinomyces LICA does not contain a repeated peptide domain, which indicates that it is a free enzyme and not a component of the multienzyme complex. While 1,3-1,4-0-D-glucanases from the rumen bacteria R. flavefaciens (Flint et al., 1993) and F. succinogenes (Teather and Airflow, 1990) have a repeated docking domain, the partial sequence identities between the lichenases of the rumen bacteria and the present lichenase are much lower than those between the present lichenase and lichenases of Bacillus strains or Clostridium thermocellum.

Although the N-terminal signal sequence of LICA is a secretory signal that is functional both in E. coli and in Orpinomyces, the cleavage sites are different. Besides the difference between E. coli and eukaryotes with respect to signal peptides and proteases as discussed hereinabove, the different cleavage sites in LICA signal sequence may also relate to the cell membrane of the anaerobic fungi.

Anaerobic fungi lack the ability to synthesize some common cell-membrane constituents such as sterol because of the absence of molecular oxygen. Instead, unusual lipids synthesized by the anaerobic pathway are incorporated into the anaerobic cell membrane (Kemp et al., 1984). In contrast, all WO 98/14595 PCT/US97/17811 previously described cloned hydrolytic enzyme genes in the fungi which contain the repeated peptide domain are neither effectively expressed nor secreted by E. coli. The expressed enzymes were also often subjected to extensive proteolysis in E. coli, perhaps due to partial removal of non-catalytic repeated domains of the enzymes (Gilbert et al., 1992; Fanutti et al., 1995).

Monocentric and polycentric anaerobic fungi are two different groups based on their morphological patterns. Very commonly, hydrolytic enzymes of monocentric Neocallimastex and Piromyces species have more than one catalytic domain in a single protein (Gilbert et al., 1992; Fanutti et al., 1995), but no such structure has been found in any cloned and sequenced genes for polycentric Orpinomyces hydrolytic enzymes so far. Neocallimastex EB188 does not appear to have a lichenase with the same properties as the lichenase disclosed herein. Since cellulases also have activity to hydrolyze bonds in lichenan and 0-glucan, the selective advantage for Orpinomyces to synthesis lichenase in the rumen ecosystem is not clear The LICA signal peptide of this invention may be used to increase yield of foreign genes in host cells in which they are expressed. Any host cell in which the signal sequence is expressed and processed may be used. The signal peptide sequence (see SEQ ID NOs. 4 and 5 for coding and amino acid sequences) from the Aureobasidium xylanase can be substituted for the exemplified LICA signal sequence. Preferred host cells are Aureobasidium species and S. cerevisiae, as well as other yeasts known to the art for fermentation, including Pichia pastoris (Sreekrishna, "Strategies for optimizing protein expression and secretion in the methylotrophic yeast Pichia pastoris," in Baltz, et al.

(eds.) Industrial Microorganisms: Basic and Applied Molecular Genetics, ASM Press, Washington, D.C. (1993) 119-126; Glick, B.R. and Pasternak, "Molecular Biotechnology Principles and Applications of Recombinant DNA," ASM Press (1994) Washington, Filamentous fungi such as Aspergillus, Trichoderma, Penicillium, etc. are also useful host organisms for expression of the DNA of this invention. (Van den Handel, et al., "Heterologous gene expression in filamentous fungi," (1991) In: Bennett, J.W. and Lasure, L.L. More gene manipulations in fungi, Academy Press, Inc., New York, 397-428). When DNA encoding the LICA signal peptide is ligated to DNA encoding other proteins expressible in these hosts, the gene products are secreted from these organisms with the help of the signal peptide.

In addition the coding region for both the signal peptide and the mature LICA protein may be expressed in such hosts. Alternatively, the LICA mature protein coding region isolated from the signal sequence may be expressed in such hosts, or the coding region for the signal peptide isolated from the mature protein coding region may be expressed in such hosts.

In a preferred embodiment, vectors suitable for transformation of the host, preferably S.

cerevisiae, with the licA gene, cDNA encoding the LICA mature protein, or the LICA signal peptide cDNA coding sequence in combination with a suitable foreign gene expressible in S. cerevisiae, are prepared with the gene under control of a promoter expressible in the host, preferably S. cerevisiae.

Preferably the promoter is a constitutive promoter such as the yeast enolase promoter (Sangadala et WO 98/14595 PCT/US97/17811 al., (1994) "Preparation and characterization of the site-directed E211Q mutant of yeast enolase," In: Abstracts of University System of Georgia 1994 Research Symposium: Advances in Biotechnology, Georgia State University, Atlanta, GA, USA) or a strong inducible promoter such as the yeast alcohol dehydrogenase promoter (Pacitti, et al. (1994), "High level expression and purification of the enzymatically active cytoplasmic region of human CD45 phosphatase from yeast," Biochimica et Biophysica Acta 1222:277-286). The vector is used to transform the host either by integration into the chromosome or otherwise. The host organism is then cultured under conditions allowing expression of the gene and the product recovered from the culture medium.

Additionally, it will be recognized by those skilled in the art that allelic variations may occur in the licA coding sequence from different strains of Orpinomyces or other fungi which will not significantly change activity of the amino acid sequences of the proteins which these sequences encode.

All such equivalent DNA sequences are included within the scope of this invention and the definition of the LICA mature protein coding region and signal sequence coding region. The skilled artisan understands that the amino acid sequence of the exemplified LICA polypeptide and signal peptide can be used to identify and isolate additional, nonexemplified nucleotide sequences which will encode functional equivalents to the polypeptides defined by the amino acid sequences given in SEQ ID NO:2, or an amino acid sequence of greater than 90% identity thereto and having equivalent biological activity. DNA sequences having at least about 70%, 80% and/or 85% homology to the DNA sequences of SEQ ID NO:1 (nucleotides 210 to 857) and encoding polypeptides with the same function are considered equivalent to the sequences of SEQ ID NO: 1 and are included in the definition of "DNA encoding the LICA mature protein" and the "licA gene." Following the teachings herein, the skilled worker will be able to make a large number of operative embodiments having equivalent DNA sequences to those listed herein.

It is further understood that codons for conservative amino acid substitutions can change the primary amino acid sequence of a lichenase protein without significantly affecting the function of that protein. Such conservative amino acid substitutions are well known to the art (See, Dayhoff et al. (1978) in Atlas of Protein Sequence and Structure, Vol. 5, Supplement 3, Chapter 22, pages 345- 352). Dayhoff et al.'s frequency tables are based on comparisons of amino acid sequences for proteins having the same function from a variety of evolutionarily different sources.

As used herein, a recombinant DNA molecule is not naturally occurring; it is produced by the hand of man in the laboratory. DNA segements or sequences from different sources can be joined by chemical synthesis, enzymatic ligation or by directed recombination.

Monoclonal or polyclonal antibodies, preferably monoclonal, specifically reacting with a lichenase encoded by a particular coding sequence may be made by methods known in the art. See, Harlow and Lane (1988) Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratories; Goding (1986) Monoclonal Antibodies: Principles and Practice, 2d ed., Academic Press, New York.

WO 98/14595 PCT/US97/17811 Standard techniques for cloning, DNA isolation, amplification and purification, for enzymatic reactions involving DNA ligase, DNA polymerase, restriction endonucleases and the like, and various separation techniques are those known and commonly employed by those skilled in the art. A number of standard techniques are described in Sambrook et al. (1989) Molecular Cloning, Second Edition, Cold Spring Harbor Laboratory, Plainview, New York; Maniatis et al. (1982)Molecular Cloning, Cold Spring Harbor Laboratory, Plainview, New York; Wu (1993) Meth. Enzymol. 218, Part I; Wu (1979) Meth Enzymol. 68; Wu et al. (eds.) (1983) Meth. Enzymol. 100 and 101; Grossman and Moldave (eds.) Meth. Enzymol. 65; Miller (1972) Experiments in Molecular Genetics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York; Old and Primrose (1981) Principles of Gene Manipulation, University of California Press, Berkeley; Schleif and Wensink (1982) Practical Methods in Molecular Biology; Glover (1985) DNA Cloning Vol. I and II, IRL Press, Oxford, UK; Hames and Higgins (eds.) (1985) Nucleic Acid Hybridization, IRL Press, Oxford, UK; and Setlow and Hollaender (1979) Genetic Engineering: Principles and Methods, Vols. 1-4, Plenum Press, New York. Abbreviations and nomenclature, where employed, are deemed standard in the field and commonly used in professional journals such as those cited herein.

All references cited in the present application are incorporated by reference herein.

The following examples are provided for illustrative purposes, and are not intended to limit the scope of the invention as claimed herein. Any variations in the exemplified articles which occur to the skilled artisan are intended to fall within the scope of the present invention.

EXAMPLES

Example 1: Fungal Strain, Culture Condition, and Vectors Orpinomyces sp strain PC-2 was isolated and described by Borneman et al. (1989); Neocallimastix sp. EB188 was provided by Dr. Calza (Washington State University). For enzyme production, the fungi were grown at 39 0 C for 7 day in 2 L round bottles, each containing 1 L of basic medium (Barichievich and Calza, 1990) and 0.3% of coastal Bermudagrass (CBG). The medium was autoclaved for 30 min, and then cooled under a stream of CO 2 Penicillin (334 U/ml), streptomycin sulfate (80 and chloramphenicol (10 /g/ml) were filter sterilized (0.22 pm) (alt 230) and added to the stated final concentrations just prior to inoculation. Escherichia coli XL-Blue, XZAPII, pBluescript were products of Stratagene Cloning Systems (La Jolla, CA).

Example 2: Recovery of Extracellular. Periplasmic and Cellular 1.3-1.4-,-D-glucanase in Recombinant E. coli Expression of endo-1,3-1,4-p-D-glucanase activity was detected according to the procedures of Neu and Heppel (1965) and Cornelis et al. (1982). E. coli was harvested by centrifugation at 3,200 g for 10 min (Beckman CS-6R). Cell free culture media were used for extracellular enzyme preparation. The cell pellet was washed twice in half the volume of the culture with 10 mM Tris-HCl WO 98/14595 PCT/US97/17811 pH 8.0 and suspended in the same volume of 25% sucrose 5 mM EDTA. The suspension was shaken for 10 min at room temperature. After centrifugation, the cells were suspended in the same volume of ice-cold water, and the suspension was shaken for 10 min at 4°C. After centrifugation, the supernatant was used as the periplasmic fraction. The cell pellet was sonicated to release intracellular 1,3-1,4-/3-D-glucanase activity.

Example 3: Construction and Screening of an Orpinomvces cDNA Library Extraction of RNA, purification of mRNA, and construction of a cDNA library from Orpinomyces PC-2 were described previously (Chen et al.,1995).

Top agar of NZY plates containing 5 mM isopropyl-l-thio--D-galactopyranoside (IPTG) and 0.2% lichenan (Sigma Chemical Co., St. Louis, MO) was used to isolate 1, 3 -1,4-f3-D-glucanaseproducing clones. After growth at 37 0 C overnight, plates were stained by flooding with 0. 1% Congo red for 20 min: clear haloes around colonies on the background indicate fl-glucanase activity.

Improved clear zones were obtained by treatment of stained agar plates with 1 M NaCI for 20 min.

before observation. Pure positive clones were obtained after a secondary screening. Positive X clones were converted to pBluescript SK- clones by in vivo excision. Single colonies were picked from the LB plates and separately inoculated into 5 ml LB+ampicillin (100 /g/ml) medium. The cultures were shaken for 7-8 hours at 250 rpm, 37 0 C until the ODw of the cultures reached about 1.5, and then A1 of 0.5 M IPTG was added to each culture and the tubes were incubated for another 5 hours. The cultures were then sonicated. After centrifugation, the clear supernatants were used for testing lichenase and CMCase activities. The pBluescript DNAs were purified from overnight cultures in LB medium containing 50 jg/ml ampicillin using the WizardT Maxipreps plasmid purification system (Promega, Madison, WI). Nucleotide sequences of insert DNA were determined with an automatic PCR sequencer (Applied Biosystems Foster City, CA). Both universal and specific primers were used to sequence both strands of the inserts. Sequence data were analyzed using the Genetic Computer Group (GCG) version 8 (University of Wisconsin Biotechnology Center, Madison, WI) on the VAX/VMS system of the BioScience Computing Resource at the University of Georgia). The nucleotide sequence of licA of Orpinomyces sp. PC-2 has been assigned accession number U63813.

Example 4: Sodium Dodecvl Sulfate-Polvacrvlamide Gel Electrophoresis (SDS-PAGE) SDS-PAGE was carried out in Laemmli's buffer (Laemmli, U.K. (1970), Nature 227:680) with Coomassie brilliant blue R-250 (Sigma Chemical Co., St. Louis, MO). To visualize enzyme activity, samples were pretreated by incubating for 1 h at 40 0 C in sample buffer and proteins were sizeseparated using SDS-PAGE at 4 0 C. To enhance removal of SDS and recovery of enzymatic activity following SDS-PAGE, gels were washed in 50 mM sodium citrate buffer, pH 6.0 with 1% (w/v) bovine serum albumin (BSA) (McGrew and Green, 1983).

WO 98/14595 PCT/US97/17811 Lichenase and CMCase activities were detected using the zymogram method of Beguin (1983) with a overlay containing 0.3% lichenan or carboxymethylcellulose and agarose w/v) in mM sodium citrate buffer, pH 6.0. The bands of enzyme activity were detected by staining the agarose gel with Congo red and destraining with 1M NaCI.

Example 5: Enzyme Assay All enzyme assays were carried out in duplicate in 50 mM sodium citrate buffer (pH 6.0) at 0 C unless otherwise stated.

0-Glucanase activity was assayed by mixing a 0.2 ml aliquot of appropriately diluted enzyme with 0.4 ml buffer containing 0.4% lichenan or barley 0-glucan (Sigma Chemical Co., St.

Louis, MO). The reaction was for 15 min and terminated by the addition 1.2 ml of 31 mM dinitrosalicylic acid (DNS) (Miller, 1959). The reaction tube was then placed in boiling water for min before determining the absorbance at 550 nm. Glucose was used as standard. Activities on other polysaccharides were assayed in assays similar to that using lichenan.

One unit of enzyme activity was defined as the amount of enzyme releasing one imol glucose per min. Specific activity was expressed as units per mg of protein. Protein concentration was determined by the Bradford method and the Coomassie protein assay reagent (Pierce Chemical Co., Rockford, IL) in duplicate sets using BSA as standard.

Example 6: Enzyme Purification An overnight culture (10 ml) of E. coli XLl-blue (pBluescript-licA) was inoculated into 500 ml LB-ampicillin (50 pg/ml) medium and grown to an ODo of 1.5 to 2.0. (-Glucanase expression was induced by the addition of 1 mM IPTG, and each culture was aerated for an additional 8 h at 37 0 C. A cell-free supernatant was obtained by centrifuging the culture at 4 0 C, 7,000 x g for 10 min.

The cell pellet was set aside, and the supernatant was concentrated to a volume of about 50 ml by using an ultrafiltration cell (Amicon Co., Beverly, Mass.) equipped with a PM 10 membrane. The concentrated supernatant was dialyzed against 500 ml of 20 mM potassium phosphate, pH Ammonium sulfate was added to a concentration of 0.8 M. The solution was centrifuged at 4 0 C and 20,000 x g for 10 min to remove precipitated material. The clear solution was loaded on a Phenyl Superose 10/10 column (7.85 ml) equilibrated with 20 mM potassium phosphate, pH 7.0, containing 0.8 M ammonium sulphate. fl-Glucanase was eluted with a 200 ml linear gradient of ammonium sulphate, from 0.8 to 0 M, then further with 100 ml distilled water. Fractions containing 0-glucanase activity were pooled and concentrated, and the buffer was changed to 20 mM piperazine-HC1, pH The solution was applied to a Mono Q 5/5 anion exchange column (1 ml) equilibrated with 20 mM piperazine-HCI buffer, pH 5.5. The 3-glucanase fractions did not bind to the column, and the enzyme was eluted by applying 5 column volumes of the buffer. The fl-glucanase-containing fractions were pooled and concentrated, and the buffer was changed to 20 mM sodium acetate, pH 5.0. The enzyme WO 98/14595 PCTIS97/17811 sample applied to a cation exchange Resource S column (1 ml). It did not adsorb to the column, and it was eluted out by further passing through 5 column volumes of the buffer. Final purification was achieved by gel filtration over Superdex 75 10/30 column (composite of cross-linked agarose and dextran gel filtration resin, Pharmacia, Piscataway, NJ) equilibrated with 20 mM sodium phosphate, 100 mM NaCI, pH 6.0. Fractions exhibiting /-glucanase activity were combined and stored at -20 0

C.

For partial purification of native P-glucanase from the culture supernatant of Orpinomyces PC-2 culture, purification procedures as above were employed.

Example 7: N-Terminal Amino Acid Sequencing Amino acid sequencing was done with protein bands isolated and purified after SDS-PAGE.

The proteins were transferred onto a poly-vinylidene difluoride (PVDF) membrane in a Mini Trans- Blot cell (Bio-Rad Laboratories, Hercules, CA). The transferred proteins were visualized by Ponceau S staining and then excised with a razor blade. N-terminal amino acid sequencing was performed on an Applied Biosystems model 477A gas-phase sequencer equipped with an automatic on-line phenylthiohydantoin analyzer.

Example 8: Enzyme Characterization The pH optimum was determined at 40 0 C using the following buffers: 0.1 M sodium acetate (pH 4.2 to sodium phosphate (pH 5.8 to and Hepes-NaOH (pH 8.2 and 8.6) with increments of 0.4. Enzyme stability at different pH values was determined by measuring the residual activity after incubating the enzyme for 24 h at 4°C at pH 3.0 to 10.2 (glycine-HCl buffer for pH to 3.4; Hepes-NaOH for pH 9.0; piperazine-HCl for pH 9.4 to 10.2). For other pH ranges, buffers were the same as those used for optimum pH determinations).

The effect of temperature on (-glucanase activity was determined by assaying the enzyme at temperatures from 30 to 65°C with increments of 5'C. Thermostability was measured by incubating the enzyme in 50 mM sodium citrate buffer, pH 6.0 for 5 min to 24 h at temperatures from 40 to with increments of 5°C. The enzyme solution was chilled in an ice bath for 5 min and then analyzed by running the standard assay at 40°C. In all these assays, lichenan was used as substrate.

For determination of Km and suitably diluted 0-glucanase was incubated with lichenan and barley-3-glucan at concentrations ranging from 0.02 to 1.0% under the assay conditions given. Km and V. values were obtained from Lineweaver-Burk plots.

Analysis of lichenan and barley-(3-glucan degradation products was carried out with 5 U of the purified recombinant /-glucanase with 5 mg individual substrate in 1 ml of a 50 mM sodium citrate buffer, pH 6.0, at 40°C. Samples were periodically withdrawn and hydrolysis was stopped by placing the reaction in boiling water for 5 min. A 10 1l portion of each sample was spotted onto thinlayer chromatography (TLC) silica gel plate (Analtech, Inc., Newark, DE) and chromatographed in a solvent system containing chloroform, glacial acetic acid, and water vol/vol) (Lake and WO 98/14595 PCT/US97/17811 Goodwin, 1976). Plates were sprayed with a reagent consisting of aniline (2 ml), diphenylamine (2 acetone (100 ml), and 85% H 3

PO

4 (15 ml). Then sugars were visualized by heating the plate for min at 105 0 C (Hansen, 1975). Glucose, cellobiose, cellotriose, cellotetraose and cellopentaose were used as standards.

WO 98/14595 WO 9814595PCTIUS97/17811 Table 1. Homology comparison between Orpinzomyces PC-2 LICA and other fl-glucanases Strain No. of AA overlap Identity Bacillus polymyxa 207 58 Bacillus subtilis 199 56.8 Closbidum tlzermocellum 243 52.7 Bacillus macerans 204 58.3 Bacillus licheniformis 200 57 Bacillus amyloliquefaciens 200 55.5 Clostridium thermoceilum 194 55.2 Ruminococcus 201 55.7 flavefaciens Fibrobacter succino genes 170 30.6 Table 2. Summary of the purification of the recombinant LICA Step Supernatanit Phenyl Superose, mono Q Resource S Superdex 75 Enzyme

U

4,388 3,149 2,648 2,421 1,909 Specific activity U mg', 156.7 1,850 2,400 2,950 3,786 WO 98/14595 WO 9814595PCT[US97/1781 1 Table 3. Substrate specificity of purified recombinant LICA of Orpinomyces PC-2' Substrate Linkage Specific% activity U Mg 1

I

Lichenan 0-1,3; 0-1,4 3,786 100 Barley fl-glucan 0-1,3; fl-1,4 5,317 140 L aminarin 0-1,3; A3-1,6 0 0 Pachyman 0-1,3 0 0 CMC 0-1,4 0 0 Acid swollen cellulose 0-1,4 0 0 Pustulan 0-1,6 0 0 aThe following substrates were not hydrolyzed: Avicel, arabinogalactan, mannan, araban, starch, xylan, pullulan, galactan, and Gum arabic (0.35% wt PNP-fl-D-xyloside, PNP-fl-D-glucoside, and PNP-13-Dcellobiose (1 mM4).

WO 98/14595 PCTIUS97/1781 1 Table 4. Nucleotide and deduced amino acid sequences of a 3-1, 4glucanase (lichenase) cDNA (licA) of Orpinomyces PC-2

AATAAAAGAAAAAA

M KS I

ATTTCTATTGCTGCTTTATCTGTTTTAGGATTGATTTCTAAAACTATGGCTGCTCCTGCT

I S I A AL S V L G L I S K T M AA P A

CCCGCTCCTGTTCCTGGTACTCTTGGAATGGTAGTCATTGTTGATTTACTAT

P AP V P G T A W N G 9 H D V M D F N Y

~I

H E S N R F E MS N W P NCG EM FN C R

TGGACTCCAAATAATGACAAATTTGAAAATGGTAAATTAAAGCTTACTATTGATAGAGAT

W T P N N D K F E NCG K L K L T I D R D

GGTTCCGGATATACTTCTGGTGAATATCGTACTAAAAACTATTATGGATATGGTATGTTC

C S G Y T C C E Y R T K N Y Y G Y G M F

CAAGTTAATATGAAACCAATTAGAATCCAGGAGTTGTTTCTTCCTTCTTTACTTACCA

Q V NMK P I K N P G V VS S F F TY T

GGACCAAGTGATGGAACTAAGTGGGATGATTGATATAGAATTCCTTGGTTATGATACA

G P S.D G T K W D ElI D IE F L G Y D T

ACCAAGTTCATTTAACTACTACACTAATGGACAAGGTCATCATGACATATTCATTAT

T K VQ F N Y Y TNG Q G H H E H I H Y

CTTGGATTTGATGCCTCTCAAGCATCCATACCTATGGTTTCTTCTGCGCGAAATTCT

L C F D AS QCG F H T Y G F F WA R N S

ATTACATGGTATGTAGATCGTACAGCCGTTTACACTGCTTACCACAATATTCCAGATACA

I T W Y V D C T AV Y T A Y D N I P D T

CCAGGTAAGATTATGATGAATGCTTCGAATCGTATTGGAGTTGATCACTGGCTTAGACCA

PCG K I MM NA W N GCI G V D D W L R P

TTTAATGGAAGAACTAATATTAGTGCCTACTATGATTGGGTATCTTATGATCACCAAGA

F N G R TN I S A YY DW V S Y D AP R

AACTAAATTATTTAAATAAATATATAATTTTTGTTTTAAAATTTAAAAAAATATATATAT

N ATATATTATAAATTAATATGAAAAATAAAACAATGT7iAAADAAAAAAD.

1 t: Cleavage site for the recombinant protein 2. Underline: n-terminal sequence of the recombinant protein 3. 1: Cleavage site for the native protein from the fungus 4. Bold and underline: n-terminal sequence of native protein from the fungus Double underline:poly-A tail Table 5. A Lica~orpifl GubBacpo GixbEacou OubClotm GubEacl.

LamiClotm GubFibsu Lica_orpin Gub_Bacpo GubEacau GubClotm GubEacli LamiClotm GubFibsu ignment of some homologous sequences with Orpinomyces LICA sequence ALWG .I .AP PPGi3AWNRBHDMHDF& HA NRF MNKKMWF11 11ITGWPS~F.~' SIFN STW K GysLaQMM.~ MPYrE JR ,L LVTGJFHB kvtTASAQT GSFFDPF GYN GFW K, GYS MNKNR JU LMAEJLL-jl PFYKAEA jT2VN]PFVI .UF.B t~ BQW K I A MSYVIRUHJIMLVTGiFLB _GD SABAQTAGSFYEPY............ YN GLWfK -GYSM M MKR LHMOIL I PFYKAEATVN1PFVM jFRS8M. EgQwx. R. MAR. .FVB

M

T nRA BHTSL T pYNKD N* TM

IJR

K- TJ ~3G YP Ks SP yMM jTRA VBNTBLE8 p YNK D N' T M TVLEAFTGDIS YPEy F, 5s y R M TMXMXlVK,9JLA- V AAIT TIV KD a LY LEEVQ jA AAAS T LQG Lica_0rpin Gub_Eacpo C ubEacou GubClot= CubBacli LamA._Clotm GubFibou Lica_orpin Gub_Bacpo Gub_Bacou GubClotm Gub-Bacli LamiClotm GubFibsu 128 123 127 130 125 128 71 193 188 192 195 193 193 141

NN

4DIIEL 5IIEL 41E 3EL 4UED S L

SIIEL

3 3DIFL 1 S 4D3 ,r DTKVFY QN DT. VF1YYN .3 9FIYYN .5 KVFI YEN 0TKQNYN .3 KF1MY]N =PS NI MT L TT9MjS LKI. .EPM LKHR TTUHjQ E R ;QVSEJgTC rPG LM T*G LM TPGI LI TPKI LI TP~kiML Q HFL4M RP N .7 S IDNPRN* SV GB N.p E R- Tsm" ml GB~NPyH9 RT p i GK ~MYA

YPNVPQDNPTPTPTA

'3 S P RSL R P E RR P Q -E OSSES.AA GQM ESKLP FQ II KVYKYTPGQGEGGSDFTLD Lica_orpin Gub_Bacpo CubEacou CubClotm GubEacli Lam!_Clot= CubFibou 260 PSTPTNPNLPLKQDVNGDG 209 WDFTDSWKDT WO 98/14595 WO 9814595PCT/US97/17811 REFERENCES CITED Guliga, and Brant, D.A. (1986) Carbohydr. Res. 157, 139-156.

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WO 98/14595 PCT/US97/17811 SEQUENCE LISTING GENERAL INFORMATION: APPLICANT: University of Georgia Research Foundation, Inc.

Li, Xin-Liang Ljungdahl, Lars G.

Chen, Huizhong (ii) TITLE OF INVENTION: Lichenases and Coding Sequences (iii) NUMBER OF SEQUENCES: 6 (iv) CORRESPONDENCE ADDRESS: ADDRESSEE: Greenlee, Winner and Sullivan, P.C.

STREET: 5370 Manhattan Circle, Suite 201 CITY: Boulder STATE: Colorado COUNTRY: US ZIP: 80303 COMPUTER READABLE FORM: MEDIUM TYPE: Floppy disk COMPUTER: IBM PC compatible OPERATING SYSTEM: PC-DOS/MS-DOS SOFTWARE: PatentIn Release Version #1.30 (vi) CURRENT APPLICATION DATA: APPLICATION NUMBER: WO FILING DATE: 03-OCT-1997

CLASSIFICATION:

(vii) PRIOR APPLICATION DATA: APPLICATION NUMBER: US 60/027,882 FILING DATE: 04-OCT-1996 (viii) ATTORNEY/AGENT INFORMATION: NAME: Ferber, Donna M.

REGISTRATION NUMBER: 33,878 REFERENCE/DOCKET NUMBER: 55-96 WO (ix) TELECOMMUNICATION INFORMATION: TELEPHONE: (303) 499-8080 TELEFAX: (303) 499-8089 INFORMATION FOR SEQ ID NO:1: SEQUENCE CHARACTERISTICS: LENGTH: 971 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: not relevant (ii) MOLECULE TYPE: cDNA to mRNA (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE: ORGANISM: Orpinomyces STRAIN: PC2 (ix) FEATURE: NAME/KEY: CDS LOCATION: 123..860 WO 98/14595 WO 9814595PCT[US97/17811 (ix) FEATURE: NAME/KEY: mat-peptide LOCATION: 210. .857 OTHER INFORMATION: /EC number= 3.2.1.73 /product= ,mature lichenase produced by Orpinomyces PC2"1 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:1: AATAAAAGAA AAAAAAAATA TATATTAAAT A7ATAATATAT ATTAAAGTAA ATTTAAGAAA ATATTTTCAT TATATAATTA ATATTTTTTG ATAAAATAAA 120 AA ATG AAA AGT ATA ATT TCT ATT GCT GCT TTA TCT GTT TTA 167 Met Lys Ser Ile Ile Ser Ile Ala Ala Leu Ser Val Leu

ATAAAAAAAA

GATTATAATA

GGA TTG Gly Leu ATT TCT AAA ACT ATG 215 Ile Ser Lys Thr Met GCT TGG AAT GGT AGT 263 Ala Trp Asn Gly Ser GCT GCT CCT GCT CCC GCT CCT Ala Ala Pro Ala Pro Ala Pro -5 GTT CCT GGT ACT Val Pro Gly Thr 1 CAT GAT GTC His Asp Val ATG GAT Met Asp

AAC

311 Asn

AGA

359 Arg GAA ATG TCA Giu Met Ser AAC TGG CCA AAT GGT Asn Trp Pro Asn Gly GAC AAA TTT GAA AAT Asp Lys Phe Glu Asn 45 AAC TAT CAT GAA AGT Asn Tyr His Glu Ser GAA ATG TTT AAT TGT Glu Met Phe Asn Cys GGT AAA TTA AAG CTT Gly Lys Leu Lys Leu ACT CCA AAT AAT Thr Pro Asn Asn 40 ACT ATT GAT AGA GAT 407 Thr Ile Asp Arg Asp AAA AAC TAT TAT GGA 455 Lys Asn Tyr Tyr Gly AAG AAT CCA GGA GTT 503 Lys Asn Pro Gly Val GAT GGA ACT AAG TGG 551 Asp Gly Thr Lys Trp GGT TCC GGA TAT ACT Gly Ser Gly Tyr Thr 60 TAT GGT ATG TTC CAA Tyr Gly Met Phe Gin 75 GTT TCT TCC TTC TTT Val Ser Ser Phe Phe TGT GGT GAA TAT COT ACT Cys Gly Glu Tyr Arg Thr GTT AAT ATG AAA CCA ATT Val Asn Met Lys Pro Ile ACT TAC ACA GGA CCA AGT Thr Tyr Thr Gly Pro Ser GAA TTC CTT GGT TAT GAT Giu Phe Leu Gly Tyr Asp GAT GAA Asp Glu ATT GAT ATA Ile Asp Ile 100 ACA ACC 599 Thr Thr 115 105 AAA OTT CAA TTT AAC Lys Vai Gin Phe Asn 120 110 TAC TAC ACT AAT GGA Tyr Tyr Thr Asn Gly 125 CAA GGT CAT CAT Gin Gly His His 130 WO 98/14595 PCT/US97/17811 GAA CAT ATT CAT TAT 647 Glu His Ile His Tyr 135 TAT GGT TTC TTC TGG 695 Tyr Gly Phe Phe Trp 150 ACA GCC GTT TAC ACT 743 Thr Ala Val Tyr Thr 165 ATT ATG ATG AAT GCT 791 Ile Met Met Asn Ala CTT GGA TTT GAT GCC Leu Gly Phe Asp Ala 140 GCG AGA AAT TCT ATT Ala Arg Asn Ser Ile 155 GCT TAC GAC AAT ATT Ala Tyr Asp Asn Ile 170 TGG AAT GGT ATT GGA Trp Asn Gly Ile Gly TCT CAA GGA TTC CAT ACC Ser Gin Gly Phe His Thr 145 ACA TGG TAT GTA GAT GGT Thr Trp Tyr Val Asp Gly 160 CCA GAT ACA CCA GGT AAG Pro Asp Thr Pro Gly Lys 175 GTT GAT GAC TGG CTT AGA Val Asp Asp Trp Leu Arg 180 CCA TTT 839 Pro Phe 195

TAT

890 Tyr 185 AAT GGA AGA ACT AAT Asn Gly Arg Thr Asn 200 GCA CCA AGA AAC TAA Ala Pro Arg Asn

ATT

Ile 190 AGT GCC TAC TAT Ser Ala Tyr Tyr 205 GAT TGG GTA TCT Asp Trp Val Ser 210

GAT

Asp ATTATTTAAA TAAATATATA ATTTTTGTTT 215 TAAAATTTAA AAAAATATAT ATATATATAT TATAAATTAA 950 TGTAAAAAAA AAAAAAAAAA A 971 TATGAAAAAT AAAAATAAGA INFORMATION FOR SEQ ID NO:2: SEQUENCE CHARACTERISTICS: LENGTH: 246 amino acids TYPE: amino acid TOPOLOGY: linear (ii) MOLECULE TYPE: protein (xi) SEQUENCE DESCRIPTION: SEQ ID Met Lys Ser Ile Ile Ser Ile Ala Ala Leu -29 -25 -20 Ser Lys Thr Met Ala Ala Pro Ala Pro Ala -5 Trp Asn Gly Ser His Asp Val Met Asp Phe NO:2: Ser Val Leu Pro Val Pro Asn Tyr His Glu Met Phe Gly Leu Ile Gly Thr Ala 1 Glu Ser Asn Arg Trp Phe Glu Met Ser Thr Pro Asn Asn Asn Trp Pro Asn Asp Lys Phe Glu Gly Asn Cys Asn Gly Lys Leu Lys 45 Leu WO 98/145! Ile Asn Asn Gly 100 Thr His Gly Ala Met 180 Phe Asp (2) 95 Asp Arg Asp Gly Ser Gly Tyr Thr 60 Tyr Tyr Gly Tyr Gly Met Phe Gn 75 Pro Gly Val Val Ser Ser Phe Phe 90 Thr Lys Trp Asp Glu Ile Asp Ile 105 Lys Val Gin Phe Asn Tyr Tyr Thr 120 Ile His Tyr Leu Gly Phe Asp Ala 135 140 Phe Phe Trp Ala Arg Asn Ser Ile 150 155 Val Tyr Thr Ala Tyr Asp Asn Ile 165 170 Met Asn Ala Trp Asn Gly Ile Gly 185 Asn Gly Arg Thr Asn Ile Ser Ala 200 Ala Pro Arg Asn 215 INFORMATION FOR SEQ ID NO:3: SEQUENCE CHARACTERISTICS: LENGTH: 12 amino acids TYPE: amino acid STRANDEDNESS: single TOPOLOGY: not relevant (ii) MOLECULE TYPE: peptide (iii) HYPOTHETICAL: NO FRAGMENT TYPE: N-terminal Cys Val Thr 3lu Asn 125 Ser rhr Pro Val Tyr 205 Gly Asn Tyr Phe 110 Gly Gin Trp Asp Asp 190 Tyr Glu Met Thr Leu Gin Gly Tyr Thr 175 Asp Asp Tyr Lys Gly Gly Gly Phe Val 160 Pro Trp Trp PCT/US97/17811 Arg Thr Lys Pro Ile Lys Pro Ser Asp Tyr Asp Thr 115 His His Glu 130 His Thr Tyr 145 Asp Gly Thr Gly Lys Ile Leu Arg Pro 195 Val Ser Tyr 210 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:3: Gly Thr Ala Trp Asn Gly Leu His Asp Val Met Asp 1 5 INFORMATION FOR SEQ ID NO:4: SEQUENCE CHARACTERISTICS: LENGTH: 102 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: not relevant (ii) MOLECULE TYPE: cDNA to mRNA (iii) HYPOTHETICAL: NO WO 98/14595 PCT/US97/17811 (ix) FEATURE: NAME/KEY: CDS LOCATION: 1..102 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:4: ATG AAG TTC TTC GCC ACC ATT GCT GCT CTC GTT GTG GGA GCT GTT GCT 48 Met Lys Phe Phe Ala Thr Ile Ala Ala Leu Val Val Gly Ala Val Ala 1 5 10 GCC CCA GTC GCA GAG GCT GAG GCT GAG GCC AGC AGC CCC ATG CTG ATC 96 Ala Pro Val Ala Glu Ala Glu Ala Glu Ala Ser Ser Pro Met Leu Ile 25 GAA CGT 102 Glu Arg INFORMATION FOR SEQ ID SEQUENCE CHARACTERISTICS: LENGTH: 34 amino acids TYPE: amino acid TOPOLOGY: linear (ii) MOLECULE TYPE: protein (xi) SEQUENCE DESCRIPTION: SEQ ID Met Lys Phe Phe Ala Thr Ile Ala Ala Leu Val Val Gly Ala Val Ala 1 5 10 Ala Pro Val Ala Glu Ala Glu Ala Glu Ala Ser Ser Pro Met Leu Ile 25 Glu Arg INFORMATION FOR SEQ ID NO:6: SEQUENCE CHARACTERISTICS: LENGTH: 5 amino acids TYPE: amino acid STRANDEDNESS: single TOPOLOGY: not relevant (ii) MOLECULE TYPE: peptide (iii) HYPOTHETICAL: NO FRAGMENT TYPE: internal (xi) SEQUENCE DESCRIPTION: SEQ ID NO:6: Asp Glu Ile Asp Ile 1 27a "Comprises/comprising" when used in this specification is taken to specify the presence of stated features, integers, steps or components but does not preclude the presence or addition of one or more other features, integers, steps, components or groups thereof.

DATED this 26t h day of April 2000 UNITVERSITY OF GEORGIA RESEARCH FOUNDATION INC.

WATERMARK PATENT AND TRADE MARK ATTORNEYS 290 BURWOOD ROAD HAWTHORN VICTORIA 3122

AUSTRALIA

LCG:KMH:VRH P8249AU00.DOC ee a S* *s

Claims (9)

1. A lichenase protein in substantially pure form. said protein being purified from a fungus or a culture thereof or from a recombinant DNA molecule having a fungal lichenase coding sequence, wherein said lichenase has an amino acid sequence selected from the group consisting of sequences as set forth in SEQ ID NO:2 from amino acid I through amino acid 216 or a functionally equivalent sequence with at least 70% amino acid sequence identity thereto and from amino acid -8 through amino acid 216 or a functionally equivalent sequence with at least 70% identity thereto or from amino acid -29 through amino acid 216 or a functionally equivalent sequence with at least 70% amino acid sequence identity thereto.

2. An isolated recombinant DNA molecule comprising a nucleotide sequence encoding a fungal lichenase of claim 1 wherein said lichenase has an amino acid sequence as given in SEQ !D NO:2 from amino acid I through amino acid 216 or a functionally equivalent sequence with at least identity thereto. from about amino acid -8 through amino acid 216 or a functionally equivalent sequence with at least 70% identity thereto, from amino acid -29 through amino acid 216 or a functionally equivalent sequence with at least 70% identity thereto.

3. The isolated recombinant DNA molecule of claim 2 wherein said lichenase is encoded by the nucleotide sequence as given in SEQ ID NO: 1 from nucleotide 210 through nucleotide 857 or a functionally equivalent sequence with at least 70% identity thereto, from nucleotide 186 through nucleotide 857 or a functionally equivalent sequence with at least 70% identity thereto, from nucleotide 123 through nucleotide 857 or a functionally equivalent sequence with at least about identity thereto.

4. The isolated recombinant DNA molecule of claim 3 or claim 4 wherein the lichenase nucleotide sequence as given in SEQ ID NO:1 or a sequence having at least 70% nucleotide sequence homologous thereto and encoding a functional lichenase additionally comprising DNA encoding a signal peptide immediately up stream of and operably linked to the nucleotide sequence encoding the mature lichenase protein.

The isolated recombinant DNA molecule of claim 5 wherein said signal peptide has an amino acid sequence as given in SEQ ID

6. A host cell comprising the recombinant DNA molecule of any of claims 2 to 5, wherein said host cell is a member of a species selected from the group consisting of Escherichia coli, Saccharomyces cerevisiae, Aspergillus, Penicillium, Trichoderma reesei, Penicillium, Aureobasidium, Strepromyces and Bacillus. AME 28 AMENDED SHEET

7. A method of using the recombinant DNA molecule of any of claims 2 to 5 to produce a lichenase in a host cell other than Orpinomyces sp. strain PC-2, said method comprising the steps of: a) infecting or transforming said host cell capable of expressing a lichenase coding region with a vector comprising a promoter active in said host cell wherein said promoter is operably linked to the coding region for said lichenase, and b) culturin the infected or transformed host cell under conditions suitable for expression of said lichenase coding sequence.

8. The method of claim 7 wherein said host cell is one of Escherichia coli, Saccharomnces cerevisiae. Aspergillus. Penicillium. Trichodenna reesei. Pichia, Streptomyces and Bacillus.

9. The method of claim 7 wherein said vector further comprises a nucleotide sequence encoding a signal peptide operably linked between said promoter and said coding region. The method of claim 7 wherein said signal peptide has an amino acid sequence as given in SEQ ID P3