WO2008016385A2 - Deacylase polypeptides, deacylase polynucleotides, and methods of use thereof - Google Patents

Abstract

The present invention provides isolated deacylase polypeptides; and deacylase nucleic acids. The present invention further provides methods for identifying inhibitors of a bacterial deacylase and that are candidates for treating a periodontal disease. The present invention further provides antibodies specific for a subject deacylase polypeptide. The present invention further provides diagnostic methods for detecting silent bacterial infections of the gum tissues; diagnostic methods for detecting conditions and disorders that are sequelae of periodontitis; and diagnostic methods for monitoring a patient's response to treatment for a periodontal disease.

Description

DEACYLASE POLYPEPTIDES, DEACYLASE POLYNUCLEOTIDES, AND METHODS OF USE THEREOF

CROSS-REFERENCE [0001] This application claims the benefit of U.S. Provisional Patent Application No.

60/760,556, filed January 20, 2006, which application is incorporated herein by reference in its entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

[0002] The U.S. government may have certain rights in this invention, pursuant to grant no.

DE 12768 awarded by the National Institutes of Health.

BACKGROUND

[0003] One important component of bacterial pathogenesis is the ability to coordinately express virulence genes in response to host microenvironments. With respect to lipopolysaccharide (LPS) it has been shown that Salmonella typhimurium significantly alters its lipid A structural content in response to host related environmental factors. Salmonella typhimurium contains a PhoP-PhoQ sensor kinase and transcriptional activator system which regulates genes required for intracellular survival and cationic peptide resistance. One of the genes regulated by the PhoP-PhoQ sensor kinase system is PagL, a deacylase that removes select fatty acids from the lipid A moiety of LPS. The removal of fatty acids from lipid A significantly alters the innate host response.

[0004] Periodontitis is a chronic inflammatory disease with stages of active bone loss and remission. Periodontitis affects approximately 85% of the adult population, and is a major cause of tooth loss. Periodontal tissue is highly vascularized, and thus accessible to serum soluble and cellular components of the innate host defense system. Porphyromonas gingivalis (formerly known as Bacteroides gingivalis) is gram-negative bacterium that is an important etiologic agent of human adult-type periodontitis. P. gingivalis releases copious amounts of outer membrane vesicles containing LPS, which can penetrate periodontal tissue, and thus participate in the destructive innate host response associated with disease. Literature

[0005] Geurtsen et. al.( 2005) Journal of Biological Chemistry 280: 88248-8259; GenBank

Accession No. NP_905755; Darveau et al. (2004) Infect. Immunity 72:5041-5051 ; Trent et al. (200I) J. Biol. Chem. 276:9083-9092; Coats et al. (2003) Infect. Immunity 71 :6799-6807; U.S. Patent No. 6,444,799; US Patent Publication No. 2002/0172976; Kumada et al. (1995) J. Bacteriol. 177:2098-2106; Tanamoto et al. (1997) J. Immunol. 158:4430-4439; Tanamoto et al. (1997) Microbiol. 143:63-71; Kumada et al. (1995) J. Bacteriol. 177:2098-2106.

SUMMARY OF THE INVENTION

[0006] The present invention provides isolated deacylase polypeptides; and deacylase nucleic acids. The present invention further provides methods for identifying inhibitors of a bacterial deacylase and that are candidates for treating a periodontal disease. The present invention further provides antibodies specific for a subject deacylase polypeptide. The present invention further provides diagnostic methods for detecting silent bacterial infections of the gum tissues; diagnostic methods for detecting conditions and disorders that are sequelae of periodontitis; and diagnostic methods for monitoring a patient's response to treatment for a periodontal disease.

BRIEF DESCRIPTION OF THE DRAWINGS

[0007] Figures IA and IB depict a nucleotide sequence encoding P. gingivalis deacylase

(Figure IA; SEQ ID NO: 1), and an amino acid sequence of P. gingivalis deacylase (Figure IB; SEQ ID NO:2).

[0008] Figures 2A-C depict an alignment of amino acid sequences of PG 1626 with deacylases from B. parapertussis, P. aeruginosa, R. solanacearum, and S. typhimurium. A consensus sequence is shown. Amino acids that are identical among the sequences are boxed. Amino acids shared by three or four sequences are in bold. Conserved amino acids are underlined.

[0009] Figures 3A-C depict an alignment of amino acid sequences of PGl 626 with putative hemin receptor amino acid sequences from Bacteroides species. A consensus sequence is shown. Amino acids that are identical among the sequences are boxed. Amino acids shared by two sequences are in bold. Conserved amino acids are underlined.

[0010] Figure 4 schematically depicts generation of a targeted gene disruption in P. gingivalis by double cross-over homologous recombination.

[0011] Figures 5A-F depict MALDI-TOF analyses of lipid As derived from a wild-type P. gingivalis 33277 and a P. gingivalis 33277-PG1626 knockout clone.

[0012] Figure 6 is a graph depicting the ability of wild-type vs mutant strains of P. gingivalis to stimulate NF-κB activation via a TLR4-dependent mechanism in transiently transfected HEK293 cells.

[0013] Figure 7 schematically depicts the structure of clones 1626wt, 1626ΔN, and 1626ΔC. [0014] Figure 8 schematically depicts generation of targeted knock-in in P. gingivalis by double cross-over homologous recombination. [0015] Figures 9A-F depict MALDI-TOF analysis of lipid As of wild-type P. gingivalis 33277

(9A), PG 1626 knockout (9B), and P. gingivalis clones bearing PGl 626 modified with a C- terminal FLAG epitope tag (9C-F), grown in the presence of high hemin concentrations. [0016] . Figure 10 depicts RT-PCR analysis of PG1626 RNA expression from P. gingivalis

33277 grown in the presence of 1 μg/ml or 20 μg/ml hemin.

[0017] Figure 11 depicts a model for bacterial interactions with the periodontium.

[0018] Figure 12 depicts MALDI-TOF analysis of P. gingivalis lipid A.

[0019] Figure 13 depicts the structures of the m/z 1690 lipid A substrate; and products m/z

1435 and m/z 1449 of deacylase action on m/z 1690. [0020] Figures 14A-D depict lipid A species produced by parental wild-type P. gingivalis

33277 (Figure 14A); PG1626 knock-out clone (Figure 14B); a PG1626 wild-type restored clone (Figure 14 C); and a PG 1626 C-terminal deletion 1 clone (Figure 14D). [0021] Figures 15A-G provide an alignment of nucleotide sequences: B. fragilis hemin receptor; B. thetaiotamicron hemin receptor; and PGl 626. A consensus sequence is also provided. Amino acids that are identical among the sequences are boxed. Amino acids shared by two sequences are in bold. Conserved amino acids are underlined. [0022] Figure 16 depicts a B. thetaiotamicron (hemin receptor) deacylase amino acid sequence

(SEQ ID NO:3). [0023] Figure 17 depicts a B. fragilis (hemin receptor) deacylase amino acid sequence (SEQ

ID NO:4).

DEFINITIONS

[0024] The terms "polynucleotide" and "nucleic acid," used interchangeably herein, refer to a polymeric form of nucleotides of any length, either ribonucleotides or deoxynucleotides. Thus, this term includes, but is not limited to, single-, double-, or multi-stranded DNA or RNA, genomic DNA, cDNA, DNA-RNA hybrids, or a polymer comprising purine and pyrimidine bases or other natural, chemically or biochemically modified, non-natural, or derivatized nucleotide bases.

[0025] The terms "peptide," "polypeptide," and "protein" are used interchangeably herein, and refer to a polymeric form of amino acids of any length, which can include coded and non- coded amino acids, chemically or biochemically modified or derivatized amino acids, and polypeptides having modified peptide backbones. [0026] The term "naturally-occurring" as used herein as applied to a nucleic acid, a cell, or an organism, refers to a nucleic acid, cell, or organism that is found in nature. For example, a polypeptide or polynucleotide sequence that is present in an organism that can be isolated from a source in nature and which has not been intentionally modified by a human in the laboratory is naturally occurring.

[0027] As used herein the term "isolated" is meant to describe a polynucleotide, a polypeptide, or a cell that is in an environment different from that in which the polynucleotide, the polypeptide, or the cell naturally occurs. An isolated genetically modified host cell may be present in a mixed population of genetically modified host cells.

[0028] As used herein, the term "exogenous nucleic acid" refers to a nucleic acid that is not normally or naturally found in and/or produced by a given bacterium, organism, or cell in nature. As used herein, the term "endogenous nucleic acid" refers to a nucleic acid that is normally found in and/or produced by a given bacterium, organism, or cell in nature. An "endogenous nucleic acid" is also referred to as a "native nucleic acid" or a nucleic acid that is "native" to a given bacterium, organism, or cell.

[0029] The term "heterologous nucleic acid," as used herein, refers to a nucleic acid wherein at least one of the following is true: (a) the nucleic acid is foreign ("exogenous") to (i.e., not naturally found in) a given host microorganism or host cell; (b) the nucleic acid comprises a nucleotide sequence that is naturally found in (e.g., is "endogenous to") a given host microorganism or host cell (e.g., the nucleic acid comprises a nucleotide sequence that is endogenous to the host microorganism or host cell) but is either produced in an unnatural (e.g., greater than expected or greater than naturally found) amount in the cell, or differs in sequence from the endogenous nucleotide sequence such that the same encoded protein (having the same or substantially the same amino acid sequence) as found endogenously is produced in an unnatural (e.g., greater than expected or greater than naturally found) amount in the cell; (c) the nucleic acid comprises two or more nucleotide sequences or segments that are not found in the same relationship to each other in nature, e.g., the nucleic acid is recombinant.

[0030] The term "heterologous polypeptide," as used herein, refers to a polypeptide that is not naturally associated with a given polypeptide.

[0031] "Recombinant," as used herein, means that a particular nucleic acid (DNA or RNA) is the product of various combinations of cloning, restriction, and/or ligation steps resulting in a construct having a structural coding or non-coding sequence distinguishable from endogenous nucleic acids found in natural systems. Generally, DNA sequences encoding the structural coding sequence can be assembled from cDNA fragments and short oligonucleotide linkers, or from a series of synthetic oligonucleotides, to provide a synthetic nucleic acid which is capable of being expressed from a recombinant transcriptional unit contained in a cell or in a cell-free transcription and translation system. Such sequences can be provided in the form of an open reading frame uninterrupted by internal non- translated sequences, or introns, which are typically present in eukaryotic genes. Genomic DNA comprising the relevant sequences can also be used in the formation of a recombinant gene or transcriptional unit. Sequences of non- translated DNA may be present 5' or 3' from the open reading frame, where such sequences do not interfere with manipulation or expression of the coding regions, and may indeed act to modulate production of a desired product by various mechanisms (see "DNA regulatory sequences," below).

[0032] Thus, e.g., the term "recombinant" polynucleotide or "recombinant" nucleic acid refers to one which is not naturally occurring, e.g., is made by the artificial combination of two otherwise separated segments of sequence through human intervention. This artificial combination is often accomplished by either chemical synthesis means, or by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques. / Such is done to replace a codon with a redundant codon encoding the same or a conservative amino acid, while typically introducing or removing a sequence recognition site. Alternatively, it is performed to join together nucleic acid segments of desired functions to generate a desired combination of functions. This artificial combination is often accomplished by either chemical synthesis means, or by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques.

[0033] Similarly, the term "recombinant" polypeptide refers to a polypeptide which is not naturally occurring, e.g., is made by the artificial combination of two otherwise separated segments of amino sequence through human intervention. Thus, e.g., a polypeptide that comprises a heterologous amino acid sequence is recombinant.

[0034] By "construct" or "vector" is meant a recombinant nucleic acid, generally recombinant

DNA, which has been generated for the purpose of the expression and/or propagation of a specific nucleotide sequence(s), or is to be used in the construction of other recombinant nucleotide sequences.

[0035] The terms "DNA regulatory sequences," "control elements," and "regulatory elements," used interchangeably herein, refer to transcriptional and translational control sequences, such as promoters, enhancers, polyadenylation signals, terminators, protein degradation signals, and the like, that provide for and/or regulate expression of a coding sequence and/or production of an encoded polypeptide in a host cell. [0036] The term "transformation" is used interchangeably herein with "genetic modification" and refers to a permanent or transient genetic change induced in a cell following introduction of new nucleic acid (i.e., DNA exogenous to the cell). Genetic change ("modification") can be accomplished either by incorporation of the new DNA into the genome of the host cell (such that the exogenous DNA is genomically integrated), or by transient or stable maintenance of the new DNA as an episomal element. Where the cell is a eukaryotic cell, a permanent genetic change is generally achieved by introduction of the DNA into the genome of the cell. In prokaryotic cells, permanent changes can be introduced into the chromosome or via extrachromosomal elements such as plasmids and expression vectors, which may contain one or more selectable markers to aid in their maintenance in the recombinant host cell. Suitable methods of genetic modification include viral infection, transfection, conjugation, protoplast fusion, electroporation, particle gun technology, calcium phosphate precipitation, direct microinjection, and the like. The choice of method is generally dependent on the type of cell being transformed and the circumstances under which the transformation is taking place (i.e. in vitro, ex vivo, or in vivo). A general discussion of these methods can be found in Ausubel, et al, Short Protocols in Molecular Biology, 3rd ed., Wiley & Sons, 1995.

[0037] "Operably linked" refers to a juxtaposition wherein the components so described are in a relationship permitting them to function in their intended manner. For instance, a promoter is operably linked to a coding sequence if the promoter affects its transcription or expression. As used herein, the terms "heterologous promoter" and "heterologous control regions" refer to promoters and other control regions that are not normally associated with a particular nucleic acid in nature. For example, a "transcriptional control region heterologous to a coding region" is a transcriptional control region that is not normally associated with the coding region in nature.

[0038] A "host cell," as used herein, denotes an in vivo or in vitro eukaryotic cell, a prokaryotic cell, or a cell from a multicellular organism (e.g., a cell line) cultured as a unicellular entity, which eukaryotic or prokaryotic cells can be, or have been, used as recipients for a nucleic acid (e.g., an expression vector that comprises a nucleotide sequence encoding all or part of a deacylase), and include the progeny of the original cell which has been genetically modified by the nucleic acid. It is understood that the progeny of a single cell may not necessarily be completely identical in morphology or in genomic or total DNA complement as the original parent, due to natural, accidental, or deliberate mutation. A "recombinant host cell" (also referred to as a "genetically modified host cell") is a host cell into which has been introduced a heterologous nucleic acid, e.g., an expression vector. For example, a subject prokaryotic host cell is a genetically modified prokaryotic host cell (e.g., a bacterium), by virtue of introduction into a suitable prokaryotic host cell a heterologous nucleic acid, e.g., an exogenous nucleic acid that is foreign to (not normally found in nature in) the prokaryotic host cell, or a recombinant nucleic acid that is not normally found in the prokaryotic host cell; and a subject eukaryotic host cell is a genetically modified eukaryotic host cell, by virtue of introduction into a suitable eukaryotic host cell a heterologous nucleic acid, e.g., an exogenous nucleic acid that is foreign to the eukaryotic host cell, or a recombinant nucleic acid that is not normally found in the eukaryotic host cell.

[0039] "Bacteroides" are well known in the art. See, e.g., Shah, H. N. 1992. The genus

Bacteroides and related taxa, p. 3593-3607. hi A. Balows, H. G. Truper, M. Dworkin, W. Harder, and K.-H. Schleifer (ed.), The Prokaryotes, 2nd ed, vol. 4. Springer- Verlag, New York. Bacteroides include B. fragilis, B. thetaiotaomicron, B. vulgatus, B. ovatus, B. distasonis, B. uniformis, B. stercoris, B. eggerthii, B. merdae, B. caccae, and Tanner ella forsythia (previously Bacteroides forsythus; see, Maiden et al. (2003) Int 7 J. Systematic and Evolutionary Microbiol. 53:2111-2112). Bacteroides include pathogenic Bacteroides, including oral pathogens; and Bacteroides resident in the intestine.

[0040] The term "conservative amino acid substitution" refers to the interchangeability in proteins of amino acid residues having similar side chains. For example, a group of amino acids having aliphatic side chains consists of glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having aliphatic-hydroxyl side chains consists of serine and threonine; a group of amino acids having amide-containing side chains consists of asparagine and glutamine; a group of amino acids having aromatic side chains consists of phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic side chains consists of lysine, arginine, and histidine; and a group of amino acids having sulfur-containing side chains consists of cysteine and methionine. Exemplary conservative amino acids substitution groups are: valine-leucine-isoleucine, phenylalanine-tyrosine, lysine-arginine, glutamic acid-aspartic acid, alanine-valine, and asparagine-glutamine.

[0041] A polynucleotide or polypeptide has a certain percent "sequence identity" to another polynucleotide or polypeptide, meaning that, when aligned, that percentage of bases or amino acids are the same, and in the same relative position, when comparing the two sequences. Sequence similarity can be determined in a number of different manners. To determine sequence identity, sequences can be aligned using the methods and computer programs, including BLAST, available over the world wide web at ncbi.nlm.nih.gov/BLAST. See, e.g., Altschul et al. (1990), J. MoI. Biol. 215:403-10. Another alignment algorithm is FASTA, available in the Genetics Computing Group (GCG) package, from Madison, Wisconsin, USA, a wholly owned subsidiary of Oxford Molecular Group, Inc. Other techniques for alignment are described in Methods in Enzymology, vol. 266: Computer Methods for Macromolecular Sequence Analysis (1996), ed. Doolittle, Academic Press, Inc., a division of Harcourt Brace & Co., San Diego, California, USA. Of particular interest are alignment programs that permit gaps in the sequence. The Smith-Waterman is one type of algorithm that permits gaps in sequence alignments. See Meth. MoI. Biol. 70: 173-187 (1997). Also, the GAP program using the Needleman and Wunsch alignment method can be utilized to align sequences. See J. MoI. Biol. 48: 443-453 (1970).

[0042] A nucleic acid is "hybridizable" to another nucleic acid, such as a cDNA, genomic

DNA, or RNA, when a single stranded form of the nucleic acid can anneal to the other nucleic acid under the appropriate conditions of temperature and solution ionic strength. Hybridization and washing conditions are well known and exemplified in Sambrook, J., Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor (1989), particularly Chapter 11 and Table 11.1 therein; and Sambrook, J. and Russell, W., Molecular Cloning: A Laboratory Manual, Third Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor (2001). The conditions of temperature and ionic strength determine the "stringency" of the hybridization. Stringency conditions can be adjusted to screen for moderately similar fragments, such as homologous sequences from distantly related organisms, to highly similar fragments, such as genes that duplicate functional enzymes from closely related organisms.

[0043] Hybridization conditions and post-hybridization washes are useful to obtain the desired determine stringency conditions of the hybridization. One set of illustrative post-hybridization washes is a series of washes starting with 6 x SSC (where SSC is 0.15 M NaCl and 15 mM citrate buffer), 0.5% SDS at room temperature for 15 minutes, then repeated with 2 x SSC, 0.5% SDS at 45°C for 30 minutes, and then repeated twice with 0.2 x SSC, 0.5% SDS at 50°C for 30 minutes. Other stringent conditions are obtained by using higher temperatures in which the washes are identical to those above except for the temperature of the final two 30 minute washes in 0.2 x SSC, 0.5% SDS, which is increased to 60°C. Another set of highly stringent conditions uses two final washes in 0.1 x SSC, 0.1% SDS at 65°C. Another example of stringent hybridization conditions is hybridization at 50°C or higher and 0. IxSSC (15 mM sodium chloride/1.5 mM sodium citrate). Another example of stringent hybridization conditions is overnight incubation at 42⁰C in a solution: 50% formamide, 5 x SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5 x Denhardt's solution, 10% dextran sulfate, and 20 μg/ml denatured, sheared salmon sperm DNA, followed by washing the filters in 0.1 x SSC at about 65°C. Stringent hybridization conditions and post- hybridization wash conditions are hybridization conditions and post-hybridization wash conditions that are at least as stringent as the above representative conditions.

[0044] Hybridization requires that the two nucleic acids contain complementary sequences, although depending on the stringency of the hybridization, mismatches between bases are possible. The appropriate stringency for hybridizing nucleic acids depends on the length of the nucleic acids and the degree of complementation, variables well known in the art. The greater the degree of similarity or homology between two nucleotide sequences, the greater the value of the melting temperature (Tm) for hybrids of nucleic acids having those sequences. The relative stability (corresponding to higher Tm) of nucleic acid hybridizations decreases in the following order: RNA:RNA, DNA:RNA, DNA:DNA. For hybrids of greater than 100 nucleotides in length, equations for calculating Tm have been derived (see Sambrook et al., supra, 9.50-9.51). For hybridizations with shorter nucleic acids, i.e., oligonucleotides, the position of mismatches becomes more important, and the length of the oligonucleotide determines its specificity (see Sambrook et al., supra, 11.7-11.8). Typically, the length for a hybridizable nucleic acid is at least about 10 nucleotides. Illustrative minimum lengths for a hybridizable nucleic acid are: at least about 15 nucleotides; at least about 20 nucleotides; and at least about 30 nucleotides. Furthermore, the skilled artisan will recognize that the temperature and wash solution salt concentration may be adjusted as necessary according to factors such as length of the probe.

[0045] A "biological sample" encompasses a variety of sample types obtained from an individual and can be used in a diagnostic or monitoring assay. The definition encompasses blood and other liquid samples of biological origin, solid tissue samples such as a biopsy specimen or tissue cultures or cells derived therefrom and the progeny thereof. The definition also includes samples that have been manipulated in any way after their procurement, such as by treatment with reagents, solubilization, or enrichment for certain components, such as polynucleotides or polypeptides. The term "biological sample" encompasses a clinical sample, and also includes cells in culture, cell supernatants, cell lysates, serum, plasma, biological fluid, and tissue samples.

[0046] As used herein, the term "target nucleic acid region" or "target nucleic acid" or "target molecules" refers to a nucleic acid molecule with a "target sequence" to be detected (e.g., by amplification). The target nucleic acid may be either single-stranded or double-stranded and may or may not include other sequences besides the target sequence (e.g., the target nucleic acid may or may not include nucleic acid sequences upstream or 5' flanking sequence, may or may not include downstream or 3' flanking sequence, and in some embodiments may not include either upstream (5') or downstream (3') nucleic acid sequence relative to the target sequence. Where detection is by amplification, these other sequences in addition to the target sequence may or may not be amplified with the target sequence.

[0047] The term "target sequence" or "target nucleic acid sequence" refers to the particular nucleotide sequence of the target nucleic acid to be detected (e.g., through amplification). The target sequence may include a probe-hybridizing region contained within the target molecule with which a probe will form a stable hybrid under desired conditions. The "target sequence" may also include the complexing sequences to which the oligonucleotide primers complex and be extended using the target sequence as a template. Where the target nucleic acid is originally single-stranded, the term "target sequence" also refers to the sequence complementary to the "target sequence" as present in the target nucleic acid. If the "target nucleic acid" is originally double-stranded, the term "target sequence" refers to both the plus (+) and minus (-) strands. Moreover, where sequences of a "target sequence" are provided herein, it is understood that the sequence may be either DNA or RNA. Thus where a DNA sequence is provided, the RNA sequence is also contemplated and is readily provided by substituting "T" of the DNA sequence with "U" to provide the RNA sequence.

[0048] The term "primer" or "oligonucleotide primer" as used herein, refers to an oligonucleotide which acts to initiate synthesis of a complementary nucleic acid strand when placed under conditions in which synthesis of a primer extension product is induced, e.g., in the presence of nucleotides and a polymerization-inducing agent such as a DNA or RNA polymerase and at suitable temperature, pH, metal concentration, and salt concentration. Primers are generally of a length compatible with its use in synthesis of primer extension products, and are usually are in the range of between 8 to 100 nucleotides (nt) in length, such as 10 to 75, 15 to 60, 15 to 40, 18 to 30, 20 to 40, 21 to 50, 22 to 45, 25 to 40 nt, and so on, more typically in the range of between 18-40, 20-35, 21-30 nucleotides long, and any length between the stated ranges. Typical primers can be in the range of between 10-50 nucleotides long, such as 15-45, 18-40, 20-30, 21-25 and so on, and any length between the stated ranges. In some embodiments, the primers are usually not more than about 10, 12, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, or 70 nucleotides in length.

[0049] Primers are usually single-stranded for maximum efficiency in amplification, but may alternatively be double-stranded. If double-stranded, the primer is usually first treated to separate its strands before being used to prepare extension products. This denaturation step is typically effected by heat, but may alternatively be carried out using alkali, followed by neutralization. Thus, a "primer" is complementary to a template, and complexes by hydrogen bonding or hybridization with the template to give a primer/template complex for initiation of synthesis by a polymerase, which is extended by the addition of covalently bonded bases linked at its 3' end complementary to the template in the process of DNA synthesis.

[0050] A "primer pair" as used herein refers to first and second primers having nucleic acid sequence suitable for nucleic acid-based amplification of a target nucleic acid. Such primer pairs generally include a first primer having a sequence that is the same or similar to that of a first portion of a target nucleic acid, and a second primer having a sequence that is complementary to a second portion of a target nucleic acid to provide for amplification of the target nucleic acid or a fragment thereof. Reference to "first" and "second" primers herein is arbitrary, unless specifically indicated otherwise. For example, the first primer can be designed as a "forward primer" (which initiates nucleic acid synthesis from a 5' end of the target nucleic acid) or as a "reverse primer" (which initiates nucleic acid synthesis from a 5' end of the extension product produced from synthesis initiated from the forward primer). Likewise, the second primer can be designed as a forward primer or a reverse primer.

[0051] As used herein, the term "probe" or "oligonucleotide probe", used interchangeable herein, refers to a structure comprised of a polynucleotide, as defined above, that contains a nucleic acid sequence complementary to a nucleic acid sequence present in the target nucleic acid analyte (e.g., a nucleic acid amplification product). The polynucleotide regions of probes may be composed of DNA, and/or RNA, and/or synthetic nucleotide analogs. Probes are generally of a length compatible with its use in specific detection of all or a portion of a target sequence of a target nucleic acid, and are usually are in the range of between 8 to 100 nucleotides in length, such as 8 to 75, 10 to 74, 12 to 72, 15 to 60, 15 to 40, 18 to 30, 20 to 40, 21 to 50, 22 to 45, 25 to 40, and so on, more typically in the range of between 18-40, 20-35, 21-30 nucleotides long, and any length between the stated ranges. The typical probe is in the range of between 10-50 nucleotides long, such as 15-45, 18-40, 20-30, 21-28, 22-25 nt and so on, and any length between the stated ranges. In some embodiments, the primers are usually not more than about 10, 12, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, or 70 nucleotides in length.

[0052] Probes contemplated herein include probes that include a detectable label. As used herein, the terms "label" and "detectable label" refer to a molecule capable of detection, including, but not limited to, radioactive isotopes, fluorescers, chemiluminescers, chromophores, enzymes, enzyme substrates, enzyme cofactors, enzyme inhibitors, chromophores, dyes, metal ions, metal sols, ligands (e.g., biotin, avidin, strepavidin or haptens) and the like. The term "fluorescer" refers to a substance or a portion thereof which is capable of exhibiting fluorescence in the detectable range.

[0053] The terms "hybridize" and "hybridization" refer to the formation of complexes between nucleotide sequences which are sufficiently complementary to form complexes via Watson- Crick base pairing. Where a primer "hybridizes" with target (template), such complexes (or hybrids) are sufficiently stable to serve the priming function required by, e.g., the DNA polymerase to initiate DNA synthesis.

[0054] The term "stringent conditions" refers to conditions under which a primer will hybridize preferentially to, or specifically bind to, its complementary binding partner, and to a lesser extent to, or not at all to, other sequences. Put another way, the term "stringent hybridization conditions" as used herein refers to conditions that are compatible to produce duplexes on an array surface between complementary binding members, e.g., between probes and complementary targets in a sample, e.g., duplexes of nucleic acid probes, such as DNA probes, and their corresponding nucleic acid targets that are present in the sample, e.g., their corresponding mRNA analytes present in the sample.

[0055] The term "assessing" includes any form of measurement, and includes determining if an element is present or not. The terms "determining," "measuring," "evaluating," "assessing," and "assaying" are used interchangeably and includes quantitative and qualitative determinations. Assessing may be relative or absolute. "Assessing the presence of includes determining the amount of something present, and/or determining whether it is present or absent. As used herein, the terms "determining," "measuring," and "assessing," and "assaying" are used interchangeably and include both quantitative and qualitative determinations.

[0056] The term "binds specifically," in the context of antibody binding, refers to high avidity and/or high affinity binding of an antibody to a specific polypeptide i.e., epitope of a polypeptide, e.g., a subject deacylase. For example, antibody binding to an epitope on a specific a subject deacylase or fragment thereof is stronger than binding of the same antibody to any other epitope, particularly those which may be present in molecules in association with, or in the same sample, as the specific polypeptide of interest, e.g., binds more strongly to a specific subject deacylase polypeptide than to any other deacylase epitopes so that by adjusting binding conditions the antibody binds almost exclusively to the specific subject deacylase epitope and not to any other deacylase epitope, or to any other polypeptide which does not comprise the epitope. Antibodies that bind specifically to a polypeptide may be capable of binding other polypeptides at a weak, yet detectable, level (e.g., 10% or less of the binding shown to the polypeptide of interest). Such weak binding, or background binding, is readily discernible from the specific antibody binding to a subject deacylase polypeptide, e.g. by use of appropriate controls. In general, specific antibodies bind to a given polypeptide with a binding affinity of 10^"7 M or more, e.g., 10^"8 M or more (e.g., 10^~9 M, 10^"10 M, 10^"11 M, etc.). In general, an antibody with a binding affinity of 10^"6 M or less is not useful in that it will not bind an antigen at a detectable level using conventional methodology currently used.

[0057] Before the present invention is further described, it is to be understood that this invention is not limited to particular embodiments described, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only by the appended claims.

[0058] Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limit of that range and any other stated or intervening value in that stated range, is encompassed within the invention. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges, and are also encompassed within the invention, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the invention.

[0059] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can also be used in the practice or testing of the present invention, the preferred methods and materials are now described. All publications mentioned herein are incorporated herein by reference to disclose and describe the methods and/or materials in connection with which the publications are cited.

[0060] It must be noted that as used herein and in the appended claims, the singular forms "a,"

"and," and "the" include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to "a deacylase polypeptide" includes a plurality of such polypeptides and reference to "the deacylase nucleic acid" includes reference to one or more deacylase nucleic acids and equivalents thereof known to those skilled in the art, and so forth. It is further noted that the claims may be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as "solely," "only" and the like in connection with the recitation of claim elements, or use of a "negative" limitation.

[0061] The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention. Further, the dates of publication provided may be different from the actual publication dates which may need to be independently confirmed.

DETAILED DESCRIPTION

[0062] The present invention provides isolated deacylase polypeptides; and deacylase nucleic acids. The present invention further provides methods for identifying inhibitors of a bacterial deacylase and that are candidates for treating a periodontal disease. The present invention further provides antibodies specific for a subject deacylase polypeptide. The present invention further provides diagnostic methods for detecting silent bacterial infections of the gum tissues; diagnostic methods for detecting conditions and disorders that are sequelae of periodontitis; and diagnostic methods for monitoring a patient's response to treatment for a periodontal disease.

[0063] A role for the deacylase in general pathogenesis is illustrated in Figure 11, which depicts a model for bacterial interactions with the periodontium. P. gingivalis releases outer membrane vesicles containing LPS, which can penetrate periodontal tissue, and participate in the destructive innate host response associated with disease. An increase in local concentrations of hemin results in increased activity of P, gingivalis deacylase, which is present in the cell wall and which modifies lipid A structures in the LPS of the cell wall. Modification of the penta-acylated lipid A structures into tetra-acylated lipid A structures allows the bacterium to at least partially evade immune responses. Under high hemin concentrations, the LPS presents mostly tetra-acylated lipid A.

[0064] MALDI-TOF analysis of the lipid A substrate and products of the P. gingivalis deacylase is provided in Figure 12. The peak designated "1690" is a penta-acylated lipid A substrate. The peaks designated "1435" and "1449" are tetra-acylated products of deacylase action on the lipid A substrate. Figure 13 depicts the structures of the m/z 1690 lipid A substrate; and products m/z 1435 and m/z 1449 of deacylase action on m/z 1690. ISOLATED POLYPEPTIDES

[0065] The present invention provides isolated deacylase polypeptides; as well as fragments of isolated deacylase polypeptides. The term "deacylase polypeptide" includes full-length deacylase polypeptides; fusion proteins comprising a deacylase polypeptides; and fragments of a deacylase polypeptide (including fragments that retain deacylase activity (but, for example, lack hemin-binding) and fragment that retain hemin-binding activity but lack deacylase activity).

[0066] In some embodiments, a subject deacylase polypeptide differs in amino acid sequence by at least one amino acid from the amino acid sequence set forth in SEQ ID NO:2. In some embodiments, the naturally-occurring amino acid sequence set forth in SEQ ID NO:2 is specifically excluded. Homologs or proteins (or fragments thereof) that vary in sequence from the amino acid sequence set forth in SEQ ID NO:2 at least about 75%, at least about 80%, at least about 90%, at least about 95%, at least about 97%, at least about 98%, or at least about 99% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO: 2, and/or to a hemin-binding region and/or a deacylase active site (as described in more detail below). Percent amino acid sequence identity is readily determined using known programs, e.g., MegAlign, DNAstar (1998) clustal algorithm as described in D. G. Higgins and P.M. Sharp, "Fast and Sensitive multiple Sequence Alignments on a Microcomputer," (1989) CABIOS, 5: 151-153. (Parameters used are ktuple 1, gap penalty 3, window, 5 and diagonals saved 5). In certain embodiments, homologs of interest have much higher sequence identity, e.g., 75%, 80%, 85%, 90% or higher (e.g., 98%, 99%, 99.5%, 99.8%, 99.9%).

[0067] In some embodiments, a subject deacylase polypeptide differs in amino acid sequence by at least one amino acid from the amino acid sequence set forth in SEQ ID NO:3 or SEQ ID NO:4 (as shown in Figures 16 and 17, respectively). In some embodiments, the naturally- occurring amino acid sequence set forth in SEQ ID NO:3 or SEQ ID NO:4 is specifically excluded. Homologs or proteins (or fragments thereof) that vary in sequence from the amino acid sequence set forth in SEQ ID NO:3 or SEQ ID NO:4 at least about 75%, at least about 80%, at least about 90%, at least about 95%, at least about 97%, at least about 98%, or at least about 99% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO: 3 or SEQ ID NO:4, and/or to a hemin-binding region and/or a deacylase active site (as described in more detail below). Percent amino acid sequence identity is readily determined using known programs, e.g., MegAlign, DNAstar (1998) clustal algorithm as described in D. G. Higgins and P.M. Sharp, "Fast and Sensitive multiple Sequence Alignments on a Microcomputer," (1989) CABIOS, 5: 151-153. (Parameters used are ktuple 1, gap penalty 3, window, 5 and diagonals saved 5). In certain embodiments, homologs of interest have much higher sequence identity, e.g., 75%, 80%, 85%, 90% or higher (e.g., 98%, 99%, 99.5%, 99.8%, 99.9%). [0068] In some embodiments, a subject deacylase protein is isolated, e.g., present in a non- naturally occurring environment. In certain embodiments, the subject proteins are provided as purified proteins, where by purified is meant that the protein is present in a composition that is substantially free of proteins other than a subject protein, where by substantially free is meant that less than 90 %, usually less than 60 % and more usually less than 50 % of the composition is made up of proteins other than a subject deacylase protein.

[0069] The proteins may also be provided substantially free of other proteins and other naturally occurring biologic molecules, such as oligosaccharides, lipopolysaccharides, lipids, polynucleotides and fragments thereof, and the like, where the term "substantially free" in this instance means that less than 70 %, usually less than 60% and more usually less than 50 % of the composition containing the isolated protein is some other naturally occurring biological molecule. In certain embodiments, the proteins are present in substantially pure form, where by "substantially pure form" is meant at least 95%, usually at least 97% and more usually at least 99% pure.

[0070] For those proteins of the subject invention that are naturally occurring proteins, the proteins are present in a non-naturally occurring environment, e.g., are separated from their naturally occurring environment. In certain embodiments, the subject proteins are present in a composition that is enriched for the subject protein as compared to its naturally occurring environment. For example, purified protein is provided, where by purified is meant that the protein is present in a composition that is substantially free of non-deacylase proteins, where by substantially free is meant that less than 90 %, usually less than 60 % and more usually less than 50 % of the composition is made up of non-deacylase proteins. A subject deacylase protein may also be present as an isolate, by which is meant that the protein is substantially free of other proteins and other naturally occurring biologic molecules, such as oligosaccharides, polynucleotides and fragments thereof, and the like, where the term "substantially free" in this instance means that less than 70 %, usually less than 60% and more usually less than 50 % of the composition containing the isolated protein is some other naturally occurring biological molecule. In certain embodiments, the proteins are present in substantially pure form, where by "substantially pure form" is meant at least 95% pure, at least 97% pure, or at least 99% pure.

[0071] In certain embodiments, a subject deacylase polypeptide is a fusion protein, e.g., a fusion deacylase polypeptide comprises a deacylase polypeptide and a fusion partner. The fusion partner is a heterologous polypeptide, e.g., a polypeptide other than a deacylase polypeptide. Suitable fusion partners include, but are not limited to, immunological tags such as epitope tags, including, but not limited to, hemagglutinin, FLAG, and the like; proteins that provide for a detectable signal, including, but not limited to, fluorescent proteins, enzymes (e.g., β-galactosidase, luciferase, horse radish peroxidase, alkaline phosphatase, etc.), and the like; polypeptides that facilitate purification or isolation of the fusion protein, e.g., metal ion binding polypeptides such as polyhistidine (e.g., 6His) tags, glutathione-S-transferase, and the like; polypeptides that provide for subcellular localization; and polypeptides that provide for secretion from a cell. Suitable fluorescent protein fusion partners include, but are not limited to, a green fluorescent protein (GFP), including, but not limited to, a GFP derived from Aequoria victoria or a derivative thereof, a number of which are commercially available; a GFP from a species such as Renilla reniformis, Renilla mulleri, or Ptilosarcus guernyi, as described in, e.g., WO 99/49019 and Peelle et al. (2001) J. Protein Chem. 20:507-519; any of a variety of fluorescent and colored proteins from Anthozoan species, as described in, e.g., Matz et al. (1999) Nature Biotechnol. 17:969-973, U.S. Patent Publication No. 2002/0197676, or U.S. Patent Publication No. 2005/0032085; and the like.

[0072] In some embodiments, a subject deacylase fusion protein comprises a heterologous protein ("fusion partner") covalently linked to the N-terminus of a subject deacylase protein. In other embodiments, a subject deacylase fusion protein comprises a heterologous protein covalently linked to the C-terminus of a subject deacylase protein. In still other embodiments, a subject deacylase protein comprises a heterologous protein inserted internally within the deacylase protein (e.g., between the hemin binding domain and the deacylase active site).

[0073] In some embodiments, the deacylase polypeptide is detectably labeled. The detectable label can be any suitable detectable label, such as a radionuclide, a immunodetectable epitope and/or fluorescent polypeptide provided in a heterologous polypeptide attached to the deacylase polypeptide (e.g., as described above).

[0074] Fragments of a deacylase are also provided. Suitable fragments include biologically active fragments and/or fragments corresponding to functional domains; and including fusions of the fragments to other proteins or parts thereof. Fragments of interest will typically be at least about 10 amino acids (aa) in length, at least about 50 aa in length, or at least about 250 aa in length or longer, and will generally not exceed about 500 aa in length, where the fragment will have a stretch of amino acids that is identical to the subject protein of at least about 10 aa, at least about 15 aa, or at least about 50 aa in length. In some embodiments, the subject polypeptides are about 25 aa, about 50 aa, about 75 aa, about 100 aa, about 125 aa, about 150 aa, about 200 aa, about 210 aa, about 220 aa, about 230 aa, about 250 aa, or about 270 aa in length. In some embodiments, a protein fragment retains all or substantially all of a biological property of a full-length deacylase protein (e.g., hemin binding; deacylase activity (e.g., removal of a fatty acid chain from a lipid A substrate)). In some embodiments, a subject polypeptide comprises the hemin-binding portion of a deacylase polypeptide, e.g., a hemin-binding polypeptide comprising from about amino acid 1 to about amino acid 290, from about amino acid 1 to about amino acid 270, from about amino acid 1 to about amino acid 250, from about amino acid 10 to about amino acid 290, from about amino acid 10 to about amino acid 270, or from about amino acid 10 to about amino acid 250 of the amino acid sequence set forth in any one of SEQ ID NO:2 (depicted in Figure IB), SEQ ID NO:3 (B. thetaiotamicron hemin binding protein; Figure 16), and SEQ ID NO:4 (B.fragilis hemin binding protein; Figure 17). In some embodiments, a subject polypeptide comprises the hemin-binding portion of a deacylase polypeptide, e.g., a hemin-binding polypeptide comprising from about 10 to about 15, from about 15 to about 25, from about 25 to about 50, from about 50 to about 75, from about 75 to about 100, from about 100 to about 150, from about 150 to about 200, or from about 200 to about 250 contiguous amino acids of amino acids 1 to about 270 of the amino acid sequence set forth in any one of SEQ ID NO:2 , SEQ ID NO:3, and SEQ ID NO:4. In some embodiments, a subject polypeptide comprises the hemin- binding portion of a deacylase polypeptide, e.g., a hemin-binding polypeptide comprising an amino acid sequence that shares at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or at least about 98% amino acid sequence identity with an amino acid sequence of from about 10 to about 15, from about 15 to about 25, from about 25 to about 50, from about 50 to about 75, from about 75 to about 100, from about 100 to about 150, from about 150 to about 200, or from about 200 to about 250 contiguous amino acids of amino acids 1 to about 270 of the amino acid sequence set forth in any one of SEQ ID NO:2 , SEQ ID NO:3, and SEQ ID NO:4. In some embodiments, a subject polypeptide comprises the hemin-binding portion of a deacylase polypeptide, e.g., a hemin-binding polypeptide comprising from about amino acid 1 to about amino acid 290, from about amino acid 1 to about amino acid 270, from about amino acid 1 to about amino acid 250, from about amino acid 10 to about amino acid 290, from about amino acid 10 to about amino acid 270, or from about amino acid 10 to about amino acid 250 of an amino acid sequence that shares at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or at least about 98% amino acid sequence identity with at least the hemin-binding portion of the amino acid sequence set forth in SEQ ID NO:2, SEQ ID NO:3, or SEQ ID NO:4. In certain of these embodiments, the polypeptide will lack the deacylase active site that carries out removal of a fatty acid chain from a lipid A substrate. [0076] In some embodiments, a subject deacylase polypeptide is a fusion protein comprising at least a hemin-binding portion of a deacylase polypeptide, as described above, and a fusion partner, where suitable fusion partners include those discussed above. In some embodiments, a subject deacylase fusion protein comprises a heterologous protein ("fusion partner") covalently linked to the N-terminus of at least a hemin-binding portion of a deacylase polypeptide. In other embodiments, a subject deacylase fusion protein comprises a heterologous protein covalently linked to the C-terminus of at least a hemin-binding portion of a deacylase polypeptide.

[0077] In some embodiments, a subject polypeptide comprises the deacylase active site of a deacylase polypeptide, e.g. a polypeptide comprising from about amino acid 270 to about amino acid 554, from about amino acid 280 to about amino acid 554, from about amino acid 290 to about amino acid 554, from about amino acid 300 to about amino acid 554, from about amino acid 270 to about amino acid 450, from about amino acid 280 to about amino acid 450, from about amino acid 290 to about amino acid 450, of the amino acid sequence set forth in SEQ ID NO:2. In some embodiments, a subject polypeptide comprises the deacylase active site of a deacylase polypeptide, e.g. a polypeptide comprising from about amino acid 270 to about amino acid 534, from about amino acid 280 to about amino acid 534, from about amino acid 290 to about amino acid 534, from about amino acid 300 to about amino acid 534, from about amino acid 270 to about amino acid 450, from about amino acid 280 to about amino acid 450, from about amino acid 290 to about amino acid 450, of the amino acid sequence set forth in SEQ ID NO:3. In some embodiments, a subject polypeptide comprises the deacylase active site of a deacylase polypeptide, e.g. a polypeptide comprising from about amino acid 270 to about amino acid 527, from about amino acid 280 to about amino acid 534, from about amino acid 290 to about amino acid 527, from about amino acid 300 to about amino acid 527, from about amino acid 270 to about amino acid 450, from about amino acid 280 to about amino acid 450, from about amino acid 290 to about amino acid 450, of the amino acid sequence set forth in SEQ ID NO:4.

[0078] In some embodiments, a subject polypeptide comprises the deacylase active site of a deacylase polypeptide, e.g. a deacylase active site polypeptide comprising from about 10 to about 15, from about 15 to about 25, from about 25 to about 50, from about 50 to about 75, from about 75 to about 100, from about 100 to about 150, from about 150 to about 200, or from about 200 to about 250 contiguous amino acids of amino acids 270 to 554 of SEQ ID NO:2, or of amino acids 270 to 534 of SEQ ID NO:3, or of amino acids 270 to 527 of SEQ ID NO:4. In some embodiments, a subject polypeptide comprises the deacylase active site of a deacylase polypeptide, e.g. a deacylase active-site polypeptide comprising from about 10 to about 15, from about 15 to about 25, from about 25 to about 50, from about 50 to about 75, from about 75 to about 100, from about 100 to about 150, from about 150 to about 200, or from about 200 to about 250 contiguous amino acids of an amino acid sequence that shares at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or at least about 98% amino acid sequence identity with at least the deacylase active site domain of SEQ ID NO:2 (e.g., amino acids 270 to 554 of SEQ ID NO:2), SEQ ID NO:3 (e.g., amino acids 270 to 534 of SEQ ID NO:3), or SEQ ID NO:4 (e.g., amino acids 270 to 527 of SEQ ID NO:4).

[0079] The "deacylase active site" (also referred to as a "deacylase domain") is the portion of the deacylase polypeptide that catalyzes the removal of a fatty acid chain from a lipid A substrate. In general the deacylase active site is defined by the consensus sequence HXSN, where the amino acid sequence of the P. gingivalis deacylase active site is HTSN as set out in SEQ ID NO:2.

[0080] In some embodiments, a subject polypeptide comprising the deacylase active site of a deacylase polypeptide, e.g. from about amino acid 270 to about amino acid 554, from about amino acid 280 to about amino acid 554, from about amino acid 290 to about amino acid 554, from about amino acid 300 to about amino acid 554, from about amino acid 270 to about amino acid 450, from about amino acid 280 to about amino acid 450, from about amino acid 290 to about amino acid 450, of an amino acid sequence that shares at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or at least about 98% amino acid sequence identity with at least the deacylase active site of the amino acid sequence set forth in SEQ ID NO:2. SEQ ID NO:3, or SEQ ID NO:4. In certain of these embodiments, the polypeptide will lack the hemin-binding portion of the deacylase polypeptide.

[0081] In some embodiments, a subject deacylase polypeptide is a fusion protein comprising at least a deacylase active site of a deacylase polypeptide, as described above, and a fusion partner, where suitable fusion partners include those discussed above. A heterologous protein is in some embodiments covalently linked to the N-terminus of at least a deacylase active site of a deacylase polypeptide. A heterologous protein is in some embodiments covalently linked to the C -terminus of at least a deacylase active site of a deacylase polypeptide.

[0082] The subject deacylase proteins are in many embodiments synthetically or recombinantly produced. For example, the subject proteins may be derived by recombinant means, e.g. by expressing a recombinant gene or nucleic acid coding sequence encoding the protein of interest in a suitable host, as described above. Any convenient protein purification procedures may be employed, where suitable protein purification methodologies are described in Guide to Protein Purification, (Deuthser ed.) (Academic Press, 1990). For example, a lysate may be prepared from the original source and purified using high performance liquid chromatography, size exclusion chromatography, gel electrophoresis, affinity chromatography, and the like. DEACYLASE NUCLEIC ACIDS

[0083] The present invention provides deacylase nucleic acids. In some embodiments, a subject deacylase nucleic acid comprises a nucleotide sequence that encodes a deacylase polypeptide that exhibits one or more activities, and is useful in the production of isolated deacylase polypeptide. Activities exhibited by the encoded deacylase polypeptide include one or more of: 1 ) hemin binding; and 2) enzymatic cleavage of a fatty acid chain from a lipid A substrate. In other embodiments, a subject deacylase nucleic acid finds use in detecting the presence of deacylase nucleic acids in a biological sample, and therefore finds use in certain embodiments in diagnostic methods, e.g., methods for detecting pathogenic oral bacteria.

[0084] In some embodiments, a subject deacylase nucleic acid comprises a nucleotide sequence encoding any of the deacylase polypeptides described above. In some embodiments, a subject deacylase nucleic acid comprises a nucleotide sequence having at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or at least about 98%, or greater, nucleotide sequence identity to the nucleotide sequence set forth in SEQ ID NO:1 (P. gingivalis deacylase nucleic acid; Figure IA), SEQ ID NO:5 (B. thetaiotamicron deacylase nucleic acid; Figure 15A-G), or SEQ ID NO:6 (B.fragilis deacylase nucleic acid; Figures 15A-G). In some embodiments, the nucleotide sequence set forth in one or more of SEQ ID NO:1, SEQ ID NO:5, and SEQ ID NO:6 is specifically excluded. Sequence similarity is calculated based on a reference sequence, which may be a subset of a larger sequence, such as a conserved motif, coding region, flanking region, etc. A reference sequence will usually be at least about 18 nt long, more usually at least about 30 nt long, and may extend to the complete sequence that is being compared. Algorithms for sequence analysis are known in the art, such as BLAST, described in Altschul et al. (1990), J. MoI. Biol. 215:403-10 (using default settings, i.e. parameters w=4 and T=I 7). The sequences provided herein are essential for recognizing related and homologous nucleic acids in database searches.

[0085] In some embodiments, a subject deacylase nucleic acid comprises a nucleotide sequence that encodes all or a fragment of a subject deacylase, including nucleic acids encoding a deacylase domain and/or a hemin-binding domain as set out above, as well as fusion proteins as described herein. For example, in some embodiments, a subject deacylase nucleic acid comprises a nucleotide sequence that encodes a fragment of from about amino acid 1 to about amino acid 270, or from about amino acid 271 to about amino acid 554 of the amino acid sequence set forth in SEQ ID NO:2 In other embodiments, a subject nucleic acid comprises a nucleotide sequence that encodes a fragment of from about amino acid 1 to about amino acid 270, or from about amino acid 271 to about amino acid 534 of the amino acid sequence set forth in SEQ ID NO:3. In other embodiments, a subject nucleic acid comprises a nucleotide sequence that encodes a fragment of from about amino acid 1 to about amino acid 270, or from about amino acid 271 to about amino acid 527 of the amino acid sequence set forth in SEQ ID NO:4. In some embodiments, a subject deacylase nucleic acid comprises a nucleotide sequence that encodes a deacylase fusion protein, as described above.

[0086] Also provided are nucleic acids that hybridize to a nucleic acid having the nucleotide sequence set forth in SEQ ID NO:1, SEQ ID NO:5, or SEQ ID NO:6, or to a fragment of such a nucleic acid, under stringent conditions. An example of stringent hybridization conditions is hybridization at 5O⁰C or higher and 0. IxSSC (15 mM sodium chloride/1.5 mM sodium citrate). Another example of stringent hybridization conditions is overnight incubation at 42°C in a solution: 50 % formamide, 5 x SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH7.6), 5 x Denhardt's solution, 10% dextran sulfate, and 20 μg/ml denatured, sheared salmon sperm DNA, followed by washing the filters in 0.1 x SSC at about 65⁰C. Stringent hybridization conditions are hybridization conditions that are at least as stringent as the above representative conditions, where conditions are considered to be at least as stringent if they are at least about 80% as stringent, typically at least about 90% as stringent as the above specific stringent conditions. Other stringent hybridization conditions are known in the art and may also be employed to identify nucleic acids of this particular embodiment of the invention. Recombinant nucleic acids

[0087] In some embodiments, a subject deacylase nucleic acid is a recombinant nucleic acid.

In some embodiments, a subject recombinant nucleic acid comprises a nucleotide sequence encoding a subject deacylase polypeptide (e.g., a full-length deacylase polypeptide, a fragment of a deacylase polypeptide, or a deacylase fusion protein), where the deacylase-encoding nucleotide sequence is operably linked to one or more control elements. In certain embodiments, the control element is a promoter. In some embodiments, the promoter is one that is functional in a prokaryotic cell. In some embodiments, the promoter is an inducible promoter. [0088] Suitable promoters for use in prokaryotic host cells (including, e.g., PGl 626-knock-out bacterial host cells) include, but are not limited to, a bacteriophage T7 RNA polymerase promoter; a trp promoter; a lac operon promoter; a hybrid promoter, e.g., a lac/tac hybrid promoter, a tac/trc hybrid promoter, a trp/lac promoter, a T7/lac promoter; a trc promoter; a tac promoter, and the like; an araBAD promoter; in vivo regulated promoters, such as an ssaG promoter or a related promoter (see, e.g., U.S. Patent Publication No. 20040131637), apagC promoter (Pulkkinen and Miller, J. BacterioL, 1991 : 173(1): 86-93; Alpuche-Aranda et al., PNAS, 1992; 89(21): 10079-83), a nirB promoter (Harborne et al. (1992) MoI. Micro. 6:2805- 2813), and the like {see, e.g., Dunstan et al. (1999) Infect. Immun. 67:5133-5141; McKelvie et al. (2004) Vaccine 22:3243-3255; and Chatfield et al. (1992) Biotechnol. 10:888-892); a sigma70 promoter, e.g., a consensus sigma70 promoter (see, e.g., GenBank Accession Nos. AX798980, AX798961, and AX798183); a stationary phase promoter, e.g., a dps promoter, an spv promoter, and the like; a promoter derived from the pathogenicity island SPI-2 (see, e.g., WO96/17951); an actA promoter (see, e.g., Shetron-Rama et al. (2002) Infect. Immun. 70:1087-1096); an rpsM promoter (see, e.g., Valdivia and Falkow (1996). MoI. Microbiol. 22:367-378); a tet promoter (see, e.g., Hillen,W. and Wissmann,A. (1989) In Saenger,W. and Heinemann,U. (eds), Topics in Molecular and Structural Biology, Protein— Nucleic Acid Interaction. Macmillan, London, UK, Vol. 10, pp. 143-162); an SP6 promoter (see, e.g., Melton et al. (1984) Nucl. Acids Res. 12:7035-7056); and the like. In some embodiments, a subject recombinant nucleic acid will include a lac I repressor coding region operably linked to a strong promoter.

[0089] Non-limiting examples of suitable eukaryotic promoters (promoters functional in eukaryotic cells) include CMV immediate early, HSV thymidine kinase, early and late SV40, LTRs from retrovirus, and mouse metallothionein-I. In some embodiments, e.g., for expression in a yeast cell, a suitable promoter is a constitutive promoter such as an ADHl promoter, a PGKl promoter, an ENO promoter, a PYKl promoter and the like; or a regulatable promoter such as a GALl promoter, a GALlO promoter, an ADH2 promoter, a PHO5 promoter, a CUPl promoter, a GAL7 promoter, a MET25 promoter, a MET3 promoter, and the like. Selection of the appropriate vector and promoter is well within the level of ordinary skill in the art. The expression vector may also contain a ribosome binding site for translation initiation and a transcription terminator. The expression vector may also include appropriate sequences for amplifying expression.

[0090] In yeast, a number of vectors containing constitutive or inducible promoters may be used. For a review see, Current Protocols in Molecular Biology, Vol. 2, 1988, Ed. Ausubel, et al., Greene Publish. Assoc. & Wiley Interscience, Ch. 13; Grant, et al., 1987, Expression and Secretion Vectors for Yeast, in Methods in Enzymology, Eds. Wu & Grossman, 31987, Acad. Press, N.Y., Vol. 153, pp.516-544; Glover, 1986, DNA Cloning, Vol. II, IRL Press, Wash., D. C, Ch. 3; and Bitter, 1987, Heterologous Gene Expression in Yeast, Methods in Enzymology, Eds. Berger & Kimmel, Acad. Press, N.Y., Vol. 152, pp. 673-684; and The Molecular Biology of the Yeast Saccharomyces, 1982, Eds. Strathern et al., Cold Spring Harbor Press, VoIs. I and II. A constitutive yeast promoter such as ADH or LEU2 or an inducible promoter such as GAL may be used (Cloning in Yeast, Ch. 3, R. Rothstein In: DNA Cloning Vol. 11, A Practical Approach, Ed. DM Glover, 1986, IRL Press, Wash., D.C.). Alternatively, vectors may be used which promote integration of foreign DNA sequences into the yeast chromosome.

[0091] Inducible promoters suitable for use in any desired host cell are well known in the art.

Suitable inducible promoters include, but are not limited to, the pL of bacteriophage λ; Plac; Ptrp; Ptac (Ptrp-lac hybrid promoter); an isopropyl-beta-D-thiogalactopyranoside (IPTG)- inducible promoter, e.g., a lacZ promoter; a tetracycline-inducible promoter; an arabinose inducible promoter, e.g., P_BAD (see, e.g., Guzman et al. (1995) J. Bacteriol. 177:4121-4130); a xylose-inducible promoter, e.g., Pxyl (see, e.g., Kim et al. (1996) Gene 181 :71-76); a GALl promoter; a tryptophan promoter; a lac promoter; a T7/lac promoter; an alcohol-inducible promoter, e.g., a methanol-inducible promoter, an ethanol-inducible promoter; a raffinose- inducible promoter; a heat-inducible promoter, e.g., heat inducible lambda P_L promoter, a promoter controlled by a heat-sensitive repressor (e.g., CI857-repressed lambda-based expression vectors; see, e.g., Hoffmann et al. (1999) FEMS Microbiol Lett. 177(2):327-34); and the like.

[0092] In some embodiments, the inducible promoter is a tightly regulated promoter, e.g., the basal level of transcription (e.g., the level of transcription in the absence of the inducer) is very low, e.g., at nearly undetectable or undetectable levels. Thus, e.g., where the deacylase polypeptide is toxic or growth inhibiting, and the deacylase-encoding nucleotide sequence is under control of a tightly regulated inducible promoter, the amount of deacylase polypeptide that is produced in a cell is low or undetectable, or at least does not substantially inhibit the growth of the cell, or is otherwise substantially not toxic to the cell. Constructs

[0093] The present invention further provides recombinant vectors ("constructs") comprising a subject nucleic acid. In some embodiments, a subject recombinant vector provides for amplification of a subject nucleic acid. In some embodiments, a subject recombinant vector provides for production of an encoded deacylase polypeptide in a prokaryotic cell, in a eukaryotic cell, or in a cell-free transcription/translation system. Suitable expression vectors include, but are not limited to, baculovirus vectors, bacteriophage vectors, plasmids, phagemids, cosmids, fosmids, bacterial artificial chromosomes, viral vectors (e.g. viral vectors based on vaccinia virus, poliovirus, adenovirus, adeno-associated virus, SV40, herpes simplex virus, and the like), Pl -based artificial chromosomes, yeast plasmids, yeast artificial chromosomes, and any other vectors specific for specific hosts of interest (such as prokaryotic cells, yeast, or other eukaryotic cells).

[0094] Certain types of vectors allow a subject nucleic acid to be amplified. Other types of vectors are necessary for efficient introduction of a subject nucleic acid to cells and their stable expression once introduced. Any vector capable of accepting a subject nucleic acid is contemplated as a suitable recombinant vector for the purposes of the invention. The vector may be any circular or linear length of DNA that either integrates into the host genome or is maintained in episomal form. Vectors may require additional manipulation or particular conditions to be efficiently incorporated into a host cell (e.g., many expression plasmids), or can be part of a self-integrating, cell specific system (e.g., a recombinant virus). The vector is in some embodiments functional in a prokaryotic cell, where such vectors function to propagate the recombinant vector and/or provide for expression of a subject nucleic acid. The vector is in some embodiments functional in a eukaryotic cell, where the vector will in many embodiments be an expression vector.

[0095] Numerous suitable expression vectors are known to those of skill in the art, and many are commercially available. The following vectors are provided by way of example; for bacterial host cells: pBluescript (Stratagene, San Diego, Calif.), pQE vectors (Qiagen), pBluescript plasmids, pNH vectors, lambda-ZAP vectors (Stratagene); pTrc (Amann et al., Gene, 69:301-315 (1988)); pTrc99a, pKK223-3, pDR540, and pRIT2T (Pharmacia); for eukaryotic host cells: pXTl, pSG5 (Stratagene), pSVK3, pBPV, pMSG, and pSVLSV40 (Pharmacia).

[0096] A subject recombinant vector will in many embodiments contain one or more selectable marker genes to provide a phenotypic trait for selection of transformed host cells. Suitable selectable markers include, but are not limited to, dihydrofolate reductase, neomycin resistance for eukaryotic cell culture; and tetracycline resistance, erythromycin resistance, or ampicillin resistance in prokaryotic host cells such as E. coli.

[0097] Generally, recombinant expression vectors will include origins of replication and selectable markers permitting transformation of the host cell, e.g., the ampicillin resistance gene of E. coli, the S. cerevisiae TRPl gene, etc.; and a promoter derived from a highly- expressed gene to direct transcription of the coding sequence. Such promoters can be derived from operons encoding glycolytic enzymes such as 3-phosphoglycerate kinase (PGK), α- factor, acid phosphatase, or heat shock proteins, among others.

[0098] In some embodiments, the recombinant construct is a plasmid. In some embodiments, the plasmid is a low copy number plasmid. In other embodiments, the plasmid is a medium copy number plasmid. In other embodiments, the plasmid is a high copy number plasmid. Low copy number plasmids generally provide for fewer than about 20 plasmid copies per cell. Medium copy number plasmids generally provide for from about 20 plasmid copies per cell to about 50 plasmid copies per cell, or from about 20 plasmid copies per cell to about 80 plasmid copies per cell. High copy number plasmids generally provide for from about 80 plasmid copies per cell to about 200 plasmid copies per cell, or more. In some embodiments, a nucleic acid comprising a nucleotide sequence encoding a deacylase is a high copy number plasmid vector comprising a nucleic acid comprising a nucleotide sequence encoding deacylase. Suitable high copy number plasmids include, but are not limited to, pUC vectors (e.g., pUC8, pUC18, pUC19, and the like), pBluescript vectors, pGEM vectors, and pTZ vectors.

[0099] In some embodiments, a subject construct is generated in vitro in a cell-free system, e.g., using standard methods involving one or more of a polymerase chain reaction, a cell-free ligation reaction (e.g., using a DNA ligase), etc.

Compositions

[00100] The present invention further provides compositions comprising a subject nucleic acid.

The present invention further provides compositions comprising a subject recombinant vector. Compositions comprising a subject nucleic acid or a subject expression vector will in many embodiments include one or more of: a salt, e.g., NaCl, MgCl, KCl, MgSO₄, etc.; a buffering agent, e.g., a Tris buffer, N-(2-Hydroxyethyl)piperazine-N'-(2-ethanesulfonic acid) (HEPES), 2-(N-Morpholino)ethanesulfonic acid (MES), 2-(N-Morpholino)ethanesulfonic acid sodium salt (MES), 3-(N-Morpholino)propanesulfonic acid (MOPS), N-tris[Hydroxymethyl]methyl-3- aminopropanesulfonic acid (TAPS), etc.; a solubilizing agent; a detergent, e.g., a non-ionic detergent such as Tween-20, etc.; a nuclease inhibitor; and the like. In some embodiments, a subject nucleic acid or a subject recombinant vector is lyophilized. Host cells

[00101] The present invention provides genetically modified host cells, e.g., host cells that have been genetically modified with a subject nucleic acid or a subject recombinant vector. In many embodiments, a subject genetically modified host cell is an in vitro host cell. In other embodiments, a subject genetically modified host cell is an in vivo host cell.

[00102] In other embodiments, the host cell is a prokaryotic cell. Suitable prokaryotic cells include, but are not limited to, any of a variety of laboratory strains of Escherichia coli, Lactobacillus sp., Salmonella sp., Shigella sp., and the like. See, e.g., Carrier et al. (1992) J. Immunol. 148:1176-1181 ; U.S. Patent No. 6,447,784; and Sizemore et al. (1995) Science 270:299-302. Examples of Salmonella strains which can be employed in the present invention include, but are not limited to, Salmonella typhi and S. typhimurium. Suitable Shigella strains include, but are not limited to, Shigella flexneri, Shigella sonnei, and Shigella disenteriae. Typically, the laboratory strain is one that is non-pathogenic. Non-limiting examples of other suitable bacteria include, but are not limited to, Bacillus subtilis, Pseudomonas pudita, Pseudomonas aeruginosa, Pseudomonas mevalonii, Rhodobacter sphaeroides, Rhodobacter capsulatus, Rhodospirillum rubrum, Rhodococcus sp., and the like. In some embodiments, the host cell is Escherichia coli.

[00103] In some embodiments, the prokaryotic host cell is a pathogenic oral bacterium. In some embodiments, the prokaryotic host cell is a Bacteroides species. In other embodiments, the prokaryotic host cell is Porphyromonas gingivalis.

[00104] In some embodiments, a subject genetically modified host cell is a prokaryotic host cell that is genetically modified with a subject nucleic acid, where the nucleic acid is a knock-out construct, resulting in a knock-out of an endogenous deacylase coding region, such that the genetically modified host cell does not synthesize endogenous deacylase. In some embodiments, a subject genetically modified host cell comprising a knock-out of an endogenous deacylase coding region produces penta-acylated lipid A, and does not produce tetra-acylated lipid A.

[00105] In some embodiments, the host cell is a eukaryotic cell. Suitable eukaryotic host cells include, but are not limited to, yeast cells, mammalian cells, insect cells, plant cells, fungal cells, and algal cells. Suitable eukaryotic host cells include, but are not limited to, Pichia pastoris, Pichia finlandica, Pichia trehalophila, Pichia koclamae, Pichia membranaefaciens, Pichia opuntiae, Pichia thermotolerans, Pichia salictaria, Pichia guercuum, Pichia pijperi, Pichia stiptis, Pichia methanolica, Pichia sp., Saccharomyces cerevisiae, Saccharomyces sp., Hansenula polymorpha, Kluyveromyces sp., Kluyveromyces lactis, Candida albicans, Aspergillus nidulans, Aspergillus niger, Aspergillus oryzae, Trichoderma reesei, Chrysosporium lucknowense, Fusarium sp., Fusarium gramineum, Fusarium venenatum, Neurospora crassa, Chlamydomonas reinhardtii, and the like. [00106] Suitable mammalian host cells include primary cells, immortalized cell lines, and the like. Suitable immortalized cell lines include cell lines derived from human, mouse, rat, hamster, non-human primates, etc. Suitable cell lines include, but are not limited to, NIH 3T3 cells (e.g., ATCC CRL-1658), HEK293T cells (e.g., ATCC CRL-1573), CHO cells (e.g., ATCC CCL-61), HeLa cells (e.g., ATCC CCL-2), and the like. Derivatives of such cell lines are also suitable for use. Many such cells are available from the American Type Culture Collection (ATCC).

[00107] To generate a subject genetically modified host cell, a subject nucleic acid or a subject recombinant construct is introduced stably or transiently into a parent host cell, using established techniques, including, but not limited to, electroporation, calcium phosphate precipitation, DEAE-dextran mediated transfection, liposome-mediated transfection, and the like. For stable transformation, a nucleic acid will generally further include a selectable marker, e.g., any of several well-known selectable markers such as neomycin resistance, ampicillin resistance, tetracycline resistance, chloramphenicol resistance, kanamycin resistance, and the like. Methods of producing a deacylase polypeptide

[00108] The present invention provides methods of producing a subject deacylase polypeptide.

The methods generally involve culturing a subject genetically modified host cell under conditions that favor production of the encoded deacylase; and recovering the deacylase so produced. Compositions comprising a subject genetically modified host cell

[00109] The present invention further provides compositions comprising a subject genetically modified host cell. A subject composition comprises a subject genetically modified host cell, and will in some embodiments comprise one or more further components, which components are selected based in part on the intended use of the genetically modified host cell. Suitable components include, but are not limited to, salts; buffers; stabilizers; protease-inhibiting agents; nuclease-inhibiting agents; cell membrane- and/or cell wall-preserving compounds, e.g., glycerol, dimethylsulfoxide, etc.; nutritional media appropriate to the cell; and the like. In some embodiments, the cells are lyophilized. Nucleic acid probes

[00110] In some embodiments, a subject deacylase nucleic acid is a nucleic acid probe that hybridizes to a target deacylase nucleic acid, e.g., hybridizes under stringent hybridization conditions to a target deacylase nucleic acid. Such nucleic acid probes are useful for detecting the presence of a bacterium, e.g., P. gingivalis, in a sample. Such probes can provide for detection of a target sequence contained in, for example, a nucleic acid encoding a hemin- binding domain of a deacylase, a deacylase active site of a deacylase, or both (e.g., using two probes). Nucleic acid probes are generally from about 12 nucleotides to about 150 nucleotides in length, e.g., from about 12 nt to about 15 nt, from about 15 nt to about 20 nt, from about 20 nt to about 50 nt, from about 50 nt to about 75 nt, from about 75 nt to about 100 nt, or from about 100 nt to about 150 nt in length. In some embodiments, a subject nucleic acid probe is immobilized on an insoluble support. In some embodiments, a subject nucleic acid probe comprises a detectable label.

[00111] The present invention provides a kit comprising a subject nucleic acid probe. In some embodiments, the kit will include components for carrying out nucleic acid hybridization. In some embodiments, the kit will include components for detecting a detectably labeled nucleic acid probe. In some embodiments, the kit will include positive and negative controls, where a positive control will include, e.g., a deacylase nucleic acid that hybridizes under stringent hybridization conditions to a nucleic acid probe in the kit; and where a negative control will include, e,g., an unrelated nucleic acid (e.g., an albumin-encoding nucleic acid) that does not hybridize under stringent hybridization conditions to the nucleic acid probe.

[00112] The present invention provides a kit comprising a first nucleic acid probe and a second nucleic acid probe, where the first nucleic acid probe hybridizes specifically to a P. gingivalis deacylase nucleic acid, and where the second nucleic acid probe hybridizes to a Porphyromonas gingivalis deacylase nucleic acid and to deacylase nucleic acid of at least one Bacteroides species. Such a composition is useful for detecting the presence of P. gingivalis specifically, and simultaneously detecting bacterial species other than P. gingivalis.

[00113] In some embodiments, the second nucleic acid probe hybridizes to a nucleotide sequence encoding the amino acid sequence HXSNXXIK.

[00114] In some embodiments, a subject nucleic acid probe comprises from about 10 to about

15, from about 15 to about 20, from about 20 to about 25, from about 25 to about 30, from about 30 to about 35, from about 35 to about 40, from about 40 to about 45, or from about 45 to about 50 contiguous nucleotides of a nucleotide sequence depicted in Figures 15A-G. In some embodiments, a subject nucleic acid probe comprises from about 10 to about 15, from about 15 to about 20, from about 20 to about 25, from about 25 to about 30, from about 30 to about 35, from about 35 to about 40, from about 40 to about 45, or from about 45 to about 50 contiguous nucleotides of the complement of a nucleotide sequence depicted in Figures 15A- G. Primer pairs

[00115] In some embodiments, the invention provides isolated nucleic acids that, when used as primers in a polymerase chain reaction, amplify a target deacylase polynucleotide. Generally, the nucleic acids are used in pairs in a polymerase chain reaction, where they are referred to as "forward" and "reverse" primers. The isolated nucleic acids that, when used as primers in a polymerase chain reaction, amplify a target deacylase polynucleotide, are from about 10 nucleotides (nt) to about 15 nt, from about 15 nt to about 20 nt, from about 20 nt to about 30 nt, from about 30 nt to about 40nt, or from about 40 nt to about 50 nt in length. The amplified deacylase polynucleotide is from about 20 to about 50, from about 50 to about 75, from about 75 to about 100, from about 100 to about 125, from about 125 to about 150, from about 150 to about 175, from about 175 to about 200, from about 200 to about 250, from about 250 to about 300, from about 300 to about 350 nucleotides in length.

[00116] In some embodiments, a subject pair of isolated nucleic acids ("primer pair") comprises a first nucleic acid and a second nucleic acid, each from about 10 to 50 nucleotides in length, where the first nucleic acid of the pair comprises a sequence of at least 10 contiguous nucleotides having 100% sequence identity to the nucleotide sequence of a subject deacylase- encoding nucleic acid, where the second nucleic acid molecule of the pair comprises a sequence of at least 10 contiguous nucleotides having 100% sequence identity to the reverse complement of the nucleotide sequence of the deacylase-encoding nucleic acid, and where the sequence of the second nucleic acid molecule is located 3' of the nucleotide of the first nucleic acid of the deacylase-encoding nucleic acid.

[00117] In some embodiments, a subject pair of isolated nucleic acids ("primer pair") comprises a first nucleic acid and a second nucleic acid, each from about 10 to 50 nucleotides in length, where the first nucleic acid of the pair comprises a sequence of at least 10 contiguous nucleotides having 100% sequence identity to the nucleotide sequence set forth in SEQ ID NO: 1, where the second nucleic acid molecule of the pair comprises a sequence of at least 10 contiguous nucleotides having 100% sequence identity to the reverse complement of the nucleotide sequence set forth in SEQ ID NO:1, and where the sequence of the second nucleic acid molecule is located 3' of the nucleotide of the first nucleic acid in SEQ ID NO:1.

[00118] In some embodiments, a subject nucleic acid primer comprises from about 10 to about

15, from about 15 to about 20, from about 20 to about 25, from about 25 to about 30, from about 30 to about 35, from about 35 to about 40, from about 40 to about 45, or from about 45 to about 50 contiguous nucleotides of a nucleotide sequence depicted in Figures 15A-G. In some embodiments, a subject nucleic acid primer comprises from about 10 to about 15, from about 15 to about 20, from about 20 to about 25, from about 25 to about 30, from about 30 to about 35, from about 35 to about 40, from about 40 to about 45, or from about 45 to about 50 contiguous nucleotides of the complement of a nucleotide sequence depicted in Figures 15A- G.

[00119] In some embodiments, a subject nucleic acid primer pair includes a first primer that comprises from about 10 to about 15, from about 15 to about 20, from about 20 to about 25, from about 25 to about 30, from about 30 to about 35, from about 35 to about 40, from about 40 to about 45, or from about 45 to about 50 contiguous nucleotides of a nucleotide sequence depicted in Figures 15A-G; and a second primer that comprises from about 10 to about 15, from about 15 to about 20, from about 20 to about 25, from about 25 to about 30, from about 30 to about 35, from about 35 to about 40, from about 40 to about 45, or from about 45 to about 50 contiguous nucleotides of the reverse complement of a nucleotide sequence depicted in Figures 15A-G.

[00120] It will be appreciated that primer pairs useful in the invention include a first primer having a sequence that is the same or similar to that of a deacylase nucleotide sequence provided herein, and a second primer having a sequence that is complementary to a deacylase sequence provided herein to provide for amplification of a deacylase target nucleic acid region described herein or a fragment thereof (e.g., the first primer is a "forward" primer and the second primer is a "reverse" primer). It will be further understood that primer pairs useful in the invention also include a first primer having a sequence that is complementary to that of a deacylase sequence provided herein, and a second primer having a sequence that is the same or similar to a deacylase sequence provided herein to provide for amplification of a deacylase target nucleic acid region described herein or a fragment thereof (e.g., the first primer is a "reverse" primer and the second primer is a "forward" primer). The primer nucleic acids are prepared using any known method, e.g., automated synthesis, and the like.

[00121] In some embodiments, the first and/or the second primer comprise a detectable label.

Suitable labels include fluorochromes, e.g. fluorescein isothiocyanate (FITC), rhodamine, Texas Red, phycoerythrin, allophycocyanin, 6-carboxyfluorescein (6-FAM), 2',7'-dimethoxy- 4',5'-dichloro-6-carboxyfluorescein (JOE), 6-carboxy-X-rhodamine (ROX), 6-carboxy- 2^t,4',7',4,7-hexachlorofluorescein (HEX), 5-carboxyfluorescein (5-FAM) or N,N,N',N'- tetramethyl-6-carboxyrhodarnine (TAMRA); radioactive labels, e.g. ³²P, ³⁵S, ³H; etc. The label may be a two stage system, where the amplified DNA is conjugated to biotin, haptens, etc. having a high affinity binding partner, e.g. avidin, specific antibodies, etc., where the binding partner is conjugated to a detectable label. The label may be conjugated to one or both of the primers. Alternatively, the pool of nucleotides used in the amplification is labeled, so as to incorporate the label into the amplification product. Target regions for primers and probes

[00122] Deacylase target regions that are suitable for amplification using a subject primer pair and/or for detection using a probe as described above, are in some embodiments deacylase targets that, when amplified and/or detected by specific hybridization, identify at least one of a P. gingivalis deacylase polynucleotide, and a deacylase polynucleotide of at least one additional bacterial species, e.g., a Bacteroides deacylase polynucleotide, a B. thetaiotamicron deacylase polynucleotide, a B. fragilis deacylase polynucleotide, a deacylase polynucleotide from pathogenic oral bacterium, etc. In other embodiments, a deacylase target region is a deacylase target that, when amplified by a subject primer pair and/or detected by specific hybridization using a probe, provides for specific detection of P. gingivalis, e.g., the target region and primer pairs (and/or probes) are chosen such that a P. gingivalis deacylase polynucleotide, but not a deacylase polynucleotide from a different species, is detected (e.g., by amplification and/or specific hybridization), e.g., to allow for distinguishing between a deacylase-encoding sequence of any of P. gingivalis and Bacteroides.

[00123] In some embodiments, a subject primer pair primes the synthesis of an amplification product in the presence of a target deacylase polynucleotide from P. gingivalis and at least one Bacteroides species (e.g., a Bacteroides oral pathogen species; a. Bacteroides species resident in the intestinal tract; B. thetaiotamicron, B. fragilis, etc.) Target deacylase sequences that provide for detection of a deacylase polynucleotide from P. gingivalis and at least one Bacteroides species (e.g., a Bacteroides oral pathogen species; B. thetaiotamicron, B. fragilis, etc.) include a stretch of from about 25 to about 50, from about 50 to about 75, from about 75 to about 100, from about 100 to about 125, from about 125 to about 150, from about 150 to about 175, from about 175 to about 200, from about 200 to about 225, from about 225 to about 250, or from about 250 to about 275 contiguous nucleotides of the sequence designated "consensus" sequence in Figures 15A-G.

[00124] In some embodiments, a subject primer pair provides for specific detection of a P. gingivalis deacylase polynucleotide, e.g., the primer pair does not substantially prime the synthesis of a nucleic acid other than a P. gingivalis deacylase polynucleotide. In some embodiments, a subject primer pair provides for specific detection of a B. fragilis deacylase polynucleotide, e.g., the primer pair does not substantially prime the synthesis of a nucleic acid other than a B. fragilis deacylase polynucleotide. In some embodiments, a subject primer pair provides for specific detection of a B. thetaiotamicron deacylase polynucleotide, e.g., the primer pair does not substantially prime the synthesis of a nucleic acid other than a B. thetaiotamicron deacylase polynucleotide. [00125] Target deacylase sequences that provide for specific detection of a P. gingivalis deacylase polynucleotide include the following: [00126] 1 ) a Target Region 1 , flanked by: a) 5 '- ATGAGG ATC AAGCCCTCTCTG AAAACG-

3' (SEQ ID NO: 16) and b) 5'-TCTTTCAACAATGGTGCTATCAATGACTAC-S ' (SEQ ID

NO: 17. Target Region 1 includes a region encoding the N-terminal portion of PGl 626. [00127] 2) a Target Region 2, flanked by: a) 5'-

TCTTTCAACAATGGTGCTATCAATGACTAC-3' (SEQ ID NO: 18) and b) 5'-

GC AATGAC AATGTCGTATCGCTTCTGA-S' (SEQ ID NO: 19). Target Region 2 includes a region encoding the C-terminal portion of PG 1626. [00128] 3) a Target Region 3, flanked by: a) 5'-ATGAGGATCAAGCCCTCTCTGAAAACG-

3' (SEQ ID NO:20) and b) 5'-GCAATGACAATGTCGTATCGCTTCTGA-S ' (SEQ ID

NO:21). Target Region 3 includes the entire PG1626 coding sequence. [00129] Suitable primer pairs for amplification of Target Region 1 include:

[00130] Primer pair 1 (Target Region 1 amplification):

[00131] 5'-ATGAGGATCAAGCCCTCTCTG-S' (forward primer; SEQ ID NO:22); and

[00132] 5'-TTGATAGCACCATTGTTGAAAGA-S ' (reverse primer; SEQ ID NO:23).

Amplification of a target nucleic acid with Primer pair 1 (Target Region 1 amplification) yields an approximately 842 base pair amplification product. [00133] Primer pair 2 (Target Region 1 amplification):

[00134] 5'-GCACAGAGCTTGGAGGTTCG-S' (forward primer; SEQ ID NO:24); and

[00135] 5'-GACATAACCGATACCCGTGA-S ' (reverse primer; SEQ ID NO:25).

Amplification of a target nucleic acid with Primer pair 2 (Target Region 1 amplification) yields an approximately 229 base pair amplification product.

[00136] Suitable primer pairs for amplification of Target Region 2 include:

[00137] Primer pair 1 (Target Region 2 amplification):

[00138] 5'-AATGGTGCTATCAATGACTAC-S ' (forward primer; SEQ ID NO:26); and

[00139] 5'-GAAGCGATACGACATTGTCATTGC-S' (reverse primer; SEQ ID NO:27).

Amplification of a target nucleic acid with Primer pair 1 (Target Region 2 amplification) yields an approximately 833 base pair amplification product. [00140] Primer pair 2 (Target Region 2 amplification):

[00141] 5'-TATCGGTATCGGAGCCATCT-3' (forward primer; SEQ ID NO:28); and [00142] 5'-TCATAATCCATACTGAGAAGGC-S ' (reverse primer; SEQ ID NO:29).

Amplification of a target nucleic acid with Primer pair 2 (Target Region 2 amplification) yields an approximately 284 base pair amplification product.

[00143] Suitable primer pairs for amplification of Target Region 3 include:

[00144] Primer pair 1 (Target Region 3 amplification):

[00145] 5'-ATGAGGATCAAGCCCTCTCTG-S ' (forward primer; SEQ ID NO:22); and

[00146] 5'-GAAGCGATACGACATTGTCATTGC-S ' (reverse primer; SEQ ID NO:27).

Amplification of a target nucleic acid with Primer pair 1 (Target Region 3 amplification) yields an approximately 1662 base pair amplification product.

[00147] Target deacylase nucleic acids that provide for specific detection of a B. fragilis deacylase polynucleotide include the following:

[00148] 1) a Target Region 4, flanked by: a) 5'-GCAAAGATTTAAATGGAACAGCT-S '

(SEQ ID NO:30); and b) 5'-ATCGATGGTCTTATGATAACAT-S ' (SEQ ID NO:31), including a nucleotide sequence encoding an N-terminal portion of B. fragilis deacylase.

[00149] 2) a Target Region 5, flanked by: a) 5'-GTTTTGACTTTAAGATGGGAGCTA-S '

(SEQ ID NO:32); and b) 5'-TAGCCATCGGTGCTGAATATG-S' (SEQ ID NO:33), including a nucleotide sequence encoding a C-terminal portion of B. fragilis deacylase.

[00150] Suitable primer pairs for amplification of Target Region 4 include:

[00151] 5'-GCAAAGATTTAAATGGAACAGCT-S ' (forward primer; SEQ ID NO:30); and

[00152] 5'-ATGTTATCATAAGACCATCGAT-S ' (reverse primer; SEQ ID NO:34). This exemplary Target Region 4-amplifying primer pair generates an approximately 221 -base pair amplification product with Target Region 4 as a target nucleic acid; and amplifies a nucleic acid encoding an N-terminal portion of B. fragilis deacylase nucleic acid.

[00153] Suitable primer pairs for amplification of Target Region 5 include:

[00154] 5'- GTTTTGACTTTAAGATGGGAGCTA-S' (forward primer; SEQ ID NO:32); and

[00155] 5'-CATATTCAGCACCGATGGCTA-S' (reverse primer; SEQ ID NO:35). This exemplary Target Region 5-amplifying primer pair generates an approximately 306-base pair amplification product with Target Region 5 as a target nucleic acid; and amplifies a nucleic acid encoding a C-terminal portion of B. fragilis deacylase nucleic acid.

[00156] Target deacylase nucleic acids that provide for specific detection of a B. thetaiotamicron deacylase polynucleotide include the following:

[00157] 1) a Target Region 6, flanked by: a) 5'-AGAAGGATTTGAATGGAACTGCC-S '

(SEQ ID NO:36); and b) 5'-GACTCGTGGATCATTTGATAATAT-S' (SEQ ID NO:37), including a nucleotide sequence encoding an N-terminal portion of B. thetaiotamicron deacylase.

[00158] 2) a Target Region 7, flanked by: a) 5 '-TTAAGTTTGGAGCTATCGTGCG-S ' (SEQ

ID NO:38); and b) 5'-TCGCTATTGGAGCAGAATATGAAT-S ' (SEQ ID NO:39), including a nucleotide sequence encoding a C-terminal portion of B. thetaiotamicron deacylase. [00159] Suitable primer pairs for amplification of Target Region 6 include:

[00160] 5'-AGAAGGATTTGAATGGAACTGCC-S ' (forward primer; SEQ ID NO:36); and

[00161] 5'-ATATTATCAAATGATCCACGAGTC-S' (reverse primer; SEQ ID NO:40). This exemplary Target Region 6-amplifying primer pair generates an approximately 221 -base pair amplification product with Target Region 6 as a target nucleic acid; and amplifies a nucleic acid encoding an N-terminal portion of B. thetaiotamicron deacylase nucleic acid. [00162] Suitable primer pairs for amplification of Target Region 7 include:

[00163] 5'- TTAAGTTTGGAGCTATCGTGCG-S' (forward primer; SEQ ID NO:38); and

[00164] 5'-ATTCATATTCTGCTCCAATAGCGA-S' (reverse primer; SEQ ID NO:41). This exemplary Target Region 7-amplifying primer pair generates an approximately 288-base pair amplification product with Target Region 7 as a target nucleic acid; and amplifies a nucleic acid encoding a C-terminal portion of B. thetaiotamicron deacylase nucleic acid.

Kits

[00165] The invention further provides a kit comprising a pair of nucleic acids (primer pairs), one or more probes, or both, where the primer pairs and probes are those as described above. The nucleic acids are present in a suitable storage medium, e.g., buffered solution, typically in a suitable container. The kit includes the primers and/or probes, and may further include a buffer; reagents (e.g., for polymerase chain reaction (e.g., deoxynucleotide triphosphates (dATP, dTTP, dCTP, and dGTP), a thermostable DNA polymerase, a buffer suitable for polymerase chain reaction, a solution containing Mg²⁺ ions (e.g., MgCl₂), and other components well known to those skilled in the art for carrying out a polymerase chain reaction)). The kit may further include instructions for use of the kit, which instructions may be provided in a variety of forms, e.g., as printed information, on a compact disc, and the like. The kit may further include reagents necessary for extraction of DNA (or mRNA) from a biological sample (e.g., gingival tissue, saliva, gingival cervicular fluid, etc.) from an individual. The kit may further include reagents necessary for reverse transcription of an mRNA, to make a cDNA copy of the mRNA.

[00166] The kit may further include positive and negative controls. An example of a positive control is a deacylase nucleic acid that includes a region that will be amplified by primer pairs included in the kit. An example of a negative control is a nucleic acid (e.g., an albumin- encoding nucleic acid) that will not be amplified by nucleic acid primers included in the kit. The kits are useful in diagnostic applications, as described in more detail below. For example, the kit is useful to determine whether a given DNA sample (or an mRNA sample) isolated from an individual comprises a deacylase nucleic acid.

[00167] A kit will in some embodiments provide a standard for normalization of a level of a deacylase polynucleotide to a standard, e.g., a level of a glucose-6-phosphate dehydrogenase polynucleotide (e.g, a G6PDH mRNA or cDNA copy of a G6PDH mRNA).

[00168] Exemplary kits include at least one primer, usually at least two primers (a 5' and a 3' primer), usually at least two primers and a probe, as described above. Kits may also contain instructions for using the kit to detect a P. gingivalis and/or Bacteroides spp. that produces a deacylase in a sample using the methods described above, including the above discussed PCR methods. Also included in the subject kits may be buffers, dNTPs, and controls, (e.g., positive and negative control nucleic acids) for performing the subject methods. Primers in the subject kits may be detectably labeled or unlabeled).

[00169] In some embodiments, a subject kit comprises one or more of the following: (a) a nucleic acid primer pair, as described above; (b) a first nucleic acid probe; and a second nucleic acid probe; where the first nucleic acid probe hybridizes specifically to a P. gingivalis deacylase nucleic acid; where the second nucleic acid probe hybridizes to a P. gingivalis deacylase nucleic acid and to a deacylase nucleic acid of at least one species other than P. gingivalis, e.g., to a deacylase nucleic acid of a Bacteroides species; and c) a combination of a nucleic acid primer pair as described above, and first and second nucleic acid probes, as described above and in (b), where at least one of the first and second nucleic acid probes hybridize to a target sequence amplified by the primer pair (and/or to an amplification product generated by the primer pair). ANTIBODIES SPECIFIC FOR A DEACYLASE POLYPEPTIDE

[00170] The present invention provides antibodies that bind specifically to a subject deacylase polypeptide. A subject antibody is useful for detecting a subject deacylase, and therefore finds use in certain embodiments in diagnostic methods, e.g., methods involving detection of pathogenic oral bacteria. In certain embodiments, a subject antibody is isolated, e.g., is in an environment other than its naturally-occurring environment. Suitable antibodies are obtained by immunizing a host animal with peptides comprising all or a portion of the subject protein. Suitable host animals include mouse, rat sheep, goat, hamster, rabbit, etc. The host animal will generally be from a different species than the immunogen where the immunogen is from a naturally occurring source, e.g., a bacterial species, where representative host animals include, but are not limited to, e.g., rabbits, goats, rats, mice, etc.

[00171] The immunogen may comprise the complete protein, or fragments and derivatives thereof. Generally, immunogens comprise all or a part of the protein, where these residues contain the post-translation modifications found on the native target protein. Immunogens are produced in a variety of ways known in the art, e.g., expression of cloned genes using conventional recombinant methods, preparation of fragments of a subject deacylase protein using well-known methods, etc.

[00172] For preparation of polyclonal antibodies, the first step is immunization of the host animal with the target protein, where the target protein will preferably be in substantially pure form, comprising less than about 1% contaminant. The immunogen may comprise the complete target protein, fragments or derivatives thereof. To increase the immune response of the host animal, the target protein may be combined with an adjuvant, where suitable adjuvants include alum, dextran, sulfate, large polymeric anions, and oil-and-water emulsions, e.g. Freund's adjuvant, Freund's complete adjuvant, and the like. The target protein may also be conjugated to synthetic carrier proteins or synthetic antigens. A variety of hosts may be immunized to produce the polyclonal antibodies. Such hosts include rabbits, guinea pigs, rodents, e.g. mice, rats, sheep, goats, and the like. The target protein is administered to the host, usually intradermally, with an initial dosage followed by one or more, usually at least two, additional booster dosages. Following immunization, the blood from the host will be collected, followed by separation of the serum from the blood cells. The Ig present in the resultant antiserum may be further fractionated using known methods, such as ammonium salt fractionation, DEAE chromatography, and the like.

[00173] Monoclonal antibodies are produced by conventional techniques. Generally, the spleen and/or lymph nodes of an immunized host animal provide a source of plasma cells. The plasma cells are immortalized by fusion with myeloma cells to produce hybridoma cells. Culture supernatant from individual hybridomas is screened using standard techniques to identify those producing antibodies with the desired specificity. Suitable animals for production of monoclonal antibodies include mouse, rat, hamster, guinea pig, rabbit, etc. The antibody may be purified from the hybridoma cell supematants or ascites fluid by conventional techniques, e.g. affinity chromatography using protein bound to an insoluble support, protein A sepharose, etc.

[00174] The antibody may be produced as a single chain, instead of the normal multimeric structure. Single chain antibodies are described in Jost et al. (1994) J.B.C. 269:26267-73, and others. DNA sequences encoding the variable region of the heavy chain and the variable region of the light chain are ligated to a spacer encoding at least about 4 amino acids of small neutral amino acids, including glycine and/or serine. The protein encoded by this fusion allows assembly of a functional variable region that retains the specificity and affinity of the original antibody.

[00175] Also provided are "artificial" antibodies, e.g., antibodies and antibody fragments produced and selected in vitro. In some embodiments, such antibodies are displayed on the surface of a bacteriophage or other viral particle. In many embodiments, such artificial antibodies are present as fusion proteins with a viral or bacteriophage structural protein, including, but not limited to, Ml 3 gene III protein. Methods of producing such artificial antibodies are well known in the art. See, e.g., U.S. Patent Nos. 5,516,637; 5,223,409; 5,658,727; 5,667,988; 5,498,538; 5,403,484; 5,571,698; and 5,625,033.

[00176] Antibody fragments, such as Fv, F(ab')₂ and Fab may be prepared by cleavage of the intact protein, e.g. by protease or chemical cleavage. Alternatively, a truncated gene is designed. For example, a chimeric gene encoding a portion of the F(ab')₂ fragment would include DNA sequences encoding the CHl domain and hinge region of the H chain, followed by a translational stop codon to yield the truncated molecule.

[00177] Expression vectors include plasmids, retroviruses, YACs, EBV derived episomes, and the like. A convenient vector is one that encodes a functionally complete human CH or CL immunoglobulin sequence, with appropriate restriction sites engineered so that any VH or VL sequence can be easily inserted and expressed. In such vectors, splicing usually occurs between the splice donor site in the inserted J region and the splice acceptor site preceding the human C region, and also at the splice regions that occur within the human CH exons. Polyadenylation and transcription termination occur at native chromosomal sites downstream of the coding regions. The resulting chimeric antibody may be joined to any strong promoter, including retroviral LTRs, e.g. SV-40 early promoter, (Okayama et al. (1983) MoI. Cell. Bio. 3:280), Rous sarcoma virus LTR (Gorman et al. (1982) P.N.A.S. 79:6777), and moloney murine leukemia virus LTR (Grosschedl et al. (1985) Cell 41 :885); native Ig promoters, etc.

[00178] A subject antibody will in some embodiments be detectably labeled, e.g., with a radioisotope, an enzyme which generates a detectable product, a fluorescent protein, a chromogenic protein, and the like. A subject antibody may be further conjugated to other moieties, such as members of specific binding pairs, e.g., biotin (member of biotin-avidin specific binding pair), and the like. A subject antibody may also be bound to a solid support, including, but not limited to, polystyrene plates or beads, magnetic beads, and the like. SCREENING METHODS

[00179] The present invention provides methods of identifying agents that inhibit an activity of a subject deacylase polypeptide, or of a deacylase polypeptide produced by a pathogenic oral bacterium.

[00180] The methods generally involve contacting a subject deacylase with a test agent, and determining the effect, if any, of the test agent on a deacylase activity. Deacylase activities include hemin binding and enzymatic activity (e.g., enzymatic removal of a fatty acid chain from a lipid A substrate).

[00181] A test agent of interest is one that inhibits deacylase enzymatic activity and/or hemin binding by at least about 10%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 80%, at least about 90%, or more, when compared to a control in the absence of the test agent. A test agent that inhibits deacylase enzymatic activity and/or hemin binding is a candidate agent for treating an infection by an oral bacterial pathogen, e.g., such a test agent is a candidate agent for treating gingivitis, periodontitis, etc.

[00182] The terms "candidate agent," "test agent," "agent," "substance," and "compound" are used interchangeably herein. Candidate agents encompass numerous chemical classes, e.g., synthetic, semi-synthetic, or naturally-occurring inorganic or organic molecules. Candidate agents include those found in large libraries of synthetic or natural compounds. For example, synthetic compound libraries are commercially available from Maybridge Chemical Co. (Trevillet, Cornwall, UK), ComGenex (South San Francisco, CA), and MicroSource (New Milford, CT). A rare chemical library is available from Aldrich (Milwaukee, Wis.). Alternatively, libraries of natural compounds in the form of bacterial, fungal, plant and animal extracts are available from Pan Labs (Bothell, WA) or are readily producible.

[00183] Candidate agents may be small organic or inorganic compounds having a molecular weight of more than 50 and less than about 10,000 daltons, less than about 5,000 daltons, or less than about 2,500 daltons. Candidate agents may comprise functional groups necessary for structural interaction with proteins, particularly hydrogen bonding, and may include at least an amine, carbonyl, hydroxyl or carboxyl group, and may contain at least two of the functional chemical groups. The candidate agents may comprise cyclical carbon or heterocyclic structures and/or aromatic or polyaromatic structures substituted with one or more of the above functional groups. Candidate agents are also found among biomolecules including peptides, saccharides, fatty acids, steroids, purines, pyrimidines, derivatives, structural analogs or combinations thereof.

[00184] Assays of the invention include controls, where suitable controls include a sample (e.g., a sample comprising a deacylase protein, or a cell that synthesizes deacylase) in the absence of the test agent. Generally a plurality of assay mixtures is run in parallel with different agent concentrations to obtain a differential response to the various concentrations. Typically, one of these concentrations serves as a negative control, i.e. at zero concentration or below the level of detection.

[00185] Where the screening assay is a binding assay, one or more of the molecules may be joined to a label, where the label can directly or indirectly provide a detectable signal. Various labels include radioisotopes, fluorescers, chemiluminescers, enzymes, specific binding molecules, particles, e.g. magnetic particles, and the like. Specific binding molecules include pairs, such as biotin and streptavidin, digoxin and antidigoxin etc. For the specific binding members, the complementary member would normally be labeled with a molecule that provides for detection, in accordance with known procedures.

[00186] A variety of other reagents may be included in the screening assay. These include reagents like salts, neutral proteins, e.g. albumin, detergents, etc that are used to facilitate optimal protein-protein binding and/or reduce non-specific or background interactions. Reagents that improve the efficiency of the assay, such as protease inhibitors, nuclease inhibitors, anti-mi crobial agents, etc. may be used. The components of the assay mixture are added in any order that provides for the requisite binding or other activity. Incubations are performed at any suitable temperature, typically between 4⁰C and 4O⁰C. Incubation periods are selected for optimum activity, but may also be optimized to facilitate rapid high-throughput screening. Typically between 0.1 hour and 1 hour will be sufficient.

[00187] The screening methods may be designed a number of different ways, where a variety of assay configurations and protocols may be employed, as are known in the art. For example, one of the components may be bound to a solid support, and the remaining components contacted with the support bound component. The above components of the method may be combined at substantially the same time or at different times.

[00188] Where the assay is a binding assay, following the contact and incubation steps, the subject methods will generally, though not necessarily, further include a washing step to remove unbound components, where such a washing step is generally employed when required to remove label that would give rise to a background signal during detection, such as radioactive or fluorescently labeled non-specifϊcally bound components. Following the optional washing step, the presence of bound complexes will then be detected.

[00189] In some embodiments, the assay is an in vitro cell-free assay. A cell-free assay is generally conducted with substantially pure deacylase polypeptide. In other embodiments, the assay is an in vitro cell-based assay. Cell-based assays are conducted using cells that produce the deacylase.

[00190] Inhibitors of the deacylase enzymatic function (e.g., removal of a fatty acid chain from a lipid A substrate) are identified using the following non-limiting exemplary procedure. The enzymatic active site portion (e.g., amino acids 270-554) of a subject deacylase, or the whole deacylase protein, is incubated with purified Pgi₆₉₀ lipid A (see Figure 13) and the release of hydroxyl fatty acids is detected by gas chromatography. A test agent that inhibits enzymatic activity of the deacylase is identified by a reduction in the amount of hydroxyl fatty acids released from the lipid A substrate. Inhibitors of the deacylase function are identified by contacting a test agent with the deacylase protein or enzymatic active site-containing fragment thereof and looking for a decrease in the amount of fatty acids liberated compared to a control in the absence of the test agent.

[00191] Hemin binding assays will in some embodiments be an enzyme-linked immunosorbent assay (ELISA) or other immunological assay. For example, a subject deacylase polypeptide, or a hemin-binding fragment of a subject deacylase polypeptide, is immobilized on an insoluble support (e.g., a well of multi-well ELISA plate). Hemin is added to the wells of the plate in the presence or absence of the test agent. After allowing for binding of the hemin to the immobilized deacylase polypeptide, and optionally washing to remove unbound hemin, bound hemin is detected using a detectably labeled antibody specific for hemin. In the presence of a test agent that inhibits hemin binding to the immobilized deacylase polypeptide, the signal produced by the detectably labeled antibody is reduced. A reduction in hemin binding is thus detected by a reduction in the amount of bound antibody. A reduction in hemin binding, compared to the level of hemin binding in a control sample in the absence of the test agent, indicates that the test agent inhibits hemin binding to the deacylase. UTILITY

[00192] A subject isolated or recombinant deacylase polypeptide is useful for generating specific antibodies (as described above), which in turn are useful in a diagnostic method, e.g., for detecting the presence of P. gingivalis in a sample (described below). A subject deacylase is also useful in some embodiments for generating modified lipid A, as described in more detail below. [00193] A subject nucleic acid is useful in some embodiments for generating a subject genetically modified host cell. In some embodiments, a subject genetically modified host cell is useful for producing a deacylase polypeptide. A subject nucleic acid probe is useful in diagnostic assays, e.g., for detecting the presence of a bacterium that produces a deacylase. Similarly, a subject primer pair is useful in diagnostic assays, e.g., for detecting the presence of a bacterium that produces a deacylase. Detection methods

[00194] The present invention provides methods of detecting a P. gingivalis in a sample. The methods are useful in some embodiments for diagnosing a periodontal disease. For example, in some embodiments, a subject method involves detecting the presence of deacylase nucleic acid or deacylase polypeptide using nucleic acids or antibodies that will specifically detect P. gingivalis in an oral sample. In other embodiments, a subject method detects, in addition to P. gingivalis deacylase nucleic acid or deacylase polypeptide, a deacylase nucleic acid or deacylase polypeptide of a bacterium other than P. gingivalis, e.g., a Bacteroides species. In other embodiments, a subject method detects a deacylase nucleic acid or a deacylase polypeptide that is specific to one or more Bacteroides species.

[00195] In some embodiments, an original sample (e.g., a sample from gum tissue) has been processed such that it no longer includes bacteria, e.g., an original sample is processed to substantially isolate nucleic acids and/or proteins. In such cases, detection of a deacylase nucleic acid and/or a deacylase polypeptide in a processed sample provides for detection of a bacterium in the original sample from which the processed sample is derived.

[00196] The methods are also useful in some embodiments for diagnosing periodontitis. In some embodiments, the methods are useful for determining the extent or stage of periodontitis. The methods are also useful for assessing the efficacy of a treatment for gingivitis or periodontitis. For example, a patient is treated for gingivitis or periodontitis; and, after a period of time following treatment, an oral sample is analyzed for the presence of P. gingivalis, using a subject detection method. A subject detection method will in some embodiments detect "silent" P, gingivalis infection. In particular, in some embodiments, the P. gingivalis that is detected using a subject method is a P. gingivalis that has an altered lipid A structure (e.g., at least a portion of the lipid A is converted from penta-acylated lipid A to tetra-acylated lipid A).

[00197] A subject method of detecting a deacylase nucleic acid or a deacylase polypeptide will in some embodiments be useful in diagnosis of a conditions or diseases that are sequelae of periodontitis. Such conditions include, but are not limited to, coronary artery disease (see, e.g., Beck and Offenbacher (2001) Annals Periodontal. 6:9-15); pre-term birth of babies; and stroke.

Detecting a deacylase nucleic acid in a biological sample

[00198] The present invention provides a method of detecting a Porphyromonas gingivalis in a sample. The method generally involves detecting the presence or absence of a Porphyromonas gingivalis deacylase nucleic acid in a sample suspected of having a Porphyromonas gingivalis, wherein the presence of a Porphyromonas gingivalis deacylase nucleic acid in the sample indicates the presence of Porphyromonas gingivalis in the sample. In some embodiments, the level of a P. gingivalis deacylase nucleic acid is detected; and normalized to a suitable standard, e.g., a G6PDH mRNA (or cDNA) level.

[00199] In some embodiments, a decrease in the level of a P. gingivalis deacylase nucleic acid correlates with or is indicative of a diseased state. Thus, in some embodiments, a level of a P. gingivalis deacylase nucleic acid that is lower than a control sample indicates the presence of P. gingivalis in the sample and/or indicates persistence of a P. gingivalis infection. In particular, in some embodiments, the P. gingivalis that is detected using a subject method is a P. gingivalis that has an altered lipid A structure (e.g., at least a portion of the lipid A is converted from penta-acylated lipid A to tetra-acylated lipid A).

[00200] A number of methods are available for analyzing nucleic acids for the presence and/or level of a specific mRNA in a cell. The mRNA may be assayed directly or reverse transcribed into cDNA for analysis. The nucleic acid may be amplified by conventional techniques, such as the polymerase chain reaction (PCR), to provide sufficient amounts for analysis. The use of the polymerase chain reaction is described in Saiki, et al. (1985), Science 239:487, and a review of techniques may be found in Sambrook, et al. Molecular Cloning: A Laboratory Manual, CSH Press 1989, pp.14.2-14.33.

[00201] In some embodiments, the method involves contacting the sample under stringent hybridization conditions with a subject deacylase nucleic acid probe and detecting binding, if any, of the probe to a nucleic acid in the sample. A variety of nucleic acid hybridization methods are well known to those skilled in the art, and any known method can be used. In many embodiments, the deacylase nucleic acid probe will be detectably labeled. Amplification with nucleic acid primer pairs

[00202] In some embodiments, the method involves contacting the sample (e.g., under stringent hybridization conditions) with a subject nucleic acid primer pair, where the primer pair, under conditions that permit primer-initiated nucleic acid amplification, amplifies any target deacylase nucleic acid present in the sample, generating an amplification product (where amplification product is generated when target deacylase nucleic acid present in the sample).

[00203] Conditions that permit primer-initiated nucleic acid amplification and catalytic nucleic acid activity are well known to those skilled in the art, and include the presence of a DNA polymerase; deoxynucleotide triphosphates; and magnesium ions. Suitable reaction conditions are well known to those skilled in the art of nucleic acid amplification. Exemplary, non- limiting reaction conditions are described in the Examples. The DNA polymerase is generally one that has high affinity for binding at the 3 '-end of an oligonucleotide hybridized to a nucleic acid strand. The DNA polymerase is generally one that has little or no 5' — >^• 3' exonuclease activity so as to minimize degradation of primer, termination or primer extension polynucleotides. The DNA polymerase is generally one that has little to no proofreading activity. In many embodiments, the DNA polymerase is thermostable, e.g., is catalytically active at temperatures in excess of about 75⁰C. DNA polymerases that are suitable for use in a subject method include, but are not limited to, DNA polymerases discussed in U.S. Pat. Nos. 5,648,211 and 5744312, which include exo^" Vent (New England Biolabs), exo^" Deep Vent (New England Biolabs), Bst (BioRad), exo^" PfU (Stratagene), Bca (Panvera), sequencing grade Taq (Promega); thermostable DNA polymerases from Thermoanaerobacter thermohydrosulfuricus; and the like. In some embodiments, the reaction mixture includes an RNAse H.

[00204] Magnesium ions are typically present in the reaction mix in a concentration of from about 1 mM to about 100 mM, e.g., from about 1 mM to about 3 mM, from about 3 mM to about 5 mM, from about 5 mM to about 10 mM, from about 10 mM to about 25 mM, from about 25 mM to about 50 mM, from about 50 mM to about 75 mM, or from about 75 mM to about 10O mM.

[00205] Usually the reaction mixture will comprise four different types of dNTPs corresponding to the four naturally occurring bases are present, i.e. dATP, dTTP, dCTP and dGTP. In the subject methods, each dNTP will typically be present at a final concentration in the reaction, ranging from about 10 μM to 5000 μM, e.g., from about 10 μM to about 50 μM, from about 50 μM to about 100 μM, from about 100 μM to about 200 μM, from about 200 μM to about 500 μM, from about 500 μM to about 1000 μM, from about 1000 μM to about 2000 μM, from about 2000 μM to about 3000 μM, from about 3000 μM to about 4000 μM, or from about 4000 μM to about 5000 μM. In some embodiments, each dNTP will be present at a final concentration in the reaction of from about 20 μM to 1000 μM, from about 100 μM to about 200 μM, or from about 50 μM to about 200 μM. [00206] The amplification reaction mixture typically includes an aqueous buffer medium that includes a source of monovalent ions, a source of divalent cations and a buffering agent. Any convenient source of monovalent ions, such as KCl, K-acetate, NH₄-acetate, K-glutamate, NH₄Cl, ammonium sulfate, and the like may be employed. The divalent cation may be magnesium, manganese, zinc and the like, where the cation will typically be magnesium. Any convenient source of magnesium cation may be employed, including MgCl₂, Mg-acetate, and the like. Representative buffering agents or salts that may be present in the buffer include Tris, Tricine, HEPES, MOPS and the like, where the amount of buffering agent will typically range from about 5 to 150 mM, usually from about 10 to 100 mM, and more usually from about 20 to 50 mM, where in certain preferred embodiments the buffering agent will be present in an amount sufficient to provide a pH ranging from about 6.0 to 9.5, e.g., pH 7.3 at 72 °C. Other agents which may be present in the buffer medium include chelating agents, such as EDTA, EGTA and the like.

[00207] Each primer nucleic acid is present in the reaction mixture at a concentration of from about 50 nM to about 900 nM, e.g., the 3' primer and the 5' primer nucleic acid are each independently present at a concentration of from about 50 nM to about 75 nM, from about 75 nM to about 100 nM, from about 100 nM to about 150 nM, from about 150 nM to about 200 nM, from about 200 nM to about 250 nM, from about 250 nM to about 300 nM, from about 300 nM to about 400 nM, from about 400 nM to about 500 nM, from about 500 nM to about 600 nM, from about 600 nM to about 700 nM, from about 700 nM to about 800 nM, or from about 800 nM to about 900 nM.

[00208] A detectable label may be included in an amplification reaction. Suitable labels include fluorochromes, e.g. fluorescein isothiocyanate (FITC), rhodamine, Texas Red, phycoerythrin, allophycocyanin, 6-carboxyfluorescein (6-FAM), 2', 7'-dimethoxy-4',5'-dichloro-6- carboxyfluorescein (JOE), 6-carboxy-X-rhodamine (ROX), 6-carboxy-2',4',7',4,7- hexachlorofluorescein (HEX), 5-carboxyfluorescein (5-FAM) or N,N,N',N'-tetramethyl-6- carboxyrhodamine (TAMRA), radioactive labels, e.g. ³²P, ³⁵S, ³H; etc. The label may be a two stage system, where the amplified DNA is conjugated to biotin, haptens, etc. having a high affinity binding partner, e.g. avidin, specific antibodies, etc., where the binding partner is conjugated to a detectable label. The label may be conjugated to one or both of the primers. Alternatively, the pool of nucleotides used in the amplification is labeled, so as to incorporate the label into the amplification product.

[00209] In one embodiment, a subject method involves amplifying nucleic acids from a sample, which amplifying step follows a reverse transcription step to provide a cDNA template for amplification. If a diagnostic nucleic acid is obtained, the presence or absence of deacylase- encoding nucleic acid, and thus a P. gingivalis and/or Bacteroides species in a sample can be indicated. In general, amplification-based methods involve reverse transcription of mRNA in a sample and amplifying the resulting cDNA from the sample using a primer and at least one other primer, as described above, and assessing the amplified nucleic acids.

[00210] As is known in the art, an amplified nucleic acid may be assessed by a number of methods, including, for example, determining the presence or absence of the nucleic acid, determining the size of the nucleic acid or determining the abundance of a nucleic acid in relation to another amplified nucleic acid. In most embodiments, an amplified nucleic acid is assessed using gel electrophoresis, nucleic acid hybridization, sequencing, and/or detection of a signal from a label bound to the amplified nucleic acid. Methods of amplifying (e.g., by polymerase chain reaction) nucleic acid, methods of performing primers extension, and methods of assessing nucleic acids are generally well known in the art (e.g., see Ausubel, et al, Short Protocols in Molecular Biology, 3rd ed., Wiley & Sons, 1995 and Sambrook, et al, Molecular Cloning: A Laboratory Manual, Third Edition, (2001) Cold Spring Harbor, N. Y.) and need not be described in any great detail.

[00211] For example, primers and probes described above may be used in polymerase chain reaction (PCR)-based techniques to detect deacylase-encoding nucleic acid in biological samples. PCR is a technique for amplifying a desired target nucleic acid sequence contained in a nucleic acid molecule or mixture of molecules. In PCR, a pair of primers is employed in excess to hybridize to the complementary strands of the target nucleic acid. The primers are each extended by a polymerase using the target nucleic acid as a template. The extension products become target sequences themselves after dissociation from the original target strand. New primers are then hybridized and extended by a polymerase, and the cycle is repeated to geometrically increase the number of target sequence molecules. The PCR method for amplifying target nucleic acid sequences in a sample is well known in the art and has been described in, e.g., Innis et al. (eds.) PCR Protocols (Academic Press, NY 1990); Taylor (1991) Polymerase chain reaction: basic principles and automation, in PCR: A Practical Approach, McPherson et al. (eds.) IRL Press, Oxford; Saiki et al. (1986) Nature 324: 163; as well as in U.S. Pat. Nos. 4,683,195, 4,683,202 and 4,889,818, all incorporated herein by reference in , their entireties.

[00212] In particular, PCR uses relatively short oligonucleotide primers which flank the target nucleotide sequence to be amplified, oriented such that their 3' ends face each other, each primer extending toward the other. The polynucleotide sample is extracted and denatured, preferably by heat, and hybridized with first and second primers which are present in molar excess. Polymerization is catalyzed in the presence of the four deoxyribonucleotide triphosphates (dNTPs—dATP, dGTP, dCTP and dTTP) using a primer- and template-dependent polynucleotide polymerizing agent, such as any enzyme capable of producing primer extension products, for example, E. coli DNA polymerase I, Kl enow fragment of DNA polymerase I, T4 DNA polymerase, thermostable DNA polymerases isolated from Thermus aquaticus (Taq), available from a variety of sources (for example, Perkin Elmer), Thermus thermophilus (United States Biochemicals), Bacillus stereothermophilus (Bio-Rad), or Thermococcus litoralis ("Vent" polymerase, New England Biolabs). This results in two "long products" which contain the respective primers at their 5' ends covalently linked to the newly synthesized complements of the original strands.

[00213] The reaction mixture is then returned to polymerizing conditions, e.g., by lowering the temperature, inactivating a denaturing agent, or adding more polymerase, and a second cycle is initiated. The second cycle provides the two original strands, the two long products from the first cycle, two new long products replicated from the original strands, and two "short products" replicated from the long products. The short products have the sequence of the target sequence with a primer at each end. On each additional cycle, an additional two long products are produced, and a number of short products equal to the number of long and short products remaining at the end of the previous cycle. Thus, the number of short products containing the target sequence grows exponentially with each cycle. PCR is typically carried out with a commercially available thermal cycler, e.g., Perkin Elmer.

[00214] RNAs encoding a deacylase of interest can be amplified by reverse transcribing the mRNA into cDNA, and then performing PCR (RT-PCR), as described above. Alternatively, a single enzyme may be used for both steps as described in U.S. Pat. No. 5,322,770. mRNA may also be reverse transcribed into cDNA, followed by asymmetric gap ligase chain reaction (RT- AGLCR) as described by Marshall et al. (1994) PCR Meth. App. 4:80-84.

[00215] The fluorogenic 5' nuclease assay, known as the TAQMAN™ assay (Perkin-Elmer), is a powerful and versatile PCR-based detection system for nucleic acid targets. For a detailed description of the TAQMAN™ assay, reagents and conditions for use therein, see, e.g., Holland et al., Proc. Natl. Acad. Sci, U.S.A. (1991) 88:7276-7280; U.S. Pat. Nos. 5,538,848, 5,723,591, and 5,876,930, all incorporated herein by reference in their entireties. Hence, primers and probes derived from regions of a deacylase-encoding nucleic acid as described herein can be used in TAQMAN analyses to detect the presence of infection in a biological sample. Analysis is performed in conjunction with thermal cycling by monitoring the generation of fluorescence signals. The assay system dispenses with the need for gel electrophoretic analysis, and has the capability to generate quantitative data allowing the determination of, for example, bacterial infection load.

[00216] The fluorogenic 5' nuclease assay is conveniently performed using, for example,

AMPLITAQ GOLD™ DNA polymerase, which has endogenous 5' nuclease activity, to digest an internal oligonucleotide probe labeled with both a fluorescent reporter dye and a quencher (see, Holland et al., Proc. Natl. Acad.Sci. USA (1991) 88:7276-7280; and Lee et al., Nucl. Acids Res. (1993) 21 :3761-3766). Assay results are detected by measuring changes in fluorescence that occur during the amplification cycle as the fluorescent probe is digested, uncoupling the dye and quencher labels and causing an increase in the fluorescent signal that is proportional to the amplification of target nucleic acid.

[00217] The amplification products can be detected in solution or using solid supports. In this method, the TAQMAN™ probe is designed to hybridize to a target sequence within the desired PCR product. The 5' end of the TAQMAN™ probe contains a fluorescent reporter dye. The 3' end of the probe is blocked to prevent probe extension and contains a dye that will quench the fluorescence of the 5' fluorophore. During subsequent amplification, the 5' fluorescent label is cleaved off if a polymerase with 5' exonuclease activity is present in the reaction. Excision of the 5' fluorophore results in an increase in fluorescence which can be detected.

[00218] In particular, the oligonucleotide probe is constructed such that the probe exists in at least one single-stranded conformation when unhybridized where the quencher molecule is near enough to the reporter molecule to quench the fluorescence of the reporter molecule. The oligonucleotide probe also exists in at least one conformation when hybridized to a target polynucleotide such that the quencher molecule is not positioned close enough to the reporter molecule to quench the fluorescence of the reporter molecule. By adopting these hybridized and unhybridized conformations, the reporter molecule and quencher molecule on the probe exhibit different fluorescence signal intensities when the probe is hybridized and unhybridized. As a result, it is possible to determine whether the probe is hybridized or unhybridized based on a change in the fluorescence intensity of the reporter molecule, the quencher molecule, or a combination thereof. In addition, because the probe can be designed such that the quencher molecule quenches the reporter molecule when the probe is not hybridized, the probe can be designed such that the reporter molecule exhibits limited fluorescence unless the probe is either hybridized or digested. [00219] Accordingly, the present invention provides methods for amplifying a target nucleotide sequence using a nucleic acid polymerase having 5' to 3' nuclease activity, one or more primers capable of hybridizing to the target sequence or its extension product, and an oligonucleotide probe capable of hybridizing to the target sequence 3' relative to the primer. During amplification, the polymerase digests the oligonucleotide probe when it is hybridized to the target sequence, thereby separating the reporter molecule from the quencher molecule. As the amplification is conducted, the fluorescence of the reporter molecule is monitored, with fluorescence corresponding to the occurrence of nucleic acid amplification. The reporter molecule is preferably a fluorescein dye and the quencher molecule is preferably a rhodamine dye.

[00220] The deacylase-encoding nucleic acids described herein may also be used as a basis for transcription-mediated amplification (TMA) assays. TMA provides a method of identifying target nucleic acids present in very small amounts in a biological sample. Such nucleic acids may be difficult or impossible to detect using direct assay methods. In particular, TMA is an isothemal, autocatalytic nucleic acid target amplification system that can provide more than a billion RNA copies of a target sequence. The assay can be done qualitatively, to accurately detect the presence or absence of the target sequence in a biological sample. The assay can also provide a quantitative measure of the amount of target sequence over a concentration range of several orders of magnitude. TMA provides a method for autocatalytically synthesizing multiple copies of a target nucleic acid sequence without repetitive manipulation of reaction conditions such as temperature, ionic strength and pH.

[00221] Generally, TMA includes the following steps: (a) isolating nucleic acid from the biological sample of interest suspected of having a bacterium that produces a deacylase as described herein (e.g., P. gingivalis or a Bacteroides spp.); and (b) combining into a reaction mixture (i) the isolated nucleic acid, (ii) first and second oligonucleotide primers, the first primer having a complexing sequence sufficiently complementary to the 3' terminal portion of an RNA target sequence, if present (for example the (+) strand), to complex therewith, and the second primer having a complexing sequence sufficiently complementary to the 3' terminal portion of the target sequence of its complement (for example, the (-) strand) to complex therewith, wherein the first oligonucleotide further comprises a sequence 5' to the complexing sequence which includes a promoter, (iii) a reverse transcriptase or RNA and DNA dependent DNA polymerases, (iv) an enzyme activity which selectively degrades the RNA strand of an RNA-DNA complex (such as an RNAse H) and (v) an RNA polymerase which recognizes the promoter. [00222] The components of the reaction mixture may be combined stepwise or at once. The reaction mixture is incubated under conditions whereby an oligonucleotide/target sequence is formed, including DNA priming and nucleic acid synthesizing conditions (including ribonucleotide triphosphates and deoxyribonucleotide triphosphates) for a period of time sufficient to provide multiple copies of the target sequence. The reaction advantageously takes place under conditions suitable for maintaining the stability of reaction components such as the component enzymes and without requiring modification or manipulation of reaction conditions during the course of the amplification reaction. Accordingly, the reaction may take place under conditions that are substantially isothermal and include substantially constant ionic strength and pH. The reaction conveniently does not require a denaturation step to separate the RNA- DNA complex produced by the first DNA extension reaction.

[00223] Suitable DNA polymerases include reverse transcriptases, such as avian myeloblastosis virus (AMV) reverse transcriptase (available from, e.g., Seikagaku America, Inc.) and Moloney murine leukemia virus (MMLV) reverse transcriptase (available from, e.g., Bethesda Research Laboratories).

[00224] Promoters or promoter sequences suitable for incorporation in the primers are nucleic acid sequences (either naturally occurring, produced synthetically or a product of a restriction digest) that are specifically recognized by an RNA polymerase that recognizes and binds to that sequence and initiates the process of transcription whereby RNA transcripts are produced. The sequence may optionally include nucleotide bases extending beyond the actual recognition site for the RNA polymerase which may impart added stability or susceptibility to degradation processes or increased transcription efficiency. Examples of useful promoters include those which are recognized by certain bacteriophage polymerases such as those from bacteriophage T3, T7 or SP6, or a promoter from E. coli. These RNA polymerases are readily available from commercial sources, such as New England Biolabs and Epicentre.

[00225] Some of the reverse transcriptases suitable for use in the methods herein have an

RNAse H activity, such as AMV reverse transcriptase. It may, however, be preferable to add exogenous RNAse H, such as E. coli RNAse H, even when AMV reverse transcriptase is used. RNAse H is readily available from, e.g., Bethesda Research Laboratories.

[00226] The RNA transcripts produced by these methods may serve as templates to produce additional copies of the target sequence through the above-described mechanisms. The system is autocatalytic and amplification occurs autocatalytically without the need for repeatedly modifying or changing reaction conditions such as temperature, pH, ionic strength or the like. [00227] Another method of detection involves use of target sequence-specific oligonucleotide probes, which contain a region of complementarity to the target sequence described above. The probes may be used in hybridization protection assays (HPA). In this embodiment, the probes are conveniently labeled with acridinium ester (AE), a highly chemiluminescent molecule. See, e.g., Nelson et al. (1995) "Detection of Acridinium Esters by Chemiluminescence" in Nonisotopic Probing, Blotting and Sequencing, Kricka L. J. (ed) Academic Press, San Diego, Calif; Nelson et al. (1994) "Application of the Hybridization Protection Assay (HPA) to PCR" in The Polymerase Chain Reaction, Mullis et al. (eds.) Birkhauser, Boston, Mass.; Weeks et al., Clin. Chem. (1983) 29:1474-1479; Berry et al., Clin. Chem. (1988) 34:2087-2090. One AE molecule is directly attached to the probe using a non-nucleotide-based linker arm chemistry that allows placement of the label at any location within the probe. See, e.g., U.S. Pat. Nos. 5,585,481 and 5,185,439. Chemiluminescence is triggered by reaction with alkaline hydrogen peroxide which yields an excited N-methyl acridone that subsequently collapses to ground state with the emission of a photon. Additionally, AE causes ester hydrolysis which yields the nonchemiluminescent-methyl acridinium carboxylic acid.

[00228] When the AE molecule is covalently attached to a nucleic acid probe, hydrolysis is rapid under mildly alkaline conditions. When the AE-labeled probe is exactly complementary to the target nucleic acid, the rate of AE hydrolysis is greatly reduced. Thus, hybridized and unhybridized AE-labeled probe can be detected directly in solution, without the need for physical separation.

[00229] HPA generally consists of the following steps: (a) the AE-labeled probe is hybridized with the target nucleic acid in solution for about 15 to about 30 minutes. A mild alkaline solution is then added and AE coupled to the unhybridized probe is hydrolyzed. This reaction takes approximately 5 to 10 minutes. The remaining hybrid-associated AE is detected as a measure of the amount of target present. This step takes approximately 2 to 5 seconds. Preferably, the differential hydrolysis step is conducted at the same temperature as the hybridization step, typically at 50 to 70 degrees Celsius. Alternatively, a second differential hydrolysis step may be conducted at room temperature. This allows elevated pHs to be used, for example in the range of 10-11, which yields larger differences in the rate of hydrolysis between hybridized and unhybridized AE-labeled probe. HPA is described in detail in, e.g., U.S. Pat. Nos. 6,004,745; 5,948,899; and 5,283,174, the disclosures of which are incorporated by reference herein in their entireties.

[00230] TMA is described in detail in, e.g., U.S. Pat. No. 5,399,491, the disclosure of which is incorporated herein by reference in its entirety. In one example of a typical assay, an isolated nucleic acid sample, suspected of containing a deacylase-encoding nucleic acid as described herein, is mixed with a buffer concentrate containing the buffer, salts, magnesium, nucleotide triphosphates, primers, dithiothreitol, and spermidine. The reaction is optionally incubated at about 100°C for approximately two minutes to denature any secondary structure. After cooling to room temperature, reverse transcriptase, RNA polymerase, and RNAse H are added and the mixture is incubated for two to four hours at 37°C. The reaction can then be assayed by denaturing the product, adding a probe solution, incubating 20 minutes at 60°C, adding a solution to selectively hydrolyze the unhybridized probe, incubating the reaction six minutes at 6O⁰C, and measuring the remaining chemiluminescence in a luminometer.

[00231] Subject oligonucleotides will in some embodiments be used in nucleic acid sequence- based amplification (NASBA). This method is a promoter-directed, enzymatic process that induces in vitro continuous, homogeneous and isothermal amplification of a specific nucleic acid to provide RNA copies of the nucleic acid. The reagents for conducting NASBA include a first DNA primer with a 5' tail comprising a promoter, a second DNA primer, reverse transcriptase, RNAse-H, T7 RNA polymerase, NTP's and dNTP's. Using NASBA, large amounts of single-stranded RNA are generated from either single-stranded RNA or DNA, or double-stranded DNA. When RNA is to be amplified, the ssRNA serves as a template for the synthesis of a first DNA strand by elongation of a first primer containing an RNA polymerase recognition site. This DNA strand in turn serves as the template for the synthesis of a second, complementary, DNA strand by elongation of a second primer, resulting in a double-stranded active RNA-polymerase promoter site, and the second DNA strand serves as a template for the synthesis of large amounts of the first template, the ssRNA, with the aid of a RNA polymerase. The NASBA technique is known in the art and described in, e.g., European Patent 329,822, International Patent Application No. WO 91/02814, and U.S. Pat. Nos. 6,063,603, 5,554,517 and 5,409,818, all of which are incorporated herein in their entireties.

[00232] The deacylase-encoding nucleic acid sequences described herein are also useful in nucleic acid hybridization and amplification techniques that utilize branched DNA molecules. In a basic nucleic acid hybridization assay, single-stranded analyte nucleic acid is hybridized to a labeled single-stranded nucleic acid probe and resulting labeled duplexes are detected. Variations of this basic scheme have been developed to facilitate separation of the duplexes to be detected from extraneous materials and/or to amplify the signal that is detected. One method for amplifying the signal uses amplification multimers that are polynucleotides with a first segment that hybridizes specifically to the analyte nucleic acid or a strand of nucleic acid bound to the analyte and iterations of a second segment that hybridizes specifically to a labeled probe. The amplification is theoretically proportional to the number of iterations of the second segment. The multimers may be either linear or branched. Two general types of branched mul timers are useful in these techniques: forked and combed. Methods for making and using branched nucleic acid molecules are known in the art and described in, e.g., U.S. Pat. No. 5,849,481, incorporated herein by reference in its entirety.

[00233] As is readily apparent, design of the assays described herein is subject to a great deal of variation, and many formats are known in the art. The above descriptions are merely provided as guidance and one of skill in the art can readily modify the described protocols, using techniques well known in the art.

Detecting the presence of deacylase polypeptides in a sample

[00234] The present invention provides a method of detecting a Porphyromonas gingivalis in a sample, where the method generally involves contacting the sample with an antibody that binds specifically to a Porphyromonas gingivalis deacylase polypeptide; and detecting binding between the antibody and any deacylase polypeptide present in the sample, wherein the presence of a Porphyromonas gingivalis deacylase in the sample indicates that presence of Porphyromonas gingivalis.

[00235] Deacylase-specific antibodies are added to the sample, and incubated for a period of time sufficient to allow binding to the epitope, usually from about 30 seconds to about 10 minutes. The antibody will in some embodiments be labeled with radioisotopes, enzymes, fluorescers, chemiluminescers, or other labels for direct detection. Alternatively, a second stage antibody or reagent is used to amplify the signal. Such reagents are well known in the art. For example, the primary antibody may be conjugated to biotin, with horseradish peroxidase-conjugated avidin added as a second stage reagent. Final detection uses a substrate that undergoes a color change in the presence of the peroxidase. Alternatively, the secondary antibody conjugated to a fluorescent compound, e.g. fluorescein, rhodamine, Texas red, etc. The absence or presence of antibody binding may be determined by various methods, including flow cytometry of dissociated cells, microscopy, radiography, scintillation counting, etc.

[00236] Suitable immunological assays include enzyme-linked immunosorbent assays (ELISA), radioimmunoassay (RIA), immunoprecipitation assays, and protein blot ("Western" blot) assays. MODIFIED LIPID A

[00237] The present invention provides a method of generating a modified lipid A. The method generally involves: a) contacting a lipid A substrate with a subject deacylase polypeptide where the subject deacylase polypeptide cleaves at least one fatty acid chain from the lipid A substrate, generating a modified lipid A; and b) isolating the modified lipid A. The present invention further provides a modified lipid A generated using a subject method. In some embodiments, the lipid A substrate is penta-acylated; and the modified lipid A is tetra-acylated.

[00238] In some embodiments, a subject deacylase polypeptide is contacted with a whole bacterium, or with a cell wall preparation (e.g., a cell wall extract). In other embodiments, a subject deacylase polypeptide is contacted with substantially purified lipid A substrate.

[00239] The source of the lipid A substrate is any of a number of bacteria. Suitable bacterial sources of lipid A substrate include, but are not limited to, oral bacteria; oral bacteria residing in subgingival plaque; intestinal bacteria; Bacteroides species; Fusobacterium nucleatum; oral gram negative bacteria that belong to the clusters described by Socransky et al. ((1998) J. CHn. Periodontal. 25:134-144); and the like.

[00240] The present invention further provides modified lipid A generated using the above- described method. The modified lipid A is isolated, e.g., free of bacterial components, enzymes, or other contaminants. In certain embodiments, the modified lipid A is purified, e.g., at least about 90% pure, at least about 95% pure, at least about 98% pure, or at least about 99% pure.

[00241] A subject purified modified lipid A is useful in some embodiments as an adjuvant or an immunomodulator, and thus will in some embodiments be useful in immunogenic compositions together with one or more antigenic substances.

EXAMPLES

[00242] The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the present invention, and are not intended to limit the scope of what the inventors regard as their invention nor are they intended to represent that the experiments below are all or the only experiments performed. Efforts have been made to ensure accuracy with respect to numbers used (e.g. amounts, temperature, etc.) but some experimental errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, molecular weight is weight average molecular weight, temperature is in degrees Celsius, and pressure is at or near atmospheric. Standard abbreviations may be used, e.g., bp, base pair(s); kb, kilobase(s); pi, picoliter(s); s or sec, second(s); min, minute(s); h or hr, hour(s); aa, amino acid(s); kb, kilobase(s); bp, base pair(s); nt, nucleotide(s); i.m., intramuscular(ly); i.p., intraperitoneal(ly); s.c, subcutaneous(ly); and the like. EXAMPLE 1 : IDENTIFICATION OF A LIPID A DEACYLASE IN P. GINGIVALIS W83

[00243] Geurtsen et. al. ((2005) J. Biol. Chem.. 280: 88248-8259) reported lipid A deacylases

(PagL) in a variety of Gram negative bacterial species. Various permutations of putative active site of Pag L proteins, based around the amino acid sequence, HFSNAGIK, were used to perform basic BLAST searches of the TIGR (The Institute for Genomic Research) database for the P. gingivalis W83 theoretical proteome. There were no significant hits identified in this initial screen.

[00244] Subsequently, a relaxed Prosite pattern search was performed, using the putative active site residues, HXSN. The relaxed Prosite pattern search identified TIGR# PGl 626 (GenBank NP-905755) as encoding the theoretical gene product bearing the best homology for the deacylase active site from the P. gingivalis W83 genome. Analysis of PG 1626 with Psortb also suggested that PG 1626 is a potential outer-membrane protein in P. gingivalis. The nucleotide sequence of the coding region and the amino acid sequence of PGl 626 from P. gingivalis W83 are shown in Figures IA and IB, respectively.

[00245] ClustalW from Vector NTI software was used to align known PagL deacylase amino acid sequences with the PG 1626 amino acid sequence (Figure 2). Identical amino acids are in boxes. In Figure 2, the core putative active site, HXSN, is identified in this alignment. This alignment indicated that the amino-terminal half of the PG 1626 gene product did not align with the deacylases but that the carboxyl -terminal half the PGl 626 gene product did align with the deacylases. This suggested that the PG 1626 protein might encode an additional functional domain. Subsequently, a BLAST search was performed using the amino terminal half of the PG 1626 amino acid sequence. Significant homology was obtained with proteins encoded by Bacteroides fragilis and Bacteroides thetaiotaomicron that were identified by the NCBI database as putative hemin receptors. Subsequent alignment of the amino acid sequences revealed that the homology between these putative hemin receptors and PGl 626 spans the entire lengths of the proteins and that they are all of a similar length (~560 aa) (Figure 3). In Figure 3, identical amino acids are in boxes. EXAMPLE 2: CHARACTERIZATION OF PG1626 Generation of PG1626 knock-outs

[00246] To test the hypothesis that PG 1626 gene product functions in the putative hemin/deacylase pathway of P. gingivalis lipid A metabolism, gene eliminations ("knockouts") for the PG 1626 coding region were designed and created in both P. gingivalis strains W83 and 33277. Briefly, the methodology of this technique involves the generation of a vector carrying approximately 1000 base-pair segments of the 5' and 3' flanking regions respectively of the PG 1626 coding region in which an erythromycin (ERM) resistance cassette has been used to replace the PG 1626 coding sequence. Upon introduction of this vector into P. gingivalis host bacterium by electroporation, a percentage of the bacteria integrate the erythromycin cassette in place of the native PGl 626 coding region by a double-crossover homologous recombination event between the homologous flanking regions of the vector and chromosomal sequences of the bacteria (Figure 4). Bacteria that gained erythromycin resistance were selected, analyzed by polymerase chain reaction DNA amplification, and clones that were confirmed to have lost the PGl 626 coding sequence were chosen for further analysis. MALDI-TOF analysis

[00247] Matrix Assisted Laser Desorption Ionization Time-of- flight Mass Spectrometry

(MALDI-TOF) analysis of P. gingivalis PG1626 knock-outs revealed that the PG1626 gene product influences the hemin-dependent composition of lipid A species in P. gingivalis LPS. In order to examine the effects of knocking out PGl 626 on lipid A biosynthesis and metabolism, lipid A species isolated from 33277 wild-type or a 33277 PG 1626 knockout clone were examined by MALDI-TOF analysis. The setup for the experiment was as follows: P. gingivalis 11211 wild-type and P. gingivalis 33277 knock-out clone were each grown in culture media containing either [1 μg/ml] hemin or [15 μg/ml] hemin. Resulting LPSs were isolated, lipid As were derivatized from the LPSs and subjected to MALDI-TOF analysis. The data are presented in Figure 5A-D.

[00248] The results of this preliminary analysis yielded compelling evidence that the genetic disruption of the PGl 626 coding sequence eliminates the ability of P. gingivalis 33277 to produce LPS bearing tetra-acylated lipid A species regardless of the concentration of hemin used to propagate the bacterial culture. Note that the 33277 wild-type bacterium, 33277 WT, produces penta-acylated lipid A species (negative mass ion= 1690) in low hemin conditions whereas tetra-acylated lipid A species predominate in high hemin (negative mass ion = 1435/1449) (Figures 5A and 5B respectively). In contrast, the 33277 knock-out clone,33277 D, only produced penta-acylated lipid A species (negative mass ion=1690) regardless of the hemin concentration (Figures 5C and 5D respectively). These results have been reproduced several times and provide strong evidence that the gene product from PG 1626 plays an important role in the hemin-regulated deacylation of the penta-acylated form of P. gingivalis LPS. This is the first identification of a single bacterial protein implicated in sensing the environmental concentrations of hemin and modulating the acylation state of LPS. Importantly, both of these functions are implicated as major virulence factors for oral bacteria in humans.

Comparison of the abilities of P. gingivalis wild-type and P. gingivalis 1626 knockout bacteria to stimulate NF-κB activation through the toll-like receptor 4 pathway.

[00249] In humans, the toll-like receptor 4 receptor (TLR4) system is recognized as the major

LPS receptor capable of eliciting immune cell activation in response to Gram-negative bacterial LPS. NF-κB activation is one of the major transcription factors that is activated upon LPS engagement of the TLR4 and is a reliable indicator of TLR4 activation. P. gingivalis penta-acylated LPS, but not tetra-acylated LPS, can activate TLR4 in human endothelial cells (Reife et. al. (2005) Cellular Microbiology. In Press). The ability of P. gingivalis wild-type bacteria to stimulate NF-κB activation was compared with that of P. gingivalis 1626 knockout bacteria in a human embryonic kidney (HEK) cell line that has been transiently transfected with recombinant human TLR4, recombinant human MD-2, and the recombinant human membrane form of the co factor, CD 14. P. gingivalis wild-type bacteria were grown in conditions expected to produce tetra-acylated LPS; the P. gingivalis PGl 626 knock-out bacteria were expected to produce penta-acylated LPS.

[00250] Briefly, live transiently-transfected HEK293 cells were exposed to 10⁸ heat-killed (HK)

P. gingivalis bacteria (either wild-type or 1626 knockout) or 10 native (non-heat killed) P. gingivalis bacteria (either wild-type or 1626 knockout) for 4 hours at 37⁰C in a humidified cell growth chamber. Subsequently, the reactions were terminated and NF-κB activation was determined. For this experiment, both W83 and 33277 strains of P. gingivalis were examined (Figure 6). Error bars represent the standard deviation of a triplicate determination. The results of this experiment indicated that both heat-killed and native P. gingivalis bearing disrupted PG 1626 genes were slightly more active than wild-type bacteria in eliciting TLR4-dependent NF-κB activation. This was the case for both strains W83 and 33277. EXAMPLE 3: CLONING AND EXPRESSING PGl 626 IN E. COLI

[00251] To gain more direct detailed information regarding the molecular function of the

PG1626 gene product, cloning and expression of PG1626 from P. gingivalis 33277 was attempted. A plasmid vector capable of high copy replication (200-400 copies per cell) and IPTG inducible promoter was used for protein expression in E. coli. The initial strategy was to use high fidelity polymerase chain reaction (PCR) amplification of P. gingivalis genomic DNA to generate a full-length version of PG 1626 (1626wt), the amino-terminal half of the molecule (1626ΔC), and the carboxyl-terminal half of the molecule (1626ΔN), with each fragment bearing a FLAG epitope fused in-frame at their respective carboxyl-termini to allow for detection and purification of the recombinant proteins following expression in E. coli (Figure 7). These recombinant proteins are then analyzed in vitro to determine the functional properties of the PG 1626 gene product. In Figures 7, the cross-hatched region indicates the N- terminal region that is not homologous to PagL type deacylases; the hatched region indicates the C-terminal region that is homologous to Pag L type deacylases; the dotted box indicates the FLAG epitope that was engineered into each construct to allow detection and purification.

[00252] In addition, purified recombinant PG 1626 proteins will be used to generate antibodies capable of detecting endogenous PGl 626 protein in P. gingivalis. For the first attempt at cloning, the plasmid vector, pGΕM-T easy (Promega) was used. pGΕM-T easy replicates at a high copy number in E. coli hosts. This vector also bears a lac operator used to drive high level expression of gene products placed directly downstream from it. PCR amplification of genomic DNA from 33277 to generate the three desired fragments of PGl 626 generated products of the expected size using primer sets derived from the W83 genomic sequence. Initial colony numbers for the full-length version of PG 1626 in pGem-T Easy occurred at unusually low efficiency and provided an early indication that the PG 1626 gene product might be toxic in E. coli. This indicated that use of the pGem-T Easy vector to clone PGl 626 fragments might be problematic since this vector was expected to produce constitutive amounts of cloned gene products at high levels due to high plasmid copy number and potential "leaky" lac operon promoter control.

[00253] Subsequently, the plasmid pETBlue-1 (Novagen) was used as an alternative vector to attempt to clone the desired versions of PG 1626. Like pGem-T easy, pETBlue-1 affords high copy number replication, but includes a more stringently controlled promoter region. In this case, a T7 phage promoter is under the control of the lac operon. Thus expression of the cloned gene products is not expected to occur in E. coli hosts that do not express T7 RNA polymerase. Following this attempt at cloning the three desired polymerase chain reaction fragments of PG 1626, it was noted that low colony numbers were again obtained for all of the fragments. PCR was used to determine that the all of the desired fragments were present in some of the selected clones. The sequences of selected clones from this experiment were analyzed to gain more detailed information to help explain the low efficiency of cloning these versions of PGl 626.

[00254] Sequence analysis of four independent clones of pET1626wt revealed numerous nucleotide substitutions resulting in either drastic amino acid changes or premature translation termination codons relative to the W83 sequence. Sequence analysis of multiple independent clones of either pET 1626ΔC or pET1626ΔN showed a similar degree of sequence anomalies, although one clone of pET1626ΔN bearing a perfect match to the amino acid sequence of the corresponding region in W83 was obtained. Taken together, these observations suggested that the pETBlue-1 vector was still supporting a basal level of expression of the toxic gene products in the E. coli hosts. Since the host cells used for cloning the fragments do not express T7 RNA polymerase, most likely, the "basal" level expression of the gene products in this vector are due to leaky read-through transcription from promoters located distally upstream on the plasmid that depend upon E. coli RNA polymerase. In this case, endogenous lad repressor levels are apparently not sufficient to eliminate such read-through transcription.

[00255] In a further attempt to clone the PGl 626 gene products in E. coli, the commercially available vector, pETcoco-2 (Novagen), was employed as a means to circumvent the issue of toxicity. This vector provides the most stringent levels of control that are currently available for cloning/expression plasmids. Like the pET-1 vector, this vector contains a T7 promoter that is controlled by the lac operon. One unique feature that this vector contains is a low copy number origin of replication that is capable of limiting the plasmid replication to 1-2 copies per E. coli cell. The vector is also capable of medium levels of replication (10-40 copies per cell) in the presence of arabinose. Another unique feature of this vector is that it encodes a copy of the lad repressor under the control of a strong promoter. These additional features allowed for the successful cloning as judged by efficient colony formation of both the 1626wt and the 1626ΔC fragments from P. gingivalis 33277. Sequence analyses of selected clones confirmed the identity and that the amino acid sequences of PG1626 from 33277 is identical to the amino acid sequence of W83 PGl 626.

[00256] In an attempt to demonstrate expression of the cloned fragments of PG 1626, selected pETcoco clones were transformed into a strain of E. coli that expresses T7 RNA polymerase, cultured in Luria Broth containing IPTG in order to overcome lad repressor activity. Subsequently, cultures were harvested and crude protein extracts were analyzed by denaturing polyacrylamide gel electrophoresis and subjected to Western blotting analysis using a monoclonal anti-FLAG antibody to detect the FLAG epitope encoded at the carboxyl-terminus of the recombinant PG 1626 proteins. Two independent attempts at expressing and detecting expression of the cloned PG 1626 gene fragments failed to produce positive results. This suggests that the PG 1626 gene product is extremely toxic to E. coli and that only cells that have modified or lost the gene survive or that expression levels of the gene product are held to extremely low levels in the E. coli host and that this precludes detection by conventional means. EXAMPLE 4: CLONING AND EXPRESSING P1626 IN P. GINGIVALIS

[00257] In light of the difficulties that were encountered trying to express recombinant PG 1626 gene fragments in E. coli, alternative approaches were considered. Given the fact that this unusual protein occurs naturally in P. gingivalis and that homologous recombination events occur efficiently in P. gingivalis 11211 as evidenced by the ability to generate a number of gene knockout clones in this strain, it was considered that an appropriate host to express recombinant PG 1626 gene products is P. gingivalis. Therefore, a "knock-in" of a synthetic version of the PGl 626 gene product bearing a FLAG-epitope tag into the P. gingivalis genome was generated.

[00258] The strategy for generating the P1626-FLAG knock-in is almost identical to the

"knock-out" approach with the exception that the erythromycin resistance cassette is inserted between the coding region of PG 1626 and the 3' flanking region of PG 1626 of the knock-in cassette (Figure 8). In Figure 8, crossed lines indicate hypothetical cross-over events; and red box indicates the FLAG epitope fused to the PG 1626 coding region. In this case a FLAG epitope tag was fused in- frame at the carboxyl -terminus of the PG 1626 coding region. Upon electroporation of this construct into P. gingivalis 33277 wild-type, a double crossover homologous recombination event between the PGl 626 genomic locus and the knock-in cassette was predicted to yield clones that bear PG 1626 with a FLAG epitope at the carboxyl- terminus of the gene product.

[00259] This procedure was carried out and yielded multiple clones carrying the desired FLAG epitope-tagged PGl 626 gene product as determined by PCR analysis of the genomic DNA from the erythromycin resistant clones. For further analysis of these clones, 4 independent clones were selected for MALDI-TOF analysis to confirm the functionality of the PG 1626 FLAG tagged proteins in generating tetra-acylated lipid A species when the bacteria were grown in high hemin conditions [15 μg/ml] (Figure 9A-F) . In parallel, control MALDI-TOF profiles of lipid As from either P. gingivalis wild-type or a P. gingivalis 1626 knock-out that were grown in identical hemin conditions were examined for comparison. WtPg33277: wild- type P. gingivalis 33277; D3-1626-2: PG1626 knock-out bacteria; Clone 1626WtFIg-Al to Clone 1626WtFIg- A4: FLAG epitope-tagged PG 1626 clones.

[00260] As seen in Figure 9 A-F, lipid A profiles from the wild-type bacteria yielded tetra- acylated species (negative mass ions = 1435/1449) (Figure 9A) and lipid A profiles from the PGl 626 knock-out bacteria yielded exclusively penta-acylated species (negative mass ions =1690) (Figure 9B) as expected. Unexpectedly, the four independent clones bearing FLAG epitope-tagged PGl 626 coding sequences did not yield tetra-acylated lipid A species but instead exhibited a knock-out phenotype displaying penta-acylated lipid A species (negative mass ions =1690) (Figures 9C-9F). These results suggest that either the bacteria are not appropriately expressing the recombinant protein, or the presence of the FLAG epitope tag at the carboxyl-terminus has a deleterious effect on the function and/or expression of the protein.

[00261] Reverse transcription-polymerase chain reaction analysis demonstrated that transcription of DNA into RNA for the recombinant PGl 626 genes occurred in all of the selected clones. However, Western blot analysis of crude protein lysates failed to detect recombinant protein when the blots were probed with a monoclonal anti-FLAG antibody. These data indicate that P. ginigivalis will not express functional PG 1626 gene products that bear carboxyl-terminal FLAG epitope tags and indicate that additional alternative approaches to expressing and purifying recombinant gene products must be employed. These data also provide the first biochemical evidence that the carboxyl-terminal region of the PG 1626 protein may perform an indispensable function with regard to its ability to mediate lipid A deacylation. EXAMPLE 5: EFFECT OF HEMIN CONCENTRATION ON THE EXPRESSION LEVELS OF PGl 626 RNA

[00262] The observation that P. gingivalis 33277 lipid A deacylation occurs in high hemin concentrations [> 10 μg/ml] and not in low hemin concentrations [< 1 μg/ml] suggested the possibility that the PGl 626 gene product levels might be modulated depending upon the concentration of hemin. Accordingly, the RNA profiles of PG 1626 and three critical LPS biosynthesis related genes (ipxA, ipxD, and htrB) were examined. Importantly, in bacteria, gene transcription into RNA is intimately coupled with RNA translation into protein and serves as a reasonable gauge for changes in protein expression. For these types of experiments, P. gingivalis 33277 cultures were grown in medium including either [1 μg/ml] hemin or [20 μg/ml] hemin. The RNA was then isolated, and subjected to reverse transcription-polymerase chain reaction (RT-PCR) analysis using primers designed to detect the appropriate RNA targets.

[00263] Figure 10 presents and RT-PCR analysis of PGl 626 RNA expression from P. gingivalis 33277grown in various hemin concentrations. RNA was isolated from P. gingivalis 33277 cultures grown in the presence of the indicated concentrations of hemin and subjected to reverse transcription polymerase chain reaction analysis with primer sets designed to detect the gene products indicated on the right side of the figure. As shown in Figure 10, the results indicated that the RNA expression levels of several biosynthetic LPS enzymes were significantly up-regulated while the RNA expression level of the deacylase, PGl 626, was significantly down-regulated in the presence of high hemin. These data are consistent with a dynamic hemin sensing molecule that exerts catabolic effects on LPS metabolism as compared to the anabolic effects of ipxA, ipxD, and htrB gene products. These gene expression data establish an important foundation for using more sophisticated genomic expression array analyses for the identification of gene products relevant to the PG 1626 pathway. These data also point to the usefulness of PG 1626 RNA and LPS biosynthetic enzyme RNA expression levels as diagnostic markers with respect to the LPS status of P. gingivalis in oral isolates. EXAMPLE 6: CREATION OF P. GINGIVALIS KNOCK-IN CLONES BEARING EITHER A WILD-TYPE

PG1626 CODING REGION OR A C-TERMINAL DELETION PG1626 CODING REGION

[00264] As discussed above in Figure 9, P. gingivalis knock-in clones bearing a wild-type

PGl 626 coding region encoding a C-terminal FLAG epitope were inactive in generating tetra- acylated lipid A species. This data suggests that either the C-terminal region of this protein is critical to its function and will not tolerate an epitope tag at its C-terminus or that the methodology used to generate these constructs was flawed in design.

[00265] To distinguish between these two possibilities, two additional types of knock-in clones were generated. The first clone was created by re-introducing the PGl 626 wild-type coding region (without an epitope tag) back into the parental PG 1626 knock-out clone in order to test for the viability of the methodology and is designated "PGl 626 wild-type restored". The second clone is designated "PG 1626 C-terminal deletion 1" and was created by knocking-in a modified PG 1626 coding region that lacks sequences encoding the last 20 amino acids in the C-terminus of the protein product.

[00266] The abilities of these two clones to generate lipid A species when grown in high hemin concentrations were compared to the respective abilities of the parental wild-type 33277 and PG 1626 knock-out clones grown in the same conditions (Figures 14A-D). As depicted in Figure 14A, the wild-type 33277 was fully capable of generating tetra-acylated lipid A species. As expected, the PG 1626 knock-out clone generates penta-acylated, but not tetra-acylated lipid A species (Figure 14 B). The PG 1626 wild-type restored clone is fully capable of generating tetra-acylated lipid A species (Figure 14 C) whereas the PG 1626 C-terminal deletion 1 clone does not (Figure 14 D).

[00267] These data demonstrate that the methodology developed for introducing recombinant

PGl 626 sequences into P. gingivalis works well and that a region contained in the C-terminal 20 amino acids are critical to the functioning of the PGl 626 gene product. These data also provide further evidence that is it not desirable to place epitope tags at the C-terminal region of this protein for expression and purification purposes in the production of a protein having full deacylase activity. Thus, constructs encoding N-terminally tagged PGl 626 gene products are of particular interest.

While the present invention has been described with reference to the specific embodiments thereof, it should be understood by those skilled in the art that various changes may be made and equivalents may be substituted without departing from the true spirit and scope of the invention. In addition, many modifications may be made to adapt a particular situation, material, composition of matter, process, process step or steps, to the objective, spirit and scope of the present invention. All such modifications are intended to be within the scope of the claims appended hereto.

Claims

CLAIMSWhat is claimed is:

1. A method of screening a test agent for inhibition of an activity of a Porphyromonas gingivalis deacylase polypeptide, the method comprising: a) contacting the Porphyromonas gingivalis deacylase polypeptide with a test agent; and b) determining the effect, if any, of the test agent on the activity of the Porphyromonas gingivalis deacylase polypeptide.

2. The method of claim 1 , wherein the Porphyromonas gingivalis deacylase activity is hemin binding.

3. The method of claim 1 , wherein the Porphyromonas gingivalis deacylase activity is catalytic removal of a fatty acid chain from a lipid A substrate.

4. A method of generating a modified lipid A, the method comprising: a) contacting a lipid A substrate with the deacylase polypeptide of claim 1 , wherein the deacylase polypeptide cleaves at least one fatty acid chain from the lipid A substrate, generating a modified lipid A; and b) isolating the modified lipid A.

5. A modified lipid A generated using the method according to claim 4.

6. An isolated polypeptide having deacylase activity, wherein said polypeptide consists essentially of an amino acid sequence having at least about 75% amino acid sequence identity to one of: amino acids 270-554 of the amino acid sequence set forth in SEQ ID NO:2, amino acids 270-534 of the amino acid sequence set forth in SEQ ID NO:3, and amino acids 270 to 527 of the amino acid sequence set forth in SEQ ID NO:4.

7. The polypeptide of claim 6, wherein said polypeptide comprises an amino acid sequence having at least about 80% amino acid sequence identity to one of: amino acids 270-554 of the amino acid sequence set forth in SEQ ID NO:2, amino acids 270-534 of the amino acid sequence set forth in SEQ ID NO:3, and amino acids 270 to 527 of the amino acid sequence set forth in SEQ ID NO:4.

8. The polypeptide of claim 6, wherein said polypeptide comprises an amino acid sequence having at least about 95% amino acid sequence identity to one of: amino acids 270-554 of the amino acid sequence set forth in SEQ ID NO:2, amino acids 270-534 of the amino acid sequence set forth in SEQ ID NO:3, and amino acids 270 to 527 of the amino acid sequence set forth in SEQ ID NO:4.

9. The polypeptide of claim 6, wherein said deacylase polypeptide is a fusion protein comprising a heterologous polypeptide selected from an epitope tag, an enzyme that generates a detectable signal, and a fluorescent protein.

10. An isolated polypeptide having hemin binding activity, wherein said polypeptide consists essentially of an amino acid sequence having at least about 75% amino acid sequence identity to amino acids 1-270 of the amino acid sequence set forth in SEQ ID NO:2, SEQ ID NO:3, or SEQ ID NO:4.

11. The polypeptide of claim 10, wherein said polypeptide comprises an amino acid sequence having at least about 80% amino acid sequence identity to amino acids 1 -270 of the amino acid sequence set forth in SEQ ID NO:2, SEQ ID NO:3, or SEQ ID NO:4.

12. The polypeptide of claim 10, wherein said polypeptide comprises an amino acid sequence having at least about 95% amino acid sequence identity to amino acids 1-270 of the amino acid sequence set forth in SEQ ID NO:2, SEQ ID NO:3, or SEQ ID NO:4.

13. A polypeptide comprising: a) at least one of a hemin-binding domain having at least about 75% amino acid sequence identity to amino acids 1-270 of the amino acid sequence set forth in SEQ ID NO:2, SEQ ID NO:3, or SEQ ID NO:4; or a deacylase polypeptide having at least about 75% amino acid sequence identity to one of amino acids 270-554 of the amino acid sequence set forth in SEQ ID NO:2, amino acids 270-534 of the amino acid sequence set forth in SEQ ID NO:3, and amino acids 270 to 527 of the amino acid sequence set forth in SEQ ID NO:4; and b) a heterologous polypeptide selected from an epitope tag, an enzyme that generates a detectable signal, and a fluorescent protein.

14. A composition comprising the polypeptide of claim 6 or claim 10, wherein said polypeptide is at least about 90% pure.

15. A recombinant nucleic acid comprising a nucleotide sequence encoding a deacylase polypeptide according to claim 6 or claim 10 or fragment thereof, wherein said deacylase polypeptide-encoding nucleotide sequence is operably linked to a heterologous promoter.

16. The nucleic acid of claim 15, wherein the heterologous promoter is an inducible promoter.

17. The nucleic acid of claim 15, wherein the heterologous promoter is a tightly regulated promoter.

18. The nucleic acid of claim 16, further comprising a nucleotide sequence encoding a lac repressor, wherein the lac repressor-encoding sequence is operably linked to a promoter.

19. The nucleic acid of claim 15, wherein said deacylase polypeptide-encoding nucleotide sequence encodes a hemin-binding fragment said deacylase polypeptide.

20. The nucleic acid of claim 15, wherein said deacylase polypeptide-encoding nucleotide sequence encodes a fragment of said deacylase polypeptide, wherein said fragment catalyzes the cleavage of a fatty acid chain from a lipid A substrate.

21. The nucleic acid of claim 15, wherein said deacylase polypeptide is a fusion protein comprising a heterologous polypeptide selected from an epitope tag, an enzyme that generates a detectable signal, and a fluorescent protein.

22. A recombinant construct comprising the nucleic acid of claim 15.

23. The construct of claim 22, wherein said construct is a plasmid.

24. The construct of claim 22, wherein said plasmid comprises a low copy number origin of replication.

25. A host cell comprising the construct of claim 22.

26. The host cell of claim 25, wherein said host cell is a prokaryote.

27. The host cell of claim 25, wherein said host cell is a eukaryote.

28. The host cell of claim 27, wherein said eukaryote is a yeast cell or a mammalian cell.

29. A nucleic acid primer pair suitable for production of an amplification product of a deacylase target nucleotide sequence of at least one of Porphyromonas gingivalis and a Bacteroides species, wherein the deacylase target sequence is selected from a hemin-binding domain coding sequence and a deacylase fatty acid cleavage active site domain coding sequence.

30. The nucleic acid primer pair of claim 29, wherein said primer pair amplifies a target nucleotide sequence specific to a Porphyromonas gingivalis deacylase coding region.

31. The nucleic acid primer pair of claim 29, wherein said primer pair amplifies a Porphyromonas gingivalis deacylase target nucleotide sequence and a deacylase target nucleotide sequence of at least one Bacteroides species.

32. The nucleic acid primer pair of claim 31 , wherein said Bacteroides species is an oral pathogen.

33. A kit comprising at least one of the following: a) a nucleic acid primer pair according to claim 29; b) a first nucleic acid probe and a second nucleic acid probe, wherein said first nucleic acid probe hybridizes specifically to a Porphyromonas gingivalis deacylase nucleic acid, and wherein said second nucleic acid probe hybridizes to a Porphyromonas gingivalis deacylase nucleic acid and to deacylase nucleic acid of at least one Bacteroides species; and c) a combination of a nucleic acid primer pair according to claim 29 and said first and second nucleic acid probes, wherein the first and second nucleic acid probes hybridize to a target sequence amplified by the primer pair.

34. The kit of claim 33, wherein the second nucleic acid probe hybridizes to a nucleotide sequence encoding the amino acid sequence HXSNXXIK.

35. An isolated antibody that binds specifically to a deacylase polypeptide, wherein the deacylase polypeptide comprises an amino acid sequence having at least about 75% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO:2, SEQ ID NO:3, or SEQ ID NO:4.

36. The antibody of claim 35, wherein said antibody is a monoclonal antibody.

37. A method of detecting a Porphyromonas gingivalis in a sample, the method comprising: detecting the presence or absence of a Porphyromonas gingivalis deacylase nucleic acid in a sample suspected of having a Porphyromonas gingivalis; wherein the presence of a Porphyromonas gingivalis deacylase nucleic acid in the sample indicates the presence of Porphyromonas gingivalis in the sample.

38. The method of claim 37, wherein said detecting is by nucleic acid-based amplification.

39. A method of detecting a Porphyromonas gingivalis in a sample, the method comprising: contacting the sample with an antibody that binds specifically to a Porphyromonas gingivalis deacylase polypeptide; and detecting binding between the antibody and any deacylase polypeptide present in the sample, wherein the presence of a Porphyromonas gingivalis deacylase in the sample indicates that presence of Porphyromonas gingivalis.

40. The method of claim 39, wherein the antibody is detectably labeled.

41. The method of claim 39, wherein said antibody is immobilized on an insoluble support.