Lactobacillus rhamnosus polynucleotides, polypeptides and methods for using them

Abstract

Novel polynucleotides isolated from Lactobacillus rhamnosus, as well as probes and primers, genetic constructs comprising the polynucleotides, biological materials, including plants, microorganisms and multicellular organisms incorporating the polynucleotides, polypeptides expressed by the polynucleotides, and methods for using the polynucleotides and polypeptides are disclosed.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application is a continuation of U.S. patent application Ser. No. 09/971,536, filed Oct. 2, 2001, which is a continuation-in-part of U.S. patent application Ser. No. 09/634,238 filed Aug. 8, 2000, now U.S. Pat. No. 6,544,772 and U.S. patent application Ser. No. 09/724,623, now U.S. Pat. No. 6,476,209, filed Nov. 28, 2000, and claims priority to PCT International Application No. PCT/NZ01/00160 filed Aug. 8, 2001.

REFERENCE TO SEQUENCE LISTING SUBMITTED ON COMPACT DISC

[0002] This application incorporates by reference in its entirety the Sequence Listing contained in the accompanying two compact discs, one of which is a duplicate copy. Each CD contains a single file, named "1043c4 SEQLIST.txt," the size of which is 196 KB, and which was created on Dec. 20, 2005, in IBM-PC MS-Windows 2000 format pursuant to 37 CFR .sctn.1.52 (e).

TECHNICAL FIELD OF THE INVENTION

[0003] This invention relates to polynucleotides isolated from lactic acid bacteria, namely Lactobacillus rhamnosus, as well as probes and primers specific to the polynucleotides, genetic constructs comprising the polynucleotides, biological materials, including microorganisms and multicellular organisms, incorporating the polynucleotides, polypeptides encoded by the polynucleotides, and methods for using the polynucleotides and polypeptides.

BACKGROUND OF THE INVENTION

[0004] The present invention relates to polynucleotides and polypeptides isolated from a specific strain of lactic acid bacteria, namely Lactobacillus rhamnosus HN001 (L. rhamnosus HN001). Lactic acid bacteria and their enzymes are the major determinants of flavor and fermentation characteristics in fermented dairy products, such as cheese and yogurt. Flavors are produced through the action of bacteria and their enzymes on proteins, carbohydrates and lipids.

[0005] Lactobacillus rhamnosus strain HN001 are heterofermentative bacteria that are Gram positive, non-motile, non-spore forming, catalase negative, facultative anaerobic rods exhibiting an optimal growth temperature of 37.+-.1.degree. C. and an optimum pH of 6.0-6.5. Experimental studies demonstrated that dietary supplementation with Lactobacillus rhamnosus strain HN001 induced a sustained enhancement in several aspects of both natural and acquired immunity (See PCT International Publication No. WO 99/10476).

[0006] In addition, L. rhamnosus HN001 and certain other Gram-positive bacteria can specifically and directly modulate human and animal health (See, for example, Tannock et al., Applied Environ. Microbiol. 66:2578-2588, 2000; Gill et al., Brit. J Nutrition 83:167-176; Quan Shu et al., Food and Chem. Toxicol. 38:153-161, 2000; Quan Shu et al., Intl. J Food Microbiol. 56:87-96, 2000; Quan Shu et al., Intl. Dairy J. 9:831-836, 1999; Prasad et al., Intl. Dairy J. 8:993-1002, 1998; Sanders and Huis in't Veld, Antonie van Leeuwenhoek 76:293-315, 1999; Salminen et al., 1998. In: Lactic Acid Bacteria, Salminen S and von Wright A (eds)., Marcel Dekker Inc, New York, Basel, Hong Kong, pp. 203-253; Delcour et al., Antonie van Leeuwenhoek 76:159-184, 1999; Blum et al., Antonie van Leeuwenhoek 76:199-205, 1999; Yasui et al., Antonie van Leeuwenhoek 76:383-389, 1999; Hirayama and Rafter, Antonie van Leeuwenhoek 76:391-394, 1999; Ouwehand, 1998. In: Lactic Acid Bacteria, Salminen S and von Wright A (eds)., Marcel Dekker Inc, New York, Basel, Hong Kong, pp. 139-159; Isolauri et al., S 1998. In: Lactic Acid Bacteria, Salminen S and von Wright A (eds)., Marcel Dekker Inc, New York, Basel, Hong Kong, pp. 255-268; Lichtenstein and Goldin, 1998. In: Lactic Acid Bacteria, Salminen S and von Wright A (eds)., Marcel Dekker Inc, New York, Basel, Hong Kong, pp. 269-277; El-Nezami and Ahokas, 1998. In: Lactic Acid Bacteria, Salminen S and von Wright A (eds)., Marcel Dekker Inc, New York, Basel, Hong Kong, pp. 359-367; Nousianen et al., 1998. In: Lactic Acid Bacteria, Salminen S and von Wright A (eds)., Marcel Dekker Inc, New York, Basel, Hong Kong, pp. 437-473; Meisel and Bockelmann, Antonie van Leeuwenhoek 76:207-215, 1999; Christensen et al., Antonie van Leeuwenhoek 76:217-246, 1999; Dunne et al., Antonie van Leeuwenhoek 76:279-292, 1999).

[0007] Beneficial health effects attributed to dietary supplementation with these bacteria include the following:

[0008] Increased resistance to enteric pathogens and anti-infection activity, including treatment of rotavirus infection and infantile diarrhea--due to increases in antibody production caused by an adjuvant effect; increased resistance to pathogen colonization; alteration of intestinal conditions, such as pH; and the presence of specific antibacterial substances, such as bacteriocins and organic acids.

[0009] Aid in lactose digestion--due to lactose degradation by bacterial lactase enzymes (such as beta-galactosidase) that act in the small intestine.

[0010] Anti-cancer (in particular anti-colon cancer) and anti-mutagenesis activities--due to anti-mutagenic activity; alteration of procancerous enzymatic activity of colonic microbes; reduction of the carcinogenic enzymes azoreductase, beta-glucuronidase and nitroreductase in the gut and/or faeces; stimulation of immune function; positive influence on bile salt concentration; and antioxidant effects.

[0011] Liver cancer reduction--due to aflatoxin detoxification and inhibition of mould growth.

[0012] Reduction of small bowel bacterial overgrowth--due to antibacterial activity; and decrease in toxic metabolite production from overgrowth flora.

[0013] Immune system modulation and treatment of autoimmune disorders and allergies--due to enhancement of non-specific and antigen-specific defence against infection and tumors; enhanced mucosal immunity; adjuvant effect in antigen-specific immune responses; and regulation of Th1/Th2 cells and production of cytokines.

[0014] Treatment of allergic responses to foods--due to prevention of antigen translocation into blood stream and modulation of allergenic factors in food.

[0015] Reduction of blood lipids and prevention of heart disease--due to assimilation of cholesterol by bacteria; hydrolysis of bile salts; and antioxidative effects.

[0016] Antihypertensive effect--bacterial protease or peptidase action on milk peptides produces antihypertensive peptides. Cell wall components act as ACE inhibitors.

[0017] Prevention and treatment of urogenital infections--due to adhesion to urinary and vaginal tract cells resulting in competitive exclusion; and production of antibacterial substances (acids, hydrogen peroxide and biosurfactants).

[0018] Treatment of inflammatory bowel disorder and irritable bowel syndrome--due to immuno-modulation; increased resistance to pathogen colonization; alteration of intestinal conditions such as pH; production of specific antibacterial substances such as bacteriocins, organic acids, hydrogen peroxide and biosurfactants; and competitive exclusion.

[0019] Modulation of infective endocarditis--due to fibronectin receptor-mediated platelet aggregation associated with Lactobacillus sepsis.

[0020] Prevention and treatment of Helicobacter pylori infection--due to competitive colonization and antibacterial effect.

[0021] Prevention and treatment of hepatic encephalopathy--due to inhibition and/or exclusion of urease-producing gut flora.

[0022] Improved protein and carbohydrate utilization and conversion--due to production of beneficial products by bacterial action on proteins and carbohydrates.

[0023] Other beneficial health effects associated with dietary supplementation with L. rhamnosus include: improved nutrition; regulation of colonocyte proliferation and differentiation; improved lignan and isoflavone metabolism; reduced mucosal permeability; detoxification of carcinogens and other harmful compounds; relief of constipation and diarrhea; and vitamin synthesis, in particular folate.

[0024] Peptidases are enzymes that break the peptide bonds linking the amino group of one amino acid with the carboxy group (acid group) of an adjacent amino acid in a peptide chain. The bonds are broken in a hydrolytic reaction. There is a large family of peptidase enzymes that are defined by their specificity for the particular peptide bonds that they cleave (Barrett A J, Rawlings N D and Woessner J F (Eds.) 1998. Handbook of proteolytic enzymes, Academic Press, London, UK). The two main families are exopeptidases and endopeptidases.

[0025] Exopeptidases cleave amino acids from the N- or C-terminus of a peptide chain, releasing free amino acids or short (di- and tri-) peptides. Different types of exopeptidases include: [0026] Aminopeptidases--release a free amino acid from the N-terminus of a peptide chain; [0027] dipeptidyl-peptidase (also known as dipeptidyl-aminopeptidases)--release a dipeptide from the N-terminus of a peptide chain; [0028] tripeptidyl-peptidases (also known as tripeptidyl-aminopeptidases)--release a tripeptide from the N-terminus of a peptide chain); [0029] carboxypeptidases--release a free amino acid from the C-terminus of a peptide chain; [0030] peptidyl-dipeptidases--release a dipeptide from the C-terminus of a peptide chain; [0031] dipeptidases--release two free amino acids from a dipeptide; and [0032] tripeptidases--release a free amino acid and a dipeptide from a tripeptide.

[0033] Endopeptidases hydrolyze peptide bonds internally within a peptide and are classified on the basis of their mode of catalysis: [0034] serine-endopeptidases--depend on serine (or threonine) as the nucleophile in the catalytic reaction; [0035] cysteine-endopeptidases--depend on the sulphydryl group of cysteine as the nucleophile in the catalytic reaction; [0036] aspartic-endopeptidases--contain aspartate residues that act as ligands for an activated water molecule which acts as the nucleophile in the catalytic reaction; and [0037] metallo-endopeptidases--contain one or more divalent metal ions that activate the water molecule that acts as the nucleophile in the catalytic reaction.

[0038] Peptidases are important enzymes in the process of cheese ripening and the development of cheese flavor. The hydrolysis of milk caseins in cheese results in textural changes and the development of cheese flavors. The raft of proteolytic enzymes that cause this hydrolysis come from the lactic acid bacteria that are bound up in the cheese--either starter cultures that grow up during the manufacture of the cheese, or adventitious and adjunct non-starter lactic acid bacteria that grow in the cheese as it ripens (Law and Haandrikman, Int. Dairy J. 7:1-11, 1997).

[0039] Many other enzymes can also influence dairy product flavor and functional and textural characteristics, as well as influencing the fermentation characteristics of the bacteria, such as speed of growth, acid production and survival. (Urbach, Int. Dairy J 5:877-890, 1995; Johnson and Somkuti, Biotech. Appl. Biochem. 13:196-204, 1991; El Soda and Pandian, J. Dairy Sci. 74:2317-2335, 1991; Fox et al., In Cheese: chemistry, physics and microbiology. Volume 1, General aspects, 2.sup.nd edition, P Fox (ed) Chapman and Hall, London; Christensen et al., Antonie van Leeuwenhoek 76:217-246, 1999; Stingle et al., J. Bacteriol. 20:6354-6360, 1999; Stingle et al., Mol. Microbiol. 32:1287-1295, 1999; Lemoine et al., Appl. Environ. Microbiol. 63:1512-3518, 1997). Enzymes influencing the specific cellular and system characteristics and/or functions are examplified below: [0040] Lysis of cells. These enzymes are mostly cell wall hydrolases, including amidases; muramidases; lysozymes, including N-acetyl muramidase; muramidase; N-acetylglucosaminidase; and N-acetylmuramoyl-L-alanine amidase. DEAD-box helicase proteins also influence autolysis. [0041] Carbohydrate utilization. Lactose, citrate and diacetyl metabolism, and alcohol metabolism are particularly important. The enzymes involved include beta-galactosidase, lactate dehydrogenase, citrate lyase, citrate permease, 2,3 butanediol dehydrogenase (acetoin reductase), acetolactate decaboxylase, acetolactate synthase, pyruvate decarboxylase, pyruvate formate lyase, diacetyl synthase, diacetyl reductase, alcohol decarboxylase, lactate dehydrogenase, pyruvate dehydrogenase, and aldehyde dehydrogenase. [0042] Lipid degradation, modification or synthesis. Enzymes involved include lipases, esterases, phospholipases, serine hydrolases, desaturases, and linoleate isomerase. [0043] Polysaccharide synthesis. Polysaccharides are important not only for potential immune enhancement and adhesion activity but are important for the texture of fermented dairy products. The enzymes involved are a series of glucosyl transferases, including beta-(1-3) glucosyl transferase, alpha-N acetylgalactosaminyl transferase, phosphogalactosyl transferase, alpha-glycosyl transferase, UDP-N-acetylglucosamine C4 epimerase and UDP-N-acetylglucosamine transferase. [0044] Amino acid degradation. Enzymes include glutamate dehydrogenase, aminotransferases, amino acid decarboxylases, and enzymes involved in sulphur amino acid degradation including cystothione beta-lyase.

[0045] Sequencing of the genomes of numerous organisms, including humans, animals, microorganisms and various plant varieties, has been and is being carried out on a large scale. Polynucleotides identified using sequencing techniques may be partial or full-length genes, and may contain open reading frames, or portions of open reading frames, that encode polypeptides. Polypeptides may be identified based on polynucleotide sequences and further characterized. The sequencing data relating to polynucleotides thus represents valuable and useful information.

[0046] Polynucleotides and polypeptides may be analyzed for varying degrees of novelty by comparing identified sequences to sequences published in various public domain databases, such as EMBL. Newly identified polynucleotides and corresponding polypeptides may also be compared to polynucleotides and polypeptides contained in public domain information to ascertain homology to known polynucleotides and polypeptides. In this way, the degree of similarity, identity or homology of polynucleotides and polypeptides having an unknown function may be determined relative to polynucleotides and polypeptides having known functions.

[0047] Information relating to the sequences of isolated polynucleotides may be used in a variety of ways. Specified polynucleotides having a particular sequence may be isolated, or synthesized, for use in in vivo or in vitro experimentation as probes or primers. Alternatively, collections of sequences of isolated polynucleotides may be stored using magnetic or optical storage medium and analyzed or manipulated using computer hardware and software, as well as other types of tools.

SUMMARY OF THE INVENTION

[0048] The present invention provides isolated polynucleotides comprising a sequence selected from the group consisting of: (a) SEQ ID NO: 1-33; (b) complements, reverse sequences and reverse complements of SEQ ID NO: 1-33 and fragments of SEQ ID NO: 1-33; (c) open reading frames contained in SEQ ID NO: 1-33 and their variants; (d) functional domains contained in SEQ ID NO: 1-33; and (e) sequences comprising at least a specified number of contiguous residues of a sequence of SEQ ID NO: 1-33 (x-mers). Oligonucleotide probes and primers corresponding to the sequences set out in SEQ ID NO: 1-33, and their variants are also provided. All of these polynucleotides and oligonucleotide probes and primers are collectively referred to herein, as "polynucleotides of the present invention." RNA sequences, reverse sequences, complementary sequences, antisense sequences and the like, corresponding to the polynucleotides of the present invention, may be routinely ascertained and obtained using the polynucleotides identified as SEQ ID NO: 1-33 and are included in the term "polynucleotide."

[0049] The polynucleotide sequences identified as SEQ ID NO: 1-33 were derived from a microbial source, namely from fragmented genomic DNA of Lactobacillus rhamnosus strain HN001, described in PCT International Publication No. WO 99/10476. A biologically pure culture of Lactobacillus rhamnosus strain HN001 was deposited at the Australian Government Analytical Laboratories (AGAL), The New South Wales Regional Laboratory, 1 Suakin Street, Pymble, NSW 2073, Australia, as Deposit No. NM97/09514, dated 18 Aug. 1997.

[0050] The polynucleotide sequences disclosed herein are primarily "full-length" sequences, in that they represent a full-length gene encoding a full-length polypeptide and contain an open reading frame.

[0051] The present invention further provides isolated polypeptides, including polypeptides encoded by the polynucleotides disclosed herein. In certain specific embodiments, the polypeptides of the present invention comprise a sequence selected from the group consisting of SEQ ID NO: 42-75, and variants thereof. Polypeptides encoded by the polynucleotides of the present invention may be expressed and used in various assays to determine their biological activity. Such polypeptides may be used to raise antibodies, to isolate corresponding interacting proteins or other compounds, and to quantitatively determine levels of interacting proteins or other compounds. The polypeptides of the present invention may also be used as nutritional additives or supplements, and as additives in dairy processing and fermentation processing. Several polypeptides of the present invention also have human and animal health related benefits.

[0052] Genetic constructs comprising the inventive polynucleotides are provided, together with transgenic host cells comprising such constructs and transgenic organisms, such as microbes, comprising such cells.

[0053] The present invention also contemplates methods for modulating the polynucleotide and/or polypeptide content and composition of an organism, such methods optionally involving stably incorporating into the genome of the organism a genetic construct comprising a polynucleotide of the present invention. Such modulation may involve up regulating or down regulating expression from one or more polynucleotides of the present invention. Up regulation may be accomplished, for example, by providing multiple gene copies, modulating expression by modifying regulatory elements, promoting transcriptional or translational mechanisms, or the like. Similarly, down regulation may be accomplished using known antisense and gene silencing techniques, including RNAi. In one embodiment, the target organism is a microbe, preferably a microbe used in fermentation, more preferably a microbe of the genus Lactobacillus, and most preferably Lactobacillus rhamnosus, or another closely related microbial species used in the dairy industry.

[0054] In a related aspect, methods for producing a microbe having an altered genotype and/or phenotype are provided, such methods comprising transforming a microbial cell with a genetic construct of the present invention to provide a transgenic cell, and cultivating the transgenic cell under conditions conducive to growth and multiplication. Organisms having an altered genotype or phenotype as a result of modulation of the level or content of a polynucleotide or polypeptide of the present invention compared to a wild-type organism, as well as components and progeny of such organisms, are contemplated by and encompassed within the present invention.

[0055] The isolated polynucleotides of the present invention may be usefully employed for the detection of lactic acid bacteria, preferably L. rhamnosus, in a sample material, using techniques well known in the art, such as polymerase chain reaction (PCR) and DNA hybridization, as detailed below.

[0056] The inventive polynucleotides and polypeptides may also be employed in methods for the selection and production of more effective probiotic bacteria; as "bioactive" (health-promoting) ingredients and health supplements; for immune function enhancement; for reduction of blood lipids such as cholesterol; for production of bioactive material from genetically modified bacteria; as adjuvants; for wound healing; in vaccine development, particularly mucosal vaccines; as animal probiotics for improved animal health and productivity; in selection and production of genetically modified rumen microorganisms for improved animal nutrition and productivity, improved flavor and improved milk composition; in methods for the selection and production of improved natural food bacteria for improved flavor, faster flavor development, improved fermentation characteristics, vitamin synthesis and improved textural characteristics; for the production of improved food bacteria through genetic modification; and for the identification of novel enzymes for the production of, for example, flavors or aroma concentrates.

[0057] The isolated polynucleotides of the present invention also have utility in genome mapping, in physical mapping, and in positional cloning of genes of more or less related microbes. Additionally, the polynucleotide sequences identified as SEQ ID NO: 1-33, and their variants, may be used to design oligonucleotide probes and primers. Oligonucleotide probes and primers have sequences that are substantially complementary to the polynucleotide of interest over a certain portion of the polynucleotide. Oligonucleotide probes designed using the polynucleotides of the present invention may be used to detect the presence and examine the expression patterns of genes in any organism having sufficiently similar DNA and RNA sequences in their cells, using techniques that are well known in the art, such as slot blot DNA hybridization techniques. Oligonucleotide primers designed using the polynucleotides of the present invention may be used for PCR amplifications. Oligonucleotide probes and primers designed using the polynucleotides of the present invention may also be used in connection with various microarray technologies, including the microarray technology of Affymetrix (Santa Clara, Calif.).

[0058] The polynucleotides of the present invention may also incorporate regulatory elements such as promoters, gene regulators, origins of DNA replication, secretion signals, cell wall or membrane anchors for genetic tools (such as expression or integration vectors).

[0059] The polynucleotide sequences, encoded polypeptides and genetic constructs of this invention are useful for improving the properties of microbes that are used in the manufacture of milk-derived products, such as cheeses, yogurt, fermented milk products, sour milks, and buttermilk. Microbial metabolism during fermentation, which results in the breakdown of proteins, lipids and lactose in milk, influences the speed of ripening, the texture and consistency of fermented milk products, and the development of flavors and aromas during ripening. Undesirable flavors in milk products are produced, for example, by the food of milk-producing animals, microbial action and enzymatic activity during fermentation, and require removal. The present invention provides polynucleotides and polypeptides and methods for their use in modifying the flavor, aroma, texture and health-related benefits of milk-derived products.

[0060] Methods are described for modulating the polynucleotide content or composition of microbes used in the dairy industry by transforming the microbes with one or more polynucleotide sequences of Lactobacillus rhamnosus strain HN001. Certain of the inventive polynucleotides encode polypeptides that increase the survivability of microbes during industrial fermentation processes, wherein exposure to osmotic, temperature and other stresses can lead to reduced microbial viability, impaired metabolic activity and suboptimal fermentation conditions. While the present invention is described with particular reference to milk-derived products, it will be recognized that microbes such as Lactobacillus, which are used in the dairy industry, are also used in the production of other foods and beverages (e.g., fermented vegetables, beer, wines, juices and sourdough breads). The polynucleotides and polypeptides described herein and their methods of use may also be employed in the processing of these foods and beverages. In addition, the inventive polypeptides and polynucleotides may be employed to provide food products, including food products prepared from milk, that have modified properties such as, but not limited to, improved flavor, aroma, texture, nutritional benefits, immune system modulation properties and health benefits.

[0061] This invention also provides transgenic microbial populations comprising expressible polynucleotide sequences of Lactobacillus rhamnosus strain HN001 which provide health-related benefits. For example, the polypeptides encoded by the inventive sequences include enzymes that detoxify carcinogens, degrade allergenic proteins and lactose, and produce bioactive peptides and biogenic amines. Microbes transformed with these polynucleotide sequences can be taken internally as a probiotic composition or alternatively, the microbes or their encoded polypeptides can be added to products to provide health-related benefits. Nonpathogenic bacteria, preferably lactic-acid producing species of Bacillus, Lactobacillus, Sporolactobacillus or Bifidiobacterium, that are able to colonize the gastrointestinal tract, preferably the gastrointestinal tract of a mammal, are useful for preventing or reducing pathogen colonization of the gastrointestinal mucosa, and for replacing normal flora that are depleted, for example, by drug therapy. The polynucleotide sequences of this invention can be used to transform microbes for use in a therapeutic composition that is effective for treating or preventing a gastrointestinal condition or disorder caused by the presence of pathogenic microbes in the gastrointestinal tract or by the absence of normal intestinal microbes in the intestinal tract. Such probiotic compositions can be administered alone or in combination with another pharmaceutical agent, depending on the condition that is to be treated.

[0062] All references cited herein, including patent references and non-patent publications, are hereby incorporated by reference in their entireties.

BRIEF DESCRIPTION OF THE DRAWINGS

[0063] FIG. 1 shows the nucleotide sequence of L. rhamnosus strain HN001 esterase gene AA7 (SEQ ID NO: 3) showing ATG initiation and translation stop codons (boxed).

[0064] FIG. 2 shows the amino acid sequence of HN001 esterase AA7 (SEQ ID NO: 44).

[0065] FIG. 3 demonstrates the esterase activity of the AA7 fusion protein. Production of ethyl butyrate from para-nitrophenyl butyrate substrate was measured by change in OD at 410 nm. While buffer only (.diamond-solid.) and the HN001 non-esterase fusion protein (.circle-solid.) showed minimal esterase activity, the ST1 esterase from Streptococcus thermophilus (.sigma.) and the AA7 esterase fusion protein (.nu.) showed strong activity.

[0066] FIG. 4 shows the dose-response of the AA7 fusion protein. While buffer-only (.lamda.) showed no esterase activity, increasing amounts of His-patch/Thio/AA7 fusion protein; 5 .mu.l (.upsilon.), 10 .mu.l (.sigma.) and 20 .mu.l (.nu.) purified protein showed increasing rates of substrate hydrolysis. The increase in substrate hydrolysis was proportional to the amount of AA7 fusion protein added.

[0067] FIG. 5 shows the effect of the serine esterase inhibitor PMSF on esterase AA7 activity. Esterase activity of the His-patch/Thio/AA7 fusion protein was assessed in the absence (.nu.) and presence (.sigma.) of 10 mM PMSF. A buffer-only reaction (.circle-solid.) was used as a negative control. The presence of PMSF reduced HN001 esterase AA7 enzyme activity.

[0068] FIG. 6 shows the nucleotide sequence of L. rhamnosus strain HN001 autoaggregation gene AG5 (SEQ ID NO: 10) showing ATG initiation and translation stop codons (boxed).

[0069] FIG. 7 shows the amino acid sequence of HN001 autoaggregation protein AG5 (SEQ ID NO: 52).

[0070] FIGS. 8A and 8B are images of phase contrast photomicrographs. FIG. 8A illustrates an image of a phase-contrast photomicrograph (exposure 1/8 sec, final magnification.times.240) showing obvious clumping of washed L. rhamnosus strain HN001 cells in the presence of AG5 autoaggregation protein tagged with GST. FIG. 8B illustrates an image of a phase-contrast photomicrograph (exposure 1/8 sec, final magnification.times.240) showing no clumping of washed L. rhamnosus strain HN.sub.001 cells in the presence of an irrelevant (non-adhesion) HN001 protein tagged with GST, as a negative control.

[0071] FIG. 9 shows the nucleotide sequence of L. rhamnosus strain HN001 malic enzyme gene AA5 (SEQ ID NO: 2) showing ATG initiation and translation stop codons (boxed).

[0072] FIG. 10 shows the amino acid sequence of HN001 malic enzyme AA5 (SEQ ID NO: 43).

[0073] FIG. 11 demonstrates malate enzyme activity measured experimentally as rate of pyruvate reduction by crude lysate preparations of EJ1321 cell transformants. .nu. PBS buffer-only; .sigma. 3.5 .mu.g wild-type EJ1321 cell lysate; .upsilon. 3.5 .mu.g cell lysate of EJ1321 transformed with pGEX-6P-3 construct encoding an irrelevant HN001 protein (AD5); .lamda. 3.5 .mu.g cell lysate of EJ1321 transformed with pGEX-6P-3 construct encoding HN001 malic enzyme AA5.

[0074] FIG. 12 shows experimental data illustrating the effect of increasing amounts of EJ1321 crude lysate on malic enzyme activity. .nu. 5 .mu.l wild-type EJ1321 cell lysate; .sigma. 5 .mu.l cell lysate of EJ1321 transformed with pGex-6P-3 encoding AA5; .upsilon. 50 .mu.l cell lysate of EJ1321 transformed with pGex-6P-3 encoding AA5; .lamda. 200 .mu.l cell lysate of EJ1321 transformed with pGex-6P-3 encoding AA5.

[0075] FIG. 13 shows the nucleotide sequence of L. rhamnosus strain HN001 malate dehydrogenase gene AG3 (SEQ ID NO: 9) showing TTG initiation and translation stop codons (boxed).

[0076] FIG. 14 shows the amino acid sequence of HN001 malate dehydrogenase AG3 (SEQ ID NO: 51).

[0077] FIG. 15 shows the nucleotide sequence of L. rhamnosus strain HN001 dihydrodipicolinate synthase gene AI2 (SEQ ID NO: 13) showing ATG initiation and translation stop codons (boxed).

[0078] FIG. 16 shows the amino acid sequence of HN001 dihydrodipicolinate synthase AI2 (SEQ ID NO: 55).

[0079] FIG. 17 shows the nucleotide sequence of L. rhamnosus strain aspartate aminotransferase gene AH9 (SEQ ID NO: 12) showing GTG initiation and translation stop codons (boxed).

[0080] FIG. 18 shows the amino acid sequence of HN001 aspartate aminotransferase AH9 (SEQ ID NO: 54).

[0081] FIG. 19 shows the nucleotide sequence of L. rhamnosus strain HN001 serine dehydratase subunits .alpha. (AF8) and .beta. (AF7). ATG translation initiation codons and termination codons are shown, boxed for AF8, and shaded for AF7.

[0082] FIG. 20 shows the experimentally measured percentage serine utilisation by HN001 strain in liquid culture with 5 mM initial serine concentration. .nu. HN001 transformed with vector only; .upsilon. pTRKH2 construct containing HN001 serine dehydratase.

[0083] FIG. 21 shows the experimentally determined percentage serine utilization by HN001 strain in liquid culture with 12 mM initial serine concentration, .nu. HN001 transformed with vector only, and .upsilon. pTRKH2 construct containing HN001 serine dehydratase.

[0084] FIG. 22 shows the amino acid sequence of L. rhamnosus strain HN001 serine dehydratase subunit .alpha. (AF8; SEQ ID NO: 49), and the amino acid sequence of L. rhamnosus strain HN001 serine dehydratase subunit .beta. (AF7; SEQ ID NO: 48).

[0085] FIG. 23 shows the nucleotide sequence of L. rhamnosus strain HN001 histidinol-phosphate aminotransferase gene AG2 (SEQ ID NO: 8) showing ATG initiation and translation stop codons (boxed).

[0086] FIG. 24 shows the amino acid sequence of HN001 histidinol-phosphate aminotransferase AG2 (SEQ ID NO: 50).

[0087] FIG. 25 shows the nucleotide sequence of L. rhamnosus strain HN001 malY-aminotransferase gene AJ6 (SEQ ID NO: 17) showing ATG initiation and translation stop codons (boxed).

[0088] FIG. 26 shows the amino acid sequence of HN001 malY-aminotransferase AJ6 (SEQ ID NO: 59).

[0089] FIG. 27 shows the nucleotide sequence of L. rhamnosus strain HN001 malY-aminotransferase gene AJ7 (SEQ ID NO: 18) showing ATG initiation and translation stop codons (boxed).

[0090] FIG. 28 shows the amino acid sequence of HN001 malY-aminotransferase AJ7 (SEQ ID NO: 60).

[0091] FIG. 29 shows the nucleotide sequence of L. rhamnosus strain HN001 cystathione .beta.-lyase gene AC8 (SEQ ID NO: 5) showing ATG initiation and translation stop codons (boxed).

[0092] FIG. 30 shows the amino acid sequence of HN001 cystathione .beta.-lyase AC8 (SEQ ID NO: 46).

[0093] FIG. 31 shows experimental results demonstrating cystathione .beta.-lyase activity measured as rate of mercaptide formation. .upsilon. 10 .mu.l purified HN001 cystathione .beta.-lyase AC8 fusion protein; .nu. 10 .mu.l purified CAT fusion protein; .nu. 10 .mu.l H.sub.2O only; .lamda. 10 .mu.l elution buffer only.

[0094] FIG. 32 shows the experimentally determined dose-response of the AC8 fusion protein. Cystathione .beta.-lyase activity of increasing amounts of His-patch/Thio/AC8 fusion protein; 10 .mu.l (.upsilon.), 25 .mu.l (.nu.) and 50 .mu.l (.sigma.) purified protein showed increasing rates of mercaptide formation. The increase in mercaptide formation was proportional to the amount of AC8 fusion protein added.

[0095] FIG. 33 shows the nucleotide sequence of L. rhamnosus strain HN001 phosphoenolpyruvate hydratase AK4 (SEQ ID NO: 20) showing ATG initiation and translation stop codons (boxed).

[0096] FIG. 34 shows the amino acid sequence of L. rhamnosus strain HN001 phosphoenolpyruvate hydratase AK4 (SEQ ID NO: 62).

[0097] FIG. 35 shows the nucleotide sequence of L. rhamnosus strain HN001 tagatose bisphosphate aldolase AK1 (SEQ ID NO: 19) showing ATG initiation and translation stop codons (boxed).

[0098] FIG. 36 shows the amino acid sequence of L. rhamnosus strain HN.sub.001 tagatose bisphosphate aldolase AK1 (SEQ ID NO: 61).

[0099] FIG. 37 shows the nucleotide sequence of L. rhamnosus strain HN001 phosphoglycerate kinase AK6 (SEQ ID NO: 22) showing TTG initiation and translation stop codons (boxed).

[0100] FIG. 38 shows the amino acid sequence of L. rhamnosus strain HN001 phosphoglycerate kinase AK6 (SEQ ID NO: 64).

[0101] FIG. 39 shows the nucleotide sequence of L. rhamnosus strain HN001 triosephosphate isomerase AK5 (SEQ ID NO: 21) showing ATG initiation and translation stop codons (boxed).

[0102] FIG. 40 shows the amino acid sequence of L. rhamnosus strain HN001 triosephosphate isomerase AK5 (SEQ ID NO: 63).

[0103] FIG. 41 shows the nucleotide sequence of L. rhamnosus strain HN001 phosphoryl carrier protein HPR AA9 (SEQ ID NO: 4) showing ATG initiation and translation stop codons (boxed).

[0104] FIG. 42 shows the amino acid sequence of L. rhamnosus strain HN001 phosphoryl carrier protein HPR AA9 (SEQ ID NO: 45).

[0105] FIG. 43 shows the nucleotide sequence of L. rhamnosus strain HN001 glyceraldehyde-3-phosphate dehydrogenase AK7 (SEQ ID NO: 23) showing ATG initiation and translation stop codons (boxed).

[0106] FIG. 44 shows the amino acid sequence of L. rhamnosus strain HN001 glyceraldehyde-3-phosphate dehydrogenase AK7 (SEQ ID NO: 65).

[0107] FIG. 45 shows the nucleotide sequence of L. rhamnosus strain HN001 sorR transcription regulator AL3 (SEQ ID NO: 24) showing ATG initiation and translation stop codons (boxed).

[0108] FIG. 46 shows the amino acid sequence of L. rhamnosus strain HN001 sorR transcription regulator AL3 (SEQ ID NO: 66).

[0109] FIG. 47 shows the nucleotide sequence of L. rhamnosus strain fpg gene AL4 (SEQ ID NO: 25) showing ATG initiation and translation stop codons (boxed).

[0110] FIG. 48 shows the amino acid sequence of HN001 fpg AL4 (SEQ ID NO: 67).

[0111] FIG. 49 shows the nucleotide sequence of the L. rhamnosus strain HN001 acetoin dehydrogenase gene AP1 (SEQ ID NO: 32) showing ATG initiation and translation stop codons (boxed).

[0112] FIG. 50 shows the amino acid sequence of HN001 acetoin dehydrogenase AP1 (SEQ ID NO: 74).

[0113] FIG. 51 illustrates the experimental results of an acetoin reductase assay as measured by oxidation of NADH co-factor by OD at 340 nm in the presence of acetoin substrate. .lamda., elution buffer only; .nu., purified irrelevant GST-fusion protein; .nu., purified GST protein; .upsilon., purified AP1-GST fusion protein.

[0114] FIG. 52 shows the nucleotide sequence of the L. rhamnosus strain HN001 aflatoxin B.sub.1 aldehyde reductase gene AI7 (SEQ ID NO: 15) showing ATG initiation and translation stop codons (boxed).

[0115] FIG. 53 shows the amino acid sequence of HN001 aflatoxin B.sub.1 aldehyde reductase AI7 (SEQ ID NO: 57).

[0116] FIG. 54 shows the experimental results of aflatoxin B.sub.1 aldehyde reductase assay according to oxidation of the NADPH co-factor in the presence of acetoin substrate. X, water only; +, Sepharose column elution buffer only; .lamda., irrelevant GST-fusion protein; .nu., 10 .mu.l purified AP4-GST fusion protein; .sigma. 20 .mu.l purified AP4-GST fusion protein.

[0117] FIG. 55 shows the experimental determination of 6-Phospho-.beta.-galactosidase enzyme activity as measured by substrate utilization using crude lysates of strains transformed with pGex-6P-3 encoding A05 (.upsilon.), pGex-6P-3 encoding an irrelevant protein (.nu.), or using lysis buffer only (X).

[0118] FIG. 56 shows the experimentally determined 6-Phospho-.beta.-galactosidase enzyme activity as measured experimentally by substrate utilization using increasing amounts of crude lysate from strains transformed with pGex-6P-3 encoding A05-GST fusion protein. .upsilon., 50 .mu.l lysate; .nu., 100 .mu.l lysate; .sigma., 200 .mu.l lysate; .lamda., 200 .mu.l lysis buffer only.

[0119] FIG. 57 shows the nucleotide sequence of the L. rhamnosus strain HN001 aromatic aminotransferase gene AH7 (SEQ ID NO: 11) showing ATG initiation and translation stop codons (boxed).

[0120] FIG. 58 shows the amino acid sequence of HN001 aromatic aminotransferase AH7 (SEQ ID NO: 53).

[0121] FIG. 59 shows the nucleotide sequence of the L. rhamnosus strain HN001 acetate kinase gene AP5 (SEQ ID NO: 33) showing ATG initiation and translation stop codons (boxed).

[0122] FIG. 60 shows the amino acid sequence of HN001 acetate kinase AP5 (SEQ ID NO: 75).

[0123] FIG. 61 shows the nucleotide sequence of the L. rhamnosus strain HN001 basic surface protein gene AC9 (SEQ ID NO: 6) showing ATG initiation and translation stop codons (boxed).

[0124] FIG. 62 shows the amino acid sequence of HN001 basic surface protein AC9 (SEQ ID NO: 47).

[0125] FIGS. 63A-C show the nucleotide sequence of the L. rhamnosus strain HN001 aromatic outer membrane protein A AL8 (SEQ ID NO: 27) showing ATG initiation and translation stop codons (boxed).

[0126] FIG. 64 shows the amino acid sequence of HN001 outer membrane protein AL8 (SEQ ID NO: 69).

[0127] FIGS. 65A-D show the nucleotide sequence of the L. rhamnosus strain HN001 aromatic extracellular matrix binding protein AM4 (SEQ ID NO: 28) showing ATG initiation and translation stop codons (boxed).

[0128] FIGS. 66A-B show the amino acid sequence of HN001 extracellular matrix binding protein AM4 (SEQ ID NO: 70).

[0129] FIGS. 67A-D show the nucleotide sequence of the L. rhamnosus strain HN001 aromatic high-molecular-weight adhesion protein AL7 (SEQ ID NO: 26) showing ATG initiation and translation stop codons (boxed).

[0130] FIG. 68 shows the amino acid sequence of HN001 high-molecular-weight adhesion protein AL7 (SEQ ID NO: 68).

[0131] FIG. 69 shows the nucleotide sequence of the L. rhamnosus strain HN001 aromatic PEB1 AJ4 (SEQ ID NO: 16) showing ATG initiation and translation stop codons (boxed).

[0132] FIG. 70 shows the amino acid sequence of HN001 PEB1 AJ4 (SEQ ID NO: 58).

[0133] FIG. 71 shows the experimentally determined relative density of autoradiographic signals from AJ4 protein (grey bars) to dot blots of intestinal proteins, compared to a positive control (mapA, white bars) and negative control (irrelevant HN001 protein, black bars). Results for each dot (duplicates) are shown.

[0134] FIG. 72 shows the nucleotide sequence of the L. rhamnosus strain HN001 dihydrodipicolinate reductase AI3 (SEQ ID NO: 14) showing ATG initiation and translation stop codons (boxed).

[0135] FIG. 73 shows the amino acid sequence of HN001 dihydrodipicolinate reductase AI3 (SEQ ID NO: 56).

[0136] FIG. 74 shows the nucleotide sequence of the L. rhamnosus strain HN001 Fructose-bisphosphate aldolase AM8 (SEQ ID NO: 29) showing ATG initiation and translation stop codons (boxed).

[0137] FIG. 75 shows the amino acid sequence of HN001 Fructose-bisphosphate aldolase AM8 (SEQ ID NO: 71).

[0138] FIG. 76 shows the nucleotide sequence of the L. rhamnosus strain HN001 chaperone protein dnaK AM9 (SEQ ID NO: 30) showing ATG initiation and translation stop codons (boxed).

[0139] FIG. 77 shows the amino acid sequence of HN001 chaperone protein dnaK AM9 (SEQ ID NO: 72).

[0140] FIG. 78 shows the nucleotide sequence of the L. rhamnosus strain HN001 6-phospho-.beta.-galactosidase gene AO5 (SEQ ID NO: 31) showing translation stop codon (boxed).

[0141] FIG. 79 shows the amino acid sequence of HN001 6-phospho-.beta.-galactosidase AO5 (SEQ ID NO: 73).

[0142] FIGS. 80A-B show the nucleotide sequence of the L. rhamnosus strain HN001 peptidase pepO (SEQ ID NO: 1) showing ATG initiation and translation stop codons (boxed).

[0143] FIG. 81 shows the amino acid sequence of HN001 peptidase pepO (SEQ ID NO: 42).

DETAILED DESCRIPTION

[0144] The polynucleotides disclosed herein were isolated by high throughput sequencing of DNA libraries from the lactic acid bacteria Lactobacillus rhamnosus as described in Example 1. The polynucleotides and polypeptides of the present invention including cell components selected from the group consisting of: peptidoglycans, teichoic acids, lipoteichoic acids, polysaccharides, adhesion proteins, secreted proteins, surface layer or S-layer proteins, collagen binding proteins and other cell surface proteins, and antibacterial substances such as bacteriocins and organic acids produced by these bacteria. Such bacterial cell components are known to mediate immune modulation, cell adhesion and antibacterial activities, producing many beneficial effects including: resistance to enteric pathogens: modulation of cancer, including colon cancer: anti-mutagenesis effects; reduction of small bowel bacterial overgrowth; modulation of auto-immune disorders; reduction in allergic disorders; modulation of urogenital infections, inflammatory bowel disorder, irritable bowel syndrome, Helicobacter pylori infection and hepatic encephalopathy; reduction of infection with pathogens; regulation of colonocyte proliferation and differentiation; reduction of mucosal permeability; and relief of constipation and diarrhea. Polynucleotides involved in the synthesis of these proteins and in the synthesis, modification, regulation, transport, synthesis and/or accumulation of precursor molecules for these proteins are used to modulate the immune effects, antibacterial, cell adhesion and competitive exclusion effects of the bacteria or of components that might be produced by these bacteria.

[0145] In order to function effectively as probiotic bacteria, L. rhamnosus HN001 survives environmental stress conditions in the gastrointestinal tract, as well as commercial and industrial processes. Modification of particular polynucleotides or regulatory processes has been shown to be effective against a number of stresses including oxidative stress, pH, osmotic stress, dehydration, carbon starvation, phosphate starvation, nitrogen starvation, amino acid starvation, heat or cold shock and mutagenic stress. Polynucleotides involved in stress resistance often confer multistress resistance, i.e., when exposed to one stress, surviving cells are resistant to several non-related stresses. Bacterial genes and/or processes shown to be involved in multistress resistance include:

[0146] Intracellular phosphate pools--inorganic phosphate starvation leads to the induction of pho regulon genes, and is linked to the bacterial stringent response. Gene knockouts involving phosphate receptor genes appear to lead to multistress resistance.

[0147] Intracellular guanosine pools--purine biosynthesis and scavenger pathways involve the production of phosphate-guanosine compounds that act as signal molecules in the bacterial stringent response. Gene knockouts involving purine scavenger pathway genes appear to confer multistress resistance.

[0148] Osmoregulatory molecules--small choline-based molecules, such as glycine-betaine, and sugars, such as trehalose, are protective against osmotic shock and are rapidly imported and/or synthesized in response to increasing osmolarity.

[0149] Acid resistance--lactobacilli naturally acidify their environment through the excretion of lactic acid, mainly through the cit operon genes responsible for citrate uptake and utilization.

[0150] Stress response genes--a number of genes appear to be induced or repressed by heat shock, cold shock, and increasing salt through the action of specific promoters.

[0151] The isolated polynucleotides of the present invention and genetic constructs comprising such polynucleotides may be employed to produce bacteria having desired phenotypes, including increased resistance to stress and improved fermentation properties. Such genetic constructs may be used to increase production of selected polypeptides of the present invention in modified bacteria, or to produce modified levels and/or compositions of polypeptides related to polypeptides of the present invention in modified bacteria. Bacteria having desired phenotypes may also be produced by modulating the transcription and/or expression of polynucleotides of the present invention and incorporating modified regulatory elements in modified bacteria. Additionally, production of selected polypeptides of the present invention may be reduced or blocked in modified bacteria using techniques that are well known in the art, such as antisense RNAi or other gene silencing techniques. Such modified bacteria are also encompassed by the present invention.

[0152] Many enzymes are known to influence dairy product flavor, functional and textural characteristics, as well as general fermentation characteristics such as speed of growth, acid production and survival. These enzymes include those involved in the metabolism of lipids, polysaccharides, amino acids and carbohydrates, as well as those involved in the lysis of the bacterial cells.

[0153] The isolated polynucleotides and polypeptides of the present invention have been demonstrated to have the identities, functions and utilities described throughout this application and in the Examples. The polynucleotide and polypeptide SEQ ID NOs of the present invention, and corresponding identification and functional information is provided below in Table 1A. TABLE-US-00001 TABLE 1A SEQ ID SEQ ID NO: NO: Polynucleotide Polypeptide Category Identification and Description 1 42 Flavor, Peptidases are enzymes that break the peptide bonds nutrition linking the amino group of one amino acid with the carboxy group (acid group) of an adjacent amino acid in a peptide chain. Peptidases are important in the process of cheese ripening and the development of cheese flavor. 2 43 Flavor, Homolog isolated from L. rhamnosus of citM malic carbohydrate enzyme that catalyzes L-malate oxidative metabolism decarboxylation and pyruvate reductive carboxylation. It is part of the noncyclic, branched pathway "tricarboxylic acid cycle" that is characteristic of anaerobic citrate metabolism and is part of the pathway that converts L-malate to L-lactate. 3 44 Flavor Homolog isolated from L. rhamnosus of her esterase that catalyzes the lipolysis of milk fat in dairy products such that the triglycerides are hydrolyzed to free fatty acids and glycerol or mono- and diglycerides. The protein plays an essential role in the development of flavor in cheese 4 45 Survival Homolog isolated from L. rhamnosus of JP28/pbH phosphoryl carrier protein HPR, involved in the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) that is responsible for the uptake and phosphorylation of a number of carbohydrates. The gene is up-regulated on heatshock 5 46 Amino acid Homolog isolated from L. rhamnosus of metC metabolism, cystathione beta-lyase (EC 4.4.1.8) that is involved in flavor metabolism of sulpher-containing compounds with important flavor impacts. 6 47 Adhesion Homolog isolated from L. rhamnosus of basic surface protein bspA (1) that is involved in adhesion to intestinal epithelial cells and binds mucin. 7 48 Amino acid Homolog isolated from L. rhamnosus of serine metabolism, dehydratase sdhB, beta subunit that is involved in the flavor production of pyruvate from serine. It plays a role in metabolism, flavor and survival in carbohydrate poor media (including milk). 7 49 Amino acid Homolog isolated from L. rhamnosus metabolism, of the serine dehydratse alpha subunit sdhA flavor that is involved in the production of pyruvate from serine. It plays a role in metabolism, flavor and survival in carbohydrate poor media (including milk). 8 50 Amino acid Homolog isolated from L. rhamnosus of metabolism, Aminotransferase HisC that is involved in histidine flavor biosynthesis. It plays a role in the development flavor and biogenic amines. 9 51 Flavor, Homolog isolated from L. rhamnosus of malate carbohydrate dehydrogenase citH that is involved in amino acid metabolism biosynthesis as well as L-malate utilization pathways. It is important for carbohydrate metabolism and production of flavor intermediates. 10 52 Adhesion Homolog isolated from L. rhamnosus of autoaggregation protein aggH that plays a role in colonization of intestinal surface by excluding other bacteria from binding sites. 11 53 Amino acid Homolog isolated from L. rhamnosus of aromatic metabolism, amino acid transferase araT (1) that is involved in flavor production of flavor compounds. 12 54 Amino acid Homolog isolated from L. rhamnosus of aspartate metabolism, aminotransferase aspB that produces alpha- flavor ketoglutarate using L-glutamate as an amino donor. It is involved in production of important flavor determinants. 13 55 Amino acid Homolog isolated from L. rhamnosus of metabolism, dihydrodipicolinate synthase dapA (EC 4.2.1.52) that flavor converts L-aspartate 4-semialdehyde and pyruvate to l- 2,3-dihydrodipicolinate as part of the lysine biosynthesis pathway. L-aspartate 4-semialdehyde is also the first step of the glycine, serine and threonine metabolic pathways. It is involved in production of important flavor determinants. 14 56 Amino acid Homolog isolated from L. rhamnosus of metabolism, dihydrodipicolinate reductase dapB (EC 1.3.1.26) that flavor converts L-2,3-dihydrodipicolinate to L- tetrahydropicolinate as part of the lysine biosynthesis pathway. L-aspartate 4-semialdehyde is also the first step of the glycine, serine and threonine metabolic pathways. It is involved in production of important flavor determinants. 15 57 Health Homolog isolated from L. rhamnosus of Aflatoxin B1 aldehyde reductase afar that metabolizes the carcinogen aflatoxin B1 (AFB1) and that is associated with AFB1-resistance. Afar is active against particular ketones, aromatic and aliphatic aldehydes and is an antocarcinogenic. It is also useful for the production of flavor compounds. 16 58 Adhesion Homolog isolated from L. rhamnosus of pebB that mediates binding to epithelial cells, excludes binding of other bacteria and prevents pathogenic infection. It is involved in colonization of intestinal surfaces. 17 59 Amino acid Homolog isolated from L. rhamnosus of Pyridoxal-5'- metabolism, phosphate-dependent aminotransferase patB (1) that flavor has both aminotransferase and regulatory activities, including the transamination of methionine and regulation of maltose utilization. It plays a role in production of flavor intermediates and growth on particular sugars. 18 60 Amino acid Homolog isolated from L. rhamnosus of Pyridoxal-5'- metabolism, phosphate-dependent aminotransferase patB (2) that flavor has both aminotransferase and regulatory activities, including the transamination of methionine and regulation of maltose utilization. It plays a role in production of flavor intermediates and growth on particular sugars. 19 61 Survival Homolog isolated from L. rhamnosus of Tagatose 1,6- diphosphate aldolase lacD (EC 4.1.2.40), a glycolytic enzyme that is up-regulated by stress conditions and is involved in stress resistance and carbohydrate utilization. 20 62 Survival Homolog isolated from L. rhamnosus of Phosphoenolpyruvate hydratase eno (EC 4.2.1.11), a glycolytic enzyme up-regulated by stress conditions. It is involved in stress resistance and carbohydrate utilization. 21 63 Survival Homolog isolated from L. rhamnosus of triosephosphate isomerase tpi (EC 5.3.1.1), a glycolytic enzyme up-regulated by stress conditions. It is involved in stress resistance and carbohydrate utilization. 22 64 Survival Homolog isolated from L. rhamnosus of phosphoglycerate kinase pgk (EC 2.7.2.3), a glycolytic enzyme up-regulated by stress conditions. It is involved in stress resistance and carbohydrate utilization. 23 65 Cell wall Homolog isolated from L. rhamnosus of structure and Glyceraldehyde-3-phosphate dehydrogenase gapdh function (EC 1.2.1.12), a glycolytic enzyme up-regulated by stress conditions. It is involved in stress resistance and carbohydrate utilization and is also a major cell wall component. 24 66 Regulation Homolog isolated from L. rhamnosus of the positive regulator sorR in the sorbose operon. It is important in the control of carbohydrate metabolism and useful for inducible promoter for novel vectors. 25 67 Survival Homolog isolated from L. rhamnosus of Formamidopyrimidine-DNA-glycosylase fpg that is important in protecting bacterial DNA against oxidative free radicals. It removes oxidized purine residues present in DNA, including the highly mutagenic C8-oxo-guanine (8-oxoG) generated in DNA by active oxygen during metabolism. It plays an important role in stress resistance. 26 68 Adhesion Homolog isolated from L. rhamnosus of hia, that mediates binding to epithelial cells and excludes binding of other bacteria. It is involved in colonization of intestinal surfaces. 27 69 Adhesion Homolog isolated from L. rhamnosus of Outer membrane protein rompA, a surface bound molecule required for adhesion. 28 70 Adhesion Homolog isolated from L. rhamnosus of MLC36/emb that mediates binding to epithelial cells, excludes binding of other bacteria and prevents pathogenic infection. It is involved in colonization of intestinal surfaces and is involved in plasminogen binding. It plays a role in immune impacts. 29 71 Survival Homolog isolated from L. rhamnosus of Fructose- bisphosphate aldolase fba (EC 4.1.2.13), a glycolytic enzyme that catalyzes the elimination reaction of D- Fructose 1,6-bisphosphate to glycerone phosphate and D-glyceraldehyde 3-phosphate. It is Up-regulatedby shock and is involved in metabolism, as a flavor intermediates and in stress resistance. 30 72 Stress Homolog isolated from L. rhamnosus of chaperone resistance protein dnaK that plays a role in enhanced bacterial survival in industrial processes, improved colonization of human intestinal environment, altered protein translation characteristics and control of plasmid stability. 31 73 Bacterial Homolog isolated from L. rhamnosus of 6-phospho-.beta.- growth, galactosidase (EC 3.2.1.85) that catalyzes the nutrition, hydrolysis of O-glycosyl bonds of 6-phospho-beta-D- flavor galactosides to give alcohols and 6-phospho-D- development galactose, and is involved in lactose utilization. It is useful for flavor and aroma enhancement, nutritional enhancement, altered bacterial metabolic/growth characteristics and removal of bitter or undesirable flavors. 32 74 Flavor Homolog isolated from L. rhamnosus of Acetoin dehydrogenase butA (EC 1.1.1.5) that catalyzes the reduction of diacetyl to acetoin, and acetoin to 2,3- butanediol as part of the pyruvate to 2,3-butanediol pathway. Diacetyl is an important dairy flavor component. 33 75 Flavor Homolog isolated from L. rhamnosus of Acetyl kinase ackA (EC 2.7.2.1) that catalyzes the phosphotransfer between ADP and acetyl phosphate to yield ATP and acetate.

[0154] Isolated polynucleotides of the present invention include the polynucleotides identified herein as SEQ ID NO: 1-33; isolated polynucleotides comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-33; isolated polynucleotides comprising at least a specified number of contiguous residues (x-mers) of any of the polynucleotides identified as SEQ ID NO: 1-33; isolated polynucleotides comprising a polynucleotide sequence that is complementary to any of the above polynucleotides; isolated polynucleotides comprising a polynucleotide sequence that is a reverse sequence or a reverse complement of any of the above polynucleotides; antisense sequences corresponding to any of the above polynucleotides; and variants of any of the above polynucleotides, as that term is described in this specification.

[0155] The word "polynucleotide(s)," as used herein, means a single or double stranded polymer of deoxyribonucleotide or ribonucleotide bases and includes DNA and corresponding RNA molecules, including mRNA molecules, both sense and antisense strands of DNA and RNA molecules, and comprehends cDNA, genomic DNA and recombinant DNA, as well as wholly or partially synthesized polynucleotides. A polynucleotide of the present invention may be an entire gene, or any portion thereof. A gene is a DNA sequence which codes for a functional protein or RNA molecule. Operable antisense polynucleotides may comprise a fragment of the corresponding polynucleotide, and the definition of "polynucleotide" therefore includes all operable antisense fragments. Antisense polynucleotides and techniques involving antisense polynucleotides are well known in the art and are described, for example, in Robinson-Benion, et al., "Antisense techniques," Methods in Enzymol. 254(23): 363-375, 1995; and Kawasaki, et al., Artific. Organs 20 (8): 836-848, 1996.

[0156] The definitions of the terms "complement," "reverse complement," and "reverse sequence," as used herein, are best illustrated by the following examples. For the sequence 5' AGGACC 3', the complement, reverse complement, and reverse sequences are as follows: TABLE-US-00002 complement 3' TCCTGG 5' reverse complement 3' GGTCCT 5' reverse sequence 5' CCAGGA 3'

[0157] Preferably, sequences that are complements of a specifically recited polynucleotide sequence are complementary over the entire length of the specific polynucleotide sequence.

[0158] Identification of genomic DNA and heterologous species DNA can be accomplished by standard DNA/DNA hybridization techniques, under appropriately stringent conditions, using all or part of a DNA sequence as a probe to screen an appropriate library. Alternatively, PCR techniques using oligonucleotide primers that are designed based on known DNA and protein sequences can be used to amplify and identify other identical or similar DNA sequences. Synthetic DNA corresponding to the identified sequences or variants thereof may be produced by conventional synthesis methods. All of the polynucleotides described herein are isolated and purified, as those terms are commonly used in the art.

[0159] The polynucleotides identified as SEQ ID NO: 1-33 contain open reading frames ("ORFs"), or partial open reading frames, encoding polypeptides. The open reading frames are specifically identified in Example 1, below. Additionally, polynucleotides identified as SEQ ID NO: 1-33 may contain non-coding sequences such as promoters and terminators that may be useful as control elements. The open reading frames contained in polynucleotides of the present invention may be isolated and/or synthesized. Expressible genetic constructs comprising the open reading frames and suitable promoters, initiators, terminators, etc., which are well known in the art, may then be constructed. Such genetic constructs may be introduced into a host cell to express the polypeptide encoded by the open reading frame. Expression of quantities of a polypeptide of the present invention using recombinant methodologies is useful, for example, when polynucleotides of the present invention are used as nutritional supplements, as flavor and/or texture enhancers, or the like.

[0160] Genetic constructs may be also designed and constructed, as is known in the art, to enhance or silence expression of an identified polypeptide. Antisense and gene silencing genetic constructs may be designed and constructed, for example, to reduce or silence expression of polypeptides of the present invention. Genetic constructs of the present invention may thus be assembled using techniques known in the art to enhance or reduce expression of polypeptides of the present invention encoded by polynucleotides of the present invention. Suitable host cells may include various prokaryotic and eukaryotic cells. In vitro expression of polypeptides is also possible, as well known in the art.

[0161] As used herein, the term "oligonucleotide" refers to a relatively short segment of a polynucleotide sequence, generally comprising between 6 and 60 nucleotides, and comprehends both probes for use in hybridization assays and primers for use in the amplification of DNA by polymerase chain reaction.

[0162] As used herein, the term "x-mer," with reference to a specific value of "x," refers to a polynucleotide or polypeptide comprising at least a specified number ("x") of contiguous residues of any of the polynucleotides and polypeptides identified as SEQ ID NO: 1-33 and 42-75. The value of x may be from about 20 to about 600, depending upon the specific sequence.

[0163] In another aspect, the present invention provides isolated polypeptides encoded, or partially encoded, by the above polynucleotides, including the polypeptides identified as SEQ ID NO: 42-75. As used herein, the term "polypeptide" encompasses amino acid chains of any length, including full-length proteins, wherein the amino acid residues are linked by covalent peptide bonds. The term "polypeptide encoded by a polynucleotide" as used herein, includes polypeptides encoded by a polynucleotide which comprises an isolated polynucleotide sequence or variant provided herein. Polypeptides of the present invention may be naturally purified products, or may be produced partially or wholly using recombinant techniques. Such polypeptides may be glycosylated with bacterial, fungal, mammalian or other eukaryotic carbohydrates or may be non-glycosylated.

[0164] Polypeptides of the present invention may be produced recombinantly by inserting a polynucleotide that encodes the polypeptide into an expression vector and expressing the polypeptide in an appropriate host. Any of a variety of expression vectors known to those of ordinary skill in the art may be employed. Expression may be achieved in any appropriate host cell that has been transformed or transfected with an expression vector containing a polynucleotide encoding a recombinant polypeptide. Suitable host cells include prokaryotes, yeast and higher eukaryotic cells. Preferably, the host cells employed are Escherichia coli, Lactococcus lactis, Lactobacillus, insect, yeast or mammalian cell lines, such as COS and CHO. The polynucleotide(s) expressed in this manner may encode naturally occurring polypeptides, portions of naturally occurring polypeptides, or other variants thereof.

[0165] In a related aspect, polypeptides are provided that comprise at least a functional portion of a polypeptide having an amino acid sequence encoded by a polynucleotide of the present invention. As used herein, a "functional portion" of a polypeptide is that portion which contains the active site essential for affecting the function of the polypeptide, for example, the portion of the molecule that is capable of binding one or more reactants. The active site may be made up of separate portions present on one or more polypeptide chains and will generally exhibit high binding affinity.

[0166] Functional portions of a polypeptide may be identified by first preparing fragments of the polypeptide by either chemical or enzymatic digestion of the polypeptide, or by mutation analysis of the polynucleotide that encodes the polypeptide and subsequent expression of the resulting mutant polypeptides. The polypeptide fragments or mutant polypeptides are then tested to determine which portions retain biological activity, using, for example, the representative assays provided below.

[0167] Portions and other variants of the inventive polypeptides may be generated by synthetic or recombinant means. Synthetic polypeptides having fewer than about 100 amino acids, and generally fewer than about 50 amino acids, may be generated using techniques that are well known to those of ordinary skill in the art. For example, such polypeptides may be synthesized using any of the commercially available solid-phase techniques, such as the Merrifield solid-phase synthesis method, where amino acids are sequentially added to a growing amino acid chain (See Merrifield, J. Am. Chem. Soc. 85:2149-2154, 1963). Equipment for automated synthesis of polypeptides is commercially available from suppliers such as Perkin Elmer/Applied Biosystems, Inc. (Foster City, Calif.), and may be operated according to the manufacturer's instructions. Variants of a native polypeptide may be prepared using standard mutagenesis techniques, such as oligonucleotide-directed site-specific mutagensis (Kunkel, Proc. Natl. Acad. Sci. USA 82: 488-492, 1985). Sections of DNA sequences may also be removed using standard techniques to permit preparation of truncated polypeptides.

[0168] In general, the polypeptides disclosed herein are prepared in an isolated, substantially pure form. Preferably, the polypeptides are at least about 80% pure; more preferably at least about 90% pure; and most preferably at least about 99% pure.

[0169] As used herein, the term "variant" comprehends polynucleotide or polypeptide sequences different from the specifically identified sequences, wherein one or more nucleotides or amino acid residues is deleted, substituted, or added. Variants may be naturally occurring allelic variants, or non-naturally occurring variants. Variant polynucleotide and polypeptide sequences preferably exhibit at least 75%, more preferably at least 80%, more preferably yet at least 85%, and most preferably at least 90% or 95% identity to a sequence of the present invention. The percentage identity is determined by aligning the two sequences to be compared as described below, determining the number of identical residues in the aligned portion, dividing that number by the total number of residues in the inventive (queried) sequence, and multiplying the result by 100.

[0170] Polynucleotide and polypeptide sequences may be aligned, and the percentage of identical residues in a specified region may be determined against another polynucleotide or polypeptide, using computer algorithms that are publicly available. Two exemplary algorithms for aligning and identifying the similarity of polynucleotide sequences are the BLASTN and FASTA algorithms. Polynucleotides may also be analyzed using the BLASTX algorithm, which compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database. The percentage identity of polypeptide sequences may be examined using the BLASTP algorithm. The BLASTN, BLASTX and BLASTP programs are available on the NCBI anonymous FTP server and from the National Center for Biotechnology Information (NCBI), National Library of Medicine, Building 38A, Room 8N805, Bethesda, Md. 20894, USA. The BLASTN algorithm Version 2.0.11 [Jan. 20, 2000], set to the parameters described below, is preferred for use in the determination of polynucleotide variants according to the present invention. The BLASTP algorithm, set to the parameters described below, is preferred for use in the determination of polypeptide variants according to the present invention. The use of the BLAST family of algorithms, including BLASTN, BLASTP and BLASTX, is described at NCBI's website and in the publication of Altschul, et al., Nucleic Acids Res. 25: 3389-3402, 1997.

[0171] The computer algorithm FASTA is available on the Internet and from the University of Virginia by contacting the Vice Provost for Research, University of Virginia, P.O. Box 9025, Charlottesville, Va. 22906-9025, USA. FASTA Version 2.0u4 [February 1996], set to the default parameters described in the documentation and distributed with the algorithm, may be used in the determination of variants according to the present invention. The use of the FASTA algorithm is described in Pearson and Lipman, Proc. Natl. Acad. Sci. USA 85:2444-2448, 1988; and Pearson, Methods in Enzymol. 183: 63-98, 1990.

[0172] The following running parameters are preferred for determination of alignments and similarities using BLASTN that contribute to the E values and percentage identity for polynucleotide sequences: Unix running command: blastall -p blastn -d embldb -e 10 -G0 -E0 -r 1 -v 30 -b 30 -i queryseq -o results; the parameters are: -p Program Name [String]; -d Database [String]; -e Expectation value (E) [Real]; -G Cost to open a gap (zero invokes default behavior) [Integer]; -E Cost to extend a gap (zero invokes default behavior) [Integer]; -r Reward for a nucleotide match (BLASTN only) [Integer]; -v Number of one-line descriptions (V) [Integer]; -b Number of alignments to show (B) [Integer]; -i Query File [File In]; and -o BLAST report Output File [File Out] Optional.

[0173] The following running parameters are preferred for determination of alignments and similarities using BLASTP that contribute to the E values and percentage identity of polypeptide sequences: blastall -p blastp -d swissprotdb -e 10 -G 0 -E 0 -v 30 -b 30 -i queryseq -o results; the parameters are: -p Program Name [String]; -d Database [String]; -e Expectation value (E) [Real]; -G Cost to open a gap (zero invokes default behavior) [Integer]; -E Cost to extend a gap (zero invokes default behavior) [Integer]; -v Number of one-line descriptions (v) [Integer]; -b Number of alignments to show (b) [Integer]; -I Query File [File In]; -o BLAST report Output File [File Out] Optional. The "hits" to one or more database sequences by a queried sequence produced by BLASTN, FASTA, BLASTP or a similar algorithm, align and identify similar portions of sequences. The hits are arranged in order of the degree of similarity and the length of sequence overlap. Hits to a database sequence generally represent an overlap over only a fraction of the sequence length of the queried sequence.

[0174] The BLASTN, FASTA, and BLASTP algorithms also produce "Expect" values for alignments. The Expect value (E) indicates the number of hits one can "expect" to see over a certain number of contiguous sequences by chance when searching a database of a certain size. The Expect value is used as a significance threshold for determining whether the hit to a database, such as the preferred EMBL database, indicates true similarity. For example, an E value of 0.1 assigned to a polynucleotide hit is interpreted as meaning that in a database of the size of the EMBL database, one might expect to see 0.1 matches over the aligned portion of the sequence with a similar score simply by chance. By this criterion, the aligned and matched portions of the polynucleotide sequences then have a probability of 90% of being the same. For sequences having an E value of 0.01 or less over aligned and matched portions, the probability of finding a match by chance in the EMBL database is 1% or less using the BLASTN or FASTA algorithm.

[0175] According to one embodiment, "variant" polynucleotides and polypeptides, with reference to each of the polynucleotides and polypeptides of the present invention, preferably comprise sequences producing an E value of 0.01 or less using the BLASTN, FASTA, or BLASTP algorithms set at parameters described above when compared to the polynucleotide or polypeptide of the present invention. According to a preferred embodiment, a variant polynucleotide is a sequence having an E value of 0.01 or less using the BLASTN or FASTA algorithms set at parameters described above when analyzed against a polynucleotide of the present invention. Similarly, according to a preferred embodiment, a variant polypeptide is a sequence having an E value of 0.01 or less using the BLASTP algorithm set at the parameters described above when analyzed against a polynucleotide of the present invention.

[0176] As noted above, the percentage identity is determined by aligning sequences using one of the BLASTN, FASTA, or BLASTP algorithms, set at the running parameters described above, and identifying the number of identical nucleic or amino acids over the aligned portions; dividing the number of identical nucleic or amino acids by the total number of nucleic or amino acids of the polynucleotide or polypeptide sequence of the present invention; and then multiplying by 100 to determine the percentage identity. For example, a polynucleotide of the present invention having 220 nucleic acids has a hit to a polynucleotide sequence in the EMBL database having 520 nucleic acids over a stretch of 23 nucleotides in the alignment produced by the BLASTN algorithm using the parameters described above. The 23 nucleotide hit includes 21 identical nucleotides, one gap and one different nucleotide. The percentage identity of the polynucleotide of the present invention to the hit in the EMBL library is thus 21/220 times 100, or 9.5%. The polynucleotide sequence in the EMBL database is thus not a variant of a polynucleotide of the present invention.

[0177] In addition to having a specified percentage identity to an inventive polynucleotide or polypeptide sequence, variant polynucleotides and polypeptides preferably have additional structure and/or functional features in common with the inventive polynucleotide or polypeptide. Polypeptides having a specified degree of identity to a polypeptide of the present invention share a high degree of similarity in their primary structure and have substantially similar functional properties. In addition to sharing a high degree of similarity in their primary structure to polynucleotides of the present invention, polynucleotides having a specified degree of identity to, or capable of hybridizing to an inventive polynucleotide preferably have at least one of the following features: (i) they contain an open reading frame or partial open reading frame encoding a polypeptide having substantially the same functional properties as the polypeptide encoded by the inventive polynucleotide; or (ii) they contain identifiable domains in common.

[0178] Alternatively, variant polynucleotides of the present invention hybridize to the polynucleotide sequences recited in SEQ ID NO: 1-33, or complements, reverse sequences, or reverse complements of those sequences under stringent conditions. As used herein, "stringent conditions" refers to prewashing in a solution of 6.times.SSC, 0.2% SDS; hybridizing at 65.degree. C., 6.times.SSC, 0.2% SDS overnight; followed by two washes of 30 minutes each in 1.times.SSC, 0.1% SDS at 65.degree. C. and two washes of 30 minutes each in 0.2.times.SSC, 0.1% SDS at 65.degree. C.

[0179] The present invention also encompasses polynucleotides that differ from the disclosed sequences but that, as a consequence of the discrepancy of the genetic code, encode a polypeptide having similar enzymatic activity as a polypeptide encoded by a polynucleotide of the present invention. Thus, polynucleotides comprising sequences that differ from the polynucleotide sequences recited in SEQ ID NO: 1-33, or complements, reverse sequences, or reverse complements of those sequences as a result of conservative substitutions are encompassed within the present invention. Additionally, polynucleotides comprising sequences that differ from the inventive polynucleotide sequences or complements, reverse complements, or reverse sequences as a result of deletions and/or insertions totaling less than 10% of the total sequence length are also contemplated by and encompassed within the present invention. Similarly, polypeptides comprising sequences that differ from the inventive polypeptide sequences as a result of amino acid substitutions, insertions, and/or deletions totaling less than 15% of the total sequence length are contemplated by and encompassed within the present invention, provided the variant polypeptide has similar activity to the inventive polypeptide.

[0180] The polynucleotides of the present invention may be isolated from various libraries, or may be synthesized using techniques that are well known in the art. The polynucleotides may be synthesized, for example, using automated oligonucleotide synthesizers (e.g., Beckman Oligo 1000M DNA Synthesizer) to obtain polynucleotide segments of up to 50 or more nucleic acids. A plurality of such polynucleotide segments may then be ligated using standard DNA manipulation techniques that are well known in the art of molecular biology. One conventional and exemplary polynucleotide synthesis technique involves synthesis of a single stranded polynucleotide segment having, for example, 80 nucleic acids, and hybridizing that segment to a synthesized complementary 85 nucleic acid segment to produce a 5-nucleotide overhang. The next segment may then be synthesized in a similar fashion, with a 5-nucleotide overhang on the opposite strand. The "sticky" ends ensure proper ligation when the two portions are hybridized. In this way, a complete polynucleotide of the present invention may be synthesized entirely in vitro.

[0181] Polynucleotides and polypeptides of the present invention comprehend polynucleotides and polypeptides comprising at least a specified number of contiguous residues .alpha.-mers) of any of the polynucleotides and polypeptides identified as SEQ ID NO: 1-33 and 42-75 or their variants. According to preferred embodiments, the value of x is preferably at least 20, more preferably at least 40, more preferably yet at least 60, and most preferably at least 80. Thus, polynucleotides and polypeptides of the present invention include polynucleotides comprising a 20-mer, a 40-mer, a 60-mer, an 80-mer, a 100-mer, a 120-mer, a 150-mer, a 180-mer, a 220-mer a 250-mer, or a 300-mer, 400-mer, 500-mer or 600-mer of a polynucleotide or polypeptide identified as SEQ ID NO: 1-75 or a variant of one of the polynucleotides or polypeptides identified as SEQ ID NO: 1-33 and 42-75.

[0182] Oligonucleotide probes and primers complementary to and/or corresponding to SEQ ID NO: 1-33, and variants of those sequences, are also comprehended by the present invention. Such oligonucleotide probes and primers are substantially complementary to the polynucleotide of interest. An oligonucleotide probe or primer is described as "corresponding to" a polynucleotide of the present invention, including one of the sequences set out as SEQ ID NO: 1-33 or a variant, if the oligonucleotide probe or primer, or its complement, is contained within one of the sequences set out as SEQ ID NO: 1-33 or a variant of one of the specified sequences.

[0183] Two single stranded sequences are said to be substantially complementary when the nucleotides of one strand, optimally aligned and compared, with the appropriate nucleotide insertions and/or deletions, pair with at least 80%, preferably at least 90% to 95%, and more preferably at least 98% to 100%, of the nucleotides of the other strand. Alternatively, substantial complementarity exists when a first DNA strand will selectively hybridize to a second DNA strand under stringent hybridization conditions. Stringent hybridization conditions for determining complementarity include salt conditions of less than about 1 M, more usually less than about 500 mM and preferably less than about 200 mM. Hybridization temperatures can be as low as 5.degree. C., but are generally greater than about 22.degree. C., more preferably greater than about 30.degree. C. and most preferably greater than about 37.degree. C. Longer DNA fragments may require higher hybridization temperatures for specific hybridization. Since the stringency of hybridization may be affected by other factors such as probe composition, presence of organic solvents and extent of base mismatching, the combination of parameters is more important than the absolute measure of any one alone. DNA-DNA hybridization studies may performed using either genomic DNA or DNA derived by preparing cDNA from the RNA present in a sample to be tested.

[0184] In addition to DNA-DNA hybridization, DNA-RNA or RNA-RNA hybridization assays are also possible. In the first case, the mRNA from expressed genes would then be detected instead of genomic DNA or cDNA derived from mRNA of the sample. In the second case, RNA probes could be used. In addition, artificial analogs of DNA hybridizing specifically to target sequences could also be used.

[0185] In specific embodiments, the oligonucleotide probes and/or primers comprise at least about 6 contiguous residues, more preferably at least about 10 contiguous residues, and most preferably at least about 20 contiguous residues complementary to a polynucleotide sequence of the present invention. Probes and primers of the present invention may be from about 8 to 100 base pairs in length or, preferably from about 10 to 50 base pairs in length or, more preferably from about 15 to 40 base pairs in length. The primers and probes may be readily selected using procedures well known in the art, taking into account DNA-DNA hybridization stringencies, annealing and melting temperatures, potential for formation of loops and other factors, which are well known in the art. Tools and software suitable for designing probes, and especially suitable for designing PCR primers, are available on the Internet. In addition, a software program suitable for designing probes, and especially for designing PCR primers, is available from Premier Biosoft International, 3786 Corina Way, Palo Alto, Calif. 94303-4504. Preferred techniques for designing PCR primers are also disclosed in Dieffenbach and Dyksler, PCR primer: a laboratory manual, CSHL Press: Cold Spring Harbor, N.Y., 1995.

[0186] A plurality of oligonucleotide probes or primers corresponding to a polynucleotide of the present invention may be provided in a kit form. Such kits generally comprise multiple DNA or oligonucleotide probes, each probe being specific for a polynucleotide sequence. Kits of the present invention may comprise one or more probes or primers corresponding to a polynucleotide of the present invention, including a polynucleotide sequence identified in SEQ ID NO: 1-33.

[0187] In one embodiment useful for high-throughput assays, the oligonucleotide probe kits of the present invention comprise multiple probes in an array format, wherein each probe is immobilized in a predefined, spatially addressable location on the surface of a solid substrate. Array formats which may be usefully employed in the present invention are disclosed, for example, in U.S. Pat. Nos. 5,412,087, 5,545,531, and PCT Publication No. WO 95/00530, the disclosures of which are hereby incorporated by reference.

[0188] Oligonucleotide probes for use in the present invention may be constructed synthetically prior to immobilization on an array, using techniques well known in the art (See, for example, Gait, ed., Oligonucleotide synthesis a practical approach, IRL Press: Oxford, England, 1984). Automated equipment for the synthesis of oligonucleotides is available commercially from such companies as Perkin Elmer/Applied Biosystems Division (Foster City, Calif.) and may be operated according to the manufacturer's instructions. Alternatively, the probes may be constructed directly on the surface of the array using techniques taught, for example, in PCT Publication No. WO 95/00530.

[0189] The solid substrate and the surface thereof preferably form a rigid support and are generally formed from the same material. Examples of materials from which the solid substrate may be constructed include polymers, plastics, resins, membranes, polysaccharides, silica or silica-based materials, carbon, metals and inorganic glasses. Synthetically prepared probes may be immobilized on the surface of the solid substrate using techniques well known in the art, such as those disclosed in U.S. Pat. No. 5,412,087.

[0190] In one such technique, compounds having protected functional groups, such as thiols protected with photochemically removable protecting groups, are attached to the surface of the substrate. Selected regions of the surface are then irradiated with a light source, preferably a laser, to provide reactive thiol groups. This irradiation step is generally performed using a mask having apertures at predefined locations using photolithographic techniques well known in the art of semiconductors. The reactive thiol groups are then incubated with the oligonucleotide probe to be immobilized. The precise conditions for incubation, such as temperature, time and pH, depend on the specific probe and can be easily determined by one of skill in the art. The surface of the substrate is washed free of unbound probe and the irradiation step is repeated using a second mask having a different pattern of apertures. The surface is subsequently incubated with a second, different, probe. Each oligonucleotide probe is typically immobilized in a discrete area of less than about 1 mm.sup.2. Preferably each discrete area is less than about 10,000 mm.sup.2, more preferably less than about 100 mm.sup.2. In this manner, a multitude of oligonucleotide probes may be immobilized at predefined locations on the array.

[0191] The resulting array may be employed to screen for differences in organisms or samples or products containing genetic material as follows. Genomic or cDNA libraries are prepared using techniques well known in the art. The resulting target DNA is then labeled with a suitable marker, such as a radiolabel, chromophore, fluorophore or chemiluminescent agent, using protocols well known for those skilled in the art. A solution of the labeled target DNA is contacted with the surface of the array and incubated for a suitable period of time.

[0192] The surface of the array is then washed free of unbound target DNA and the probes to which the target DNA hybridized are determined by identifying those regions of the array to which the markers are attached. When the marker is a radiolabel, such as .sup.32P, autoradiography is employed as the detection method. In one embodiment, the marker is a fluorophore, such as fluorescein, and the location of bound target DNA is determined by means of fluorescence spectroscopy. Automated equipment for use in fluorescence scanning of oligonucleotide probe arrays is available from Affymetrix, Inc. (Santa Clara, Calif.) and may be operated according to the manufacturer's instructions. Such equipment may be employed to determine the intensity of fluorescence at each predefined location on the array, thereby providing a measure of the amount of target DNA bound at each location. Such an assay would be able to indicate not only the absence and presence of the marker probe in the target, but also the quantitative amount as well.

[0193] The significance of such a high-throughput screening system is apparent for applications such as microbial selection and quality control operations in which there is a need to identify large numbers of samples or products for unwanted materials, to identify microbes or samples or products containing microbial material for quarantine purposes, etc., or to ascertain the true origin of samples or products containing microbes. Screening for the presence or absence of polynucleotides of the present invention used as identifiers for tagging microbes and microbial products can be valuable for later detecting the genetic composition of food, fermentation and industrial microbes or microbes in human or animal digestive system after consumption of probiotics, etc.

[0194] In this manner, oligonucleotide probe kits of the present invention may be employed to examine the presence/absence (or relative amounts in case of mixtures) of polynucleotides in different samples or products containing different materials rapidly and in a cost-effective manner. Examples of microbial species which may be examined using the present invention, include lactic acid bacteria, such as Lactobacillus rhamnosus, and other microbial species.

[0195] Another aspect of the present invention involves collections of a plurality of polynucleotides of the present invention. A collection of a plurality of the polynucleotides of the present invention, particularly the polynucleotides identified as SEQ ID NO: 1-33, may be recorded and/or stored on a storage medium and subsequently accessed for purposes of analysis, comparison, etc. Suitable storage media include magnetic media such as magnetic diskettes, magnetic tapes, CD-ROM storage media, optical storage media, and the like. Suitable storage media and methods for recording and storing information, as well as accessing information such as polynucleotide sequences recorded on such media, are well known in the art. The polynucleotide information stored on the storage medium is preferably computer-readable and may be used for analysis and comparison of the polynucleotide information.

[0196] Another aspect of the present invention thus involves storage medium on which are recorded a collection of the polynucleotides of the present invention, particularly a collection of the polynucleotides identified as SEQ ID NO: 1-33. According to one embodiment, the storage medium includes a collection of at least 20, of the polynucleotides of the present invention, preferably at least 20 of the polynucleotides identified as SEQ ID NO: 1-33, including variants of those polynucleotides.

[0197] Another aspect of the present invention involves a combination of polynucleotides, the combination containing at least 5, preferably at least 10, more preferably at least 20 different polynucleotides of the present invention, including polynucleotides selected from SEQ ID NO: 1-33, and variants of these polynucleotides.

[0198] In another aspect, the present invention provides genetic constructs comprising, in the 5'-3' direction, a gene promoter sequence and an open reading frame coding for at least a functional portion of a polypeptide encoded by a polynucleotide of the present invention. In certain embodiments, the genetic constructs of the present invention also comprise a gene termination sequence. The open reading frame may be oriented in either a sense or antisense direction. Genetic constructs comprising a non-coding region of a gene coding for a polypeptide encoded by the above polynucleotides or a nucleotide sequence complementary to a non-coding region, together with a gene promoter sequence, are also provided. A terminator sequence may form part of this construct. Preferably, the gene promoter and termination sequences are functional in a host organism. More preferably, the gene promoter and termination sequences are common to those of the polynucleotide being introduced. The genetic construct may further include a marker for the identification of transformed cells.

[0199] Techniques for operatively linking the components of the genetic constructs are well known in the art and include the use of synthetic linkers containing one or more restriction endonuclease sites as described, for example, by Sambrook et al., in Molecular cloning: a laboratory manual, Cold Spring Harbor Laboratories Press: Cold Spring Harbor, N.Y., 1989. The genetic constructs of the present invention may be linked to a vector having at least one replication system, for example, E. coli, whereby after each manipulation, the resulting construct can be cloned and sequenced and the correctness of the manipulation determined.

[0200] Transgenic microbial cells comprising the genetic constructs of the present invention are also provided by the present invention, together with microbes comprising such transgenic cells, products and progeny of such microbes, and materials including such microbes. Techniques for stably incorporating genetic constructs into the genome of target microbes, such as Lactobacillus species, Lactococcus lactis or E. coli, are well known in the art of bacterial transformation and are exemplified by the transformation of E. coli for sequencing in Example 1, as well as the transformations described in numerous of the examples provided below.

[0201] Transgenic, non-microbial, cells comprising the genetic constructs of the present invention are also provided, together with organisms comprising such transgenic cells, and products and progeny of such organisms. Genetic constructs of the present invention may be stably incorporated into the genomes of non-microbial target organisms, such as fungi, using techniques well known in the art.

[0202] In preferred embodiments, the genetic constructs of the present invention are employed to transform microbes used in the production of food products, ingredients, processing aids, additives or supplements and for the production of microbial products for pharmaceutical uses, particularly for modulating immune system function and immunological effects; and in the production of chemoprotectants providing beneficial effects, probiotics and health supplements. The inventive genetic constructs may also be employed to transform bacteria that are used to produce enzymes or substances such as polysaccharides, flavor compounds, and bioactive substances, and to enhance resistance to industrial processes such as drying and to adverse stimuli in the human digestive system. The genes involved in antibiotic production, and phage uptake and resistance in Lactobacillus rhamnosus are considered to be especially useful. The target microbe to be used for transformation with one or more polynucleotides or genetic constructs of the present invention is preferably selected from the group consisting of bacterial genera Lactococcus, Lactobacillus, Streptococcus, Oenococcus, Lactosphaera, Trichococcus, Pediococcus and others potentially useful in various fermentation industries selected, most preferably, from the group consisting of Lactobacillus species in the following list: Lactobacillus acetotolerans, Lactobacillus acidophilus, Lactobacillus agilis, Lactobacillus alimentarius, Lactobacillus amylolyticus, Lactobacillus amylophilus, Lactobacillus amylovorus, Lactobacillus animalis, Lactobacillus arizonae, Lactobacillus aviarius, Lactobacillus bavaricus, Lactobacillus bifermentans, Lactobacillus brevis, Lactobacillus buchneri, Lactobacillus bulgaricus, Lactobacillus casei, Lactobacillus collinoides, Lactobacillus coryniformis, Lactobacillus crispatus, Lactobacillus curvatus, Lactobacillus delbrueckii, Lactobacillus delbrueckii subsp. bulgaricus, Lactobacillus delbrueckii subsp. lactis, Lactobacillus farciminis, Lactobacillus fermentum, Lactobacillus fructivorans, Lactobacillus gallinarum, Lactobacillus gasseri, Lactobacillus graminis, Lactobacillus hamsteri, Lactobacillus helveticus, Lactobacillus helveticus subsp. jugurti, Lactobacillus hetero, Lactobacillus hilgardii, Lactobacillus homohiochii, Lactobacillus japonicus, Lactobacillus johnsonii, Lactobacillus kefiri, Lactobacillus lactis, Lactobacillus leichmannii, Lactobacillus lindneri, Lactobacillus mali, Lactobacillus maltaromicus, Lactobacillus manihotivorans, Lactobacillus mucosae, Lactobacillus murinus, Lactobacillus oris, Lactobacillus panis, Lactobacillus paracasei, Lactobacillus paracasei subsp. pseudoplantarum, Lactobacillus paraplantarum, Lactobacillus pentosus, Lactobacillus plantarum, Lactobacillus pontis, Lactobacillus reuteri, Lactobacillus rhamnosus, Lactobacillus niminis, Lactobacillus sake, Lactobacillus salivarius, Lactobacillus salivarius subsp. salicinius, Lactobacillus salivarius subsp. salivarius, Lactobacillus sanfranciscensis, Lactobacillus sharpeae, Lactobacillus thermophilus, Lactobacillus vaginalis, Lactobacillus vermiforme, Lactobacillus zeae.

[0203] In yet a further aspect, the present invention provides methods for modifying the concentration, composition and/or activity of a polypeptide in a host organism, such as a microbe, comprising stably incorporating a genetic construct of the present invention into the genome of the host organism by transforming the host organism with such a genetic construct. The genetic constructs of the present invention may be used to transform a variety of organisms.

[0204] Thus, in yet another aspect, transgenic cells comprising the genetic constructs of the present invention are provided, together with organisms, such as microbes, comprising such transgenic cells, and products and progeny of such microbes. Techniques for stably incorporating genetic constructs into the genome of target organisms are well known in the art. Once the cells are transformed, cells having the genetic construct incorporated in their genome are selected. Transgenic cells may then be cultured in an appropriate medium, using techniques well known in the art.

[0205] Polynucleotides of the present invention may also be used to specifically suppress gene expression by methods such as RNA interference (RNAi), which may also include cosuppression and quelling. This and other techniques of gene suppression are well known in the art. A review of this technique is found in Science 288:1370-1372, 2000. Traditional methods of gene suppression, employing antisense RNA or DNA, operate by binding to the reverse sequence of a gene of interest such that binding interferes with subsequent cellular processes and thereby blocks synthesis of the corresponding protein. RNAi also operates on a post-transcriptional level and is sequence specific, but suppresses gene expression more efficiently.

[0206] Studies have demonstrated that one or more ribonucleases specifically bind to and cleave double-stranded RNA into short fragments. The ribonuclease(s) remains associated with these fragments, which in turn specifically bind to complementary mRNA, i.e. specifically bind to the transcribed mRNA strand for the gene of interest. The mRNA for the gene is also degraded by the ribonuclease(s) into short fragments, thereby obviating translation and expression of the gene. Additionally, an RNA polymerase may act to facilitate the synthesis of numerous copies of the short fragments, which exponentially increases the efficiency of the system. A unique feature of this gene suppression pathway is that silencing is not limited to the cells where it is initiated. The gene-silencing effects may be disseminated to other parts of an organism and even transmitted through the germ line to several generations.

[0207] Specifically, polynucleotides of the present invention are useful for generating gene constructs for silencing specific genes. Polynucleotides of the present invention may be used to generate genetic constructs that encode a single self-complementary RNA sequence specific for one or more genes of interest. Genetic constructs and/or gene-specific self-complementary RNA sequences may be delivered by any conventional method known in the art. Within genetic constructs, sense and antisense sequences flank an intron sequence arranged in proper splicing orientation making use of donor and acceptor splicing sites. Alternative methods may employ spacer sequences of various lengths rather than discrete intron sequences to create an operable and efficient construct. During post-transcriptional processing of the gene construct product, intron sequences are spliced-out, allowing sense and antisense sequences, as well as splice junction sequences, to bind forming double-stranded RNA. Select ribonucleases bind to and cleave the double-stranded RNA, thereby initiating the cascade of events leading to degradation of specific mRNA gene sequences, and silencing specific genes. Alternatively, rather than using a gene construct to express the self-complementary RNA sequences, the gene-specific double-stranded RNA segments are delivered to one or more targeted areas to be internalized into the cell cytoplasm to exert a gene silencing effect.

[0208] Using this cellular pathway of gene suppression, gene function may be studied and high-throughput screening of sequences may be employed to discover sequences affecting gene expression. Additionally, genetically modified microbes and higher order organisms may be generated.

[0209] In another aspect, the present invention provides methods for using one or more of the inventive polypeptides or polynucleotides to treat disorders in a mammal, such as a human.

[0210] In this aspect, the polypeptide or polynucleotide is generally present within a composition, such as a pharmaceutical or immunogenic composition. Pharmaceutical compositions may comprise one or more polypeptides, each of which may contain one or more of the above sequences (or variants thereof), and a physiologically acceptable carrier. Immunogenic compositions may comprise one or more of the above polypeptides and an immunostimulant, such as an adjuvant or a liposome, into which the polypeptide is incorporated.

[0211] Alternatively, a composition of the present invention may contain DNA encoding one or more polypeptides described herein, such that the polypeptide is generated in situ. In such compositions, the DNA may be present within any of a variety of delivery systems known to those of ordinary skill in the art, including nucleic acid expression systems, and bacterial and viral expression systems. Appropriate nucleic acid expression systems contain the necessary DNA sequences for expression in the patient (such as a suitable promoter and terminator signal). Bacterial delivery systems involve the administration of a bacterium (such as Bacillus Calmette-Guerin) that expresses an immunogenic portion of the polypeptide on its cell surface. In a preferred embodiment, the DNA may be introduced using a viral expression system (e.g., vaccinia or other poxvirus, retrovirus, or adenovirus), which may involve the use of a non-pathogenic, or defective, replication competent virus. Techniques for incorporating DNA into such expression systems are well known in the art. The DNA may also be "naked," as described, for example, in Ulmer et al., Science 259:1745-1749, 1993 and reviewed by Cohen, Science 259:1691-1692, 1993. The uptake of naked DNA may be increased by coating the DNA onto biodegradable beads, which are efficiently transported into the cells.

[0212] While any suitable carrier known to those of ordinary skill in the art may be employed in the pharmaceutical compositions of this invention, the type of carrier will vary depending on the mode of administration. For parenteral administration, such as subcutaneous injection, the carrier preferably comprises water, saline, alcohol, a lipid, a wax or a buffer. For oral administration, any of the above carriers or a solid carrier, such as mannitol, lactose, starch, magnesium stearate, sodium saccharine, talcum, cellulose, glucose, sucrose, and magnesium carbonate, may be employed. Biodegradable microspheres (e.g., polylactic galactide) may also be employed as carriers for the pharmaceutical compositions of this invention. Suitable biodegradable microspheres are disclosed, for example, in U.S. Pat. Nos. 4,897,268 and 5,075,109.

[0213] Any of a variety of adjuvants may be employed in the immunogenic compositions of the present invention to non-specifically enhance an immune response. Most adjuvants contain a substance designed to protect the antigen from rapid catabolism, such as aluminum hydroxide or mineral oil, and a non-specific stimulator of immune responses, such as lipid A, Bordetella pertussis or M. tuberculosis. Suitable adjuvants are commercially available as, for example, Freund's Incomplete Adjuvant and Freund's Complete Adjuvant (Difco Laboratories, Detroit, Mich.), and Merck Adjuvant 65 (Merck and Company, Inc., Rahway, N.J.). Other suitable adjuvants include alum, biodegradable microspheres, monophosphoryl lipid A and Quil A.

[0214] Routes and frequency of administration, as well as dosage, vary from individual to individual. In general, the inventive compositions may be administered by injection (e.g., intradermal, intramuscular, intravenous or subcutaneous), intranasally (e.g., by aspiration) or orally. In general, the amount of polypeptide present in a dose (or produced in situ by the DNA in a dose) ranges from about 1 pg to about 100 mg per kg of host, typically from about 10 pg to about 1 mg per kg of host, and preferably from about 100 pg to about 1 .mu.g per kg of host. Suitable dose sizes will vary with the size of the patient, but will typically range from about 0.1 ml to about 2 ml.

[0215] The following examples are offered by way of illustration and not by way of limitation.

EXAMPLE 1

Isolation and Characterization of DNA Sequences from Lactobacillus rhamnosus Strain HN001

[0216] Lactobacillus rhamnosus strain HN001 DNA libraries were constructed and screened as follows.

[0217] DNA was prepared in large scale by cultivating the bacteria in 2.times.100 ml cultures with 100 ml MRS broth (Difco Laboratories, Detroit Mich.) and 1 ml Lactobacillus glycerol stock as inoculum, placed into 500 ml culture flasks and incubated at 37.degree. C. for approx. 16 hours with shaking (220 rpm).

[0218] The cultures were centrifuged at 3500 rpm for 10 min to pellet the cells. The supernatant was removed and the cell pellet resuspended in 40 ml fresh MRS broth and transferred to clean 500 ml culture flasks. Fresh MRS broth (60 ml) was added to bring the volume back to 100 ml and flasks were incubated for a further 2 hrs at 37.degree. C. with shaking (220 rpm). The cells were pelleted by centrifugation (3500 rpm for 10 min) and supernatant removed. Cell pellets were washed twice in 20 ml buffer A (50 mM NaCl, 30 mM Tris pH 8.0, 0.5 mM EDTA).

[0219] Cells were resuspended in 2.5 ml buffer B (25% sucrose (w/v), 50 mM Tris pH 8.0, 1 mM EDTA, 20 mg/ml lysozyme, 20 .mu.g/ml mutanolysin) and incubated at 37.degree. C. for 45 min. Equal volumes of EDTA (0.25 M) was added to each tube and allowed to incubate at room temperature for 5 min. 20% SDS (1 ml) solution was added, mixed and incubated at 65.degree. C. for 90 min. 50 .mu.l Proteinase K (Gibco BRL, Gaithersburg, Md.) from a stock solution of 20 mg/ml was added and tubes incubated at 65.degree. C. for 15 min.

[0220] DNA was extracted with equal volumes of phenol:chloroform:isoamylalcohol (25:24:1). Tubes were centrifuged at 3500 rpm for 40 min. The aqueous phase was removed to clean sterile Oak Ridge centrifuge tubes (30 ml). Crude DNA was precipitated with an equal volume of cold isopropanol and incubated at -20.degree. C. overnight.

[0221] After resuspension in 500 .mu.l TE buffer, DNase-free RNase was added to a final concentraion of 100 .mu.g/ml and incubated at 37.degree. C. for 30 min. The incubation was extended for a further 30 min after adding 100 .mu.l Proteinase K from a stock solution of 20 mg/ml. DNA was precipitated with ethanol after a phenol:chloroform:isoamylalcohol (25:24:1) and a chloroform:isoamylalcohol (24:1) extraction and dissolved in 250 .mu.l TE buffer.

[0222] DNA was digested with Sau3AI at a concentration of 0.004 U/.mu.g in a total volume of 1480 .mu.l, with 996 .mu.l DNA, 138.75 .mu.l 10.times. REACT 4 buffer and 252.75 .mu.l H.sub.2O. Following incubation for 1 hour at 37.degree. C., DNA was divided into two tubes. 31 .mu.l 0.5 M EDTA was added to stop the digestion and 17 .mu.l samples were taken for agarose gel analysis. Samples were put into 15 ml Falcon tubes and diluted to 3 ml for loading onto sucrose gradient tubes.

[0223] Sucrose gradient size fractionation was conducted as follows. 100 ml of 50% sucrose (w/v) was made in TEN buffer (1M NaCl, 20 mM Tris pH 8.0, 5 mM EDTA) and sterile filtered. Dilutions of 5, 10, 15, 20, 25, 30, 35 and 40% sucrose were prepared and overlaid carefully in Beckman Polyallomer tubes, and kept overnight at 4.degree. C. TEN buffer (4 ml) was loaded onto the gradient, with 3 ml of DNA solution on top. The gradients were centrifuged at 26K for 18 hours at 4.degree. C. in a Centricon T-2060 centrifuge using a Kontron TST 28-38 rotor. After deceleration without braking (approx. 1 hour), the gradients were removed and fractions collected using an auto Densi-Flow (Haake-Buchler Instruments). Agarose gel was used to analyse the fractions. The best two pairs of fractions were pooled and diluted to contain less than 10% sucrose. TEN buffer (4 ml) was added and DNA precipitated with 2 volumes of 100% ice cold ethanol and an overnight incubation at -20.degree. C.

[0224] DNA pellets were resuspended in 300 .mu.l TE buffer and re-precipitated for approx. 6 hours at -20.degree. C. after adding 1/10 volume 3 M NaOAC pH 5.2 and 2 volumes of ethanol. DNA was pelleted at top speed in a microcentrifuge for 15 min, washed with 70% ethanol and pelleted again, dried and resuspended in 10 .mu.l TE buffer.

[0225] DNA was ligated into dephosphorylated BamHI-digested pBluescript SK II.sup.+ and dephosphorylated BamHI-digested lambda ZAP Express using standard protocols. Packaging of the DNA was done using Gigapack III Gold packaging extract (Stratagene, La Jolla, Calif.) following the manufacturer's protocols. Packaged libraries were stored at 4.degree. C.

[0226] Mass excision from the primary packaged phage library was done using XL1-Blue MRF' cells and ExAssist Helper Phage (Stratagene). The excised phagemids were diluted with NZY broth (Gibco BRL, Gaithersburg, Md.) and plated out onto LB-kanamycin agar plates containing 5-bromo-4-chloro-3-indolyl-.beta.-D-galactoside (X-gal) and isopropylthio-beta-galactoside (IPTG). After incubation, single colonies were picked for PCR size determination before the most suitable libraries were selected for sequencing.

[0227] Of the colonies picked for DNA minipreps and subsequent sequencing, the large majority contained an insert suitable for sequencing. Positive colonies were cultured in LB broth with kanamycin or ampicillin depending on the vector used, and DNA was purified by means of rapid alkaline lysis minipreps (solutions: Qiagen, Venlo, The Netherlands; clearing plates, Millipore, Bedford, Mass.). Agarose gels at 1% were used to screen sequencing templates for chromosomal contamination and concentration. Dye terminator sequencing reactions were prepared using a Biomek 2000 robot (Beckman Coulter, Inc., Fullerton, Calif.) and Hydra 96 (Robbins Scientific, Sunnyvale, Calif.) for liquid handling. DNA amplification was done in a 9700 PCR machine (Perkin Elmer/Applied Biosystems, Foster City, Calif.) according to the manufacturer's protocol.

[0228] The sequence of the genomic DNA fragments were determined using a Perkin Elmer/Applied Biosystems Division Prism 377 sequencer. The DNA clones were sequenced from the 5' and/or 3' end, and are identified as SEQ ID NO: 1-33.

[0229] This example not only shows how the sequences were obtained, but also that a bacterium (E. coli) can be stably transformed with any desired DNA fragment of the present invention for permanent marking for stable inheritance.

[0230] The determined DNA sequences were compared to and aligned with known sequences in the public databases. Specifically, the polynucleotides identified in SEQ ID NO: 1-33 were compared to polynucleotides in the EMBL database as of the end of July 2001, using BLASTN algorithm Version 2.0.11 [Jan. 20, 2000], set to the following running parameters: Unix running command: blastall -p blastn -d embldb -e 10 -G 0 -E 0 -r 1 -v 30 -b 30 -i queryseq -o results. Multiple alignments of redundant sequences were used to build up reliable consensus sequences. Based on similarity to known sequences, the isolated polynucleotides of the present invention identified as SEQ ID NO: 1-33 were identified as encoding polypeptides.

[0231] Numerous of the sequences provided in SEQ ID NO: 1-33 were found to be "full-length" and to contain open reading frames (ORFs). These full-length sequences, the location of ORFs (by nucleotide position) contained within these sequences, and the corresponding amino acid sequences are provided in Table 1B below. TABLE-US-00003 TABLE 1B Polynucleotide Polypeptide SEQ ID NO: ORF SEQ ID NO: 1 1,128-3,026 42 2 196-924 43 3 145-1,098 44 4 82-348 45 5 103-1,239 46 6 122-934 47 7 94-759 48 7 807-1,676 49 8 126-1,232 50 9 181-1,086 51 10 23-1,510 52 11 209-1,381 53 12 1-1,179 54 13 1-650 55 14 1-768 56 15 163-1,167 57 16 64-888 58 17 47-1,219 59 18 45-1,295 60 19 175-1,173 61 20 48-1,352 62 21 1,705-2,280 63 22 60-1,250 64 23 71-1,093 65 24 120-1,074 66 25 86-934 67 26 2,209-7,434 68 27 74-4,465 69 28 821-6,460 70 29 141-1,022 71 30 83-607 72 31 27-875 73 32 96-881 74 33 1-1,191 75

[0232] The polynucleotide and polypeptide sequences of SEQ ID NO: 1-33 and 42-75 were compared to sequences in the EMBL and SwissProt databases using the BLAST computer algorithms version 2.0.11 [Jan. 20, 2000]. Comparisons of polynucleotide sequences provided in SEQ ID NO: 1-33 to sequences in the EMBL database were made as of August 2001. Comparisons of amino acid sequences provided in SEQ ID NO: 42-75 to sequences in the SwissProt database were made as of August 2001. Analysis of six-frame translations of the polynucleotides of SEQ ID NO: 1-33 were also compared to and aligned with the six-frame translations of polynucleotides in the SwissProt database using the BLASTX program.

BLASTN Polynucleotide Analysis

[0233] The polynucleotide sequences of SEQ ID NO: 1-3, 5-23 and 25-33 were determined to have less than 50% identity, determined as described above, to sequences in the EMBL database using the computer algorithm BLASTN, as described above. The polynucleotide sequence of SEQ ID NO: 24 was determined to have less than 90% identity, determined as described above, to sequences in the EMBL database using BLASTN, as described above. The polynucleotide sequence of SEQ ID NO: 4 was determined to have less than 98% identity, determined as described above, to sequences in the EMBL database using BLASTN, as described above.

BLASTP Amino Acid Analysis

[0234] The amino acid sequences of SEQ ID NO: 43, 45-47, 51-53, 58, 60, 61, 63, 67, 68, 70, 71, 73 and 74 were determined to have less than 50% identity, determined as described above, to sequences in the SwissProt database using the BLASTP computer algorithm as described above. The amino acid sequences of SEQ ID NO: 48-50, 55-56, 62, 64, 66, 69, 72 and 75 were determined to have less than 75% identity, determined as described above, to sequences in the SwissProt database using the BLASTP computer algorithm as described above. The amino acid sequences of SEQ ID NO: 57 and 65 were determined to have less than 90% identity, determined as described above, to sequences in the SwissProt database using the computer algorithm BLASTP, as described above. The amino acid sequence of SEQ ID NO: 54 and 59 was determined to have less than 98% identity, determined as described above, to sequences in the SwissProt database using the computer algorithm BLASTP, as described above.

BLASTX Analysis

[0235] The six-frame translations of the polynucleotide sequences of SEQ ID NO: 1-33 were compared to and aligned with six-frame translations of polynucleotides in the EMBL database using the BLASTX program version 2.0.11 [Jan. 20, 2000] set to the following running parameters: Unix running command: blastall -p blastn -d embldb -e 10 -G 0 -E 0 -v 30 -b 30 -i queryseq -o results. The translations of the polynucleotides of SEQ ID NO: 1, 3, 5-9, 11-19, 21 and 25-32 were determined to have less than 50% identity, determined as described above, to translations of polynucleotides in the EMBL database using the computer algorithm BLASTX. The translations of the polynucleotides of SEQ ID NO: 2, 4, 10, 20, 22, 23 and 33 were determined to have less than 75% identity, determined as described above, to translations of polynucleotides in the EMBL database using the computer algorithm BLASTX. The translations of the polynucleotide sequence of SEQ ID NO: 24 was determined to have less than 90% identity, determined as described above, to translations of polynucleotides in the EMBL database using the computer algorithm BLASTX.

EXAMPLE 2

Isolation and Characterization of Peptidase from L. rhamnosus

[0236] The full-length gene sequence of a peptidase believed to be related to pepO, and referred to herein as "pepO" from L. rhamnosus strain HN001 (given in SEQ ID NO: 1 and shown in FIG. 80) was isolated essentially as described in Example 1. Primers were designed to this sequence and employed to amplify pepO from L. rhamnosus HN001 using standard PCR methodology. PepO was cloned in the vector pTRKH2 (obtained from Dr Todd Klaenhammer, North Carolina State University, North Carolina, USA) and transformed into E. coli. Competent cells of L. rhamnosus HN001 were transformed with the pTRKH2+pepO construct to overexpress the gene in strain HN001. The amino acid sequence of the expressed protein is provided in SEQ ID NO: 42 and shown in FIG. 81.

[0237] Cell extracts of the HN001 strain constructs with enhanced levels of the peptidase enzyme showed enhanced enzyme activity on the casein peptide, .alpha..sub.S1-casein(1-17). Specifically, .alpha..sub.S1-casein(1-17) was incubated with non-transformed strain HN001 (referred to as DR20 WT) and strain HN001 transformed with the pepO construct described above (referred to as DR20 PepO:1 and DR20 PepO:4). HPLC separation of the resulting peptide products was performed using a Vydac reverse phase C18 column, 4.6 mm.times.250 mm. The solvent system was solvent A, 0.1% TFA in water, solvent B, 0.08% TFA in acetonitrile and the gradient employed was 15-40% solvent B over 20 minutes. A major peak was observed at 11 minutes, together with other non-identified minor peaks corresponding to hydrolysis products of the original substrate.

[0238] With non-transformed HN001 (DR 20 WT), the major peak of unhydrolysed .alpha..sub.s1-casein(1-17) had a height of approximately 250 mAU. With each of the two transformed strains of HN001 (DR 20 PepO:1 and DR 20 PepO:4) the major peak of unhydrolysed .alpha..sub.si-casein(1-17) had a height of approximately 150 mAU, demonstrating that HN001 transformed with the pepO construct has enhanced peptidase activity compared to non-transformed HN001.

[0239] The peptidase of SEQ ID NO: 42 was not active on bradykinin, a standard substrate for measuring pepO activity (Pritchard et al., Microbiol. 140:923-30,1994). The enzyme of SEQ ID NO: 42 thus has a specificity that is significantly different from the homologous enzyme from Lactococcus.

[0240] The polypeptide of SEQ ID NO: 42 and the polynucleotide of SEQ ID NO: 1 have utility in processing food products to develop new characteristics in food products, and as supplements and additives to food products, including cheese and hydrolyzed milk protein products. This enzyme may also be used to develop non-food products. The attributes conferred by this enzyme, and the applications for use of this enzyme, include: flavor and aroma enhancement; removal of bitter peptides and undesirable flavors; nutritional enhancement; enhanced texture and functionality; production of bioactive peptides; and removal of allergenic peptides or proteins.

[0241] These attributes may be produced in food, such as dairy products, (including milk protein hydrolysates and cheese) by directed activity of the enzyme, introduced in a bacterial strain (including strain HN001 or starter cultures) comprising a polynucleotide of SEQ ID NO: 1, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 42.

EXAMPLE 3

Isolation and Characterisation of an Esterase from L. rhamnosus HN001

[0242] The full-length polynucleotide sequence of an esterase gene, given in SEQ ID NO: 3, was used to amplify the AA 7 esterase gene from L. rhamnosus HN001 using standard PCR methodology. FIG. 1 shows the nucleotide sequence of L. rhamnosus strain HN001 esterase gene AA 7, with the ATG initiation and translation stop codons shown boxed.

[0243] The AA7 esterase gene sequence was cloned into the pUniBlunt/V5-HisTopo vector (Invitrogen, Auckland, NZ) and transformed into the E. coli strain PIR1 OneShot competent cells (Invitrogen). To construct an expression plasmid the pUniBlunt/V5-HisTopo vector construct was recombined with the pBad/Thio-E vector (Invitrogen) and transformed into the E. coli strain TOP10 competent cells (Invitrogen) according to the manufacturer's instructions. The gene product was therefore cloned as a fusion protein tagged with a His-patch polypeptide and thioredoxin protein. The esterase fusion protein was expressed and purified using a Ni-NTA column (Qiagen, Auckland, NZ) according to the manufacturer's instructions and protein expression checked by SDS-PAGE. The amino acid sequence of the esterase AA7 polypeptide is given in SEQ ID NO: 44 and shown in FIG. 2.

[0244] Esterase activity was assessed using the para-nitrophenyl butyrate assay as described in Lee and Lee, Biotech. Appl. Biochem. 11:552-563, 1989, with some modifications. Briefly, esterase activity was measured spectrophotometrically using p-nitrophenyl butyrate (Sigma Chemical Co., St Louis, Mo.) as substrate. Substrate was prepared by sonicating 1 ml of 50 mM methanolic p-nitrophenyl butyrate in 18 ml 50 mM sodium phosphate buffer (pH 7.5). Aliquots of 1.9 ml were placed in cuvettes, allowed to stabilize at 30.degree. C., and between 5 and 20 .mu.l of purified AA7 esterase added. Changes in optical density (OD) 410 nm were determined. Based on the results, enzyme activity was calculated, with one unit (U) of enzyme defined as the amount required to hydrolyze 1 .mu.mol substrate per minute.

[0245] Esterase activity of the AA7 fusion protein was compared to the activity of a known esterase enzyme from Streptococcus thermophilus (ST1, as described in Liu et al., Int. Dairy J. 11:27-35, 2001), a non-esterase HN001 enzyme also expressed as a His-patch/Thioredoxin fusion protein and buffer-only.

[0246] The results are shown in FIG. 3 and the enzyme activities are given in Table 1C. FIG. 3 demonstrates the production of ethyl butyrate from para-nitrophenyl butyrate substrate as measured by change in OD at 410 nm. As shown in FIG. 3, while buffer only (.diamond-solid.) and the HN001 non-esterase fusion protein (.circle-solid.) showed minimal esterase activity, the ST1 esterase from Streptococcus thermophilus (.sigma.) and the AA7 esterase fusion protein (.nu.) showed strong activity. Thus, the AA7 esterase fusion protein showed strong esterase activity compared to the positive control, and negligible amounts of esterase was produced by the two negative controls (buffer-only and the non-esterase fusion protein). TABLE-US-00004 TABLE 1C Esterase activity of the AA7 fusion protein Enzyme activity Protein .DELTA. OD.sub.410/min (.mu.mol/min/ml) AA7 fusion protein 0.41 3.7 ST1 esterase control 0.49 4.0 Non-esterase control 0.05 0.4 Buffer-only control 0.02 0.2

[0247] The esterase activity exhibited by the AA7 fusion protein was not due to background hydrolysis of the substrate as the buffer-only control showed little or no activity. The specific enzyme activity of the His-patch/Thio/AA7 fusion protein was 1.42 .mu.mol/min/mg protein compared with 0.03 .mu.mol/min/mg for the non-esterase fusion protein, showing an almost 50-fold difference in esterase activity. Therefore, AA7 esterase activity was not due to the His-patch/Thioredoxin fusion protein tag.

[0248] The dose-response of the AA7 fusion protein was determined by comparing the esterase activity in a series of three two-fold dilutions of the purified enzyme. Results are shown in FIG. 4 and the rate of change in optical density at 410 nm and enzyme activities given in Table 2. As shown in FIG. 4, while buffer-only (.lamda.) showed no esterase activity, increasing amounts of His-patch/Thio/AA7 fusion protein; 5 .mu.l (.upsilon.), 10 .mu.l (.sigma.) and 20 .mu.l (.nu.) purified protein showed increasing rates of substrate hydrolysis. The increase in substrate hydrolysis was proportional to amount of AA7 fusion protein added. TABLE-US-00005 TABLE 2 Esterase activity for increasing amounts of AA7 fusion protein Enzyme activity Protein .DELTA. OD.sub.410/min (.mu.mol/min/ml) 5 .mu.l His-patch/Thio/AA7 0.18 5.9 10 .mu.l His-patch/Thio/AA7 0.40 6.7 20 .mu.l His-patch/Thio/AA7 0.68 5.6 1.Buffer-only 0.00 0.0

[0249] Results indicated the rate of change in OD at 410 nm was proportional to the amount of enzyme added, whilst enzyme activity remained relatively constant. Therefore, esterase activity was dependent on the amount of esterase AA7 fusion protein present.

[0250] The effect of the serine esterase inhibitor PMSF was determined using the p-nitrophenyl butyrate assay. Esterase activity of the AA7 fusion protein was assessed in the presence and absence of 10 mM PMSF. Results are shown in FIG. 5, and the rate of change in OD at 410 nm and enzyme activities given in Table 3. These results indicate that the PMSF inhibitor caused a 17.9% reduction in the esterase activity of the AA7 fusion protein. Therefore, AA7 esterase activity was inhibited by the serine esterase-specific inhibitor PMSF. TABLE-US-00006 TABLE 3 Effect of PMSF inhibitor on AA7 fusion protein esterase activity Enzyme activity Protein .DELTA. OD.sub.410/min (.mu.mol/min/ml) AA7 0.68 5.6 AA7 + 10 mM PMSF 0.50 4.1 Buffer-only 0.00 0.0

[0251] The enzymatic breakdown of milk fat plays an essential role in the development of flavor in cheese. Esterases and lipases catalyze the lipolysis of milk fat in dairy products such that the triglycerides are hydrolyzed to free fatty acids and glycerol or mono- and diglycerides. Although exogenous esterases and lipases of mammalian and fungal origins are often used to encourage extensive lipolysis in cheeses, esterases and lipases from cheese microorganisms may also contribute to lipolysis (reviewed in Fox and Wallace, Adv. Appl. Microbiol. 45:17-85, 1997 and McSweeney and Wallace, Lait 80:293-324, 2000).

[0252] The polypeptide of SEQ ID NO: 44 and the polynucleotide of SEQ ID NO: 3 have utility for processing food products and as supplements and additives to food products. This esterase may also be used to develop non-food products. The attributes conferred by this enzyme include: enhanced flavor and aroma; removal of off-flavors; altered levels of butyric acid; and altered metabolic characteristics.

[0253] These attributes may be produced in food, such as dairy products, by directed activity of the enzyme, introduced in a bacterial strain (including strain HN001 or starter cultures) comprising a polynucleotide of SEQ ID NO: 3 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 44 or a variant.

EXAMPLE 4

Isolation and Characterisation of Autoaggregation Protein AG5 from L. rhamnosus HN001

[0254] The full-length polynucleotide sequence of an autoaggregation protein from L. rhamnosus strain HN001, given in SEQ ID NO: 10, was used to amplify the AG5 autoaggregation gene from L. rhamnosus HN001 DNA using standard PCR methodology. The full-length polynucleotide sequence of L. rhamnosus strain HN001 autoaggregation gene AG5, showing ATG initiation and translation stop codons (boxed) is shown in FIG. 6.

[0255] AG5 was then cloned into the EcoRI and SalI sites of the pGEX-6P-3 expression vector (Pharmacia Biotech, Auckland, NZ) and transformed into the E. coli strain K12 XL-1Blue competent cells according to standard laboratory protocols. The amino acid sequence of the autoaggregation protein AG5 is given in SEQ ID NO: 52 and shown in FIG. 7.

[0256] The autoaggregation AG5 protein was expressed as a fusion protein with glutathione S-transferase (GST), isolated and purified using Glutathione Sepharose 4B resin (Pharmacia Biotech) according to the manufacturer's instructions and protein expression checked by SDS-PAGE.

[0257] An assay for aggregation was adapted from Roos et al., Mol. Microbiol. 32:427-436, 1999. A 10 ml overnight culture of L. rhamnosus strain HN001 was grown in Man-Rogosa-Sharpe (MRS) broth (Oxoid) with glucose at a final concentration of 1%. The bacteria were washed five times in sterile deionized water resulting in loss of endogenous aggregation. Bacteria were suspended in 1 ml PBS, and 5 .mu.l of the purified the HN001 autoaggregation protein AG5 fusion protein or an irrelevant (ie. non-adhesion) GST-fusion protein were added to 20 .mu.l aliquots of the bacterial suspension, and placed on microscope slides. The slides were rocked gently for 13 min, and aggregation monitored by light microscopy.

[0258] As shown in FIG. 8A, in the presence of the AG5 autoaggregation GST-fusion protein, L. rhamnosus strain HN001 cells readily aggregated. FIG. 8A illustrates an image of a phase-contrast photomicrograph (exposure 1/8 sec, final magnification.times.240) showing obvious clumping of washed L. rhamnosus strain HN001 cells in the presence of AG5 autoaggregation protein tagged with GST. If an irrelevant (ie. non-adhesion) GST-fusion protein was used, no aggregation occurred. FIG. 8B illustrates an image of a phase-contrast photomicrograph (exposure 1/8 sec, final magnification.times.240) showing no clumping of washed L. rhamnosus strain HN001 cells in the presence of an irrelevant (non-adhesion) HN001 protein tagged with GST, as a negative control. The GST-tagged HN001 autoaggregation protein AG5 did not form observable clumps in the absence of bacterial cells (data not shown). Thus, the HN001 autoaggregation protein AG5 mediated the autoaggregation of L. rhamnosus strain HN001 cells.

[0259] The L. rhamnosus strain HN001 is known to have probiotic properties (see Tannock et al., Appl. Environ. Microbiol. 66:2,578-2,588, 2000; Gill et al., Br. J. Nutr. 83:167-176, 2000; Prasad et al., Int. Dairy J. 8:993-1002, 1998). In order to function effectively as probiotic bacteria, L. rhamnosus HN001 must colonize (at least transiently) the gut environment, as well as exert positive health benefits, possibly through the exclusion of pathogenic bacteria from intestinal surfaces. The ability to form aggregates may be important for both survival in the gut environment and functionality of L. rhamnosus HN001. The ability to autoaggregate may assist in the formation of biofilms of L. rhamnosus HN001 and/or related species, improving the chances of colonization in the highly competitive gut environment, and then exclusion of competing bacteria, including pathogens.

[0260] The polypeptide of SEQ ID NO: 52, and the polynucleotide of SEQ ID NO: 10 have utility for processing food products and as supplements and additives to food products. This protein may also be used to develop non-food products. The attributes conferred by this enzyme include: as a prebiotic to enhance the growth of L. rhamnosus HN001 or other Lactobacillus species in the gut; as an agent to promote clumping of L. rhamnosus HN001 in media to improve survival in industrial processes; and as an agent to help prevent pathogenic colonization of mucosal surfaces.

[0261] These attributes may be produced in food, such as dairy products, by directed activity of the autoaggregation protein, introduced in a bacterial strain (including strain HN001 or starter cultures) comprising a polynucleotide of SEQ ID NO: 10 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 52 or a variant.

EXAMPLE 5

Isolation and Characterisation of Malic Enzyme from L. rhamnosus HN001

[0262] The full-length polynucleotide sequence of malic enzyme AA5, given in SEQ ID NO: 2, was amplified from L. rhamnosus HN001 DNA using standard PCR methodology. The polynucleotide sequence of L. rhamnosus strain HN001 malic enzyme gene AA5 showing ATG initiation and translation stop codons (boxed) is shown in FIG. 9. The upstream and downstream primers were tagged with EcoRI and BamHI restriction endonuclease recognition sequences to facilitate cloning.

[0263] The AA5 gene was then cloned into the EcoRI and BamHI sites of the pGEX-6P-3 expression vector (Pharmacia Biotech) and transformed into the E. coli strain DH-5.alpha. competent cells according to standard laboratory protocols. Cells were lysed by sonication and the AA5 protein, expressed as a GST fusion protein, was checked by SDS-PAGE analysis. The polypeptide sequence is given in SEQ ID NO: 43 and shown in FIG. 10.

[0264] Malic enzyme activity was assessed determining the rate of pyruvate reduction in transformed strains of an E. coli mutant. The E. coli strain EJ1321 contains multiple mutations that affect both NAD- and NADP-dependent malic enzyme activity, as well as malic enzyme regulation (Hansen and Juni, Biochem. Biophys. Res. Comm. 65:559-566, 1975). The strain was obtained from the E. coli Genetic Stock Centre (Yale University, USA), and transformed with the pGEX-6P-3 vector construct encoding the HN001 malic enzyme AA5. Transformants were selected by resistance to 100 .mu.g/ml ampicillin on M9 plates supplemented with 0.5% glucose (ie. permissive growth conditions). Ampicillin resistant EJ132 colonies were picked and grown overnight at 37.degree. C. in 10 ml LB broth with 100 .mu.g/ml ampicillin and 2 ml then used to inoculate 100 ml LB broth with 100 .mu.g/ml ampicillin. Cultures were incubated at 37.degree. C. with shaking until OD at 600 nm reached approximately 0.4 whereupon expression of the AA5 protein was induced by the addition of 100 .mu.l of 1 M IPTG. After a further 4 hours culture at 37.degree. C. with shaking, 10 ml aliquots were taken, spun at 4000 rpm for 5 min, supernatants removed and cells resuspended in 5 ml PBS. Cultures were then sonicated to produce crude lysates.

[0265] Malic enzyme activity in the crude lysates was measured according to Kobayashi et al., J. Biol. Chem. 264:3200-3205, 1989, with modifications. Briefly, total protein content of the lysates were quantitated using the BCA Protein Assay Reagent kit (Pierce, Rockford, Ill., USA) according to the manufacturer's instructions, and 3.5 mg total protein added to 990 .mu.l reaction solution containing 100 .mu.M MOPS buffer (pH 6.1), 100 .mu.M Na.sub.2CO.sub.3, 50 .mu.M NADH and 5 .mu.M MgCl.sub.2 (Sigma). Lastly, 10 .mu.l of 1 M sodium pyruvate was added as substrate and utilization of NADH measured as change in OD at 340 nm.

[0266] Malic enzyme activity was compared between PBS buffer only (20 .mu.l), crude lysate from wild type EJ1321 cells (ie. non-transformed), EJ1321 cells transformed with pGEX-6P-3 encoding an irrelevant protein (AD5), and EJ1321 cells transformed with pGEX-6P-3 encoding HN001 malic enzyme AA5 (FIG. 11). Specific activities are given in Table 4, with a unit of enzyme was defined as .mu.mole NADH used per min per mg protein.

[0267] The results indicate that although NADH was stable (ie. no change in OD in the presence of NADH and substrate), some background NADH reduction occurred when crude lysates from wild-type EJ1321 cells or EJ1321 cells expressing an irrelevant protein. Nonetheless, clear malic enzyme activity was observed when crude lysate from EJ1321 cells expressing AA5 protein was used, with over 6-fold more enzyme activity compared to background. Therefore, AA5 encodes a malic enzyme.

[0268] FIG. 11 shows malate enzyme activity measured as rate of pyruvate reduction by crude lysate preparations of EJ1321 cell transformants. .nu. PBS buffer-only; .sigma. 3.5 .mu.g wild-type EJ1321 cell lysate; .upsilon. 3.5 .mu.g cell lysate of EJ1321 transformed with pGEX-6P-3 construct encoding an irrelevant HN001 protein (AD5); .lamda. 3.5 .mu.g cell lysate of EJ1321 transformed with pGEX-6P-3 construct encoding HN001 malic enzyme AA5. TABLE-US-00007 TABLE 4 Malic enzyme activity in crude lysates of transformed and non-transformed EJ1321 cells Enzyme activity Lysate .DELTA. OD.sub.340/min (.mu.mol/min/ml) Buffer-only 0.00 0.00 Wild-type EJ1321 0.01 2.0 .times. 10.sup.2 EJ1321 with pGEX-6P-3 0.02 4.2 .times. 10.sup.2 encoding an irrelevant protein EJ1321 with pGEX-6P-3 0.12 26.8 .times. 10.sup.2 encoding AA5

[0269] The malic enzyme assay was repeated with increasing amounts of crude lysate from EJ1321 cells expressing AA5 protein to determine whether malic enzyme activity was proportional to amount of AA5 protein present (FIG. 12 and Table 5).

[0270] Results from FIG. 12 and Table 5 indicate that increased amounts of crude lysate of EJ1321 E. coli strain transformed with HN001 malic enzyme AA5 led to increased malic enzyme activity. However, as the amount of substrate became limiting at higher amounts of lysate, the increases in activity were not strictly proportional. Nonetheless, these results support the evidence that AA5 encodes the HN001 malic enzyme.

[0271] FIG. 12 shows data illustrating the effect of increasing amounts of EJ1321 crude lysate on malic enzyme activity. .nu. 5 .mu.l wild-type EJ1321 cell lysate; .sigma. 5 .mu.l cell lysate of EJ1321 transformed with pGex-6P-3 encoding AA5; .upsilon. 50 .mu.l cell lysate of EJ1321 transformed with pGex-6P-3 encoding AA5; .upsilon. 200 .mu.l cell lysate of EJ1321 transformed with pGex-6P-3 encoding AA5. TABLE-US-00008 TABLE 5 Malic enzyme activity with increasing amounts of cell lysate Enzyme activity Lysate .DELTA. OD.sub.340/min (.mu.mol/min/ml) 5 .mu.l wild-type EJ1321 0.004 3.2 .times. 10.sup.2 5 .mu.l EJ1321 with pGEX-6P-3 0.032 25.8 .times. 10.sup.2 encoding AA5 2.50 .mu.l EJ1321 with pGEX-6P- 0.216 17.3 .times. 10.sup.2 3 encoding AA5 3.200 .mu.l EJ1321 with pGEX- 0.232 4.6 .times. 10.sup.2 6P-3 encoding AA5

[0272] The NAD-dependent malic enzyme (EC 1.1.1.38) catalyzes L-malate oxidative decarboxylation and pyruvate reductive carboxylation (Murai, T. et al, Biochem. Biophys. Res. Comm. 43:875-881, 1971) and is central to citrate metabolism.

[0273] The polypeptide of SEQ ID NO: 43 and the polynucleotide of SEQ ID NO: 2 have utility for processing food products and as supplements and additives to food products, as well as in industrial processing. This malic enzyme may also be used to develop non-food products and in non-food processing systems. The attributes conferred by this enzyme include: manipulation of energy production and growth in particular media; altered survival characteristics in industrial processes; formation of common intermediates of various flavor compounds; and lactic acid production, important for antibacterial effects and acid tolerance.

[0274] These attributes may be produced in food or in other environments by directed activity of the enzyme, introduced in a bacterial strain (including strain HN001, or starter cultures) comprising a polynucleotide of SEQ ID NO: 2 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 43 or a variant.

EXAMPLE 6

Isolation and Characterisation of Malate Dehydrogenase from L. rhamnosus HN001

[0275] The full-length polynucleotide sequence of malic enzyme, given in SEQ ID NO: 9, was amplified from the AG3 malate dehydrogenase gene from L. rhamnosus HN001 DNA using standard PCR methodology. FIG. 13 shows the polynucleotide sequence of L. rhamnosus strain HN001 malate dehydrogenase gene AG3 showing the TTG initiation and translation stop codons (boxed).

[0276] AG3 was then cloned into the pUniBlunt/V5-HisTopo vector (Invitrogen) and transformed into the E. coli strain PIR1 OneShot competent cells (Invitrogen) according to the manufacturer's instructions. To construct an expression plasmid, the pUniBlunt/V5-HisTopo vector construct was recombined with the pBad/Thio-E Echo vector (Invitrogen) and transformed into the E. coli strain TOP10 competent cells (Invitrogen) according to the manufacturer's instructions. The AG3 gene product was therefore cloned as a fusion protein tagged with a His-patch polypeptide and thioredoxin protein. The fusion protein was expressed and purified using a Ni-NTA column (Qiagen, Auckland, NZ) according to the manufacturer's instructions and protein expression checked by SDS-PAGE. The polypeptide sequence is given in SEQ ID NO: 51 and shown in FIG. 14.

[0277] Malate dehydrogenase activity was assessed by gene complementation of the mutant E. coli strain UTH4606 that lacks a functional malate dehydrogenase gene (Heard et al., J. Bacteriol. 122:329-331, 1975; Shaw et al., Mutation Res., 18:247-250, 1973), provided by the E. coli Genetic Stock Centre (Yale University, USA). UTH4606 strain cells cannot utilize malate as a carbon source, in contrast to wild-type E. coli. pBAD-Thio-E construct containing the HN001 malate dehydrogenase AG3 gene or empty pBAD-Thio-E vector was transformed into the UTH4606 E. coli strain and plated onto M9 media plates containing 100 .mu.g/ml kanamycin and 0.5% glucose. Transformant colonies were picked, and plated out onto a series of selective M9 agar plates containing 100 .mu.g/ml Kanamycin and/or 0.5% glucose or 0.5% malate. Growth of the UTH4606 transformed with pBAD-Thio-E encoding the AG3 protein was compared with wild-type UTH4606 cells and UTH4606 cells transformed with empty pBAD-Thio-E vector. Plates were incubated aerobically at 37.degree. C. overnight. Growth was assessed for malate dehydrogenase complementation.

[0278] Results are shown in Table 6 and indicate that wild-type UTH780 cells grew on M9 media supplemented with glucose, but not on M9 media supplemented with malate, or on media containing Kanamycin. This confirmed the phenotype of the UTH780 strain of being unable to utilize malate as a carbon source due to the loss of malate dehydrogenase function. Transformation with empty pBAD/Thio-E vector allowed growth on media containing Kanamycin, but did not complement the malate dehydrogenase mutation. Transformation with pBAD/Thio-E encoding the HN001 malate dehydrogenase AG3 allowed growth on Kanamycin, indicating the presence of the plasmid, and on malate, indicating that the AG3 protein complemented the E. coli malate dehydrogenase deficiency. Therefore, the HN001 protein AG3 has malate dehydrogenase activity. TABLE-US-00009 TABLE 6 Results of LB agar plate assay for malate dehydrogenase gene complementation M9 agar plates containing: E. coli UTH780 0.5% 0.5% Glucose + 0.5% Malate + 0.5% transformed with: Glucose Kanamycin Kanamycin Malate -- + - - - pBAD/Thio-E + + - - pBAD/Thio-E + + + + encoding AG3 +: growth; -: no growth

[0279] Malate dehydrogenase (EC 1.1.1.37) catalyzes the reversible oxidation of malate to oxaloacetate with the concomitant reduction of NAD. As lactobacilli appear not to have a functioning Krebs cycle, the enzyme may be involved in amino acid biosynthesis or L-malate utilization pathways.

[0280] The polypeptide of SEQ ID NO: 51, and the polynucleotide of SEQ ID NO: 9 have utility for processing food and other products and as supplements and additives to food products and in industrial processing. The attributes conferred by this enzyme include: manipulation of energy production and growth in particular media; altered survival characteristics in industrial processes; and formation of common intermediates of various flavor compounds.

[0281] These attributes may be produced in food products, or in industrial processing, by directed activity of the enzyme, introduced in a bacterial strain (including strain HN001, or starter cultures) comprising a polynucleotide of SEQ ID NO: 9 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 51 or a variant.

EXAMPLE 7

Isolation and Characterisation of Dihydrodipicolinate Synthase from L. rhamnosus HN001

[0282] The full-length polynucleotide sequence of dihydrodipicolinate synthase from L. rhamnosus HN001, given in SEQ ID NO: 13 and shown in FIG. 15 with ATG initiation and translation stop codons (boxed), was used to amplify the AI2 dihydrodipicolinate synthase gene from L. rhamnosus HN001 DNA using standard PCR methodology. The upstream and downstream primers were tagged with EcoRI and SalI restriction endonuclease recognition sequences to facilitate cloning.

[0283] AI2 was then cloned into the EcoRI and SalI sites of the pGEX-6P-3 expression vector (Pharmacia Biotech) and transformed into the E. coli strain K12 XL-1Blue competent cells according to standard laboratory protocols. The dihydrodipicolinate synthase AI2 protein was expressed as a fusion protein with glutathione S-transferase (GST), bound to Glutathione Sepharose 4B resin (Pharmacia Biotech), and PreScission protease used to cleave off dihydrodipicolinate synthase AI2 protein, according to the manufacturer's instructions. An aliquot of the purified AI2 protein was checked by SDS-PAGE analysis. The polypeptide sequence is given in SEQ ID NO: 55 and is shown in FIG. 16.

[0284] Dihydrodipicolinate synthase activity was assessed by gene complementation of the mutant E. coli strain AT997 deficient in dihydrodipicolinate synthase gene function (Bukhari and Taylor, J. Bacteriol. 105:844-854, 1971), provided by the E. coli Genetic Stock Centre (Yale University, USA). AT997 cells require diaminopimelic acid (DAP) for growth, in contrast to wild-type E. coli that is DAP-independent. pGEX-6P-3 construct containing the HN001 dihydrodipicolinate synthase AI2 gene or empty pGEX-6P-3 vector was transformed into the AT997 E. coli strain. Transformed AT997 cells were plated onto LB agar plates containing ampicillin (100 .mu.g/ml) only or ampicillin and 45 .mu.g/ml DAP, at dilutions designed to allow the visualization of distinct colonies (ie. <200 colonies/plate). Plates were incubated aerobically at 37.degree. C. overnight and growth assessed as the presence of distinct colonies.

[0285] Results in Table 7 indicate that while AT997 cells transformed with either empty pGEX-6P-3 or pGEX-6P-3 containing the HN001 dihydrodipicolinate synthase AI2 grew in the presence of DAP, only cells transformed with vector containing AI2 grew without DAP. Therefore, the HN001 dihydrodipicolinate synthase protein AI2 complemented the dihydrodipicolinate synthase gene mutation in E. coli strain AT997. TABLE-US-00010 TABLE 7 Results of LB agar plate assay for dihydrodipicolinate synthase gene complementation LB agar plates containing: E. coli AT997 transformed with: Ampicillin and DAP Ampicillin only pGEX-6P-3 + - pGEX-6P-3 with AI2 + + +: growth; -: no growth

[0286] Dihydrodipicolinate synthase (EC 4.2.1.52) converts L-aspartate 4-semialdehyde and pyruvate to 1-2,3-dihydrodipicolinate as part of the lysine biosynthesis pathway. L-aspartate 4-semialdehyde is also the first step of the glycine, serine and threonine metabolic pathways.

[0287] The polypeptide of SEQ ID NO: 55 and the polynucleotide of SEQ ID NO: 13 have utility for processing food products, as additives for industrial processing, and in the commercial production of lysine or intermediates. The attributes conferred by this enzyme include: altered amino acid content, with important flavor and metabolic impacts; commercial production of lysine or intermediates; manipulation of energy production and growth in particular media; and altered survival characteristics in industrial processes.

[0288] These attributes may be produced in food products and used in food and other types of industrial processing, by directed activity of the enzyme, introduced in a bacterial strain (including strain HN001, or starter cultures) comprising a polynucleotide of SEQ ID NO: 13 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 55 or a variant.

EXAMPLE 8

Isolation and Characterisation of Dihydrodipicolinate Reductase from L. rhamnosus HN001

[0289] The full-length polynucleotide sequence of dihydrodipicolinate reductase from L. rhamnosus strain HN001, given in SEQ ID NO: 14 and shown in FIG. 72 with ATG initiation and translation stop codons (boxed), was used to amplify the AI3 dihydrodipicolinate reductase gene from L. rhamnosus HN001 DNA using standard PCR methodology. The upstream and downstream primers were tagged with EcoRI and SalI restriction endonuclease recognition sequences to facilitate cloning.

[0290] AI3 was then cloned into the EcoRI and SalI sites of the pGEX-6P-3 expression vector (Pharmacia Biotech) and transformed into the E. coli strain K12 XL-1Blue competent cells according to standard laboratory protocols. The polypeptide sequence of dihydrodipicolinate reductase AI3 is given in SEQ ID NO: 56 and is shown in FIG. 73. The dihydrodipicolinate reductase AI3 protein was expressed as a fusion protein with glutathione S-transferase (GST), bound to Glutathione Sepharose 4B resin (Pharmacia Biotech), and PreScission protease used to cleave off dihydrodipicolinate reductase AI3 protein, according to the manufacturer's instructions. An aliquot of the purified AI3 protein was checked by SDS-PAGE analysis.

[0291] Dihydrodipicolinate reductase activity was assessed by gene complementation of the mutant E. coli strain AT999 deficient in dihydrodipicolinate reductase gene function (Bukhari and Taylor, J. Bacteriol. 105:844-854, 1971), provided by the E. coli Genetic Stock Centre (Yale University, USA). AT999 cells require diaminopimelic acid (DAP) for growth, in contrast to wild-type E. coli that is DAP-independent. pGEX-6P-3 construct containing the HN001 dihydrodipicolinate reductase AI3 gene or empty pGEX-6P-3 vector was transformed into the AT999 E. coli strain. Transformed AT999 cells were plated onto LB agar plates containing ampicillin (100 .mu.g/ml) only or ampicillin and 45 .mu.g/ml DAP, at dilutions designed to allow the visualization of distinct colonies (ie. <200 colonies/plate). Plates were incubated aerobically at 37.degree. C. overnight and growth assessed as the presence of distinct colonies (Table 8).

[0292] The results in Table 8 indicate that while AT999 cells transformed with either empty pGEX-6P-3 or pGEX-6P-3 containing the HN001 dihydrodipicolinate reductase AI3 grew in the presence of DAP, only cells transformed with vector containing AI3 grew without DAP. Therefore, the HN001 dihydrodipicolinate reductase protein AI3 complemented the dihydrodipicolinate reductase gene mutation in E. coli strain AT999. TABLE-US-00011 TABLE 8 Results of LB agar plate assay for dihydrodipicolinate reductase gene complementation. LB agar plates containing: E. coli AT999 transformed with: Ampicillin and DAP Ampicillin only pGEX-6P-3 + - pGEX-6P-3 with AI3 + + +: growth; -: no growth

[0293] Dihydrodipicolinate reductase (EC 1.3.1.26) converts L-2,3-dihydro-dipicolinate to L-tetrahydropicolinate as part of the lysine biosynthesis pathway.

[0294] The polypeptide of SEQ ID NO: 56, and the polynucleotide of SEQ ID NO: 14 have utility for processing food products, as additives for industrial processing, and in the commercial production of lysine or intermediates. The attributes conferred by this enzyme include: altered amino acid content, with important flavor and metabolic impacts; commercial production of lysine or intermediates; manipulation of energy production and growth in particular media; and altered survival characteristics in industrial processes.

[0295] These attributes may be produced in food products and used in food and other types of industrial processing, by directed activity of the enzyme, introduced in a bacterial strain (including strain HN001, or starter cultures) comprising a polynucleotide of SEQ ID NO: 14 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 56 or a variant.

EXAMPLE 9

Isolation and Characterisation of Aspartate Aminotransferase from L. rhamnosus HN001

[0296] The full-length gene sequence of aspartate aminotransferase from L. rhamnosus strain HN001, given in SEQ ID NO: 12 and shown in FIG. 17 with GTG initiation and translation stop codons (boxed), was used to amplify the AH9 aspartate aminotransferase gene from L. rhamnosus HN001 DNA using standard PCR methodology. The upstream and downstream primers were tagged with EcoRI and SalI restriction endonuclease recognition sequences to facilitate cloning.

[0297] AH9 was then cloned into the EcoRI and SalI sites of the pGEX-6P-3 expression vector (Pharmacia Biotech) and transformed into the E. coli strain K12 XL-1Blue competent cells according to standard laboratory protocols. The aspartate aminotransferase AH9 protein was expressed as a fusion protein with glutathione S-transferase (GST), bound to Glutathione Sepharose 4B resin (Pharmacia Biotech), and PreScission protease used to cleave off the aspartate aminotransferase AH9 protein, according to the manufacturer's instructions. An aliquot of the purified AH9 protein was checked by SDS-PAGE analysis. The polypeptide sequence is given in SEQ ID NO: 54 and is shown in FIG. 18.

[0298] AH9 activity was assayed according to the previously published malate dehydrogenase-coupled method (Karmen, J. Clin. Invest. 34:131-133, 1955) with modifications. Briefly, 1 ml reaction mixtures containing 100 .mu.mol Tris hydrochloride buffer (pH 8.0), 100 .mu.mol L-aspartate, 10 .mu.mol of .alpha.-ketoglutarate, 0.2 .mu.mol NADH, 0.015 .mu.mol pyrodoxal 5'-phosphate (PLP), and 3 .mu.g (3.6 U) malate dehydrogenase (all chemicals from Sigma Chemical Co.) were incubated at 37.degree. C. with increasing amounts (0 to 142.5 ng) of the purified HN001 aspartate aminotransferase AH9 protein. The rationale of the assay is that aspartate aminotransferase converts .alpha.-ketoglutarate and L-aspartate to oxaloacetate and L-glutamate. The oxaloacetate is then substrate for the malate dehydrogenase, which oxidizes one molecule of NADH to NAD.sup.+ for every molecule of oxaloacetate converted to L-malate. As the first step is rate limiting, the amount of NADH oxidized in the second step is directly proportional to the aspartate aminotransferase-dependent production of oxaloacetate from .alpha.-ketoglutarate in the first step. The reaction was monitored by the decrease in absorbance at 340 nm, and results used to calculate the .mu.mol NADH oxidized per minute. One unit of enzyme was defined as the amount of enzyme that catalyzed the production of 1 .mu.mol of oxaloacetate per minute at 37.degree. C.

[0299] Results in Table 9 indicate that, while in the absence of purified HN001 aspartate aminotransferase AH9 protein there was some background oxidation of NADH, the addition of AH9 protein led to increased rates of aspartate aminotransferase-dependent NADH oxidation. Increased amounts of AH9 increased NADH oxidation in a dose-dependent manner. A similar background rate observed in reaction mixtures without the addition of AH9 protein was also observed in reaction mixtures without both AH9 protein and .alpha.-ketoglutarate substrate (data not shown), indicating that the background NADH oxidation was not aspartate aminotransferase-dependent. The addition of 142.5 ng of AH9 protein led to an over 19-fold increase in NADH oxidation. The activity of the purified HN001 aspartate aminotransferase AH9 protein was calculated to be 31 U/mg protein. Therefore, HN001 protein AH9 is an aspartate aminotransferase. TABLE-US-00012 TABLE 9 Results of the malate dehydrogenase-coupled aspartate aminotransferase assay. Concentration of purified HN001 aspartate aminotransferase AH9 NADH oxidized (ng/ml) (.mu.mol/min/ml) 0 0.20 .times. 10.sup.-3 23.8 0.80 .times. 10.sup.-3 47.5 1.13 .times. 10.sup.-3 71.2 1.61 .times. 10.sup.-3 95.0 1.95 .times. 10.sup.-3 118.8 2.57 .times. 10.sup.-3 142.5 3.82 .times. 10.sup.-3

[0300] .alpha.-Ketoglutarate is an important chemical mediator in lactic acid bacteria, and the addition of this compound to cheese curd has positive impacts on cheese flavor (Yvon et al., Int. Dairy J. 8:889-898, 1998). The formation of .alpha.-ketoglutarate using L-glutamate as an amino donor, catalysed by aspartate aminotransferase, is an important pathway in maintaining intracellular .alpha.-ketoglutarate levels.

[0301] The polypeptide of SEQ ID NO: 54 and the polynucleotide of SEQ ID NO: 12 have utility for processing food products and as supplements and additives to food products. This esterase may also be used to develop non-food products. The attributes conferred by this enzyme include: altered amino acid content, with important flavor and metabolic impacts; manipulation of energy production and growth in particular media; and altered survival characteristics in industrial processes, including food processing These attributes may be produced in food, such as dairy products, and in other industrial processes, by directed activity of the enzyme, introduced in a bacterial strain (including strain HN001, or starter cultures) comprising a polynucleotide of SEQ ID NO: 12 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 54 or a variant.

EXAMPLE 10

Isolation and Characterisation of Serine Dehydratase subunits .alpha. and .beta. from L. rhamnosus HN001

[0302] The full-length polynucleotide sequence of serine dehydratase subunits .alpha. and .beta., given in SEQ ID NO: 7, was used to amplify the AF8 serine dehydratase cc subunit and AF7 serine dehydratase .beta. subunit from L. rhamnosus HN001 DNA as a single operon using standard PCR methodology. The polynucleotide sequence of L. rhamnosus strain HN001 serine dehydratase subunits .alpha. (AF8) and .beta. (AF7) is shown in FIG. 19, with ATG translation initiation codons and termination codons shown boxed for AF8 and shaded for AF7.

[0303] The AF8 serine dehydratase cc subunit and AF7 serine dehydratase .beta. subunit were amplified from L. rhamnosus HN001 DNA as a single operon using standard PCR methodology. The AF8 and AF7 genes were cloned in the vector pTRKH2 (obtained from Dr Todd Klaenhammer, North Carolina State University, North Carolina, USA) and transformed into E. coli DH5.alpha. cells. Positive transformants were selected, grown overnight and the plasmid isolated by standard laboratory techniques. Competent L. rhamnosus HN001 cells were then transformed with the pTRKH2 construct containing the HN001 serine dehydratase subunits .alpha. and .beta. to overexpress the genes in strain HN001. The amino acid sequences of the expressed proteins AF8 serine dehydratase .alpha. and AF7 serine dehydratase .beta. are given in SEQ ID NO: 49 and 48, respectively, and shown in FIGS. 22A and 22B, respectively.

[0304] Serine dehydratase enzyme activity was assessed by comparing serine utilization in liquid cultures of HN001 strain cells transformed with either the pTRKH2 construct containing the HN001 serine dehydratase or empty pTRKH2 vector only.

[0305] The results shown in FIGS. 20 and 21 indicate that the presence of the expression plasmid encoding HN001 serine dehydratase subunits .alpha. (AF8) and .beta. (AF7) significantly increased the utilization of serine by HN001 strain cells, compared to cells transformed with empty expression vector only. Therefore the HN001 genes AF7 and AF8 encode the serine dehydratase enzyme. FIG. 20 shows the percentage serine utilization by HN001 strain in liquid culture with 5 mM initial serine concentration: .nu. HN001 transformed with vector only; .upsilon. pTRKH2 construct containing HN001 serine dehydratase. FIG. 21 shows the percentage serine utilization by HN001 strain in liquid culture with 12 mM initial serine concentration: .nu. HN001 transformed with vector only, .upsilon. pTRKH2 construct containing HN001 serine dehydratase.

[0306] Serine dehydratase (EC 4.2.1.13), comprising .alpha. and .beta. subunits, catalyzes the irreversible deamination of serine to pyruvate and ammonia (Ogawa et al., J. Biol. Chem. 264:15818-15822, 1989; Grabowski et al., Trends in Biochem. Sci. 18:297-300, 1993).

[0307] The polypeptides of SEQ ID NO: 48 and 49, and the polynucleotide of SEQ ID NO: 7 have utility for processing food products and in other types of industrial processing, and in the production of ammonia. Applications for the HN001 serine dehydratase subunits AF7 and AF8 of the present invention include: energy supply from amino acids present in growth media or environment; production of ammonia, regarded as a flavor compound; altered pyruvate levels--pyruvate is a highly reactive compound, and is important in a number of flavor pathways; and altered survival characteristics in industrial processes.

[0308] These applications may be implemented by directed activity of the enzyme, introduced in a bacterial strain (including strain HN001, or starter cultures) comprising a polynucleotide of SEQ ID NO: 7 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 48 and/or 49, or variants.

EXAMPLE 11

Isolation and Characterisation of Histidinol-Phosphate Aminotransferase from L. rhamnosus HN001

[0309] The full-length polynucleotide sequence of histidinol-phosphate amino-transferase from L. rhamnosus strain HN001, given in SEQ ID NO: 8 and shown in FIG. 23 with ATG initiation and translation stop codons (boxed), was used to amplify the AG2 histidinol-phosphate aminotransferase gene from L. rhamnosus HN001 DNA using standard PCR methodology. The upstream and downstream primers were tagged with EcoRI and BamHI restriction endonuclease recognition sequences to facilitate cloning.

[0310] AG2 was then cloned into the EcoRI and BamHI sites of the pGEX-6P-3 expression vector (Pharmacia Biotech) and transformed into E. coli strain DH-5.alpha. at competent cells according to standard laboratory protocols. Cells were lysed by sonication and the presence of AG2 protein, expressed as a GST fusion protein, checked by SDS-PAGE analysis. The polypeptide sequence of AG2 is given in SEQ ID NO: 50 and shown in FIG. 24.

[0311] Histidinol-phosphate aminotransferase activity was assessed by gene complementation of the mutant E. coli strain UTH780 that lacks a functional his C gene that encodes histidinol-phosphate aminotransferase (Goldschmidt et al., Genetics, 66:219-229, 1970), provided by the E. coli Genetic Stock Centre (Yale University, USA). UTH780 cells require L-histidine for growth, in contrast to wild-type E. coli that is L-histidine-independent. pGEX-6P-3 construct encoding HN001 histidinol-phosphate aminotransferase AG2 was transformed into the UTH780 E. coli strain and plated onto LB agar plates containing 100 .mu.g/ml ampicillin. Ampicillin-resistant transformant colonies were picked and plated out onto selective media (ie. M9 media plates with and without 100 .mu.g/ml L-histidine, with and without 100 .mu.g/ml ampicillin). Growth of UTH780 transformed with AG2 was compared with the growth of wild-type UTH780 cells and UTH780 cells transformed with a pGex-6P-3 construct encoding a non-histidinol-phosphate aminotransferase (AE8). Plates were incubated aerobically at 37.degree. C. overnight and growth assessed as the presence of distinct colonies.

[0312] Results in Table 10 indicate that while wild-type UTH780 cells grew in the presence of histidine, no growth was observed when ampicillin was added to the media. Therefore, ampicillin resistance in transformed UTH780 was due to the presence of pGEX-6P-3 vector. UTH780 cells transformed with either empty pGEX-6P-3 or pGEX-6P-3 encoding an irrelevant protein (AE9) grew in the presence of histidine and ampicillin, but remained auxotrophic for hisitidine, indicating that the H is C phenotype was not complemented. UTH780 cells transformed with pGEX-6P-3 encoding HN001 histidinol-phosphate aminotransferase AG2 grew on M9 media without histidine. Therefore, the AG2 protein complemented the his C mutation of UTH780 strain E. coli cells. TABLE-US-00013 TABLE 10 Results of M9 agar plate assay for histidinol-phosphate aminotransferase gene complementation. M9 agar plates containing: E. coli UTH780 Ampicillin and L- transformed with: L-histidine only histidine Ampicillin only -- + - - pGEX-6P-3 + + - pGEX-6P-3 + + - encoding AE9 pGEX-6P-3 + + + encoding AG2 +: growth; -: no growth

[0313] Histidinol-phosphate aminotransferase (EC 2.6.1.9) catalyzes the transamination of histidinol phosphate and 2-oxoglutarate to 3-(Imidazol-4-yl)-2-oxopropyl phosphate and glutamate, as the eighth step in histidine biosynthesis (Martin et al., J. Bio. Chem. 242:1168-1174, 1967). Some lactic acid bacteria are known to decarboxylate amino acids, such that histidine can be converted to histamine, which has undesirable physiological effects (Lonvaud-Funel, FEMS Microb. Lett. 199:9-13, 2001).

[0314] The polypeptide of SEQ ID NO: 50 and the polynucleotide of SEQ ID NO: 8 have utility for processing food products and as supplements and additives to food products. This histidinol-phosphate aminotransferase may also be used to develop non-food products. The attributes conferred by this enzyme include: altered levels of particular amino acids, leading to flavor and metabolic changes; affect aromatic amino acid metabolism, a source of important flavor compounds; and modulate production of biogenic amines.

[0315] These attributes may be produced in food, and other products, by directed activity of the enzyme, introduced in a bacterial strain (including strain HN001, or starter cultures) comprising a polynucleotide of SEQ ID NO: 8 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 50 or a variant.

EXAMPLE 12

Isolation and Characterisation of malY-Aminotransferase from L. rhamnosus HN001

[0316] The full-length polynucleotide sequence of malY aminotransferase from L. rhamnosus strain HN001, given in SEQ ID NO: 17 and shown in FIG. 25 with ATG initiation and translation stop codons (boxed), was used to amplify the AJ6 aminotransferase gene from L. rhamnosus HN001 DNA using standard PCR methodology. The upstream and downstream primers were tagged with EcoRI and BamHI restriction endonuclease recognition sequences to facilitate cloning.

[0317] AJ6 was then cloned into the EcoRI and BamHI sites of the pGEX-6P-3 expression vector (Pharmacia Biotech) and transformed into E. coli strain DH-5.alpha. competent cells according to standard laboratory protocols. Cells were lysed by sonication and the presence of AJ6 protein, expressed as a GST fusion protein, checked by SDS-PAGE analysis. The polypeptide sequence of AJ6 is given in SEQ ID NO: 59 and shown in FIG. 26.

[0318] A feature of malY-aminotransferases is the ability to complement mutations of the E. coli cystathione .beta.-lyase protein metC (Zdych et al., J. Bacteriol. 177:5035-5039, 1995). Therefore, AJ6 activity was assessed by suppression of the metC.sup.- phenotype in the E. coli strain CAG18527 (Singer et al., Microbiol. Rev. 53:1-24, 1989) provided by the E. coli Genetic Stock Centre (Yale University, USA). CAG18527 cells require L-methionine for growth, in contrast to wild-type E. coli that is L-methionine-independent. A pGEX-6P-3 construct encoding the HN001 aminotransferase AJ6 was transformed into the CAG18527 E. coli strain and plated onto LB agar plates containing 100 .mu.g/ml ampicillin. Ampicillin-resistant transformant colonies were picked and plated out onto selective media (M9 plates with and without 1 mM L-methionine, with and without 5 .mu.g/ml ampicillin). Growth of the CAG18527 transformed with AJ6 was compared with the growth of wild-type CAG18527 cells and CAG18527 cells transformed with a pGEX-6P-3 construct encoding a non-aminotransferase irrelevant protein. Plates were incubated aerobically at 37.degree. C. for 48 hrs and growth assessed.

[0319] Results in Table 11 indicate that while wild-type CAG18527 cells grew in the presence of methionine, no growth was observed in the presence of ampicillin. This confirmed the ampicillin-sensitive, methionine-auxotrophic phenotype of the CAG18527 strain. CAG18527 cells transformed with either empty pGEX-6P-3 or pGEX-6P-3 encoding an irrelevant HN001 protein (AC9) grew in the presence of methionine and ampicillin, but not in the absence of methionine, indicating that the metC- phenotype was not suppressed. CAG18527 cells transformed with pGEX-6P-3 encoding HN001 aminotransferase AJ6 were ampicillin resistant and grew on M9 media without methionine. Therefore, the AJ6 protein suppressed the metC.sup.- mutation of CAG18527 strain E. coli cells. TABLE-US-00014 TABLE 11 Results of M9 agar plate assay for suppression of the metC phenotype. M9 agar plates containing: E. coli CAG18527 L-methionine Ampicillin and L- transformed with: only methionine Ampicillin only -- + - - pGEX-6P-3 + + - pGEX-6P-3 + + - encoding AC9 pGEX-6P-3 + + + encoding AJ6 +: growth; -: no growth

[0320] The malY/PatB pyridoxal-5'-phosphate-dependent aminotransferase family (EC 2.6.1.-) appear to have both aminotransferase and regulatory activities (Mehta and Christen, Eur. J. Biochem. 203 :373-376, 1993), including the transamination of methionine and regulation of maltose utilization (Reidl and Boos, J. Bacteriol. 173:4862-4876, 1991), as well as other activities (Chu et al., Infect. Imm. 63: 4448-4455, 1995).

[0321] The polypeptide of SEQ ID NO: 59 and the polynucleotide of SEQ ID NO: 17 have utility for processing food products and as supplements and additives to food products. This aminotransferase may also be used to develop non-food products. The attributes conferred by this enzyme include: altered levels of particular amino acids, leading to flavor and metabolic changes; altered expression of catabolite or other regulons; modulation of hemolytic activity; and probiotic effects.

[0322] These attributes may be produced in food products by directed activity of the enzyme, introduced in a bacterial strain (including strain HN001, or starter cultures) comprising a polynucleotide of SEQ ID NO: 17 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 59 or a variant.

EXAMPLE 13

Isolation and Characterisation of malY-Aminotransferase from L. rhamnosus HN001

[0323] The full-length polynucleotide sequence of a second malY-aminotransferase from L. rhamnosus strain HN001, given in SEQ ID NO: 18 and shown in FIG. 27 with ATG initiation and translation stop codons (boxed), was used to amplify the AJ7 aminotransferase gene from L. rhamnosus HN001 DNA using standard PCR methodology. The upstream and downstream primers were tagged with EcoRI and BamHI restriction endonuclease recognition sequences to facilitate cloning.

[0324] AJ7 was then cloned into the EcoRI and BamHI sites of the pGEX-6P-3 expression vector (Pharmacia Biotech) and transformed into E. coli strain DH-5.alpha. competent cells according to standard laboratory protocols. Cells were lysed by sonication and the presence of AJ7 protein, expressed as a GST fusion protein, checked by SDS-PAGE analysis. The polypeptide sequence of AJ7 is given in SEQ ID NO: 60 and shown in FIG. 28.

[0325] A feature of malY-aminotransferases is the ability to complement mutations of the E. coli cystathione .beta.-lyase protein metC (Zdych et al., J. Bacteriol. 177:5035-5039, 1995). Therefore, AJ7 activity was assessed by suppression of the metC.sup.- phenotype in the E. coli strain CAG18527 (Singer et al., Microbiol. Rev. 53:1-24, 1989) provided by the E. coli Genetic Stock Centre (Yale University, USA). CAG18527 cells require L-methionine for growth, in contrast to wild-type E. coli that is L-methionine-independent. pGEX-6P-3 construct encoding the HN001 aminotransferase AJ7 was transformed into the CAG18527 E. coli strain and plated onto LB agar plates containing 100 .mu.g/ml ampicillin. Ampicillin-resistant transformant colonies were picked and plated out onto selective media (M9 plates with and without 1 mM L-methionine, with and without 5 .mu.g/ml ampicillin). Growth of the CAG18527 transformed with AJ7 was compared with the growth of wild-type CAG18527 cells and CAG18527 cells transformed with a pGEX-6P-3 construct encoding a irrelevant protein. Plates were incubated aerobically at 37.degree. C. for 48 hrs and growth assessed.

[0326] Results in Table 12 indicate that while wild-type CAG18527 cells grew in the presence of methionine, no growth was observed in the presence of ampicillin. This confirmed the ampicillin-sensitive, methionine-auxotrophic phenotype of the CAG18527 strain. CAG18527 cells transformed with either empty pGEX-6P-3 or pGEX-6P-3 encoding an irrelevant HN001 protein (AC9) grew in the presence of methionine and ampicillin, but not in the absence of methionine, indicating that the metC- phenotype was not suppressed. CAG18527 cells transformed with pGEX-6P-3 encoding HN001 aminotransferase AJ7 were ampicillin resistant and grew on M9 media without methionine. Therefore, the AJ7 protein suppressed the metC.sup.- mutation of CAG18527 strain E. coli cells. TABLE-US-00015 TABLE 12 Results of M9 agar plate assay for suppression of the metC phenotype. M9 agar plates containing: E. coli CAG18527 L-methionine Ampicillin and L- transformed with: only methionine Ampicillin only -- + - - pGEX-6P-3 + + - pGEX-6P-3 + + - encoding AC9 pGEX-6P-3 + + + encoding AJ7 +: growth; -: no growth

[0327] The malY/PatB pyridoxal-5'-phosphate-dependent aminotransferase family (EC 2.6.1.-) appear to have both aminotransferase and regulatory activities (Mehta and Christen, Eur. J. Biochem. 203:373-376, 1993), including the transamination of methionine and regulation of maltose utilization (Reidl and Boos, J. Bacteriol. 173:4862-4876, 1991), as well as other activities (Chu et al., Infect. Imm. 63: 4448-4455, 1995).

[0328] The polypeptide of SEQ ID NO: 60 and the polynucleotide of SEQ ID NO: 18 have utility for processing food products and as supplements and additives to food products. This aminotransferase may also be used to develop non-food products. The attributes conferred by this enzyme include: altered levels of particular amino acids, leading to flavor and metabolic changes; altered expression of catabolite or other regulons; modulation of hemolytic activity; and probiotic effects.

[0329] These attributes may be produced in food, such as dairy products, by directed activity of the enzyme, introduced in a bacterial strain (including strain HN001, or starter cultures) comprising a polynucleotide of SEQ ID NO: 18 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 60 or a variant.

EXAMPLE 14

Isolation and Characterisation of Cystathione .beta.-Lyase from L. rhamnosus HN001

[0330] The full-length polynucleotide sequence of cystathione .beta.-lyase from L. rhamnosus strain HN001, given in SEQ ID NO: 5 and shown in FIG. 29 with ATG initiation and translation stop codons (boxed), was used to amplify the AC8 cystathione .alpha.-lyase gene from L. rhamnosus HN001 DNA using standard PCR methodology.

[0331] AC8 was cloned into the pUniBlunt/V5-HisTopo vector (Invitrogen) and transformed into the E. coli strain PIR1 OneShot competent cells (Invitrogen). To construct an expression plasmid, the pUniBlunt/V5-HisTopo vector construct was recombined with the pBad/Thio-E vector (Invitrogen) and transformed into the E. coli strain TOP10 competent cells (Invitrogen) according to the manufacturer's instructions. The AC gene product was therefore cloned as a fusion protein tagged with a His-patch polypeptide and thioredoxin protein. The AC8 fusion protein was expressed and purified using a Ni-NTA column (Qiagen, Auckland, NZ) according to the manufacturer's instructions and protein expression checked by SDS-PAGE. The polypeptide sequence of AC8 is given in SEQ ID NO: 46 and shown in FIG. 30.

[0332] Cystathione .beta.-lyase activity was assessed according to the method of Uren, Methods in Enzymol. 143:483-496, 1987, with modifications. Briefly, aliquots of the purified AC8-GST fusion protein were added to 1 ml cuvettes containing 780 .mu.l of 0.1 M Tris-HCl pH 9.0, 200 .mu.l of 10 mM L-cystathionine, and 20 .mu.l of 0.1 M potassium phosphate, with pyridoxal-5'-phosphate added to a final concentration of 20 .mu.M, on ice. Change in OD was measured at 412 nm over time, and one unit of enzyme defined as the formation of 1 .mu.mol of mercaptide per minute at 37.degree. C. Cystathione .beta.-lyase activity of the AC8 fusion protein was compared with activity of an irrelevant protein (pBAD/Thio-E/Uni-CAT expression control vector, Invitrogen), and reactions containing water or Ni-NTA column elution buffer.

[0333] The results are shown in FIG. 31, with rates of change of OD and enzyme activity given in Table 13. These results indicate that similar background rates of mercaptide formation were observed in reactions containing water only, elution buffer only or 10 .mu.l purified CAT fusion protein. Significantly greater mercaptide formation was observed in reactions containing 10 .mu.l purified HN001 cystathione .alpha.-lyase AC8 fusion protein. Therefore, AC8 protein has cystathione .alpha.-lyase activity. FIG. 31 shows cystathione .beta.-lyase activity measured as rate of mercaptide formation. .upsilon. 10 .mu.l purified HN001 cystathione .beta.-lyase AC8 fusion protein; .nu. 10 .mu.l purified CAT fusion protein; .sigma. 10 .mu.l H.sub.2O only; .lamda. 10 .mu.l elution buffer only. TABLE-US-00016 TABLE 13 Cystathione .beta.-lyase activity of AC8 compared with irrelevant protein, H.sub.2O and elution buffer controls. Enzyme activity Protein .DELTA. OD.sub.412/min (.mu.mol/min/ml) AC8 fusion protein 0.00328 16.31 CAT fusion protein 0.00242 12.03 H.sub.2O only 0.00232 11.53 Elution buffer-only 0.00233 11.58

[0334] The dose-response of the HN001 cystathione .beta.-lyase activity AC8 was determined by comparing mercaptide formation in a series of dilutions of the purified enzyme. Results are shown in FIG. 32, and the rate of change in optical density and enzyme activities given in Table 14.

[0335] These results indicate that the increased rate of mercaptide peptide was proportional to the amount of AC8 fusion protein, supporting that AC8 encodes HN001 cystathionine .beta.-lyase. FIG. 32 shows the experimentally determined dose-response of the AC8 fusion protein. Cystathione .beta.-lyase activity of increasing amounts of His-patch/Thio/AC8 fusion protein; 10 .mu.l (.upsilon.), 25 .mu.l (.nu.) and 50 .mu.l (.sigma.) purified protein showed increasing rates of mercaptide formation. The increase in mercaptide formation was proportional to amount of AC8 fusion protein added. TABLE-US-00017 TABLE 14 Cystathione .beta.-lyase activity in increasing amounts of AC8 protein Amount of purified AC8 Enzyme activity fusion protein .DELTA. OD.sub.410/min (.mu.mol/min/ml) 10 .mu.l 0.00319 15.8 25 .mu.l 0.00378 18.8 50 .mu.l 0.00496 24.7

[0336] Cystathionine .beta.-lyase (EC 4.4.1.8) deaminates cystathionine to L-homocysteine, ammonia and pyruvate (Dwivedi et al., Biochem. 21:3064-3069, 1982), and may also have active on L-cystine and related substrates (Uren, Methods in Enzymol. 143:483-486, 1987; Alting et al., Appl. Environ. Microbiol. 61:4037-4042, 1995). Thus, cystathionine .beta.-lyase is involved in a number of pathways including methionine metabolism and catabolism of sulphur-containing compounds. L-homocysteine has been shown to have important health impacts in humans (Nittynen et al., Ann. Med. 31:318-326, 1999; Giles et al., Am. Heart J. 139:446-453, 2000).

[0337] The polypeptide of SEQ ID NO: 46 and the polynucleotide of SEQ ID NO: 5 have utility for processing food products and as supplements and additives to food products. This lyase may also be used to develop non-food products. The attributes conferred by this enzyme include: altered flavor and metabolic characteristics through changes in levels of particular amino acids; altered levels of important sulphur-containing flavor compounds; and health impacts through the modulation of L-homocysteine levels.

[0338] These attributes may be produced in food products by directed activity of the enzyme, introduced in a bacterial strain (including strain HN001, or starter cultures) comprising a polynucleotide of SEQ ID NO: 5 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 46 or a variant.

EXAMPLE 15

Isolation and Characterisation of Phosphoenolpyruvate Hydratase from L. rhamnosus HN001

[0339] HN001 phosphoenolpyruvate hydratase AK4 was isolated by a series of experiments designed to identify HN001 strain proteins that were up-regulated in response to physiological stresses encountered during industrial processes. Cells were subjected to heat or osmotic shock, proteins radiolabeled with [.sup.35S]-methionine and [.sup.35S]-cysteine (Amersham, USA), and cell-free extracts from shocked and non-shocked HN001 cultures compared by 2-D analysis and N-terminal sequencing as below.

[0340] Shock proteins were radiolabeled according to standard laboratory methods. Heat shock was performed by incubation at 50.degree. C. on both log phase and stationary phase HN001 strain cultures, and salt (osmotic) shock on late log phase by HN001 strain cultures by transfer into MRS broth containing 0.6 M sodium chloride. Immediately after heat or osmotic shock, approximately 5 .mu.Ci ml.sup.-1 each of L-[.sup.35S]-methionine and L-[.sup.35S]-cysteine were added to the culture medium and incubated for 30 min, followed by the addition of excess of cold 1 mM L-cysteine hydrochloride and 1 mM L-methionine, and cultures then placed on ice. Radiolabeled cells were collected by centrifugation, washed twice in washing buffer (0.1 M Tris-HCl, 1 mM EDTA, pH 7.5) and resuspended in resuspension buffer (10 mM Tris-HCl, 5 mM MgCl.sub.2, 2 mM PMSF, pH 7.5). About 0.5 ml cell suspension was mixed with 0.5 g of 0.17-0.18 mm glass beads and homogenized using Shake-it-Baby (Biospec products). After homogenization for 25 min, the suspension was centrifuged and the supernatant was collected. 2-D Gel electrophoresis was performed on the cell free extract containing 50-75 .mu.g of protein. Excess chilled methanol was added and kept at -80.degree. C. for 1 hr followed by centrifugation at 13,000 rpm to collect the pellet. The pellet was vacuum-dried and resuspended in rehydration buffer (8M urea, 2% Triton X 100, 0.5% (v/v) IPG buffer (Amersham Pharmacia Biotech, USA) and few grains of bromophenol blue). Endonuclease (Sigma) was added (150 U) to the rehydrated sample and incubated at room temperature for 20 min. The solution was then added to IPG strips and rehydrated overnight at 20.degree. C. The rehydrated IPG strips were placed on a flat bed electrophoresis unit (Amersham Pharmacia Biotech, USA) and focused at 300 Volts for 30 min followed by 3,000 volts for 4 hrs. The focused strips were equilibrated (15 min) in equilibration buffer (50 mM Tris-HCl, pH 8.8, 6 M Urea, 30% (v/v) glycerol, 2% (w/v) SDS and few grains bromophenol blue) containing either dithioerythritol (1.0% w/v) or iodoacetamide (2.5% w/v). After equilibration, the strips were placed on the second dimensional (vertical SDS-PAGE homogeneous) gels a using PROTEAN II xi cell (Bio-Rad). The second dimension was carried out at 20 mA per plate for 15 min and 40 mA per plate for 4 hrs.

[0341] Gels were then equilibrated in protein transfer buffer (24.8 mM Tris, pH 8.3, 192 mM Glycine and 10% (v/v) methanol) and blotted on a PVDF membrane using a Trans-blot apparatus (Bio-Rad) at 24 volts overnight at 4.degree. C. PVDF membranes were exposed to Hyperfilm-.beta.max (Amersham Pharmacia Biotech, USA) for up to two weeks using standard procedures. Resultant autoradiograms were scanned using the Fluor-S Multimager system (Bio-Rad) and patterns compared using PDQuest software. For N-terminal sequencing, membranes were stained with Coommassie Brilliant Blue R-250. The desired spots were excised and N-terminal sequencing carried out using a protein sequencer (Applied BioSystems, Model 476A) according to standard methods.

[0342] A protein up-regulated by heat and osmotic shock was N-terminal sequenced and the amino acid sequence is given in SEQ ID NO: 83. This sequence was used to search an HN001 sequence database using the TBLASTN program (NCBI) and the corresponding polynucleotide and polypeptide sequences are given in SEQ ID NO: 20 and 62, and shown in FIGS. 33 and 34, respectively. Similarity searching using BLAST software revealed closest amino acid sequence similarity to phosphoenolpyruvate hydratase sequences but with significant differences.

[0343] Phosphoenolpyruvate hydratase (EC 4.2.1.11) is a glycolytic pathway enzyme that hydrolyzes 2-phospho-D-glycerate to give phosphoenolpyruvate (Malmstroem, B. G, The Enzymes, 2nd. Ed., Boyer, P. D., Lardy, H., Myrback, K., eds., 5:471-494, 1961).

[0344] The polypeptide of SEQ ID NO: 62 and the polynucleotide of SEQ ID NO: 20 have utility for processing food products and as supplements and additives to food products. This hydratase may also be used to develop non-food products. The attributes conferred by this enzyme include: enhanced bacterial survival in industrial processes; improved colonization of human intestinal environment; and altered metabolic characteristics through changes in carbohydrate utilization.

[0345] These attributes may be produced in food products by directed activity of the enzyme, introduced in a bacterial strain (including strain HN001, or starter cultures) comprising a polynucleotide of SEQ ID NO: 20 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 62 or a variant.

EXAMPLE 16

Isolation and Characterisation of Tagatose Bisphosphate Aldolase from L. rhamnosus HN001

[0346] HN001 tagatose bisphosphate aldolase AK1 was isolated by a series of experiments designed to identify HN001 strain proteins that were up-regulated in response to physiological stresses encountered during industrial processes. Cells were subjected to heat or osmotic shock, proteins radiolabeled with [.sup.35S]-methionine and [.sup.35S]-cysteine (Amersham, USA), and cell-free extracts from shocked and non-shocked HN001 cultures compared by 2-D analysis and N-terminal sequencing as described for Example 15 (HN001 phosphoenolpyruvate hydratase AK4).

[0347] A protein up-regulated by heat and osmotic shock was N-terminal sequenced and the polypeptide sequence is given in SEQ ID NO: 81. This was used to search an HN001 sequence database using the TBLASTN program (NCBI) and the corresponding polynucleotide and polypeptide sequences are given in SEQ ID NO: 19 and 61, and shown in FIGS. 35 and 36, respectively. Similarity searching using BLAST software revealed closest amino acid sequence similarity to tagatose bisphosphate aldolase sequences but with significant differences.

[0348] Tagatose bisphosphate aldolase (EC 4.1.2.40) is involved in the tagatose 6-phosphate pathway of lactose catabolism, and converts D-tagatose 1,6-bisphosphate to glycerone phosphate and D-glyceraldehyde 3-phosphate (Anderson and Markwell, Methods in Enzymol. 90:232-234, 1982).

[0349] The polypeptide of SEQ ID NO: 61 and the polynucleotide of SEQ ID NO: 19 have utility for processing food and other products, and as supplements and additives to food products. This aldolase may also be used to develop non-food products. The attributes conferred by this enzyme include: enhanced bacterial survival in industrial processes; improved colonization of human intestinal environment; and altered metabolic characteristics through changes in carbohydrate utilization.

[0350] These attributes may be produced in food products or in supplements, by directed activity of the enzyme, introduced in a bacterial strain (including strain HN001, or starter cultures) comprising a polynucleotide of SEQ ID NO: 19 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 61 or a variant.

EXAMPLE 17

Isolation and Characterisation of Phosphoglycerate Kinase from L. rhamnosus HN001

[0351] HN001 phosphoglycerate kinase AK6 was isolated by a series of experiments designed to identify HN001 strain proteins that were up-regulated in response to physiological stresses encountered during industrial processes. Cells were subjected to heat or osmotic shock, proteins radiolabeled with [.sup.35S]-methionine and [.sup.35S]-cysteine (Amersham, USA), and cell-free extracts from shocked and non-shocked HN001 cultures compared by 2-D analysis and N-terminal sequencing as described for Example 15 (HN001 phosphoenolpyruvate hydratase AK4).

[0352] A protein up-regulated by heat and osmotic shock was N-terminal sequenced and the polypeptide sequence is given in SEQ ID NO: 82. This was used to search an HN001 sequence database using the TBLASTN program (NCBI) and the corresponding polynucleotide and polypeptide sequences are given in SEQ ID NO: 22 and 64, and shown in FIGS. 37 and 38, respectively. Similarity searching using BLAST software revealed closest amino acid sequence similarity to phosphoglycerate kinase sequences but with significant differences.

[0353] Phosphoglycerate kinase (EC 2.7.2.3) is involved in the glycolysis pathway, and catalyzes the phospho-transfer reaction of ATP and 3-phospho-D-glycerate to ADP and 3-phospho-D-glyceroyl phosphate (bacterial enzyme reviewed in Suzuki and Imahori, Methods in Enzymol. 90:126-130, 1982).

[0354] The polypeptide of SEQ ID NO: 64 and the polynucleotide of SEQ ID NO: 22 have utility for processing food products, and as supplements and additives to food products. This kinase may also be used to develop non-food products. The attributes conferred by this enzyme include: enhanced bacterial survival in industrial processes; improved colonization of human intestinal environment; and altered metabolic characteristics through changes in carbohydrate utilization.

[0355] These attributes may be produced in food products and supplements by directed activity of the enzyme, introduced in a bacterial strain (including strain HN001, or starter cultures) comprising a polynucleotide of SEQ ID NO: 22 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 64 or a variant.

EXAMPLE 18

Isolation and Characterisation of Triosephosphate isomerase from L. rhamnosus HN001

[0356] HN001 triosephosphate isomerase AK5 was isolated by a series of experiments designed to identify HN001 strain proteins that were up-regulated in response to physiological stresses encountered during industrial processes. Cells were subjected to heat or osmotic shock, proteins radiolabeled with [.sup.35S]-methionine and [.sup.35S]-cysteine (Amersham, USA), and cell-free extracts from shocked and non-shocked HN001 cultures compared by 2-D analysis and N-terminal sequencing as described for Example 15 (HN001 phosphoenolpyruvate hydratase AK4).

[0357] A protein up-regulated by heat and osmotic shock was N-terminal sequenced. The polypeptide sequence is given in SEQ ID NO: 76. This sequence was used to search an HN001 sequence database using the TBLASTN program (NCBI) and the corresponding polynucleotide and polypeptide sequences are given in SEQ ID NO: 21 and 63, and shown in FIGS. 39 and 40, respectively. Similarity searching using BLAST software revealed closest amino acid sequence similarity to triosephosphate isomerase sequences but with significant differences. FIG. 39 shows the nucleotide sequence of L. rhamnosus strain HN001 triosephosphate isomerase AK5 showing ATG initiation and translation stop codons (boxed).

[0358] Triosephosphate isomerase (EC 5.3.1.1) is involved in the glycolysis pathway, and catalyzes the isomerisation reaction of D-glyceraldehyde 3-phosphate to glycerone phosphate (Fahey et al., Biochem. J. 124:77P, 1971).

[0359] The polypeptide of SEQ ID NO: 63 and the polynucleotide of SEQ ID NO: 21 have utility for processing food and other products and as supplements and additives to food products. This isomerase may also be used to develop non-food products. The attributes conferred by this enzyme include: enhanced bacterial survival in industrial processes, including food processing; improved colonization of human intestinal environment; and altered metabolic characteristics through changes in carbohydrate utilization.

[0360] These attributes may be produced in food products or supplements by directed activity of the enzyme, introduced in a bacterial strain (including strain HN001, or starter cultures) comprising a polynucleotide of SEQ ID NO: 21 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 63 or a variant.

EXAMPLE 19

Isolation and Characterisation of Fructose-bisphosphate Aldolase from L. rhamnosus HN001

[0361] HN001 fructose-bisphosphate aldolase AM8 was isolated by a series of experiments designed to identify HN001 strain proteins that were up-regulated in response to physiological stresses encountered during industrial processes. Cells were subjected to heat or osmotic shock, proteins radiolabeled with [.sup.35S]-methionine and [.sup.35S]-cysteine (Amersham, USA), and cell-free extracts from shocked and non-shocked HN001 cultures compared by 2-D analysis and N-terminal sequencing as described in Example 15.

[0362] A protein upregulated by heat and osmotic shock was N-terminal sequenced. The amino acid is given in SEQ ID NO: 77. This was used to search an HN001 sequence database using the TBLASTN program (NCBI). The corresponding polynucleotide and polypeptide sequences are given in SEQ ID NO: 29 and 71, and shown in FIGS. 74 and 75, respectively.

[0363] Fructose-bisphosphate aldolase (EC 4.1.2.13) is involved in the glycolysis pathway, and catalyzes the elimination reaction of D-fructose 1,6-bisphosphate to glycerone phosphate and D-glyceraldehyde 3-phosphate (bacterial enzyme reviewed in: Ujita and Kimura, Methods in Enzymol. 90: 235-241, 1982).

[0364] The polypeptide of SEQ ID NO: 71 and the polynucleotide of SEQ ID NO: 29 have utility for processing food and other products and as supplements and additives to food and other products. This aldolase may also be used to develop non-food products. The attributes conferred by this enzyme include: enhanced bacterial survival of industrial processes; improved colonization of human intestinal environment; and altered metabolic characteristics through changes in carbohydrate utilization.

[0365] These attributes may be produced in food products and supplements by directed activity of the enzyme, introduced in a bacterial strain (including strain HN001, or starter cultures) comprising a polynucleotide of SEQ ID NO: 29 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 71 or a variant.

EXAMPLE 20

Isolation and Characterisation Phosphoryl Carrier Protein HPR from L. rhamnosus HN001

[0366] HN001 phosphoryl carrier protein HPR AA9 was isolated by a series of experiments designed to identify HN001 strain proteins that were up-regulated in response to physiological stresses encountered during industrial processes. Cells were subjected to heat or osmotic shock, proteins radiolabeled with [.sup.35S]-methionine and [.sup.35S]-cysteine (Amersham, USA), and cell-free extracts from shocked and non-shocked HN001 cultures compared by 2-D analysis and N-terminal sequencing as described for Example 15.

[0367] A protein upregulated by heat and osmotic shock was N-terminal sequenced, with the determined amino acid sequence being given in SEQ ID NO: 78. This sequence was used to search an HN001 sequence database using the TBLASTN program (NCBI) and the corresponding polynucleotide and polypeptide sequences are given in SEQ ID NO: 4 and 45, and shown in FIGS. 41 and 42, respectively. Similarity searching using BLAST software revealed closest amino acid sequence similarity to phosphoryl carrier protein HPR sequences but with significant differences.

[0368] Phosphoryl carrier protein HPR is involved in the phosphoenol-pyruvate:carbohydrate phosphotransferase system (PTS) responsible for the uptake and phosphorylation of a number of carbohydrates (De Reuse et al., Gene 35:199-207, 1985; Gonzy-Treboul et al., Mol. Microbiol. 3:103-112, 1989). PTS is also involved in the regulation of various bacterial functions by various mechanisms, including catabolite repression, inducer exclusion, and inducer expulsion (reviewed in Postma et al., Microbiol. Rev. 57:543-594, 1993; Reizer et al., Crit. Rev. Microbiol. 15:297-338, 1988; Saier et al., Microbiol 142:217-230, 1996).

[0369] The polypeptide of SEQ ID NO: 45 and the polynucleotide of SEQ ID NO: 4 have utility for processing food products and as supplements and additives to food products. This aldolase may also be used to develop non-food products. The attributes conferred by this enzyme include: enhanced bacterial survival in industrial processes; improved colonization of human intestinal environment; altered metabolic characteristics through changes in carbohydrate utilization; and control of catabolite regulation.

[0370] These attributes may be produced in food, such as dairy products, by directed activity of the enzyme, introduced in a bacterial strain (including strain HN001, or starter cultures) comprising a polynucleotide of SEQ ID NO: 4 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 45 or a variant.

EXAMPLE 21

Isolation and Characterisation of Chaperone Protein dnaK from L. rhamnosus HN001

[0371] HN001 dnaK chaperone protein AM9 was isolated by a series of experiments designed to identify HN001 strain proteins that were up-regulated in response to physiological stresses encountered during industrial processes. Cells were subjected to heat or osmotic shock, proteins radiolabeled with [.sup.35S]-methionine and [.sup.35S]-cysteine (Amersham, USA), and cell-free extracts from shocked and non-shocked HN001 cultures compared by 2-D analysis and N-terminal sequencing as described for Example 15.

[0372] A protein up-regulated by heat and osmotic shock was N-terminal sequenced. The determined amino acid sequence is given in SEQ ID NO: 79. This sequence was used to search an HN001 sequence database using the TBLASTN program (NCBI). The corresponding polynucleotide and polypeptide sequences are given in SEQ ID NO: 30 and 72 and shown in FIGS. 76 and 77, respectively. Similarity searching using BLAST software revealed closest amino acid sequence similarity to chaperone protein dnaK sequences but with significant differences.

[0373] Chaperone protein dnaK is a 70 kDa heat shock protein (HSP). DnaK chaperones act by binding and protecting exposed regions on unfolded or partially folded protein chains, and are involved in reactivating proteins that become aggregated after heat shock (reviewed in Lund, Adv. Microbial Physiol. 44:93-140, 2001). Overexpression may contribute to plasmid instability (Lobacz and Wolska, Acta Microbiol. Pol. 46:393-397, 1977).

[0374] The polypeptide of SEQ ID NO: 72 and the polynucleotide of SEQ ID NO: 30 have utility for processing food products and as supplements and additives to food products. This chaperone protein may also be used to develop non-food products. The attributes conferred by this protein include: enhanced bacterial survival in industrial processes; improved colonization of human intestinal environment; altered protein translation characteristics; and methods to control plasmid stability.

[0375] These attributes may be produced in food, such as dairy products, by directed activity of the enzyme, introduced in a bacterial strain (including strain HN001, or starter cultures) comprising a polynucleotide of SEQ ID NO: 30 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 72 or a variant.

EXAMPLE 22

Isolation and Characterisation of Glyceraldehyde-3-phosphate Dehydrogenase from L. rhamnosus HN001

[0376] HN0001 glyceraldehyde-3-phosphate dehydrogenase AK7 was isolated by a series of experiments designed to identify HN001 strain proteins that were up-regulated in response to physiological stresses encountered during industrial processes. Cells were subjected to heat or osmotic shock, proteins radiolabeled with [.sup.35S]-methionine and [.sup.35S]-cysteine (Amersham, USA), and cell-free extracts from shocked and non-shocked HN001 cultures compared by 2-D analysis and N-terminal sequencing as described for Example 15.

[0377] A protein up-regulated by heat and osmotic shock was N-terminal sequenced and the determined amino acid sequence is given in SEQ ID NO: 80. This sequence was used to search an HN001 sequence database using the TBLASTN program (NCBI). The corresponding polynucleotide and polypeptide sequences are given in SEQ ID NO: 23 and 65, and shown in FIGS. 43 and 44, respectively. Similarity searching using BLAST software revealed the closest amino acid sequence similarity to glyceraldehyde-3-phosphate dehydrogenase sequences but with significant differences.

[0378] A second experiment was also performed to identify surface layer proteins extracted from Lactobacillus rhamnosus HN0001 strain. Surface layer proteins were extracted using the method of Turner et al., J. Bacteriol. 179:3310-3316, 1997. Briefly, 100 ml stationary phase HN001 culture was pelleted by centrifugation, washed with an equal volume of 0.15M NaCl, resuspended in 1 ml of 5M LiCl.sub.2 and kept on ice for 15 min. The crude lysate was centrifuged at 13,000 rpm using a microcentrifuge and analyzed by SDS-PAGE on a 12.5% gel. To facilitate better extraction of surface layer proteins, freeze-dried DR20 was extracted with 0.2% SDS and 5M LiCl.sub.2 as described by Brennan et al., Infect. Imm. 52:840-845, 1986 and Toba et al., J Imm. Methods 182:193-207, 1995. After 1-D electrophoresis according to standard laboratory methods, gels were blotted on a PVDF membrane using a Semi-dry blotting apparatus (Bio-Rad). A major surface protein with molecular weight between 30 and 46 kDa was excised and N-terminal sequencing performed using a protein sequencer (Applied BioSystems, Model 476A). The determined N-terminal sequence was identical to that obtained from the heat and osmotic shock experiments described above. Therefore, HN001 gene AK7 encodes glyceraldehyde-3-phosphate dehydrogenase, which is up-regulated by shock and is a major cell surface protein.

[0379] Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) is part of the glycolytic pathway and catalyzes the redox reaction of D-glyceraldehyde 3-phosphate, phosphate and NAD.sup.+ to 3-phospho-D-glyceroyl phosphate and NADH (for bacterial enzyme see Amelunxen, Methods in Enzymol. 41:268-273, 1975; D'Alessio and Josse, J. Biol. Chem. 246:4326-4333, 1971). The enzyme has also been found to be a major cell-surface component of several bacterial species including Saccharomyces cerevisiae (Delgado et al., Microbiol. 147:411-417, 2001), Candida albicans (Gil-Navarro et al., J. Bacteriol. 179: 4992-4999, 1997) and group A Streptococci (Pancholi and Fischetti, Proc. Natl. Acad. Sci. USA 90:8154-8158, 1993).

[0380] The polypeptide of SEQ ID NO: 65 and the polynucleotide of SEQ ID NO: 23 have utility for processing food products and as supplements and additives to food products. This dehydrogenase may also be used to develop non-food products. The attributes conferred by this enzyme include: flavor and aroma enhancement; enhanced bacterial survival in industrial processes; prolonged survival in storage; improved colonization of human intestinal environment; enhanced textural properties; enhanced adhesion to intestinal cell surfaces; and altered metabolic characteristics.

[0381] These attributes may be produced in food, such as dairy products, by directed activity of the enzyme, introduced in a bacterial strain (including strain HN001, or starter cultures) comprising a polynucleotide of SEQ ID NO: 23 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 65 or a variant.

EXAMPLE 23

Isolation and Characterisation of Transcription Regulator sorR from L. rhamnosus HN001

[0382] The full-length polynucleotide sequence of a transcription regulator sorR, given in SEQ ID NO: 24 and shown in FIG. 45, was used to amplify the AL3 transcription regulator sorR gene from L. rhamnosus HN001 DNA using standard PCR methodology. The upstream and downstream primers were tagged with BamHI and PstI restriction endonuclease recognition sequences to facilitate cloning. The polypeptide sequence of AL3 is given in SEQ ID NO: 66 and shown in FIG. 46.

[0383] Full-length HN001 sorR transcription regulator AL3 was cloned into BamHI and PstI cut pFX3 vector (an E. coli/Lactococcus lactis shuttle vector as used in Xu et al., FEMS Microbiol. Lett. 61:55-59, 1991), and transformed into competent E. coli DH5.alpha. cells according to standard laboratory methods. Positive transformants were selected, grown overnight, and the plasmid construct isolated using a QIAprep Spin Miniprep Kit (Qiagen). The pFX3 construct encoding the HN001 sorR transcription regulator AL3 was digested using the restriction enzymes EcoRI and NruI, which released a 500 bp internal AL3 fragment that was cloned into the pBEryl vector cut with EcoRI and SmaI. The 3.6 kb pBEryl vector was constructed using the replicon and multiple cloning site (MCS) from the phagemid pBlueScript (pBS-SK+) (Stratagene, La Jolla Calif., USA). The ampicillin resistance gene in pBS-SK+ was removed by digestion with RcaI (Roche, Auckland, New Zealand) and the 1,953 bp fragment containing the ColE1 origin and multiple cloning site purified and treated with Klenow enzyme (Roche) to give a blunt-ended fragment. A gene encoding resistance to erythromycin (Em) was isolated on a 1.6 kb fragment obtained after cutting pVA891 (Macrina et al., Gene 25:145-50, 1983) with ClaI and HindIII and treatment with Klenow to give blunt ends. The 1.6 kb Em fragment was ligated to the 1,953 bp pBS-SK+ fragment, transformed into E. coli TG1 (Gibson T J, Studies on the Epstein-Barr virus genome. Ph.D. Thesis, University of Cambridge, Cambridge, England, 1984), and plated on LB agar plates containing 200 .mu.g/ml Em. Maintenance of .alpha.-complementation for blue/white color selection of recombinant pBEry1 clones was confirmed by growing E. coli colonies on agar plates containing IPTG/X-gal.

[0384] The resulting pBEryl construct encoding the HN001 sorR transcription regulator AL3 gene was transformed into competent HN001 cells and grown anaerobically for 48 hrs at 37.degree. C. on MRS lactobacilli agar (Difco, Detroit Mich.) containing 2.5 .mu.g/ml Em. Erythromycin-resistant HN001 were checked for integration of the plasmid construct into the sorR gene by PCR using vector-specific (T3 or T7) and AL3 internal fragment-specific primers. Colonies giving PCR patterns consistent with the insertional inactivation of the endogenous HN001 sorR transcription regulator AL3 gene were assessed for sorbose auxotrophy.

[0385] Auxotrophy of selected HN001 mutants for metabolism of sorbose was tested by growing pure cultures (1% inoculum) overnight at 37.degree. C. on MRS agar in the presence of 1% sorbose or 1% glucose, compared to wild-type HN001 and undefined mutant HN001 (Em-resistant cultures with intact sorR transcription regulator AL3 gene, the result of a random integration event) cultures.

[0386] As shown in Table 15, the results indicate that the AL3.sup.- HN001 mutant strain failed to utilize sorbose as a carbon source in contrast to wild type HN001 and undefined mutant HN001 strain. This result was confirmed by growing pure cultures (1% inoculum) overnight at 37.degree. C. in liquid MRS broth with 1% sorbose or 1% glucose and measuring absorbance at 600 nm. Again, results showed a clear difference in growth between the AL3.sup.- mutant strain, and the wild-type and undefined mutant HN001 strains containing intact the AL3 gene. Thus, the AL3 gene is required for sorbose metabolism in HN001, and encodes the sorR transcriptional regulator. TABLE-US-00018 TABLE 15 Results of assessment of sorbose auxotrophy. MRS Wild type Undefined HN001 AL3.sup.- mutant plates with: HN001 mutant HN001 1% glucose + + + 1% sorbose + + - +: growth; -: no growth

[0387] The sorR transcriptional regulator is required for the transcription of the sorbose operon, thereby regulating the utilization of L-sorbose as a carbon source, and its expression is induced by sorbose (Yebra et al., J. Bacteriol. 182:155-163, 2000; Sprenger and Lengeler, Mol. Gen. Genetics 209:352-359, 1987).

[0388] The polypeptide of SEQ ID NO: 66 and the polynucleotide of SEQ ID NO: 24 have utility as transcriptional regulators in L. rhamnosus and other bacterial species. Specifically, applications for the HN001 sorR transcriptional regulator include: reagents for the control or modification of metabolic processes; and construction of sorbose-inducible HN001 expression vectors using the sorR gene promoter.

EXAMPLE 24

Isolation and Characterisation of Formamidopyirimidine-DNA-Glycosylase from L. rhamnosus HN001

[0389] The full-length polynucleotide sequence of formamidopyrimidine-DNA-glycosylase (fpg) from L. rhamnosus strain HN001, given in SEQ ID NO: 25 and shown in FIG. 47 with ATG initiation and translation stop codons (boxed), was used to amplify the AL4 fpg gene from L. rhamnosus HN001 DNA using standard PCR methodology. The upstream and downstream primers were tagged with EcoRI and SalI restriction endonuclease recognition sequences to facilitate cloning.

[0390] AL4 was then cloned into the EcoRI and SalI sites of the pKK223-3 expression vector (Pharmacia Biotech) and transformed into the E. coli strain DH5.alpha. competent cells according to standard laboratory protocols. The polypeptide sequence of AL4 is given in SEQ ID NO: 67 and shown in FIG. 48. Expression of the fpg AL4 protein was confirmed by SDS-PAGE analysis.

[0391] AL4 fpg activity was assayed according to previously published methods (Duwat et al., Microbiol. 141:411-417, 1995; Zhang et al., Nucleic Acids Res. 26:4669-4675, 1998) that examine the ability of fpg to suppress the spontaneous mutator phenotype of fpg or mutY mutants of E. coli. The E. coli strain CSH117 (Miller, in: A short course in Bacterial Genetics, Cold Spring Harbor Press, Cold Spring Harbor, N.Y., 1992) that contains a mutated mutY gene was obtained from the E. coli Genetic Stock Centre (Yale University, USA) and transformed with the pKK223-3 construct encoding the HN.sub.001 fpg AL4 gene according to standard laboratory methods. Positive transformants were selected according to ampicillin resistance, and used to innoculate 7 ml LB broth cultures containing 100 .mu.g/ml ampicillin and incubated aerobically at 37.degree. C. with shaking. Cultures containing pKK223-3 constructs encoding AL4 or empty pKK223-3 vector were grown to similar OD at 600 nm, serially diluted, and plated in triplicate on LB plates with and without 100 .mu.g/ml rifampicin (Sigma). Plates were incubated overnight at 37.degree. C. and colonies counted. Results are shown in Table 16 as mean plate counts from three independent experiments.

[0392] These results indicate that there was a significant difference in the frequency of mutations leading to rifampicin resistance in E. coli CSH117 transformed with pKK223-3 encoding HN001 fpg AL4 and empty pKK22-3 vector (p<0.001 by paired Student's t-test (1-tailed)). Because the presence of AL4 suppressed the spontaneous mutation rate, it was concluded that AL4 encoded the HN001 fpg protein. TABLE-US-00019 TABLE 16 Spontaneous mutagenesis in E. coli CHS117 expressing the HN001 fpg AL4 gene. E. coli CSH117 Counts on Counts on LB transformed with LB plates (no plates with pKK223-3 rifampicin) rifampicin) Mutation Expt: encoding: (10.sup.8/ml) (10.sup.1/ml) frequency* 1 Empty 13.8 20.0 14.5 AL4 11.0 3.7 3.4 2 Empty 13.0 25.8 20 AL4 10.3 9.5 9.3 3 Empty 12.1 24.4 20.1 AL4 11.6 8.6 7.7 *expressed as the number of rifampicin-resistant mutants per 10.sup.8 cells

[0393] The fpg protein (EC 3.2.2.23) is a DNA glycosylase/AP lyase that removes oxidized purine residues present in DNA, including the highly mutagenic C8-oxo-guanine (8-oxoG) generated in DNA by active oxygen during metabolism (Laval et al., Mutation Res. 233:73-79, 1990; Boiteux et al., EMBO J. 6: 3177-3183, 1987). The fpg protein exhibits three catalytic activities in vitro (Olga et al., J. Biol. Chem. 275:9924-9929, 2000): a DNA glycosylase that excises modified nucleotide bases (Laval et al., Mutation Res. 402:93-102, 1998), an AP lyase that incises DNA at abasic sites by an elimination mechanism, and a deoxyribophosphodiesterase that removes 5'-terminal deoxyribose phosphate residues.

[0394] The polypeptide of SEQ ID NO: 67 and the polynucleotide of SEQ ID NO: 25 have utility for processing food products, and as supplements and additives to food products. This glycosylase may also be used to develop non-food products. The applications for and attributes conferred by this enzyme include: reagents or techniques to improve the survival of HN001 in aerobic conditions; enhanced bacterial survival in industrial processes; and enhanced bacterial survival in the intestinal environment. These attributes may be produced in food, such as dairy products, by directed activity of the enzyme, introduced in a bacterial strain (including strain HN001, or starter cultures) comprising a polynucleotide of SEQ ID NO: 25 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 67 or a variant.

EXAMPLE 25

Isolation and Characterisation of Acetoin Dehydrogenase from L. rhamnosus HN001

[0395] The full-length polynucleotide sequence of acetoin dehydrogenase from L. rhamnosis strain HN001, given in SEQ ID NO: 32 and shown in FIG. 49 with ATG initiation and translation stop codons (boxed), was used to amplify the AP1 acetoin dehydrogenase gene from L. rhamnosus HN001 DNA using standard PCR methodology. The upstream and downstream primers were tagged with EcoRI and SalI restriction endonuclease recognition sequences to facilitate cloning.

[0396] AP1 was then cloned into the EcoRI and SalI sites of the pGEX-6P-3 expression vector (Pharmacia Biotech) and transformed into E. coli strain K12 XL-1Blue competent cells according to standard laboratory protocols. The polypeptide sequence of acetoin dehydrogenase AP1 is given in SEQ ID NO: 74 and shown in FIG. 50. The acetoin dehydrogenase AP1 protein was expressed as a fusion protein with glutathione S-transferase (GST), and purified using Glutathione Sepharose 4B resin (Pharmacia Biotech) according to the manufacturer's instructions. An aliquot of purified AP1-GST fusion protein was confirmed by SDS-PAGE analysis.

[0397] Acetoin dehydrogenase activity was assayed according to published methods (Rattray et al., Int. Dairy J. 10:781-789, 2000) with some modifications. Briefly, acetoin dehydrogenase activity was measured spectrophotometrically by monitoring the change in absorbance of the cofactor NADH at 340 nm. Aliquots of the purified AP4-GST fusion protein solution were added to reaction mixtures containing 50 mM 2[N-morpholino]ethanesulphonic acid (MES, Sigma) buffer pH 5.5 at 30.degree. C. and the reactions started by the addition of 0.5 mM NADH and 37 mM diacetyl (Sigma) in a total volume of 1 ml. The change in optical density at 340 nm was measured, and rates of NADH utilization measured as an indicator of acetoin dehydrogenase activity. Enzyme activity was calculated as the amount of protein required to convert 1 .mu.mol diacetyl and NADH to acetoin and NAD.sup.+ per minute at pH 5.5 at 30.degree. C. Enzyme activity of AP1-GST fusion protein was compared to that of an irrelevant GST-fusion protein, GST protein and elution buffer only.

[0398] Results presented in FIG. 51 and Table 17 indicate significant background utilization of NADH in the reactions. Similar rates were observed for elution buffer, GST protein and irrelevant fusion protein, indicating that the GST fusion protein did not exhibit acetoin reductase activity. Nonetheless, presence of the AP1-GST fusion protein gave significantly greater acetoin dehydrogenase activity than background, indicating that HN001 AP1 protein encodes acetoin dehydrogenase. FIG. 51 shows the results of an acetoin reductase assay as measured by oxidation of NADH co-factor by OD at 340 nm in the presence of acetoin substrate: .lamda., elution buffer only; .nu., purified irrelevant GST-fusion protein; .sigma., purified GST protein; .upsilon., purified AP1-GST fusion protein. TABLE-US-00020 TABLE 17 Acetoin reductase activity of AP1 GST-fusion protein compared to elution buffer, GST protein, and irrelevant GST-fusion protein controls. .DELTA. OD/min Enzyme activity (.mu.mol/min/ml) AP1-GST fusion protein 3.54 .times. 10.sup.-3 14.07 Irrelevant GST-fusion 2.77 .times. 10.sup.-3 11.13 protein GST protein 2.68 .times. 10.sup.-3 10.77 Elution buffer only 2.38 .times. 10.sup.-3 9.56

[0399] Acetoin dehydrogenase (EC 1.1.1.5) catalyzes the reduction of diacetyl to acetoin, and acetoin to 2,3-butanediol as part of the pyruvate to 2,3-butanediol pathway (reviewed in Sarmiento and Burgos, Methods in Enzymol. 89:516-523, 1982). Diacetyl is an important flavor component in a variety of dairy products including butter, buttermilk, sour cream, fermented cream and cheese. Like its metabolites or related compounds acetoin, acetaldehyde and 2,3-butanediol, diacetyl plays a role in flavor when present in trace amounts (reviewed in Escamilla-Hurtado et al., Rev. Latinoamerican Microbiol. 38:129-37, 1996). A mixture of all these compounds is produced during lactic acid fermentation, and particular proportions of these compounds lead to characteristic flavors in dairy products.

[0400] The polypeptide of SEQ ID NO: 74 and the polynucleotide of SEQ ID NO: 32 have utility for processing food products, and as supplements and additives to food products. This dehydrogenase may also be used to develop non-food products. The attributes conferred by and applications for use of this enzyme include: modulation of the production of important flavor compounds; modification of pyruvate metabolic pathways; industrial production of flavor compounds; and control of diacetyl levels in dairy products.

[0401] These attributes may be produced in food, such as dairy products, and the applications implemented by directed activity of the enzyme, introduced in a bacterial strain (including strain HN001, or starter cultures) comprising a polynucleotide of SEQ ID NO: 32 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 74 or a variant.

EXAMPLE 26

Isolation and Characterisation of Aflatoxin B.sub.1 Aldehyde Reductase from L. rhamnosus HN001

[0402] The full-length polynucleotide sequence of aflatoxin B.sub.1 aldehyde reductase from L. rhamnosus strain HN001, given in SEQ ID NO: 15 and shown with ATG initiation and translation stop codons (boxed) in FIG. 52, was used to amplify the AI7 aflatoxin B.sub.1 aldehyde reductase gene from L. rhamnosus HN001 DNA using standard PCR methodology. The upstream and downstream primers were tagged with EcoRI and SalI restriction endonuclease recognition sequences to facilitate cloning.

[0403] AI7 was then cloned into the EcoRI and SalI sites of the pGEX-6P-3 expression vector (Pharmacia Biotech) and transformed into E. coli strain DH5.alpha. competent cells according to standard laboratory protocols. The polypeptide sequence of aflatoxin B, aldehyde reductase AI7 is given in SEQ ID NO: 57 and shown in FIG. 53. The aflatoxin B.sub.1 aldehyde reductase AI7 protein was expressed as a fusion protein with glutathione S-transferase (GST) and purified using Glutathione Sepharose 4B resin (Pharmacia Biotech) according to the manufacturer's instructions. An aliquot of the purified AI7 protein was checked by SDS-PAGE analysis.

[0404] AI7 activity was assayed by the previously published method of Ellis and Hayes (Biochem. J. 312:535-541, 1995) with some modifications. Briefly, the aldehyde- and ketone-reducing activity of aflatoxin B.sub.1 aldehyde reductase was assayed using 4-nitrobenzyl alcohol as substrate and NADPH as a cofactor. Enzyme activity was assessed spectrophotometrically by monitoring the utilization of NADPH at an OD of 340 nm. Reaction volumes of 1 ml containing 100 mM sodium phosphate pH 6.6 and 0.2 mM NADPH were prepared, aliquots of purified AI7 protein added, and the changes in OD measured. Enzyme activity was compared between reactions containing AI7-GST fusion protein, irrelevant GST-fusion protein, elution buffer used during protein purification and water only. Enzyme activity was calculated as .mu.mol NADP used/min/ml.

[0405] As shown in FIG. 54 and Table 18, the results indicate that HN001 AI7 protein fused with GST exhibited significant aldehyde reductase activity, while the irrelevant GST-fusion protein, as well as the water and elution buffer controls, showed no activity whatsoever. Therefore, the aflatoxin B.sub.1 aldehyde reductase activity of the AP4-GST fusion protein was due to the AI7 moiety rather than the GST. Also, the results showed increased rate of substrate utilization proportional to the amount of AI7 protein added, indicating that aflatoxin B.sub.1 aldehyde reductase activity of AI7 was dose dependent. Therefore, AI7 encodes HN001 aflatoxin B.sub.1 aldehyde reductase.

[0406] FIG. 54 shows the experimental results of aflatoxin B.sub.1 aldehyde reductase assay according to oxidation of the NADPH co-factor in the presence of acetoin substrate. X, water only; +, Sepharose column elution buffer only; .lamda., irrelevant GST-fusion protein; .nu., 10 .mu.l purified AP4-GST fusion protein; .sigma. 20 .mu.l purified AP4-GST fusion protein. TABLE-US-00021 TABLE 18 Aflatoxin B.sub.1 aldehyde reductase activity of AI7 GST-fusion protein compared to elution buffer, water and irrelevant GST-fusion protein controls. .DELTA. OD/min at 340 nm Enzyme activity (.mu.mol/min/ml) Elution 0.00 0 buffer only Water only 0.00 0 10 .mu.l 0.00 0 Irrelevant protein 10 .mu.l AI7 0.038 606 20 .mu.l AI7 0.087 690

[0407] Aflatoxin B.sub.1 aldehyde reductase metabolizes the carcinogen aflatoxin B.sub.1 (AFB.sub.1) by converting the protein-binding dialdehyde form of AFB.sub.1-dihydrodiol to the non-binding di-alcohol metabolite, and is associated with AFB.sub.1-resistance in animal studies (Ellis et al., Proc. Natl. Acad. Sci. USA 90:10350-10354, 1993; Hayes et al., Cancer Res. 53:3887-3894, 1993). The enzyme is also active against other substrates including a particular class of ketone (ketone groups on adjacent carbon atoms, e.g. 9,10-phenanthrenequinone), as well as aromatic and aliphatic aldehydes (Ellis and Hayes, Biochem. J. 312:535-541, 1995).

[0408] The polypeptide of SEQ ID NO: 57 and the polynucleotide of SEQ ID NO: 15 have utility for processing food products, and as supplements and additives to food products. This reductase also has applications in non-food products and processes. The attributes conferred by and applications for use of this enzyme include: anti-carcinogenic or chemoprotectant reagents; probiotic bacterial strains with anti-cancer effects; research tools for cancer research; enhanced flavor or aroma characteristics; removal of undesirable flavors; and description and application of novel metabolic pathways.

[0409] These attributes may be produced and applications implemented by directed activity of the enzyme, introduced in a bacterial strain (including strain HN001, or starter cultures) comprising a polynucleotide of SEQ ID NO: 15 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 57 or a variant.

EXAMPLE 27

Isolation and Characterisation of 6-Phospho-.beta.-galactosidase from L. rhamnosus HN001

[0410] The full-length polynucleotide sequence of 6-phospho-.beta.-galactosidase, given in SEQ ID NO: 31 and shown with the translation stop codon (boxed) in FIG. 78, was used to amplify the A05 6-phospho-.alpha.-galactosidase gene from L. rhamnosus HN001 DNA using standard PCR methodology. The upstream and downstream primers were tagged with EcoRI and SalI restriction endonuclease recognition sequences to facilitate cloning.

[0411] A05 was then cloned into the EcoRI and SalI sites of the pGEX-6P-3 expression vector (Pharmacia Biotech) and transformed into E. coli strain DH5.alpha. competent cells according to standard laboratory protocols. The polypeptide sequence of AO5 is given in SEQ ID NO: 73 and shown in FIG. 79. The 6-phospho-.beta.-galactosidase AO5 protein was expressed as a fusion protein with glutathione S-transferase (GST) and purified using Glutathione Sepharose 4B resin (Pharmacia Biotech) according to the manufacturer's instructions. An aliquot of the purified AO5 protein was checked by SDS-PAGE analysis.

[0412] A05 activity was assayed using standard laboratory methods as follows. Briefly, crude cell lysates were prepared by resuspending a 10 ml overnight culture of E. coli DH5.alpha. cells in 1 ml lysis buffer (50 mM potassium phosphate pH 7.8, 400 mM NaCl, 100 mM KCl, 10% glycerol, 0.5% Triton X-100, 10 mM imidazole). Cells were sonicated and spun to sediment cell debris according to standard laboratory methods. Aliquots of 50 .mu.l of cell lysate were added to 900 .mu.l reaction buffer (100 mM KH.sub.2PO.sub.4 pH 7.0, 2 mM MgCl.sub.2) and 50 .mu.l substrate O-nitrophenyl .beta.-D-glycopyranoside (ONPG) (Sigma). Utilization of OPNG was measured spectrophotometrically by monitoring change in absorbance at 420 nm and enzyme activity was calculated as .mu.mol OPNG used/min/ml. 6-Phospho-.beta.-galactosidase enzyme activity was compared in crude lysates from E. coli DH5.alpha. transformed with pGEX-6P-3 encoding A05, pGEX-6P-3 encoding an irrelevant protein, and lysis buffer only.

[0413] Experimental results presented in FIG. 55 and Table 19 indicate that while reactions containing crude lysates from cells transformed with an irrelevant GST-fusion protein or lysis buffer only exhibited little or no enzyme activity, crude lysate from E. coli expressing AO5-GST fusion protein showed significant enzyme activity. FIG. 55 shows the experimental determination of 6-phospho-.beta.-galactosidase enzyme activity as measured by substrate utilization using crude lysates of strains transformed with pGex-6P-3 encoding A05 (.upsilon.), pGex-6P-3 encoding an irrelevant protein (.nu.), or using lysis buffer only (X). TABLE-US-00022 TABLE 19 6-Phospho-.beta.-galactosidase enzyme activity in crude cell lysates Enzyme activity Crude cell lysate expressing: .DELTA. OD/min at 420 nm (.mu.mol/min/ml) AO5-GST fusion protein 0.074 0.60 Irrelevant GST-fusion protein 0.001 0.01 Lysis buffer only 0.000 0.00

[0414] Enzyme activity was also measured in increasing amounts of crude cell lysates to assess dose-dependency. Results shown in FIG. 56 and Table 20 indicate that increasing amounts of cell lysates from cells expressing the A05-GST fusion protein led to proportional increases in 6-phospho-.beta.-galactosidase enzyme activity. Therefore, A05 encodes HN001 6-phospho-.beta.-galactosidase. FIG. 56 shows 6-phospho-.beta.-galactosidase enzyme activity as measured experimentally by substrate utilisation using increasing amounts of crude lysate from strains transformed with pGex-6P-3 encoding A05-GST fusion protein. .upsilon., 50 .mu.l lysate; .nu., 100 .mu.l lysate; .sigma., 200 .mu.l lysate; .lamda., 200 .mu.l lysis buffer only. TABLE-US-00023 TABLE 20 6-Phospho-.beta.-galactosidase enzyme activity in increasing amounts of crude cell lysates. Crude cell lysate expressing Enzyme activity AO5-GST fusion protein .DELTA. OD/min at 420 nm (.mu.mol/min/ml) 50 .mu.l 0.074 0.60 100 .mu.l 0.113 0.92 200 .mu.l 0.169 1.38 200 .mu.l 0.000 0.00 Lysis buffer only

[0415] 6-Phospho-.beta.-galactosidase (EC 3.2.1.85) catalyzes the hydrolysis of O-glycosyl bonds of 6-phospho-beta-D-galactosides to give alcohols and 6-phospho-D-galactose, and is involved in lactose utilization (Hengstenberg and Morse, Methods in Enzymol. 42:491-494, 1975).

[0416] The polypeptide of SEQ ID NO: 73 and the polynucleotide of SEQ ID NO: 31 have utility for processing food products and as supplements and additives to food products. This galactosidase may also be used to develop non-food products. The attributes conferred by this enzyme include: flavor and aroma enhancement; nutritional enhancement; altered bacterial metabolic/growth characteristics; and removal of bitter or undesirable flavors.

[0417] These attributes may be produced in food, such as dairy products, by directed activity of the enzyme, introduced in a bacterial strain (including strain HN001, or starter cultures) comprising a polynucleotide of SEQ ID NO: 31 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 73 or a variant.

EXAMPLE 28

Isolation and Characterisation of Aromatic Aminotransferase from L. rhamnosus HN001

[0418] The full-length polynucleotide sequence of aromatic aminotransferase of L. rhamnosus strain HN001, given in SEQ ID NO: 11 and shown in FIG. 57 with ATG initiation and translation stop codons (boxed), was used to amplify the AH7 aromatic aminotransferase gene from L. rhamnosus HN001 DNA using standard PCR methodology. The upstream and downstream primers were tagged with EcoRI and SalI restriction endonuclease recognition sequences to facilitate cloning.

[0419] AH7 was then cloned into the EcoRI and SalI sites of the pGEX-6P-3 expression vector (Pharmacia Biotech) and transformed into E. coli strain DH5.alpha. competent cells according to standard laboratory protocols. The polypeptide sequence of aromatic aminotransferase AH7 is given in SEQ ID NO: 53 and shown in FIG. 58. The aromatic aminotransferase AH7 protein was expressed as a fusion protein with glutathione S-transferase (GST) and purified using Glutathione Sepharose 4B resin (Pharmacia Biotech) according to the manufacturer's instructions. An aliquot of the purified AH7 protein was checked by SDS-PAGE analysis.

[0420] Aromatic aminotransferase activity was assayed according to previously published methods (Yvon et al., Appl. Environ. Microbiol. 63:414-419, 1997) with modifications. The assay is composed of two parts: the first is an aminotransferase reaction using the aromatic amino acid phenylalanine as substrate and results in the production of glutamate from .alpha.-ketoglutarate. The second part of the assay is the colorimetric determination of the glutamate. For the phenylalanine transamination, 250 .mu.l reaction mixtures containing 70 mM Tris-HCl pH 8.0, 3 mM L-phenylalanine, 10 mM .alpha.-ketoglutarate and 0.05 .mu.M pyridoxal 5' phosphate were incubated with purified proteins or elution buffer at 37.degree. C. for 15 min. Aliquots of 20 .mu.l were then taken and glutamate levels determined by adding to a reaction mixture containing 65 mM Tris pH 9.0, 1.3 mM EDTA, 40 mM hydrazine, 19.5 mM NAD.sup.+ and 65 mM ADP, with and without 2.4 U glutamate dehydrogenase in a total volume of 250 .mu.l in the wells of a microtitre plate. Reactions were incubated at 37.degree. C. for 40 min and absorbance at 340 nm measured using a plate reader (Molecular Devices, Sunnyvale Calif.). Enzyme activity of the purified AH7-His-Thio fusion protein was compared a purified irrelevant His-Thio-fusion protein, elution buffer used to elute the purified proteins from the Ni-NTA columns and water only and results are shown in Table 21. Glutamate concentrations were calculated using a standard curve, and assays on all samples and standards were performed in triplicate. Enzyme activities were calculated as .mu.mol glutamate produced/min/ml and specific activities calculated using protein concentrations obtained using the BCA protein assay kit (Pierce) according to the manufacturer's instructions. While the irrelevant fusion protein, elution buffer and water resulted in little glutamate production, AH7 fusion protein exhibited significant aminotransferase activity using phenylalanine as substrate, demonstrating that HN001 AH7 encodes an aromatic amino acid transaminase. TABLE-US-00024 TABLE 21 Aromatic amino acid transaminase activity in HN001 AH7 purified protein as measured by glutamate production. mM glutamate Enzyme Specific per activity activity reaction (.mu.mol/min/ml) (.mu.mol/min/.mu.g) Water only 0.044 146 -- 10 .mu.l elution buffer 0.031 103 -- 10 .mu.l irrelevant His-Thio- 0.030 100 0.52 fusion protein solution 10 .mu.l His-Thio-AH7 fusion 1.120 3733 17.7 protein solution

[0421] Aromatic amino acid transaminase (EC 2.6.1.57) catalyzes the transfer of amino groups between an aromatic amino acid and .alpha.-ketoglutarate to its aromatic oxo-acid and L-glutamate (Mavrides and Orr, J. Biol. Chem. 250:4128-4133, 1975). The products of enzymatic amino acid degradation play a major role in cheese flavor development. Degradation products from aromatic amino acids have both positive and negative impacts on cheese flavor (Dunn and Lindsay, J. Dairy Sci. 68:2859-2874, 1985; Engels et al., Int. Dairy J. 7:225-263, 1997). Therefore, the applications of HN001 aromatic amino acid aminotransferase AH7 include: flavor and aroma enhancement; removal of off-flavors; altered levels of biogenic amines; and altered metabolic characteristics.

[0422] These attributes may be produced in food, such as dairy products, by directed activity of the enzyme, introduced in a bacterial strain (including strain HN001 or starter cultures) comprising a polynucleotide of SEQ ID NO: 11, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 53.

EXAMPLE 29

Isolation and Characterisation of Acetate Kinase from L. rhamnosus HN001

[0423] The full-length polynucleotide sequence of acetate kinase, given in SEQ ID NO: 33 and shown in FIG. 59 with ATG initiation and translation stop codons (boxed), was used to amplify the AP5 acetate kinase gene from L. rhamnosus strain. The upstream and downstream primers were tagged with EcoRI and SalI restriction endonuclease recognition sequences to facilitate cloning.

[0424] AP5 was then cloned into the EcoRI and SalI sites of the pGEX-6P-3 expression vector (Pharmacia Biotech) and transformed into E. coli strain K12 XL-1Blue competent cells according to standard laboratory protocols. The polypeptide sequence of the acetate kinase AP5 polypeptide is given in SEQ ID NO: 75 and shown in FIG. 60. This was expressed as a fusion protein with glutathione S-transferase (GST) and purified using Glutathione Sepharose 4B resin (Pharmacia Biotech) according to the manufacturer's instructions. An aliquot of the purified AP5 protein was checked by SDS-PAGE analysis.

[0425] AP5 activity was assayed based on a published method for analysis of the related carbamate kinase (Crow and Thomas, J. Bacteriol. 150:1024-1032, 1982). Briefly, the assay uses a couple reaction such that acetyl phosphate and ADP is converted to CO.sub.2, NH3 and ATP in the presence of acetate kinase. The produced ATP is then combined with glucose by the enzyme hexokinase to give glucose-6-phosphate, which in turn is reduced by glucose-6-phosphate dehydrogenase using the NADP.sup.+ cofactor. Because the hexokinase glucose-6-phosphate dehydrogenase enzymes are provided in excess, acetate kinase activity can be assessed spectrophotometrically by monitoring NADPH production at an OD of 340 nm. Reaction mixtures of 730 .mu.l 200 mM Tris-HCL pH 7.9, 73 .mu.l 200 mM acetyl phosphate, 36.5 .mu.l 200 mM ADP, 36.5 .mu.l 200 mM MgCl.sub.2, 73 .mu.l 500 mM glucose, 7 .mu.l 100 mM NADP.sup.+ and 7 .mu.l hexokinase glucose-6-phosphate dehydrogenase were prepared and allowed to equilibrate at 37.degree. C. Purified AP5-GST fusion protein and sterile milliQ water was added to a final volume of 1 ml, and changes in OD at 340 nm measured. Enzyme activity was compared between purified AP5-GST fusion protein, irrelevant fusion protein, and elution buffer used to elute the purified proteins off the Sepharose column. The results are shown in Table 22. Enzyme activities were calculated as .mu.mol NAPDH produced/min/ml, and specific activities calculated using protein concentrations obtained using the BCA protein assay kit (Pierce) according to the manufacturer's instructions. The results indicate that while elution buffer and irrelevant GST-fusion protein showed little or no enzyme activity, the AP5-GST fusion protein exhibited significant activity. Therefore, AP5 encodes HN001 acetate kinase. TABLE-US-00025 TABLE 22 Acetate kinase activity of HN001 protein AP5. Enzyme Specific .DELTA. OD/min activity activity at 340 nm (.mu.mol/min/.mu.l) (.mu.mol/min/.mu.g) 20 .mu.l elution buffer 0.0 0.0 -- 1 .mu.l irrelevant GST-fusion 0.13 0.05 0.025 protein solution 2 .mu.l AP5-GST fusion 1.72 0.35 0.172 protein solution

[0426] Acetyl kinase (EC 2.7.2.1) catalyzes the phosphotransfer between ADP and acetyl phosphate to give ATP and acetate (Nishimura and Griffith, Methods in Enzymol. 71:311-316, 1981). Acetate, a flavor compound in its own right, can give ammonia and carbon dioxide, both of which have important flavor and texture impacts in cheese (Fox et al., Crit. Rev. Food Sci. Nutr. 29:237-53, 1990).

[0427] The polypeptide of SEQ ID NO: 75 and the polynucleotide of SEQ ID NO: 33 have utility for processing food products and as supplements and additives to food products. This kinase may also be used to develop non-food products. The attributes conferred by this enzyme include: flavor and aroma enhancement; removal of off-flavors; altered texture characteristics; and altered metabolic characteristics.

[0428] These attributes may be produced in food, such as dairy products, by directed activity of the enzyme, introduced in a bacterial strain (including strain HN001, or starter cultures) comprising a polynucleotide of SEQ ID NO: 33 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 75 or a variant.

EXAMPLE 30

Isolation and Characterisation of Basic Surface Protein from L. rhamnosus HN001

[0429] The full-length polynucleotide sequence of basic surface protein from L. rhamnosus strain HN001, given in SEQ ID NO: 6 and shown in FIG. 61 with ATG initiation and translation stop codons (boxed), was used to amplify the AC9 basic surface protein gene, but excluding the predicted N-terminal Type II signal sequence. The primer sequences used (SEQ ID NO: 34 and 35) and were tagged with EcoRI and BamHI restriction endonuclease recognition sequences, respectively, to facilitate cloning. AC9 sequence was then amplified from HN001 strain genomic DNA, purified, cloned into EcoRI/BamHI-cut pGEX-6P-3 expression vector, and transformed into E. coli DH5.alpha. cells according to standard laboratory methods. The polypeptide sequence of basic surface protein AC9 is given in SEQ ID NO: 47 and shown in FIG. 62. The basic surface protein AC9 was expressed as a fusion protein with glutathione S-transferase (GST), bound to Glutathione Sepharose 4B resin (Pharmacia Biotech), and PreScission protease used to cleave off the basic surface protein AC9 protein, according to the manufacturer's instructions. An aliquot of the purified AC9 protein was checked by SDS-PAGE analysis.

[0430] Purified AC9 protein (14 .mu.g) was labeled by radio-iodination with 0.1 mCi iodine-125 (Amersham Pharmacia) using IODO-BEADS iodination reagent (Pierce) following the manufacturer's instructions. The radio-iodinated protein was separated from unincorporated iodine-125 and excess sodium iodide-125 using a PD-10 desalting column (Amersham-Pharmacia) according to the manufacturer's instructions, except that the elution was performed in phosphate buffered saline in twelve 500 .mu.l aliquots. Radioactivity in eluted fractions was quantitated on a Bioscan Quick Count QC-4000/XER Benchtop Radioisotope Counter (Bioscan, Inc.) and fractions containing the first peak of radioactivity (corresponding to labeled AC9 protein) were pooled and bovine serum albumin added to a final concentration of 10 mg/ml.

[0431] To analyze the binding of polypeptide AC9 to proteins associated with intestinal surface proteins known to act as ligands for bacterial adhesins, different intestinal protein ligands were dot blotted onto a nitrocellulose membrane using a Convertible Filtration Manifold System (Life Technologies) following the manufacturer's instructions. Duplicate dots of approximately 1 .mu.g of type I collagen from calf skin, type IV collagen from human placenta, fibronectin from human plasma, laminin from the basement membrane of Engelbreth-Holm-Swarm mouse sarcoma and type III mucin partially purified from porcine stomach and bovine serum albumin included as a negative control (all proteins were obtained from Sigma) were blotted. The blot was incubated at room temperature on an orbital shaker in 10 ml phosphate buffered saline, pH 7.4, containing 0.1% Tween 20 and 5 mg/ml bovine serum albumin for 1 hour. Radio-iodinated AC9 protein was then added to a final concentration of approximately 500 ng/ml, and incubated at room temperature for a further hour. The blot was washed three times in approximately 40 ml phosphate buffered saline, pH 7.4, containing 0.1% Tween 20 at room temperature for 10 minutes, then autoradiographed against X-ray film at -80.degree. C. overnight. The autoradiograph was developed and the resulting image digitized with a Fluor S MultiImager (BioRad). Binding by AC9 protein to the intestinal protein ligands was quantitated using Bio-Rad Quantity One software by measuring the density of the signal on the autoradiograph resulting from radiolabeled AC9 protein binding to the different ligands and subtracting the background density of blank film. To quantitate relative amounts of protein ligands blotted, blots were stained with Ponceau S using standard procedures (Ausubel et al., Current Protocols in Molecular Biology, John Wiley & Sons, 2001), and quantitated as for the autoradiograhs. The density corresponding to AC9 protein binding to individual ligands was divided by the average density of Ponceau S staining of the ligand to give the relative AC9 bound to each ligand. Binding of iodinated AC9 (1.50.times.10.sup.7 dpm) was compared to binding of iodinated mucus adhesion promoting (mapA) protein of Lactobacillus reuteri (GenBank accession number AJ293860) as a positive control, and iodinated irrelevant HN001 protein (7.00.times.10.sup.6 dpm) as a negative control.

[0432] As shown in Table 23, the results indicate that while the irrelevant HN001 protein did not bind to any of the intestinal adhesin ligands, both the AC9 protein and the positive control protein mapA showed significant binding to mucin. Therefore, AC9 encodes the HN001 basic surface protein. The results represent the mean of relative density of two dots. TABLE-US-00026 TABLE 23 Density of autoradiographic signals from AC9 basic surface protein binding to dot blots of intestinal proteins, compared to a positive control (mapA) and negative control (irrelevant HN001 protein). Intestinal Relative Relative Relative Irrelevant Protein AC9 Binding mapA Binding protein Binding BSA 0.25 0.76 0.06 Collagen I 0.44 1.02 0.26 Collagen IV 0.34 0.78 0.09 Fibronectin 0.35 0.67 0.09 Laminin 0.53 0.83 0.12 Mucin 2.20 2.57 0.68

[0433] The basic surface protein of Lactobacillus fermentum is a surface-bound molecule that belongs to a family of ATP-binding cassette (ABC) receptor solute binding proteins (Turner et al., J. Bacteriol. 179:3310-3316, 1997; Tam et al., Microbiol. Rev. 57:320-346, 1993). Basic surface protein has also been shown to be involved in cysteine uptake (Turner et al., J. Bacteriol. 181:2192-2198, 1999) and has been used as an attachment site for immunodominant proteins in the development of new vaccine strategies (Turner et al., Infect. Imm. 67:5486-5489, 1999).

[0434] The polypeptide of SEQ ID NO: 47 and the polynucleotide of SEQ ID NO: 6 have utility for processing food products, and as supplements and additives. This basic surface protein may also be used to develop non-food products. The attributes conferred by this protein include: enhanced adhesion to intestinal surface and cell lines; enhanced bacterial survival in intestinal environment; altered metabolic characteristics; altered flavor or aroma characteristics; enhanced probiotic effects; reagents to block or modify adherence of bacteria to mucosal surfaces; and development of vaccine carriers.

[0435] These attributes may be produced in food, such as dairy products, or in supplements by directed activity of the enzyme, introduced in a bacterial strain (including strain HN001, or starter cultures) comprising a polynucleotide of SEQ ID NO: 6 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 47 or a variant.

EXAMPLE 31

Isolation and Characterisation of Outer Membrane Protein A from L. rhamnosus HN001

[0436] The full-length polynucleotide sequence of outer membrane protein A from L. rhamnosus strain HN001, given in SEQ ID NO: 27 and shown in FIG. 63 with ATG initiation and translation stop codons (boxed) was used to amplify the N-terminal region of AL8 outer membrane protein A gene. The primer sequences are given in SEQ ID NO: 36 and 37, respectively, and were tagged with BamHI and XhoI restriction endonuclease recognition sequences, respectively, to facilitate cloning. AL8 sequence was then amplified from HN001 strain genomic DNA, purified, cloned into BamHI/XhoI-cut pGEX-6P-3 expression vector, and transformed into E. coli DH5.alpha. cells according to standard laboratory methods. The polypeptide sequence of outer membrane protein A AL8 is given in SEQ ID NO: 69 and shown in FIG. 64. AL8 was expressed as a fusion protein with glutathione S-transferase (GST), bound to Glutathione Sepharose 4B resin (Pharmacia Biotech), and PreScission protease was used to cleave off the AL8 protein, according to the manufacturer's instructions. An aliquot of the purified AL8 protein was checked by SDS-PAGE analysis.

[0437] Purified AL8 protein (20 .mu.g) was then labeled by radio-iodination with 0.1 mCi iodine-125 (Amersham Pharmacia) using IODO-BEADS iodination reagent (Pierce) following the manufacturer's instructions. Radio-iodinated protein was separated from unincorporated iodine-125 and excess sodium iodide-125 using a PD-10 desalting column (Amersham-Pharmacia) according to the manufacturer's instructions, except that the elution was performed in phosphate buffered saline in twelve 500 .mu.l aliquots. Radioactivity in eluted fractions was quantitated on a Bioscan Quick Count QC-4000/XER Benchtop Radioisotope Counter (Bioscan, Inc.) and fractions containing the first peak of radioactivity (corresponding to labeled AL8 protein) were pooled and bovine serum albumin added to a final concentration of 10 mg/ml.

[0438] To analyze AL8 protein binding to proteins associated with intestinal surface proteins known to act as ligands for bacterial adhesins, different intestinal protein ligands were dot blotted onto a nitrocellulose membrane using a Convertible Filtration Manifold System (Life Technologies) following the manufacturer's instructions. Duplicate dots of approximately 1 .mu.g of type I collagen from calf skin, type IV collagen from human placenta, fibronectin from human plasma, laminin from the basement membrane of Engelbreth-Holm-Swarm mouse sarcoma and type III mucin partially purified from porcine stomach and bovine serum albumin included as a negative control (all proteins were obtained from Sigma) were blotted. The blot was incubated at room temperature on an orbital shaker in 10 ml phosphate buffered saline, pH 7.4, containing 0.1% Tween 20 and 5 mg/ml bovine serum albumin for 1 hour. Radio-iodinated AL8 protein was then added to a final concentration of approximately 500 ng/ml, and incubated at room temperature for a further hour. The blot was then washed three times in approximately 40 ml phosphate buffered saline, pH 7.4, containing 0.1% Tween 20 at room temperature for 10 minutes, then autoradiographed against X-ray film at -80.degree. C. overnight. The autoradiograph was developed and the resulting image digitized with a Fluor S Multilmager (BioRad). Binding by AL8 protein to the intestinal protein ligands was quantitated using Bio-Rad Quantity One software by measuring the density of the signal on the autoradiograph resulting from radiolabelled AL8 protein binding to the different ligands and subtracting the background density of blank film. To quantitate relative amounts of protein ligands blotted, blots were stained with Ponceau S using standard procedures (Ausubel et al., Current Protocols in Molecular Biology, John Wiley & Sons, 2001), and quantitated as for the autoradiograhs. The density corresponding to AL8 protein binding to individual ligands was divided by the average density of Ponceau S staining of the ligand to give the relative AL8 bound to each ligand. Binding of iodinated AL8 (3.2.times.10.sup.7 DPM) was compared to binding of iodinated mucus adhesion promoting (mapA) protein of Lactobacillus reuteri (GenBank accession number AJ293860) (6.6.times.10.sup.6 dpm) as a positive control, and iodinated irrelevant HN001 protein (7.0.times.10.sup.6 DPM) as a negative control.

[0439] The results, shown in Table 24, indicate that while the irrelevant HN001 protein did not bind to any of the intestinal adhesin ligands, both the AL8 protein and the positive control protein mapA showed significant binding to mucin. Therefore, AL8 encodes the HN001 outer membrane protein A. Results represent mean of relative density of two dots. TABLE-US-00027 TABLE 24 Density of autoradiographic signals from AL8 outer membrane protein A binding to dot blots of intestinal proteins, compared to a positive control (mapA) and negative control (irrelevant HN001 protein). Intestinal Relative Relative Relative Irrelevant Protein AL8 Binding mapA Binding protein Binding BSA 0.08 0.76 0.06 Collagen I 0.89 1.02 0.26 Collagen IV 0.16 0.78 0.09 Fibronectin 0.24 0.67 0.09 Laminin 0.47 0.83 0.12 Mucin 2.01 2.57 0.68

[0440] The outer membrane protein A of Rickettsia spp. is a 190 kDa surface bound molecule required for the adhesion of Rickettsia to host cells (Li and Walker, Microbial Path. 179:3310-3316, 1998). Rickettsial outer membrane protein A is also an immunodominant protein and has been used for the serotyping of rickettsial strains (Philip et al., J. Imm. 121:1961-1968, 1978).

[0441] The polypeptide of SEQ ID NO: 69 and the polynucleotide of SEQ ID NO: 27 have utility for processing food products and as supplements and additives. This outer membrane protein may also be used to develop non-food products. The attributes conferred by and applications for this protein include: enhanced adhesion to intestinal surface and cell lines; enhanced bacterial survival in intestinal environment; altered texture characteristics; enhanced probiotic effects; reagents to block or modify adherence of bacteria to mucosal surfaces; and development of vaccine carriers.

[0442] These attributes may be produced in food, such as dairy products, and the applications may be implemented by directed activity of the protein, introduced in a bacterial strain (including strain HN001, or starter cultures) comprising a polynucleotide of SEQ ID NO: 27 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 69 or a variant.

EXAMPLE 32

Isolation and Characterisation of Extracellular Matrix Binding Protein from L. rhamnosus HN001

[0443] The full-length polynucleotide sequence of extracellular matrix binding protein, AM4, from L. rhamnosus strain HN001, given in SEQ ID NO: 28 and shown in FIG. 65, was used to amplify the N-terminal region of AM4 extracellular matrix binding protein gene. The primer sequences used (SEQ ID NO: 38 and 39) were tagged with EcoRI and NotI restriction endonuclease recognition sequences, respectively, to facilitate cloning. AM4 sequence was then amplified from HN001 strain genomic DNA, purified, cloned into EcoRI/NotI-cut pGEX-6P-3 expression vector, and transformed into E. coli DH5.alpha. cells according to standard laboratory methods. The polypeptide sequence of extracellular matrix binding protein AM4 is given in SEQ ID NO: 70 and shown in FIG. 66. The extracellular matrix binding protein AM4 was expressed as a fusion protein with glutathione S-transferase (GST) and purified using Glutathione Sepharose 4B resin (Pharmacia Biotech), according to the manufacturer's instructions. An aliquot of the purified AM4-GST fusion protein was checked by SDS-PAGE analysis.

[0444] Purified AM4 protein (10 .mu.g) was labeled by radio-iodination with 0.1 mCi iodine-125 (Amersham Pharmacia) using IODO-BEADS iodination reagent (Pierce) following the manufacturer's instructions. Radio-iodinated protein was separated from unincorporated iodine-125 and excess sodium iodide-125 using a PD-10 desalting column (Amersham-Pharmacia) according to the manufacturer's instructions, except that the elution was performed in phosphate buffered saline in twelve 500 .mu.l aliquots. Radioactivity in eluted fractions was quantitated on a Bioscan Quick Count QC-4000/XER Benchtop Radioisotope Counter (Bioscan, Inc.) and fractions containing the first peak of radioactivity (corresponding to labeled AM4 protein) were pooled and bovine serum albumin added to a final concentration of 10 mg/ml.

[0445] To analyze binding of the AM4 protein with intestinal surface proteins known to act as ligands for bacterial adhesins, different intestinal protein ligands were dot blotted onto a nitrocellulose membrane using a Convertible Filtration Manifold System (Life Technologies) following the manufacturer's instructions. Duplicate dots were blotted of approximately 1 .mu.g of type I collagen from calf skin, type IV collagen from human placenta, fibronectin from human plasma, and laminin from the basement membrane of Engelbreth-Holm-Swarm mouse sarcoma, with type III mucin partially purified from porcine stomach and bovine serum albumin included as a negative control (all proteins were obtained from Sigma). The blot was incubated at room temperature on an orbital shaker in 10 ml phosphate buffered saline, pH 7.4, containing 0.1% Tween 20 and 5 mg/ml bovine serum albumin for 1 hour. Radio-iodinated AM4 protein was then added to a final concentration of approximately 500 ng/ml, and incubated at room temperature for a further hour. The blot was then washed three times in approximately 40 ml phosphate buffered saline, pH 7.4, containing 0.1% Tween 20 at room temperature for 10 minutes, and autoradiographed against X-ray film at -80.degree. C. overnight. The autoradiograph was developed and the resulting image digitized with a Fluor S Multilmager (BioRad). Binding by AM4 protein to the intestinal protein ligands was quantitated using Bio-Rad Quantity One software by measuring the density of the signal on the autoradiograph resulting from radiolabeled AM4 protein binding to the different ligands and subtracting the background density of blank film. To quantitate relative amounts of protein ligands blotted, blots were stained with Ponceau S using standard procedures (Ausubel et al., Current Protocols in Molecular Biology, John Wiley & Sons, 2001), and quantitated as for the autoradiograhs. The density corresponding to AM4 protein binding to individual ligands was divided by the average density of Ponceau S staining of the ligand to give the relative AM4 bound to each ligand. Binding of iodinated AM4-GST fusion protein (3.3.times.10.sup.7 DPM) was compared to binding of iodinated mucus adhesion promoting (mapA) protein of Lactobacillus reuteri (GenBank accession number AJ293860; 6.6.times.10.sup.6 DPM) as a positive control, and iodinated irrelevant HN001 protein (7.0.times.10.sup.6 dpm) as a negative control.

[0446] Results in Table 25 indicate that while the irrelevant HN001 protein did not bind to any of the intestinal adhesin ligands, the AM4 fusion protein gave a very similar binding pattern to the positive control protein mapA, with significant binding to mucin and collagen types I and IV. Therefore, AM4 encodes the HN001 extracellular matrix binding protein. Results represent mean of relative density of two dots. TABLE-US-00028 TABLE 25 Density of autoradiographic signals from AM4-GST fusion protein to dot blots of intestinal proteins, compared to a positive control (mapA) and negative control (irrelevant HN001 protein). Intestinal Relative AM4-GST Relative Relative Irrelevant Protein Binding mapA Binding Protein Binding BSA 0.37 0.76 0.06 Collagen I 1.43 1.02 0.26 Collagen IV 0.94 0.78 0.09 Fibronectin 0.53 0.67 0.09 Laminin 0.65 0.83 0.12 Mucin 1.48 2.57 0.68

[0447] The extracellular matrix binding protein is a surface bound molecule required for the adhesion of Streptococcus spp. to the extracellular matrix, exposed during tissue injury (Manganelli and van de Rijn, Infect. Imm. 67:50-56, 1999).

[0448] The polypeptide of SEQ ID NO: 70 and the polynucleotide of SEQ ID NO: 28 have utility for processing food products and as supplements and additives. This binding protein also has other applications. The attributes conferred by and applications for this enzyme include: enhanced adhesion to intestinal surface and cell lines; enhanced bacterial survival in intestinal environment; altered texture characteristics; enhanced probiotic effects; reagents to block or modify adherence of bacteria to surfaces; and development of vaccine carriers.

[0449] These attributes may be produced in food, such as dairy products, and other applications may be implemented by directed activity of the binding protein, introduced in a bacterial strain (including strain HN001, or starter cultures) comprising a polynucleotide of SEQ ID NO: 28 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 70 or a variant.

EXAMPLE 33

Isolation and Characterisation of High-Molecular-Weight Adhesion Protein from L. rhamnosus HN001

[0450] The full-length polynucleotide sequence of high-molecular-weight adhesion protein, AL7, from L. rhamnosus strain HN001, given in SEQ ID NO: 26 and shown in FIG. 67 with ATG initiation and translation stop codons (boxed), was used to amplify the N-terminal region of AL7 high-molecular-weight adhesion protein gene. The primer sequences used (SEQ ID NO: 40 and 41) were tagged with BamHI and EcoRI restriction endonuclease recognition sequences, respectively, to facilitate cloning. AL7 sequence was amplified from HN001 strain genomic DNA, purified, cloned into BamHI/EcoRI-cut pGEX-6P-3 expression vector, and transformed into E. coli DH5.alpha. cells according to standard laboratory methods. The polypeptide sequence of high-molecular-weight adhesion protein AL7 is given in SEQ ID NO: 68 and shown in FIG. 68. The high-molecular-weight adhesion protein AL7 was expressed as a fusion protein with glutathione S-transferase (GST) and expression was checked by SDS-PAGE analysis.

[0451] Lysates of DH5.alpha. clones containing pGEX-6P-3 expressing AL7-GST fusion protein, lysates of DH5.alpha. clones containing pGEX-6P-3 expressing irrelevant HN001 GST-fusion protein, and crude cell wall cytoplasmic HN001 protein preparations (prepared by standard laboratory methods) were separated by SDS-PAGE. Proteins were blotted onto nitrocellulose membranes using a Trans-Blot SD Semi-Dry Electrophoretic Transfer Cell (Bio-Rad) according to the manufacturer's instructions. The nitrocellulose blot was then blocked overnight at 4.degree. C. in phosphate buffered saline, pH 7.4, 0.1% Tween 20 (PBS-T), containing 5% non-fat dried milk. Rabbit anti-sera raised against HN001 cell wall proteins (supplied by Dr. Paul O'Toole, Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand) were diluted 1:5000 in PBS-T, 5% non-fat dried milk and incubated with the blot for 1 hr at room temperature. The blot was washed three times for 15 min each in PBS-T and incubated at room temperature in 50 ml PBS-T, 5% non-fat dried milk containing a 1:3000 dilution of a horseradish peroxidase-labeled antibody against rabbit Ig (Amersham Pharmacia) for 20 min. The blot was washed six times in PBS-T at room temperature for 15 min each, and binding visualized using the ECL Western blotting detection system (Amersham Pharmacia) according to the manufacturer's instructions.

[0452] Results of the Western blot revealed that the anti-sera detected a number of proteins from HN001 raised against the HN001 cell wall preparations. While several of these proteins were found in both the cell wall and cytoplasmic preparations of HN001, these proteins consisted of bands of approximately 66 kDa and less. In addition, a number of high molecular weight protein bands were detected in the HN001 cell wall protein preparations that were not present in the HN001 cytoplasmic protein preparations. These bands ranged from approx. 130 kDa to approx. 220 kDa or greater. Therefore the cell wall antisera specifically detected several large cell wall proteins from HN001. Of the E. coli extracts, the only signal came from the lysate of the DH5.alpha. clone containing pGEX-6P-3 expressing the N-terminal region of AL7. This strong band was approximately 97 kDa, the same size as the AL7-GST fusion protein. Lysates from E. coli clones expressing unrelated proteins showed no cross-reactivity with the HN001 cell wall anti-sera. This data indicates that AL7 encodes a high-molecular-weight adhesion protein at the cell surface.

[0453] The high-molecular-weight adhesion protein is a homologue of the surface-bound molecule of Haemophilus influenzae shown to be involved in adhesion to human cell lines (Barenkamp and St Geme, Mol. Microbiol. 19:1215-1223, 1996; St Geme et al., Proc. Natl. Acad. Sci. USA 90:2875-2879, 1993).

[0454] The polypeptide of SEQ ID NO: 68 and the polynucleotide of SEQ ID NO: 26 have utility for processing food products, as supplements and additives, and as reagents for several applications. The attributes conferred by and applications for use of this adhesion protein include: enhanced adhesion to intestinal surfaces and cell lines; enhanced bacterial survival in intestinal environment; altered texture characteristics; enhanced probiotic effects; reagents to block or modify adherence of bacteria to surfaces; and development of vaccine carriers. These attributes may be produced in food, such as dairy products, and implemented in other applications by directed activity of the adhesion protein, introduced in a bacterial strain (including strain HN001, or starter cultures) comprising a polynucleotide of SEQ ID NO: 26 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 68 or a variant.

EXAMPLE 34

Isolation and Characterisation of Periplasmic Binding Protein 1 (PEB1) from L. rhamnosus HN001

[0455] The full-length polynucleotide sequence of a periplasmic binding protein 1 (PEB1), AJ4, from L. rhamnosus strain HN001, given in SEQ ID NO: 16 and shown in FIG. 69 with ATG initiation and translation stop codons (boxed), was used to amplify the AJ4 PEB1 gene from HN001 strain genomic DNA by PCR according to standard laboratory methods. Primers were tagged with BamHI and EcoRI to facilitate cloning. AJ4 PCR products were purified, cloned into BamHI/EcoRI-cut pGEX-6P-3 expression vector, and transformed into E. coli DH5.alpha. cells according to standard laboratory methods. The polypeptide sequence of PEB1 AJ4 is given in SEQ ID NO: 58 and shown in FIG. 70. AJ4 was expressed as a fusion protein with glutathione S-transferase transferase (GST), bound to Glutathione Sepharose 4B resin (Pharmacia Biotech), and PreScission protease was used to cleave off the PEB1 AJ4 protein, according to the manufacturer's instructions. An aliquot of the purified AJ4 protein was checked by SDS-PAGE analysis.

[0456] Purified AJ4 protein (10 .mu.g) was then labeled by radio-iodination with 0.1 mCi iodine-125 (Amersham Pharmacia) using IODO-BEADS iodination reagent (Pierce) following the manufacturer's instructions. Radio-iodinated protein was separated from unincorporated iodine-125 and excess sodium iodide-125 using a PD-10 desalting column (Amersham-Pharmacia) according to the manufacturer's instructions, except that the elution was performed in phosphate buffered saline in twelve 500 .mu.l aliquots. Radioactivity in eluted fractions was quantitated on a Bioscan Quick Count QC-4000/XER Benchtop Radioisotope Counter (Bioscan, Inc.) and fractions containing the first peak of radioactivity (corresponding to labeled AJ4 protein) were pooled and bovine serum albumin added to a final concentration of 10 mg/ml.

[0457] To analyze the binding of the AJ4 protein to intestinal surface proteins known to act as ligands for bacterial adhesins, different intestinal protein ligands were dot blotted onto a nitrocellulose membrane using a Convertible Filtration Manifold System (Life Technologies) following the manufacturer's instructions. Duplicate dots were blotted of approximately 1 .mu.g of type I collagen from calf skin, type IV collagen from human placenta, fibronectin from human plasma, laminin from the basement membrane of Engelbreth-Holm-Swarm mouse sarcoma, and type III mucin partially purified from porcine stomach and bovine serum albumin included as a negative control (all proteins were obtained from Sigma). The blot was incubated at room temperature on an orbital shaker in 10 ml phosphate buffered saline, pH 7.4, containing 0.1% Tween 20 and 5 mg/ml bovine serum albumin for 1 hour. Radio-iodinated AJ4 protein was then added to a final concentration of approximately 500 ng/ml, and incubated at room temperature for a further hour. The blot was washed three times in approximately 40 ml phosphate buffered saline, pH 7.4, containing 0.1% Tween 20 at room temperature for 10 minutes, and autoradiographed against X-ray film at -80.degree. C. overnight. The autoradiograph was developed and the resulting image digitized with a Fluor S MultiImager (BioRad). Binding by AJ4 protein to the intestinal protein ligands was quantitated using Bio-Rad Quantity One software by measuring the density of the signal on the autoradiograph resulting from radio-labeled AJ4 protein binding to the different ligands and subtracting the background density of blank film. To quantitate relative amounts of protein ligands blotted, blots were stained with Ponceau S using standard procedures (Ausubel et al., Current Protocols in Molecular Biology, John Wiley & Sons, 2001), and quantitated as for the autoradiograhs. The density corresponding to AJ4 protein binding to individual ligands was divided by the average density of Ponceau S staining of the ligand to give the relative AJ4 bound to each ligand. Binding of iodinated AJ4 protein (2.6.times.10.sup.6 DPM) was compared to binding of iodinated mucus adhesion promoting (mapA) protein of Lactobacillus reuteri (GenBank accession number AJ293860; 1.3.times.10.sup.6 dpm) as a positive control, and iodinated irrelevant HN001 protein (1.4.times.10.sup.6 DPM) as a negative control.

[0458] Results shown in FIG. 71 demonstrate that while the irrelevant HN001 protein showed no significant binding to the intestinal proteins, AJ4 and the positive control protein mapA showed significant binding to mucin. AJ4 also showed some binding to laminin, fibronectin, and collagen type IV. Therefore, AJ4 encodes the HN001 PEB1. FIG. 71 shows the relative density of autoradiographic signals from AJ4 protein (grey bars) to dot blots of intestinal proteins, compared to a positive control (mapA, white bars) and negative control (irrelevant HN001 protein, black bars). Results for each dot (duplicates) are shown.

[0459] The PEB1 is a surface-bound molecule required for the adhesion of Campylobacter spp. to intestinal epithelial cells and is required for effective colonization of the gut environment (Pei et al., Infect. Imm. 66:938-943, 1998; Pei and Blaser, J. Biol. Chem. 268:18717-18725, 1993).

[0460] The polypeptide of SEQ ID NO: 58 and the polynucleotide of SEQ ID NO: 16 have utility for processing food products and as supplements and additives. This binding protein may also be used to develop non-food products. The attributes conferred by and applications for this protein include: enhanced adhesion to intestinal surface and cell lines; enhanced bacterial survival in intestinal environment; altered texture characteristics; enhanced probiotic effects; reagents to block or modify adherence of bacteria to surfaces; and development of vaccine carriers.

[0461] These attributes may be produced in food, such as dairy products, and implemented in other applications, by directed activity of the protein, introduced in a bacterial strain (including strain HN001, or starter cultures) comprising a polynucleotide of SEQ ID NO: 16 or a variant, or as an enzyme preparation comprising a polypeptide of SEQ ID NO: 58 or a variant.

[0462] SEQ ID NO: 1-83 are set out in the attached Sequence Listing. The codes for nucleotide sequences used in the attached Sequence Listing, including the symbol "n," conform to WIPO Standard ST.25 (1998), Appendix 2, Table 1.

[0463] All references cited herein, including all patent and literature references, are incorporated herein by reference in their entireties.

[0464] While in the foregoing specification this invention has been described in relation to certain preferred embodiments, and many details have been set forth for purposes of illustration, it will be apparent to those skilled in the art that the invention is susceptible to additional embodiments and that certain of the details described herein may be varied considerably without departing from the basic principles of the invention.

Sequence CWU 1

1

83 1 3215 DNA Lactobacillus rhamnosus 1 gatcatgatg gggcagcagt cgccatcaag cagtatgcaa tgggtgaagg ttaataaaaa 60 agcgagtcga attcctgata atggaagtcg actcgctttt tattttagcc gaaatagttt 120 cgtttaaatc taatctttta agtcaataat tgcctgttcc aactcctgtt tctgagctgc 180 agagatttcc ggatatttta gcggcaaagc ggtgacttcg cggttgatga tttgggacac 240 aaccagtcgg gagtaccact tatcgtctga cggaatcacg taccagggat ttgttttcgt 300 ggcggtgtgc tgaatggcat cttgataagc ttgctggtaa tcatcccaaa agcgccgttc 360 gtgaatatcc gccaatgaga acttccaatt cttttcggga atttcgattc gttttaagaa 420 gcgatttttt tgttcggcct tggaaatgtg taagaagaac ttgagcagca agatgccatt 480 gcggtgcgca taggtttcta gcgccttgat atcgttgaag cgtttggccc ataaatcgtc 540 atggacatca gcaacggtgt tgattcccgg caggttttct tttaatagca attcgggatg 600 aacccggtcg accagcactt cttcataatg ggagcgattg aacaccgtca gttcgccacc 660 agccgggaaa gcgttatgga tgcgccataa aaagtcatgg cctagttcaa gctcagtcgg 720 tactttaaac gacaccactg aggttccctg cggattgacg ccggacatga cgtgttcaat 780 catgctgtct ttgccggctg catccatccc ttgaaagata atcaagacgc tgtattgttt 840 ctgtgccgcc aagtgttgct gaactttgga gagcaccttg atgttatgat caatgtctgc 900 tttgatctgc tcttttttat tttgaaaatg ttctggcggc gcggtcgcaa acgcttgaat 960 gttaaaggtg ccagtgccgt caaaacgata tttttccaat gtcatcttat caccttcaat 1020 ttaagcttag tttcaacata gtagttacgc caaggatgtg caagcaattg acgccttggc 1080 ggattaaatc tatgctgaga ttacgacatg aaaacggagg caattgcatg acattaccaa 1140 gaattcaaga tgatttgtac ctagccgtca atggcgaatg gcaagcgaag acgccgattc 1200 cacctgacaa aagtgttgtg agtgcggata gtaatctgac cgatgatatt cgccaaaaac 1260 tagtggctga tctaagcacg atgacgaaaa cagccaaaac tttgccgctc cagtatgcag 1320 cgcggttgtt tgccaaagcc aatgaccaaa cccgccgtca gcagctaggc attgagccag 1380 ttcgtgatcg gataagcttt ttgatggcgc tcacgacgct tgatcaattt cgcagcgcta 1440 tgcccaaact ggttgctgat caatacgtct taccgatcag tccttacgtt gatgctgata 1500 tgcacgatgc cgagcataat attctgaatc ttggcgggcc agacacaatt ttacctgatg 1560 cggcgatgta ccaacatgaa gatgccgaaa atgcggcgga tctggcagcg tggtcgcaga 1620 tggcagctgc catgctggct gcggtaggat tcagtcagac tgatcaaaca gcatatgttg 1680 aagcggctaa acgatttgat cggcgtttgg ctgattatgt gccagcaaat gttgacttag 1740 cggtagatag cacgtatgac aatccattga gctggcaggc gtttgaagat gcggccggtt 1800 atttggggat cccacaagcc tttgcaactt acatgccgca aacaccggcg aaagtcaatg 1860 cggttgtacc ggcttatctt ccgcacttaa gcaaactact gacgccggac aattattcag 1920 aatggcacgc atggatggtg attaacgaat tgctaacctg cgccacttac ctcagtgatg 1980 atttacgtca attggccgga cagtatgatc ggtttttggc tggtcaacct gaggcgtcat 2040 cgtggacgaa acacgctttt gggattgcca acgagtattt tgacgatgtg attggtcagt 2100 attatggtca aacctacttt ggtgccgacg ctaaggcaga tgtgacggcc atggttaagc 2160 aaattcttgc gcaataccgc gtgcagctag aaaacaacac ttggctgagt ccggctacga 2220 agcaaaaggc gatgcgcaag ttagccacga tgcaagtcaa aatggggtat ccggagcgac 2280 tcttttcctt gtatgatcac ttgagcgtgg atgttgacga tgatttgttg acggcaattc 2340 tgaaacttag cgcacagacg caggcctttt ggtttaaaca gttaggccag acggtggatc 2400 ggaatcaatg gaatatgccg ggacacttgg tgaatgccag ttatgatccg ctgaaaaatg 2460 acatcacttt tcccgctggt atcttgcagc cgccgtatta ctcactcaaa tggacccggg 2520 cggaaaacct cggagggaca ggcgcaacga tcggtcatga aatctcgcat tcgtttgata 2580 ataacggggc gctgtatgat gaatatggta atttgcataa ctggtggaca ccagcggata 2640 agcaggcatt tgatcagctg gtaaaagcga tggcggcaca gtttgatggc cgtgactatg 2700 aaggagtcaa ggtcaacggt acactgaccg ttagtgaaaa catggcggat aacgccggca 2760 tggatgtggc gttggcgtta ctaggcgatc agccggatgt taaggatctg caggcattct 2820 tcatcactta cgctcgttca tgggccacca aaatgcgacc ggagcgggct aaaactgttt 2880 tgcggcaaga tgttcatgcg ccggctacct tacgcgtgaa tgtgccggtg caaaactttc 2940 ctgcatggta ccaggcattt aatgttcagc cacaagatgg tatgtatcgg caaccacaga 3000 agcggctgac gatttggcat cagtaatatt taaataaaag agttttatgt gaaccttttt 3060 cgagaaccgc gagatcaact gtgtgtcaca ctgttcatgg ggaagcgtaa acaaaaaggc 3120 aacgattgcc gtgagacaat cgttgccttt tttcaatctt gggacaggtc gtggtaataa 3180 tgtagccagc cggtttcgcg ttcgccgatt tgatc 3215 2 924 DNA Lactobacillus rhamnosus 2 acggctattg tgacggcttg tcagagtggg atgggcggta ctggcgacgt ggctattctc 60 agtacggcga atcggatgaa tctgatgcca tttgctcagg tggcaacacg cttgggtggc 120 gcgattaccg ttattaccat gacggcgatt ctgcggatga tcttttaaat cgactagttt 180 cgaaacttaa ggaggatgat tcacatggca aagaaggatt ttaatcaact agcgctagat 240 caagcaaaag taaatggcgg aaaattgagt gtggaaccga aagtaccaat tgagacgcgc 300 gatgatttga gtattgcgta tactccaggc gtcggggcag tttcttctgc tattgccaag 360 gatcagtcgc tcgtttatga cttaaccact aagaaaaata cggttgcagt tgtcagtgac 420 ggttcggcgg ttttagggtt aggcaatatc ggtgccgagg ctgcgatgcc ggtgatggaa 480 ggaaaagccg ctttgttcaa acggtttgct aaggttgatg ccgtgccgat tgtgttggat 540 acgcaagaca ctgaagcaat cattgcggcg gttaaagcca ttgcaccaac atttggcggg 600 atcaatcttg aggatatcag tgcgccacga tgttttgaaa tcgaagcacg actcattgat 660 gagctcaaca tcccggtgtt ccacgatgat caacatggca ctgcgattgt ggtgctcgcc 720 gctttgtaca atgccttgaa agtagcggat aaaaagattg aagacattcg cgtggtggtt 780 aatggcggcg gctcagcggg gctatccgtt gcccggcgat tcttggcagc cggagtcaaa 840 cacgtcatgg tggtggataa ggtgggcatt ttagctaaaa agaacgctga tcaactgcca 900 ccacatcaag cgggattgcc ttaa 924 3 1218 DNA Lactobacillus rhamnosus 3 gtgttaaatc caaggatcgt taaaaaacgg gcttaaaatc aaacgattag actgtcgggt 60 gacgcaccgg cagtcttttt gcgttaatat aggaataacc ttttaacacg attcgttaac 120 acgaggaaat ggaggcattc gttaatggca gatgaagagg caatgttggc aaaggttcaa 180 gcgagctggg cgcaaacggc tgctcgggat aaggcacggt acgcggatga acgggtaccg 240 gaagatgttc attgggagac ggaatatcgg tacgaacagt cggctgatcc gcagcaaacc 300 ctgaacctgt actatccggc caaaagacgc aacgcaacca tgccgaccgt catcgatatt 360 catggtggcg ggtggtttta tggtgatcgt aatttgaatc gtaattattg ccgctatttg 420 gctagtcaag gatacgcagt gatgggtatg ggctatcggt tgttaccgga tgttgattta 480 cgcggccaga ttcaagacat ctttgctagt ctgcgctggt tatcgcattt tggccctcaa 540 cgcggatttg accttgacca tgtgcttttg accggggatt cagctggcgg ccacctggcg 600 tccttggttg cctgcatcca gcagagtgcg gagttacagg aactctttgg cgtgagtcgg 660 gttaatttca acttcaccct ggtggcgctg gtttgtccag tcgcagaacc aagtaagctt 720 cccgaagcag ccggtgacat gagcgatatg gccgcgtttt atctggacaa gttaagcggc 780 ggcgatcagg cactggccga tcacctgaat ttctcgcagg ttgtcaaggg tttggacctg 840 ccgccgttta tgctgattgg cgggcaaaat gacagctttt acttgcaaag ccaagccttg 900 ttgaaggtgt tcgatgctaa tcacgtcacc tatacaacga agctatggcc ggcaagtgcg 960 gggccacacc tcaagcatgt gtttaatgtt caacattggg aatggccgga aagtattgag 1020 acgaacttgg agatgctgcg gacgtttgat gcgttaagca agcagcaaga tcaagctgaa 1080 gaaaacgaat ttgaatagtc tgcggaagtg gcagtcatag cagccgctca tccggcgata 1140 gaaaaagact cagaggcgat ctgagtcttt ttagattaaa aaaaccgcgc agtttgaagg 1200 ctacgcggag gaaatggc 1218 4 491 DNA Lactobacillus rhamnosus 4 ttgttttggg tacgagtacg cacacaaact attcggaaaa acactagaaa aatctagtta 60 atacgaagga gcagatcagt catggaaaaa cgcgaattta acattattgc agaaaccggg 120 attcacgcac gtccggcaac cttgttggta caagcagcta gcaagttcaa ctcagatatc 180 aacttggaat ataaaggtaa gagcgttaac ttgaagtcca tcatgggtgt tatgagtttg 240 ggcgttggtc aaggtgccga tgttacaatc tctgctgaag gcgctgacga agccgatgca 300 atcgctgcaa ttacggacac aatgaaaaag gaaggcttgg ctgaataatg gctgaacatt 360 tgaagggaat cgctgctagt gatgggatcg ccacagcgaa ggcctattta ctggttcaac 420 ctgatttatc atttgacaaa aagacggttg atgatccttc aaaggagatc gaccggctaa 480 agcaggcact t 491 5 1276 DNA Lactobacillus rhamnosus 5 ccaagtaatc atgccattca gctagcaaac attgcccgtc aacctgcttc attgacgggc 60 atacataaaa gaacactatt cattaaagga ggtcgggttt caatgaccca attcaatacc 120 aaactcgttc atggaccaca actaaatgtc gaccaagccg gtgccatcgt gccaccagta 180 taccaaagtg ccatgttccg ctttgctcct gatggtcagg aaacccactg ggactatgcg 240 cgcagtggta acccgacccg tgaatacctg gaacgtcaga ttgctacgct agaaaatggc 300 gatgctggct ttgcgttttc cagcggtgtt gcagcgattg caacggtgct cgcgattttc 360 cccgaccaca gtcacttcat tattggtgat tcgctctaca gtggcaccga tcgcctcatc 420 aaccagtatt tttctcaaca cggcctgacc tttacaccgg tggatacgcg tgatctggca 480 gcggtggaag ccgccatccg ccccgaaact aaagcaattt tctttgagac tttttccaat 540 ccgctcctca aagtcagcag cgtcaaggcc atcagtgccc tcgccaaaac ccatgatctg 600 ttaacgattg tcgacaacac gttcttaacc ccttattacc agcggccact tgacctcggt 660 gccgacatcg ttctacacag cgccaccaaa tacctcggtg gccacggtga cctcatcgcc 720 ggcctcgttg tctccgctca ccccgacctc agcgagaagc tcgctttcct gcaaaacacg 780 atcggtgcca ttttaagccc gcttgactgt agcctcgtca cccgcggcat tgccaccctc 840 tccgttcgcc ttgatcgtga aactgcaaac gcccaagccg tcgccgaatt tctagcgcag 900 cacccagacg tcgcccacgt ttactacccc ggacttaaaa acgatcccgg ttacgcatta 960 gcccaaaaag aaaccacggg tgccagcgga ctcctgacga tcaaactagc cgacaacatt 1020 gatcccttaa agttcgttaa cagcaccaaa attttcgact ttgccgactc acttggcacc 1080 gtctccagtc tagtcaaact accttggttt aagctcccgg aagacaaacg cgccgatttt 1140 ggtttgacac cgcaacatgt ccggattgca attggcttgg aggatcagca ggacttgatt 1200 gacgatctgc agcaggcact ggttgcagcg gaaaaatagt atccaaaata atatctatta 1260 cttttgctaa ataggc 1276 6 1032 DNA Lactobacillus rhamnosus 6 atgccattgt ctgcactttc ttagcttggg gtcagcggta tctcgaaaaa ttcacatcac 60 gctacaatgc caatgcacaa accacgcaat tataatccgc cattttgaaa ggaagaaagc 120 tatgttaaag aaaaagttgt ggttcctgtt gccgcttgtg gccttggtaa ccttcacgct 180 caccgcttgc accagcgcat catctgacac gtcaaaaaac agcgacgtca ccgccgaact 240 catcaacaaa aatgagctta ccatcggcct tgaaggtact tatgcgccat tttcttatcg 300 caaagatggc aaacttgaag gcttcgaagt ggaactgggg aaagccttag ccaagaaaat 360 cggggttaag gcaaaattcg tgcccaccca atgggattcg ctgattgcag gattaggcag 420 ccagaaattt gatctcgtac tgaatgatat tagtgaaacg cccgcacgca aaaaggtcta 480 caacttcacc actccgtaca tgtactcgcg ttatgcctta ataacccgca gcgataacac 540 caccatcaaa tcgcttgccg atattaaagg caaaacattt gtcgaaggca ccggtacacc 600 caatgccgct ttagccaaaa aatacggcgc taagatcacc ccgtctggcg actttaccgt 660 atcgcttagc cttgtgaaag aaaaacgcgc agacggaacc atcaacgcct cggctgcatg 720 gtatgccttt gccaagaata actcaaccgc gggcttaaag agtcaaaccc tcaaagatag 780 tgtcgttaaa cccgatgaag tagctggcat ggtcagcaaa aaatcgccta aactacaagc 840 cgcactttca aagggcattc aagaactacg caaagacggc acgttgaaaa aactgtcgca 900 aaaatatttt ggcaccgatt taaccaccaa gtaatcatgc cattcagcta gcaaacattg 960 cccgtcaacc tgcttcataa acgggcatac ataaaagaac actattcatt aaaggaggtc 1020 gggtttcaat ga 1032 7 1886 DNA Lactobacillus rhamnosus 7 aacatcaggg tggtaaaatc acactgatta aggaacgggt tgtcggcttg aacgactgaa 60 aacttcgact tcggtcatct aaaggagaaa actatgccag atgtacgttt tcacagcgtc 120 tttgatatta ttggaccggt tatggtgggg ccaagtagct cacatacagc cggggcagcg 180 cggattggta aagtcgtgcg cgacattttt ggcgaacccc cggagacgat tacgatttac 240 ctttacgaat catttgccaa aacctatcgc ggtcatggta ccgatgtggc gctagtagca 300 gggctgttgg ggatggcacc cgatgatccg cggttgccgg aatcgctgaa gttggcctat 360 gaccaaggca ttaaagtgag ttttgtgccg aaaagcgata aggttgatca tcctaacacg 420 gcacatattg tcttgcaagc cggtgatcac cggttagcgg tcactggggt ttccattggt 480 ggcgggaata ttcagatcac ggaaatcaat gggtttaaga tatcgttgag catgggtcag 540 ccgacttata tcaccattca tgacgatgtg ccggggatga ttgcacaggt caccaagatt 600 ttctccgatg ccggcattaa tatcgggaca atgacggtga cccgcactgc taaaggggaa 660 caggcaatta tgatcattga aacggatgat tatcatgatg atattttggc caaattgaaa 720 ttattaccgc atatgcgcaa tgtcacttac tttgagtgat gacgcgctaa caactggtta 780 cgaactggct aataaaggag cttatcatgt tttataccgt taaagaactt gtagaacaaa 840 gtcatgcctt ctcctcggtt gccgaactca tggtgcatac ggaagtcgaa aactcaacgc 900 ggactgaagc acagatccgt catttaatga gccgtaatct ggaagtgatg gaacgctcgg 960 ttaaggaagg cattgccggg gtcaaaagtg tcaccgggtt aaccggcggc gaggccaaaa 1020 agctgaacca ttatattgct gatgaccggt tcatgagcgg taaaccgatc atggaggctg 1080 ttcgcaatgc agtggcagtt aatgaagtga acgctaaaat ggggctgatt tgtgcgacgc 1140 cgactgcggg atcggcagga gttctggccg gtgttttgtt ggcgatgcgt gatcgcctgc 1200 acctgacgca tgatcagcag cttgattttc tttttaccgc tggtgcattt ggcttggtca 1260 ttgcaaataa tgccgggatt gccggagcag aaggcgggtg ccaggaagaa gttggctcgg 1320 ccagtgcgat ggctgcggcg gcgttggttt gtgctaatgg cggcagtgcc gaacaggcag 1380 ccaccgccgt tgcgattacg ttgcaaaaca tgctggggtt ggtttgtgac ccagttgccg 1440 gcttggtgga ggttccgtgt gtgaagcgaa atgcattggg agcaagtcaa gccatgattt 1500 ccgctgatat ggcattggcc ggttgcatca gtgtgattcc ggccgatgag gtgattgaag 1560 cggttaaccg cgtcggcatg cagttgccag caacattgcg ggaaaccggc gagggcggcc 1620 tagcaacgac accaactggc ttacggctga aagaacaaat cttcggcaaa aagtaattgt 1680 gattcaatga cggcacgaca aatttttgcc cggcatgagt tttatttaaa cggcgttact 1740 ggcaacaagg tatttggaaa gggtcaatcg tgattaattt atatattatt cgacatggtg 1800 aaacagcagg caatgtgcgc cgcttaattc aaggcgtgac gaattcacac ttgaatgcgc 1860 gcggacgtaa acaggcgtat gctttg 1886 8 1350 DNA Lactobacillus rhamnosus 8 gtgaaggaaa aatgagtcgc ttaaaagagc gcgataaaat caacaaatat tgacaaccga 60 ttgccagcca gcgctcacgt ttgaagctcg gccaaaccaa acaagatcac aaggaggcgt 120 tgtttatgtt taaacccacc attcatcaac ttcatcccta tacgccagaa aagcctcttg 180 ccgtattaaa agaagaactt ggcttgccac agctggtgcg gatgtcagca aacgaaaacc 240 cattcggtac cagcgtcaaa gttcagcagg ccgtgaccaa ctggaatttt acgcaaagtc 300 gtgattaccc cgatggctat gccagtcaac tacgcaccgc ggtggcaaaa catttagacg 360 ttgccgcaga gcagttggtt tttggcaatg gtctggatga agtcattgcc ttaattgccc 420 gcactttttt gagcccgggg gatgaagtca ttgaaccatg gccaacattt tccgagtacc 480 gcttgcatgc ccaaattgaa ggggccaccg tgattgatgt gcccgtcact gaaactggca 540 attttgattt atctgcaatg gcgcaggcgc taaccgcgaa aacgaaactg atttgggtgt 600 gcaacccaaa taaccccacg ggcacgctgc tgtcaattgc gacactgacc gaatggctgc 660 gacagatacc aaaagacgtg ctggttttaa tggatgaggc ttatattgag ttcactgatg 720 actatccagc cacgagcgct atcagcttat tatcaaagtt tccaaacctc gtcgtgctgc 780 gaacattttc aaaaatctat ggactggcga atttccgggt cggcttcggt gtttttccta 840 aacaacttgt taactacttg caaaccgttc ggctgcctta caatttaagc agcattgccc 900 aagttagcgc acaggcggcc ttggctgatc aagattttgt cgcgatgaca cgcaagcgag 960 tgcagcaagc gcgcgatagt tgggaacgct ttttaaccca aactggactg ccacacaccc 1020 ggagccaaac caactttcaa ttctttcagg ccccaaaaat gcaggcatcg gctttaaaaa 1080 agcgcctgct acaacaaggt tttcttgtcc gtgatggctt aaaacccggc tggctgcgcg 1140 tcacgtttgg cactgaggta caaaacacgg cggtacagcg catcattgaa acttttcagg 1200 cagaactcac tgggccaaat gcgctgaagt gattggaacc gccaccatgc aggcgtaaac 1260 taaaggtgtg gttaatggct catctgaaag gaagcattta ttttgaaaat tgccaaatta 1320 aacaaccatc cctatctgat aacgtctgca 1350 9 1275 DNA Lactobacillus rhamnosus 9 aaagcaatcg gttcgatcat catcgcattt gttgccatga ttttggcttt gctttggcca 60 ccgttaacga tcatactgga cttggtaatg ttactcttgt gggccatccc ggatcagcgg 120 gttgaacggc atttgctaca tggcccgaaa aactaaactt tgtgaaaagg ggtttttatc 180 ttggcaagaa ccattggtat tatcggtatt ggacatgttg gggtgacaac agcatttaat 240 ctcgttagca aggggattgc ggatcgtctg gtgctaattg accaaaaggc tgatttagct 300 gaaggcgaaa gttatgattt gaaggatgca cttggtggat tgccgactta taccgagatt 360 atcgtcaatg attacgatgc tttgaaagat gcagatgttg tcatttccgc ggttggcaat 420 atcggtgcga tttcaaacgg cgatcgaatt ggtgaaaccc aaacgtcaaa acaagcatta 480 gacgatgtgg caccaaagtt gaaagcgtcc ggattccatg gcgttttgct ggatatcacc 540 aatccttgtg atgctgtcac cagctattgg caatatttac ttgacctacc aaagtcccag 600 attattggca ccggcacctc gctggatact tatcggatgc ggcgcgcggt tgctgaatcg 660 ctaaatgtga atgtcgccga tgttcgcggt tataacatgg gtgagcatgg tgagtcacaa 720 tttacggcgt ggtcaacggt gcgggttaac aacgagccaa tcacggatta tgcgcaagta 780 gattatgatc aattagctga tgcggcgcgg gctggcggct ggaagattta tcaggccaaa 840 cattatacca gctacggtat tgccaccatt gctactgaaa tgacacaggc gattatcagt 900 gatgccaagc ggatttttcc gtgcgctaac tatgatcctg aattcggtat cgccatcggt 960 catccggcga cgattggcaa gctcggtgtt gttaacacgc ctaagttgaa gcttaccgat 1020 gaagagcgtg ctaagtatgt tcattccgcg ggcatcatta aagctacagt ggaaaagatg 1080 aagtaagatt aatccagtag cattgatgtc atgcataaaa agacgccaaa ttgtgaccgg 1140 tattctctaa cgttttactc caacgttgag ggtgctgatc aaatcggcgc ctttttacta 1200 gagttaattt daatgttacg ccttaataag gagtttttcg ggtatggtta aaaaatatac 1260 gttggtgact gttga 1275 10 1536 DNA Lactobacillus rhamnosus 10 ttcgaagttt aaagaactag gtttggatca tgatctctta aaggcaatcg cccagtcagg 60 ttttgaggaa gcgacgccga ttcaagcgga gacgatccca ctggttctgg aaggcaaaga 120 tgtgatcggt caagcccaga ccggtaccgg gaaaacggca gcatttggct tgccaattct 180 gcaacacatc gataaagccg accggagtat ccaagcattg gtcatttccc caactcggga 240 attggcgatt cagacccaag aagagcttta ccgtttaggc cgcgacaaga agatcaaggt 300 tcaggctgtc tatggcggcg ctgatattcg ccgccagatt cgtcagcttg ctgaccatcc 360 gcaaattgtg gttgggacac ctggtcggat tcttgatcat attggtcgtc ataccttaaa 420 gttggaacac cttgatacct tggtgttaga tgaagccgat gaaatgctcg atatgggctt 480 cattgacgat attgaaaaga ttgttgaaca aatgccgacc gagcgtcaaa cattactgtt 540 ctccgcgacg atgccggcag cgatcatgcg cttaaccaac aagttcatga aagaacctgt 600 gattgtcaag attaaggcta aggaactgac agcagatacc gttgagcaat attatgttcg 660 ggccaaggac tatgaaaagt tcgatgtcat gacacgactg tttgacgttc aggatccgga 720 cttggcactg atttttggac ggaccaagcg tcgtgttgac gaactgacac ggggattaaa 780 ggcacgcggc tatcgggctg aaggtattca cggcgattta acccagcaaa agcgaatgag 840 cgttttgcgg cagttcaaga gcggccaatt ggattttctg gttgcaaccg atgtcgctgc 900 tcgtgggttg gacatttctg gtgtcaccca tgtttacaac tatgatatcc cgcaagatcc 960 ggattcctat gttcaccgta tcggtcggac gggacgcgcc ggacataaag gggtatccgt 1020 aacctttgtc acgccaaatg aaattgaata tctgcacacc attgaagatc tcaccaagaa 1080 gcggatgtta cccatgaagc cgccgacagc tgaagaagca ttaatgggcc agatctccag 1140 cggcttagca accatcaagg aacaagttga agctaacgat accgaaaagt atgaagcaat 1200 ggctgaaacc ttgttggaaa actacacccc gttgcagctg gtttcggcgt atctcaaggc 1260 agtcagccct gacgatgcga gtgccgttcc ggttaaaatt acaccagaac gtccattacc 1320 acgccgcggc cgcaacaatc acggccatgg caacaatcgt ggcggttata aaggcggcta 1380 caaaggcaag cgacgcgatg gcggctatca aggtaatcgc gatggcaagc gcagttacga 1440 caagaagcgc aactttggcg acaaacgtaa aaacgttaag cgtaatttca aaatccgtac 1500 gggtgaataa tcaccagtac gttaatagac cggtca 1536 11 1409 DNA Lactobacillus rhamnosus 11 tatgacgttg cgtgtcgata ggcaaatgga ctatgctatt tgcatgctat tataacgcgt 60 ttgccagcgt aaaagtcagt taggcaatct tttagttgta

gccgtctaac tccgacttct 120 aactgcatcg gttcgcgttt acatcataat gcgctctcct gcccagaaat cgggtttggc 180 tcgcgcttac tttattaagg agatttgtat gacattgcaa cctttaaacg aacaactacc 240 tgccatcgag gttagtgaga ttcgacaatt tgacgaaagt gtcagtgata ttcccggtat 300 tttgaaactg acgctaggcg aacctgattt caacaccccg gaacatgtta agcaagccgg 360 gatcaaagcc attcaggaaa attactcgca ttataccggg atggttggtg atccggagtt 420 acgcgaagcc gcacaacatt tttttaaaac gaaatatgcc actgactatc gggctacaga 480 tgaaattctg gtgacagtcg gggccactga agcactggca accgccatta cgacgatcag 540 tgatccgggt gatgccatgc tggttccgtc accaatttat ccgggctaca ttccgcttct 600 gacgctgaat cacgttacgc cgctttatat ggatacgagt aaaaccgact ttgtcttgac 660 ccccgaactc attgaggcca ccatcactgc aaatcctgac gctaaaatca aaggcattat 720 ccttaactat ccaagtaatc ccaccggtgt cacgtatcgg gcggcagaag ttaaagccat 780 tgcggacatc gccgctaaac ataacctcta cattatctgt gacgaaattt attctgaact 840 gacttatggt gagccgcatg tttccatggg acaatttgcc tacgatcgta catttattgt 900 caacggtctg tctaaatcac atgcaatgac cggctggcga atcggctttt tgatgggtcc 960 ccagcagtta atcgcgcaag ccaaaaaggt gcaccaatat cttgtgactg ccgcaacgac 1020 cattgcccag cgcgctggta ttgaagctct gacgaacggt gcagacgatg ctcaggtgat 1080 gaaagcagct tacgttaaac gccgtgattt tgtttatgcc gccctcatcg acatgggctt 1140 tagcgtggct cgtcctgatg gtgcctttta tctttttgca aaaattccga cccaactgca 1200 tctaagctca cgcgaattta cgcacgcctt ggcacatgaa cagaagttag ctctgatttc 1260 aggtaccgct tttggccccg gcggcgaagg ttatatccga atcagttacg cggcatcaat 1320 gaccgatctt caagaagccg ttaagcgatt gcgcgcgttc atggccagcc acatcggcta 1380 atcaagcgta aacggaaaga atccgcacg 1409 12 1247 DNA Lactobacillus rhamnosus 12 gtgcatttag caaaaagaat cctcaacgtc gcaccgtcag cgacattggc cttaagtaat 60 cagacgaaag acttaaaggc aaaaggtgcc gacgtcattg atttgtctat tggccaacca 120 gatttttcaa cccctaaggc gattgatgac gcagctattg cggcgattca ggctggtaat 180 gccagtttct atacggcagc aaccggtatt ccggaattaa agcaggcgat tagtgaccgg 240 atatttgccc aagacggtat tcgttatgat catcgtcaaa tcgttgcaac caccggcgct 300 aagtttgctt tgtatgcctt atttcaggtt ttcttaaacc caggcgatga ggtgctgatt 360 cctgttccat actgggtttc ctacgaggaa cagattaaat tggcgagcgg cgtgccacat 420 ctggtcatgc cggcagtcgg acataaagtc agtgtcgatg atcttgaggc ggctcggacc 480 gataaaaccc gggcattgat tatcaattcg ccacaaaacc caagtggcgt tgtctatgat 540 cgcacggaac tgaccttaat tggcaattgg gcgctgaagc atcatatttt ggtagtgact 600 gacgatattt accgagatct gatttataac ggtacgactt acacctcaat gattagtatc 660 gatcccgata tcgcagcgaa tactgtttta atttccggcg tctccaagtc atatgcgatg 720 acgggttggc ggattggtta tgcggccggt ccggaaaagc tgattcaggc catggcgacc 780 tttattagcc acacgacctc taatccggca gcagtttccg aatacgccgc ggtggcagct 840 ttaactggcg atcagcaggt tgttgaaaag atgcgccgtg cttttgaaga acggctgaat 900 cttttctatg atcttctggc agatattccc ggtttcgata tgggagataa accgcaaggc 960 gccttctatc ttttcccgaa tattaagcgt gccgctcaat tgagtcatta tggtacggtt 1020 gatgatttta tcagtgcact gttgaccgaa accggggttg ccattgttcg tgctggacgg 1080 gcgtttggca tgccggatca tgcgcggatt agttattgta aagatttggc cagtctgaaa 1140 gaggccgccc ggcgtatccg ggagtttgtt ggtaaataat tattgaagtg gggagttaac 1200 gcatgacgga aaagattcgc attattgatg caaaagaaca tgtgaac 1247 13 650 DNA Lactobacillus rhamnosus 13 atgcaaagag cagaattaat caccgcgatt gtgacaccgt ttaacgaccg cgatgaaatt 60 gactatgata gtatgcaacg gttagtcgat catctcattg atcaaggcac tgacgggttt 120 gtggttggag ctacgacggg tgaagggcct acgttgagtc atgatgaaaa gatcaccctt 180 tacacccgtt ttgtggccat ggttcacggg cgcgcactcg tcattgccaa ttcagggtct 240 aacaacaccc gcgaaaccac tgattttacg catgaagtcg gtggaattgc cggaattgat 300 gctactttgg ttgtggttcc gtattacaac aagccggatc aagatggcat gatcgcgcac 360 tataccacgg ttgcggcaag tgcgcaaaaa ccgatcatta tttacaacat tccagggcga 420 accggcgtaa acatgttacc ggaaaccgtg gcaacgctgg cacaaaaccc catgattcaa 480 gggatcaagc agtgcggcag tctggcagca ctcagcgata tcatcgaccg aaccaaacac 540 gatgccttca atgtctggac cggcgaagat gctcaagcgc tgacgatcaa aacactgggc 600 gggatgggcg ttatttcagt tgcctcccac ctatatgccc atagcatccg 650 14 768 DNA Lactobacillus rhamnosus 14 ctacaagaaa ttttccaacc ccacaaccaa atgatccgct gcctgaacct tgcgaatggc 60 aacggcgacc ccttgcatga agctttggcg atcgaaggag tcttggcgga tggtgagggc 120 ttcaccggga ccgccgaaga ggacttgttc gtgggcgatg taacctggta agcggacggc 180 gtggaccggg acgtcatcaa tgcgttggcc gcgggcgtcg ttgtcgatgg tggacaatgg 240 cttttgggtg cgtccggcgg cgattttgtg cgcagtggcg atggcggtac ctgatggcgc 300 atcggctttg tcctgatgat gcatctcgat aatttcggcg tcagggaagt aggcggcggc 360 ttcctgcgcg aacttcatta agagaaccgc ggaaaggccg aagtttgggg cgattagacc 420 gccgatatga cgggcttggg cgagttcgat taagcggttt tgatcggctt gcgtcatgcc 480 gcttgtgcca acgactgggt gaatgcctgc tttgatcgcg gcttcaatgt tggcagcgac 540 ggcagtggga ttggtaaaat caacccacac atcggcaatg tcgggattga gctgatcata 600 gctcgtgagc acttttgtat cagctggtag tccatatttt tgggcatcag cggcagttgc 660 tttgggatca aaaacggcac ttaatgcgaa atctttttgt gactgaacca ttttgactgt 720 tttttgaccc atggcaccgc gaaaaccggc gacaagaacg tgaatcat 768 15 1277 DNA Lactobacillus rhamnosus 15 actaatgtgg atgacggcgt ggcgaacttt ttaacggatt tttttgagaa gtgagctttt 60 tccgtaaaaa gtggggtttc tggttgattg ttagcgaaac gtttgccacc atagagatgg 120 taaacgtttt tattttgcgg tcgtttgagg agggctttaa tcatgtatca tgcagcagct 180 gatcgttatg agaaaatgcc ggttcgccat gctggtaaga cagggttgat gttgccggtt 240 atttcgttgg gattgtggca gcattatggc aacttggatc catttggccc gcgacgctcg 300 gtgattttgg atgcgtttga tcgtggcgtt tttcattttg atgtcgctaa tcattatggt 360 aatggtgatc gtgaaccggg atttggctct agtgaaaggt tactcgggca gattctggcc 420 acggatttaa aaccgtatcg agacgaattg gtgattagta ccaaggtggg ttatgagatt 480 caccctggtc catacggtgt cgggacgtcg cgtaaagcag ttattcaagg cttgaatgat 540 tcactcaagc gcttgcagtt ggattatgtc gatatttact atgcccaccg atttgacgat 600 accgtggcct tggaagagac ggttaatgcg ctggatcaaa cggtgcgtga cggtaaggcg 660 ttgtatattg gtatttccaa ctatgatacg aagcagacca aagaagcaat tgcgatgttt 720 aaagatctgc acacgccttt tgtactgaat caatacagtt acaacatgtt taatcgcacc 780 gctgaaacgt ccggcttgat cgatgcatta aaagctgatg gtgccgggtt gattgcatac 840 ggaccgttat cagaaggctt gttatcagat cgctacctaa agggaattcc ggatactttc 900 aaaatccatc caaccaacaa ggccactttt gctaagggca aagaggctgt ggttaagcaa 960 ctaaatgcgc ttaatgaaat tgcgcatgat cgtgaccaaa ccctgagtca aatggccttg 1020 gcgtggttgt tacgggatcc ggttgtcaca agtgtgatca ttgggacgac ctcagttgaa 1080 caccttcagg ataaccttaa agcaacggaa catctgacct ttactgctga agagattcaa 1140 caaattgatg atattttaaa tgcttagttg acgtttggct gtaaaaggct aagcgtaagt 1200 ataaaaaaac ggcttcggag tgttttttga ctccggagcc gttttatttt tgaggaacaa 1260 tgcttgacag gtgctct 1277 16 964 DNA Lactobacillus rhamnosus 16 gcaatgacca cacaatccgg cttctaccca cgctggctgg cgctcacgag gagggacatt 60 aaaatggcaa aaatgtggaa acgcatgctc ctgccactgg tgttgttact attgatgata 120 ccgttaagca gctgtggcaa aagtgtggcg gatcgtgata ttttagcgaa cgccaaggca 180 accaatacga ttatttgggg cgtcaaggcc gatacccgtc tgtttggctt gatgaacatt 240 aaaaccggta aaattgaagg ctttgatgtt gatatggcca aggcgattac caagcagatt 300 ttaggcaaaa aagggaacgc ccagctggtt caggtgacca gtgatacccg cgtgccgatg 360 attaaaggtg ggaacctgga cgcggtgatc gctaccatga cgattacccc ggagcgccaa 420 aagattctgg acttttccga tgtttacttt aatgccgggc aaagtctttt agttaaaaaa 480 ggcagtccga ttaagtcagt gaaggatttg aagaaaggca ccaaagttat cggcgtgcaa 540 gggtccaatt cagttgataa tgttaaaaaa gctgctcccg acaccactgt tctgcagtta 600 gccgattatg cgcaggcgtt taccgctttg aaatcaggcc aaggtgatgc cttgaccact 660 gacaatggga ttttatacgg gatgtcagaa caggataaga actatattgt caccgggggc 720 accttcacta aagagccata cgggattgcg attaacaaag gccagaagcc gtttgtcaac 780 gcggttaata aggcgatcaa acaactcaaa caaaacggga cttatgcaaa gctaatcaag 840 aagtggttcg gcgatgtgcc aggattcagt cttaaggagg tggaataaca tgtggtcaat 900 tcttaccaat aattggaaca cctttctttc cggacttggt ttcacgttag cagcgagcat 960 ttag 964 17 1263 DNA Lactobacillus rhamnosus 17 ggatggtgca ggggcttagg cttctgtgcc tttttagaaa gaagcgatga aattgacaat 60 ttatgacttt gatcatgtta tcgatcgccg gggtacgttt agcactcaat gggattatat 120 tgctgatagg tttggccgta acgatatcct gcccttttcg atctccgata cagattttcc 180 agtaccagtt gaagtgcaag atgcgctaaa agaacggtta acacatccaa tttatggcta 240 tacacgatgg aatcatgcta cttacaaaga cagtattgtt cactggttcg agcgtgatgg 300 tcatacaaag ataaacccgg attggattgt ttatagccct agcgttgttt ttacgattgc 360 tacactcatt cgaatgaaga gcgatcccgg ggacggagtg gctgtgttta cgcctatgta 420 tgatgccttc tatggtacga ttaaacagaa cgatcgagtg ttgatcccga ttcgattagc 480 agctgcagat gaaggctatg tgattgattg ggatagtttg gcaacggtac ttgctgaaaa 540 gcagacaaaa atattcttac taacaaatcc gcataacccg acaggacatg tttttacaaa 600 atcggaatta gcacgccttt atgacttgtg tcaggcagcc catgttttct tgatctctga 660 tgatattcac cgcgatattg tttatccggg tcattcgtac gaaccaatga caaatgtcgg 720 cacaagtgat gttgcactct gctgctcagg gtcaaagaca tttaacacac caggcctgat 780 tggctcatat gccttcttac cagatcatga tgtaagggca caatttttga cggaattaaa 840 gcagaaaaat gctctgtctt ctgtaagcat ctttggcatg ctggcgcaaa ttgcggctta 900 taacggttca gaggattacg tggaacaact gactgcctat acaaaaaata atatggagtt 960 ggttgctagt tatttagagg aaaatttgcc ggaattgcag ttttcgttac cggatgccac 1020 gtacttagcc tggataaatg tgtctaaact gagattaacg tcagaggaac ttcaacatcg 1080 gttagtaaac ggcggccatg ttggcattat ggcgggcaaa acttatggtg ataccagata 1140 tctaaggatg aatattgcct gtccaaagaa gaagttagtg atggggctag aacgtttaaa 1200 gaagggaatt aggggataat atgctcttac tcagagaaat caaaatctta cgccgcctgt 1260 ccc 1263 18 1356 DNA Lactobacillus rhamnosus 18 atgactgatt gggtacttga tgacggtgga catggttcta ctggatgcgt acaatgacaa 60 caaaagcaag aaagcaggga tcattgatgg aagatttgcc aactgatatt gcaacgtttg 120 tggacacgca cttagttgat cgccataata gcaatgctgt gaagtgggac ggtctgaaag 180 aagaatttgg ccgggctgac ttgttgccta tgtggattgc cgacactgag tttaaggcgc 240 ctcaagcagt tttggatgca ttgacagttc gcgtcaagga agggacgttt ggctattcca 300 ttcgcccgca gtcttattac gaagccttca ttaactggca aaaggaacga catggcatta 360 cggttgaacc tgagtggatg cgttttggcg ttggcgttgt caaatcactg tatgcgatgg 420 tgaactggct gacagaacct ggtgatccgg tcctcatcat gcagccggtt tattatccct 480 ttatgaatgc cattaatgat cttggacgta aagtcgtatc agttgacttg caattaaccg 540 ctgatggttg gcgcatggat tttgaccaat tagaaaagac cttggcggcg aatgaaatta 600 aagcgatgat tctgtgttca ccgcacaatc cggttggtcg gatctggacc cgagatgagt 660 tagaacaact ttttgccatc acaagtcggt atgatgtgac agtggtttct gatgaaattc 720 acggtgatct tgaagtgagt gggccgaagt ttacatccgc tttacaggtc gctgaaggta 780 aagctcgaaa aaagcttgtt gtgctcaatg cgccgtcaaa aacatttaat ttagccgcct 840 tgctgaattc acacattatt attcccgatc aagcgttgcg tacgagttat gatgccttca 900 ttaagcagct gcatccggtt gatacgagct tgatggggca agtggccggt gaagctgctt 960 atcggcatgg cgctgcttgg ttagatcagg tcttacaagt ggttcgctac aattatcggc 1020 aactgcaagc tggtttagcc gcggcggccc cacaagcgac cctggccgac ttacaaggga 1080 cttatttggc ttatgttgat atcggtgctt atgttgcgcc aagtcagatc aaagactttg 1140 ttgaaggtgt gtgcggattg gctgttgatt atggtgcatg gttttcaccg caaacggcaa 1200 cttatattcg tttaaattta gctactgatc ctaagcttgt tgccgaggcg attaaccgac 1260 taaccactca tttggcacag cagccgcagc ggtgatcggg acaagaatta aattgccttt 1320 ttcaagataa aactcgaatt caaagagacg gaatgg 1356 19 1254 DNA Lactobacillus rhamnosus 19 tatagcacgc caagccaagc agctcgcagg tggtttttgg gttaaagctt ctattattga 60 ctgactttct ttgagtttca tgaaaatgat cggcgaaaaa tgtctattat tgtcattttg 120 ttctatacta atcgtgtact gaacatttaa ggattaccta ggaggtattt ttacatgtct 180 gttaaactta ctgctggtca gttagagcat ttgaagcaat tgtccaatga caacaacgtc 240 atctcggctt tagccattga ccaacgcggt tccctgaaga agatgcttgc agctgcagcg 300 aacaagccag ctgacgaaac cacgattgtt gatttcaaga aagctgtttc tgaagaatta 360 accaaatacg ccagcgcgat tctgcttgat ccagaatacg gcctgccagc tgccaaggtt 420 cgcgatccta agtccggcct cttgctttcc tatgaaaaga ccggctacga tgcgactgaa 480 cctggccgtt tcccagattt gattgataac caaagtgctt tgcgcatcaa gaacgaaggc 540 ggcgatgcag tcaagttctt actgtacatt gaccctgacg aacctgatag tatcaacgat 600 cgtaaatatg cgtttgttga acgggttggt gctgaagcta aggctaatga tctgccactg 660 ttcttggaat tagtttccta cgatggcaag accaacgaaa ccggcaccgc tgcatgggca 720 aaagcaaagc ctgaaaaagt tatcaagatc actaaggaat tcagcaaggc gcaatacaac 780 gtttctgttt tgaagcttga agttccggtt gatcaaaagt ttgttgaagg ttacaccgat 840 gaaggcgtaa cgccggttta cagcaaggaa gaagctgcta agtactacaa ggctcaatcc 900 gatgcaaccg atttgccatt catcttcctg tccgctggtg tttccaacga attgttcctt 960 gaagaactca aatttgctaa ggaagccggt tcaaccttta acggtgtgct ttgcggccgg 1020 gcaacctgga agccaggcgt taagccattt gctgctgaag gcgaagctgc cggcaagaag 1080 tggctgcaaa cggaaggtaa agctaacatc gatcgtttga acaaggtttt ggctgacact 1140 gctactcctt ggacagacaa ggttgaaggc taattctttt taactaatta atcgttcaaa 1200 aaccagccac agatgcggct ggttttttat atggtgagcg tgagccagcc cgct 1254 20 1482 DNA Lactobacillus rhamnosus 20 tctggtttca atattaaaca gccttctggc aaaaaggaga agaatatatg tctatcatta 60 ctgatgtatt ggcacgcgaa gttttagact cacgtggcaa ccctactgtt gaagttgaat 120 tgtataccga agatggcggt ttcggccgcg cattagttcc atcaggtgct tcaaccggtg 180 aacatgaagc cgttgaattg cgtgatggcg ataaggatcg ttttggcggc aagggtgttt 240 tgaaggccgt tgaccacgta aacaatgaaa ttgctaaggc tgtgattggc cttgacgtca 300 ccgaacaacg cttgattgac caaaccatga tcgatcttga tggcacgcct aataaaggca 360 agctcggtgc caatgcgatt ttgggtgttt ccttggctgc tgcccgtgct gcggctgatg 420 aagttggtct gccattgtat caatatcttg gcggcccgaa tgctcatgtt ttgccaacgc 480 caatgatgaa cgttcttaat ggtggtgcac attcaactaa caccgttgac ttccaggaat 540 tcatgatcat gcctgttggt gccaagagtg ttcgtgaagc cgttcggatg ggttcagaaa 600 ccttccacgc attgcaggca ctgctcaaga gcaagggtga catcactgct gttggtgatg 660 aaggcggctt tgcacctaac ttgaaggata acgaagaagc tttcgaattg cttgttgaag 720 cgatcaagaa ggctggctac aagccgggtg atgacattgc tttggccttc gacgttgctg 780 cttcagaaat gtacgatgct gataccaaga cgtacacaac caagtggtcc aaccctgaca 840 agaagtacac aaccgaagaa tggaccaaca tgattgacgg ctacattaac aagtatccga 900 tcgtttctgt tgaagatcca atcgatgaaa acgactggga aggctggcag acattcaccg 960 agaagatggg cgacaaagtc caaatcgttg gtgatgacct gtttgttacc aacaccgatt 1020 acctgaagaa gggtattgac atgggtgttg ctaactccat cctgatcaag ttgaaccaaa 1080 tcggtacatt gacagaaacc ttcgaagcaa tcgaaatggc caaagaagct ggttacacgg 1140 ctgttgtttc acatcgttca ggtgaaaccg aagataccac gattgctgac ttggttgttg 1200 caaccaacgc cggtgaaatc aagactggtt caatgagccg gactgaccgg attgccaagt 1260 acaatcagtt gatgcgcatc gaagatcaat taggtgctca atcacaatac aagggtcgca 1320 agtccttcta caacgttaaa gcaattgact aattaacgct tgacgttaac atgaaaagca 1380 cgtcacttca aatggtggcg tgttttttct attcttagct taagcaaaag atgaacttgc 1440 tcacgctttg tgactgaggg ctgtctggtg ccggtgcaag ca 1482 21 2407 DNA Lactobacillus rhamnosus 21 tgcttgcacc ggcaccagac agccctcagt cacaaagcgt gagcaagttc atcttttgct 60 taagctaaga atagaaaaaa cacgccacca tttgaagtga cgtgcttttc atgttaacgt 120 caagcgttaa ttagtcaatt gctttaacgt tgtagaagga cttgcgaccc ttgtattgtg 180 attgagcacc taattgatct tcgatgcgca tcaactgatt gtacttggca atccggtcag 240 tccggctcat tgaaccagtc ttgatttcac cggcgttggt tgcaacaacc aagtcagcaa 300 tcgtggtatc ttcggtttca cctgaacgat gtgaaacaac agccgtgtaa ccagcttctt 360 tggccatttc gattgcttcg aaggtttctg tcaatgtacc gatttggttc aacttgatca 420 ggatggagtt agcaacaccc atgtcaatac ccttcttcag gtaatcggtg ttggtaacaa 480 acaggtcatc accaacgatt tggactttgt cgcccatctt ctcggtgaat gtctgccagc 540 cttcccagtc gttttcatcg attggatctt caacagaaac gatcggatac ttgttaatgt 600 agccgtcaat catgttggtc cattcttcgg ttgtgtactt cttgtcaggg ttggaccact 660 tggttgtgta cgtcttggta tcagcatcgt acatttctga agcagcaacg tcgaaggcca 720 aagcaatgtc atcacccggc ttgtagccag ccttcttgat cgcttcaaca agcaattcga 780 aagcttcttc gttatccttc aagttaggtg caaagccgcc ttcatcacca acagcagtga 840 tgtcaccctt gctcttgagc agtgcctgca atgcgtggaa ggtttctgaa cccatccgaa 900 cggcttcacg aacactcttg gcaccaacag gcatgatcat gaattcctgg aagtcaacgg 960 tgttagttga atgtgcacca ccattaagaa cgttcatcat tggcgttggc aaaacatgag 1020 cattcgggcc gccaagatat tgatacaatg gcagaccaac ttcatcagcc gcagcacggg 1080 cagcagccaa ggaaacaccc aaaatcgcat tggcaccgag cttgccttta ttaggcgtgc 1140 catcaagatc gatcatggtt tggtcaatca agcgttgttc ggtgacgtca aggccaatca 1200 cagccttagc aatttcattg tttacgtggt caacggcctt caaaacaccc ttgccgccaa 1260 aacgatcctt atcgccatca cgcaattcaa cggcttcatg ttcaccggtt gaagcacctg 1320 atggaactaa tgcgcggccg aaaccgccat cttcggtata caattcaact tcaacagtag 1380 ggttgccacg tgagtctaaa acttcgcgtg ccaatacatc agtaatgata gacatatatt 1440 cttctccttt ttgccagaag gctgtttaat attgaaacca gattaatctt ggtagttagc 1500 caaggcgatg aaactgtcag gatccatcga agcgccacca actaaaccac catcaatatc 1560 aggcttagcc attaattcct tgacgttcgc tggtttaaca gagccgccgt aaagaatccg 1620 aacagcatct gccgtatctt tattatacaa cttctcaacg gttgcacgga tgtgagcaac 1680 aacttcttgt gcttgatctg cagttgctgt tttaccagtg ccgatagccc agattggttc 1740 ataagccaaa accgaaacct taacttggtc ggcacttaag cctgccaaag ctgcttcgat 1800 ttgagaagca acccagtctt cggtttgacc ggcttcacgc tgagccaaac tttcaccaca 1860 gcagataatc ggcaaaagat tgttcttaaa gatggcctta gccttcttgt tgatatcttc 1920 gtcggtttcg tggaaataac cgcgacgttc actgtgaccg ataatgacgt aatcaacgcc 1980 catttctttt aaggctttcg ggctggtttc gccggtaaaa gcaccttcgt cttcaaagta 2040 gcagttttcc gccgctgtct tcaaaggagt accttctgca ccggcaacca gtgtcgttag 2100 atcaatggca ggtgcgccaa tgactgtttc aactttgctt gcatcaggta acttaccctt 2160 aacagcatct aagaaggctt gcgtctcctt aggattctta ttcattttcc agttaccagc 2220 aatgaatggt gtccgcatga cataccttcc tttcattatg taccgacatg catcatgcat 2280 gtcgataatg actgttagat cagcatcact aacaattact tgtcagaaat ggctgcaata 2340 cctggtaagg tcttgccttc aaggtattca aggctagcac cgccaccagt ggagatgtgg 2400 gtaatct 2407 22 1407 DNA Lactobacillus rhamnosus 22 tgttgatggt aagcttaatt gaaacatcat ctttaggaaa atgaaggagg tcatatcttt 60 tggctaaatt aatcgtttca gatttagacg ttaaagacaa aaaagtcttg attcgcgttg 120 acttcaacgt gccgatcaaa gacggcgtta tcggtgatga caatcggatc gtggcagcat 180 tgccaaccat ccaatatgtc attgatcacg gcggcaaggc aattctgctg tctcaccttg 240 gccgggttaa gaccgaagaa gataaggcaa agctgacctt gaagcctgtt gcagaacgcc 300 ttagtgaatt gctgaagaag ccagttacat ttgtaccagc tacccgtggt aaagaattgg 360

aagacgcgat cgcaaagtta aatgacggcg acgtactttt gatggaaaat acgcggtttg 420 aagatcttga cggtaaaaaa gaatccggca acgatcctga actcggcaag tactgggcaa 480 gcttaggcga cttgtttgtc aatgatgcct ttggtaccgc tcaccgtaag catgcttcaa 540 acgttggtat tgcctccaac atgaaacaaa ctgctgccgg cttcttgatg gaaaaagaaa 600 tcaagttctt gggtgacgct gtggacaatc caaagcatcc attcatcgca attttgggtg 660 gtgctaaggt ttccgataag atcggtgtga ttgaaaacct ggttcctaaa gctgacaaga 720 ttctcatcgg cggcggcatg acttatacct tctatgctgc caagggtatg agcatcggta 780 attcactggt tgaaaaggac aagatcgact tagctaagaa gatcatggac caagccggtg 840 acaagctgct tttgcctgtt gattctgtgg ttgccccaga attttctaac gatgcaccgc 900 ataaggttgt tgaaggcgac attccggatg gctacatggc gttggatatc ggccctaaga 960 cgattcagga attcaaggat gcacttaagg gtgccaagac agttgtctgg aacggcccaa 1020 tgggtgtctt tgaaatgagt aactatgctg aaggcacact tgaagttggt cgtgctcttg 1080 gtgatttgaa ggatgcaact acgatcatcg gtggcggcga ctcaacagct gcagctaagc 1140 aacttggcat tgcacctaag attacccaca tctccactgg tggcggtgct agccttgaat 1200 accttgaagg caagacctta ccaggtattg cagccatttc tgacaagtaa ttgttagtga 1260 tgctgatcta acagtcatta tcgacatgca tgatgcatgt cggtacataa tgaaaggaag 1320 gtatgtcatg cggacaccat tcattgctgg taactggaaa atgaataaga atcctaagga 1380 gacgcaagcc ttcttagatg ctgttaa 1407 23 1178 DNA Lactobacillus rhamnosus 23 ccacaaactc gattttaact ggggcaaccc gttagaataa accttatttc ctaaaggagg 60 aaattttagc atgactgtta agattggtat taatggtttt ggccgtatcg gtcgtttggc 120 attccgtcgt atttacgaat tgggtgcaaa gagcaatgac attcaggttg ttgcgatcaa 180 cgatttgacc agcccaacca tgctggctca cttgctgaag tatgattcaa cccacggtac 240 tttccctggt gaagttagtg caaccgataa cggtattgtc gttgacggta aagaataccg 300 tgtctacgca gaaccgcaag cccagaacat tccttgggtt aagaacgacg gcgttgacta 360 cgttcttgaa tgcacaggct tctatacttc tgctgaaaag tcacaagctc acttggatgc 420 aggcgcaaag cgtgttctga tttctgcccc agctggcaag attaagacta tcgtttataa 480 cgttaatgat gacaccttga atgcagacga caagatcgtt tctgcaggtt cttgcacgac 540 caactgcttg gcaccaatgg cttacttcct gaaccaggaa ttcggcattg aagttggtac 600 catgaccacc gttcatgcct acacctcaac tcagatgttg cttgacggcc cagttcgtgg 660 cggcaacctg cgtgctgcac gttcagctgc tgctaacacg attcctcaca gcactggtgc 720 tgctaaggct atcggtttgg ttatcccaga attgaacggc aagttacagg gtcatgcaca 780 gcgtgtttct gttgttgacg gttccttgac tgaattggtt tccatcttga agaccaagaa 840 cgttacggct gaccaagtca acgaagctat caagaagcac accgaaaaca accctagctt 900 tggctggaac gaagacgaaa tcgtatcttc cgatgttatc ggtacgacat acggttcaat 960 cttcgatcct actcagaccg aagttacaac tgccggtgac tatcaattag ttaagacggt 1020 tgcttggtac gataacgaat atggctttac ttgccagatg atccgtacct tgctgaaatt 1080 tgctactctc taatccggag taacgctttt ctaaccgcaa catccgaagc ggagggagct 1140 ttactccctc cgcttttttt ggaaagacca ttaaaagg 1178 24 1074 DNA Lactobacillus rhamnosus 24 tcattcacaa atgttaaact taagttgtta ctaatttcac ttttgattat aattggaatg 60 taatcggtta caacgtgact gttgaataat ttcacatttg tgatttcgag gtgacatcaa 120 tgtcaaattt gcctaaacgg tatgatcgtg caactttagt caagatatcc gatctttact 180 acatgcacgg tctaactcaa caagaaatat ctaacattgc ccatattcac agaaccgaaa 240 taagtcgaat tctgaaggcg gctagggatg aaggcgtggt atctatcgca atcaatcccg 300 aaaccaccgc cgtcagccaa cttattgatt tttttaaaca aaaatacaat ttgcgagagg 360 ccgttatagt cccggcttct gaaaatggag gcaatgagtt aaacgctttg agtgtttacg 420 catcaatgtt tttatcaaga atcattaaaa gtggtgacgt aattgggtta agttggggtt 480 caacgctttc aagtgttatc agtcaatttc caacagataa aggccttcgt gatattaaag 540 ttgttccgct ggtgggtggc ccaatgggaa gaataccttc gaactatcat gtgagctatc 600 tgacacaccg gctcgccaat cggctaaacg gaacagcgtt tgtcttggat tcccctgcct 660 ttgtcagatc aaaagcgctt cgtaaagagc ttctcgccaa ccccaacacg caagaaatct 720 taggattgtg gaatcgtgtc aatatcgcga tctttggcat cggaagttca ctaattacag 780 attctcctga ttggcaagcg ttctatgaga acacaaactt caagtcttat ttcagtgccg 840 atatggtcgg agatattctt tcacaccctt tcgacaagga tggaaaatta gctcgcgata 900 tcgactccat tcttgttgcc tttccttttt cggcattgcg aaaagtacca cactccgttg 960 gaattgcttt tggggaagaa aaggtaaatg ctatccttgc cgctcttcga ggtggtctct 1020 taaacacttt aattactacc gaagcaacag caaaggcaat caaagagttg tcct 1074 25 1025 DNA Lactobacillus rhamnosus 25 gactcggctt gtttcacttg tggtaccttt gaaagtcgaa agtcattatg gaccgacctg 60 gtttgatgcg aaataaggag aactcatgcc tgaattacct gaagttgaaa cggttcgccg 120 ttccttgtta ccgttagtca aaaataaaaa aatcaccgcg attagcacaa actgggagaa 180 aatcctaatt aatggtctgg caacctttca aaaacaggtt gtgggcgctg ctgtcaacac 240 gattgatcgc cgcggtaagt atttactgat tcggcttaac aacggcatga cgattgtcag 300 tcatttgcgc atggaaggcc gctattacgt tgtttcggat gccaaaacgc cgctggataa 360 gcatgatcat gtgacgttta cctttcagga tggcagccag ttgcgttacc gcgatctgcg 420 caagtttggc cggatgcggc tgattcacac gggtcaggag caattggtgc cagcgctggc 480 caagctagga ccggagccga ctgctgctac ttttagcgaa agtgactttg cccagaaact 540 aaaacggcat cataaagcca ttaaatcggt tttgctggat caaactgttg tggccggaat 600 tggtaatatt tacgcggatg aggtcttatg gctcagcaag ctcaatccgc tgcagccagc 660 taatacctta accaaggcgg aggttcacac gttacatgat gcgattatca aggaattgga 720 cgacgccatt gccgctggcg gtaccagtgc ccatacttac gttgatgcaa aaggcaaccg 780 cggttcgttt caggacgctt tgcatgtcta tgatcgtgaa gggacgcctt gtgatcgttg 840 cggcaccacg attgtcaaaa ttaaagtcgg tcaacgcggc acgcattatt gcccgcattg 900 ccagccgtta cgtcgaaggg ggcaactggc atgacctttt tgttagggct gacgggcggc 960 attgcgtcag gcaagtcaac ggtaagccgg acatttaaag cagctgggtt tccagtggtg 1020 gatgc 1025 26 7755 DNA Lactobacillus rhamnosus 26 gattcagcag caagcacgag tgatgcaacc gattcgaaat cgctagcgac agattcagca 60 gcagtcaaac cgcaaacggt gacccaagaa gaccgctcac ttgcatccgc agctgttcag 120 acaacttcgg ccgcagcatc atcggcggct tcatctgcat cgtcacaagc atccttagca 180 gcacaatcgg caacaacaac tcaggtcaac acgcaagctc cggccaatgc aacagctgct 240 gaaaatacgc agaccattgg cgactatacc tacagtcttg atacggcaaa cggtacagca 300 acggttaccg gccgcgccaa cgccaatgtc accgatatta acattggcgc gtctgttacc 360 tataatggcc aaacttttaa agtgacggcg attaacaatg gcgcttttgc aacgcttaat 420 aatttgggta atgttaacgt ggctgatact gtcacgtcca ttggcgaaaa tgcttttgca 480 tacagtcagt ttacgggcaa cattacaatt gaaaatgcag aaagtctcgg caaagccgca 540 tttgccggaa ttaaggcagg gtcagtcacg ctgaagaaga cggctaacat ttcagagcgc 600 gccttttatt ttgctaacgt gaaagatata acgattgcag acgctcagac tatagaggca 660 caggcattct ttagtcttac agcttcatct ttaaaaattg atggtcaagc cgatattggc 720 gagtctgctt ttgaatctgc caatattgct ggggatgtca ccgttaatcg tgcaaagacg 780 atcggaaaaa atgcattcgc cactttaaag gcgcattcgt tgacgttgga caatctaacg 840 acgcttgatg aaggtgcctt tggtggtgct gtattcactg gtaatcttac aattaatggc 900 gcaaaaacta ttggcaagtc cgcattcgct tatgacaaag taaccggaga tgtcacggtg 960 agcggctcac ctgccattgg tgaaattgcc ttttatggga ttcaggcggc gacaatcacg 1020 attgatggcg cccaaaccac tttcgataag accgcgtttg gatttgccac ggcggatcac 1080 gtaacagtca atgtagccac ccttgatcat gaggcatttt atcatcttta tactgaccaa 1140 ctaacccttg gtcctgatgt tcgagatatt acagatggcg cttttcagtt tattcaaaat 1200 accaaaaaaa cagagagtaa cgctgaaaat gatactacgg acgttcaaat agcagtgttg 1260 aacctgccag ctaatgtcaa aacaatcagc ggctcggctt tttatggttc gaaagttaaa 1320 acgatcgcag ttgcagaaaa cagtcaattg acaactctcg gatttcaggc gtttgcattt 1380 tccactgcta cggcgattaa cttacccgat tcgctggagc agattggtga tcaggcgttt 1440 tatggcggga agcttgtgaa agtagcgttt ggacccaaat tgcaatcaat tggtaatctg 1500 gcctttactg aatttggccc gttggaaaat gttgacttta ctcgggccac ggcgctcgaa 1560 acaattggtg atagtgcgtt tgcctacaat acgattaaca atgcgatcac gttaccacct 1620 aagctattaa cgatcggaaa tgcggccttt gtcgggaata aaattccaaa actggttctg 1680 gatgatcggt taaagacaat cggtgacact gcttttggct ataaccagat ccaggacgca 1740 ctcgatgttc ctgacagcgt gaccgacatc ggtaagtatg catttgttta caactctatc 1800 agtaatttaa cgttaggaaa tggactgaaa acgattggcc aggaagcatt tgaagccaat 1860 gttattttaa atgcgcaaac gataccaagc agtgttacga gtattggcgc caaggcattt 1920 aaggctaatt tgattcctaa agttgttgtt gagggcacgc caaccattgg caatgatgct 1980 ttttcgaata accggatcac tgtgctgaaa gcagcgacag ccaagccgac aaccccggat 2040 gctttggagc agaatgccga tgcctataca gactcggcgc acgtaagtct aagtgatttc 2100 tttgatgtgg ccatttccgg agtgacccac caaaacatcg ttgtttcaaa catcaaagga 2160 gttaatggcg ctacggtaac ttttgatacg gcaagtaagt cgtttaaaat gccagctaag 2220 acgcagggat ttaatttcga ttggtctttg aaagggcaag acggtgttac ctacacaggc 2280 cactacattg ttcatctcga tgatccagtg attcgtgccc atgacatcag cctatttact 2340 ggccaggtat ggaagccgga actgaatttt gaaaacgcga ttaaaagcga cggtactgag 2400 gttccattga gtgagttgac ttggtcagtg acggatgaaa aaggcaatgt ggtagcatct 2460 aaggataaaa atggggttgt caccggtcat gtggataata gccagccaac gacttatgtg 2520 gtcacctata cctatggtgc agaaagcggt tctgctaaaa tcaattacaa gcaacggtta 2580 gcggcttcat atgctttgac tggtactcag accgtcaccg caacaggaag tccgattacc 2640 gtcgatgtct cccaatttgc actgagtttg ggtgacggtt ttgatgcggg gaaattagaa 2700 ttaagtgatc ttaatttctt tgatgccgat ggtaagccgg tagccgcaga tgctctgatt 2760 aaaactggcg tctacagtgt ggaattatca gaagctgcgt gggcacggat cgccaaatta 2820 acaaatgatg aaggccagtc tgctgcgggt tatgatttta ccggaacaag tacggcacaa 2880 ttaatcatcg gtctaacggc tacaggtcat ttgagcgata gcggttttgt ttatgacggc 2940 aaaacaacag ccagtcagtc taaagatttg gcggtcacgg tgacattgag tgatggcact 3000 cagaaagaaa tgaacctgac ctcagaagac ttctcattag ttgaaaaaga ttcagctaac 3060 gttggcacgt accattattt gttaaacagc gttggtttcg ctcgtttaca agcgttacta 3120 ggtgataccg tgacgattga tcaaactgcc atcaatcaaa attccggaaa aatcaccatt 3180 acgccagcac cggctacagt taatagtaat agtacggatt ttgaatatga tggcaaaacc 3240 aaggccagtg aggctaaagg tattcaagct acagtcaaac taggcgaaac tggaaaaacg 3300 attgacctga cgtcagctga cattgttgtt gagaatgatg gtgtagatgc aggcaagtac 3360 agctatgagc tgagtgacgc tggtaaagct aaattgcaag ccgcaactgg aaataactat 3420 cagttgactg cagacgatct ggctaaagtc acgggagcta tcacgattac gccagctacc 3480 acctcagttg atagcaatga cgtttcattt gaatacgatg gtaagaccaa ggccagtgaa 3540 gctgcaggta ttcaagccac aatcaagctc gacactggta aagttgtaga cttgaccgcg 3600 gccgatatta tcgttaccaa tgatgacgta aacgctggtc agtacagcta tcaactaagt 3660 gatgctggta aggctaagtt acaagccgca actggaaata actatcagtt gactgcagac 3720 gatttggcca aggttgctgg aactatcacg atcacgccag ccgttaccac agttgatagt 3780 agtgacgtat cattcgaata tgacggcaag accaaggcca gtgaagccaa gggtattcaa 3840 gctacaatca agctggacac tggtaaagtt gtagacttga ccgcggccga tattatcgtt 3900 accaacgatg acgtaaacgc tggtcagtac agctatcaac taagtgatgc tggtaaggct 3960 aagttacaag ccgcaaccgg aaataactac caactcacgg cagacgattt agctaaagtc 4020 atgggaacca tcacgatcac gccagccgct gtcacagcag acagcaatga cctttcgttc 4080 gaatatgatg gtaaaacgaa agccagtgaa gccaaaggta ttcaagccat ggtaaaacta 4140 ggcgagactg aaaaaacggt tgacctgacg tcagctgaca ttgttgttgc caacgatgac 4200 gtaaacgccg gtcagtacag ctatcagcta agtgatgctg gtaaggctaa gctgcaagct 4260 gcaactggaa ataactatca gttgactgca gacggtttgg ctaaggttgc tggaacaatc 4320 acaatcacgc cagctaccac tacagcggat agcaatgacg tttcatttga atacgatggt 4380 aagaccaagg ccagtgaagc caagggtatt caagccacaa tcaaattagg cgaaattgaa 4440 aaaacggttg acctatcgtc agctgacatt atcgttgcca atgacggagt aatcgttggc 4500 aaatacactt acagtctgag cgacagcggc aaatctaaat tacaggcggc aacaggaagt 4560 aattatcagt taacgacaga agttttggat aaggtttcag gaagcattac aatcacccct 4620 gctggagcaa tcgcaacagg caaggatgct cactttgagt acgatggaaa aacgaaagcc 4680 agtgaagcta aaggcattca agcgattttg accattgacg ggactgaaaa gactgttgac 4740 ctgaccgcgg ctgacattgt tgttgcggag gatggcgtag atgcaggcaa gtacagttat 4800 cgactgagcg atgctggtaa atctaagtta cagagggaag cagggagcga ccatcagcta 4860 accgcagacg acttggctga agtcacggga actatcacga tcacgccagc cattgccaca 4920 gcagatagta atgacgtttc atttgaatat aatggcaaga ccaaggccag tgaagctgaa 4980 ggtattcaag ccacggttat gctgggtgag tctggacaag ttgttgctct aacatcggct 5040 gatgttgttg ttgtgaatga tggtgtagat gcaggcaagt acagctatca gctgagtgat 5100 gctggtaaag ctaagctaca agccgcaacc ggaaataact accagctcac ggcagacgat 5160 ttagataaag tcacgggaac catcacgatc acgccagcta ccaccacagt tgatagcaat 5220 gacgtttcat tcgaatatga cggcaagacc aaggccggtg aagctaaggg tattcaagtt 5280 acagtcaaac taggcgaaac tgaaaaaacg gttgacctga cgtcagctga cattgttgtt 5340 gccaacgatg acgtaaacgc tggtcagtac agctatcagc taagtgatgc tggtaaggct 5400 aagttacaag ccgcaactgg aaataactac cagctaactg cagacgatct ggctaaagtc 5460 acgggaacca tcacgatcac gccagccgtt accacagcag atagcaatga cgtttcattc 5520 gaatatgacg gcaagaccaa ggccagtgaa gctaagggta ttcaagttat agtcaaacta 5580 ggcgaaactg aaaaaacggt tgacctgacg tcagctgaca ttgttgtagc caacgatgat 5640 gtaaacgctg gtcattacag ctatcagcta agtgatgctg gtaaggctaa gttgcaagcc 5700 gcaaccggaa ataactatca actaactgca gacgatttgg ccaagatcac tggaaccatc 5760 acgattaccc cagccgttgc cacagcagat agcaataacg tttcatttga atataacggc 5820 aagaccaagg ccagtgaagc tcggggcatt caagccacag tcaaactagg cgaaaatgga 5880 aaaaccgttg cgctaaccgc ggctgacatt gttgtcgtca atgacggggt caatgctggc 5940 cagtacgact ataagttaag tgctgctggt atgacaaagc tacgccaggc aacaggaact 6000 aattatcaat tcaaaaagga ggacttaacc aaacttggcg gcacggtcac gatcacgcca 6060 gctacggcat tagctgatct gaatgatgtt tcatttagtt atgatggaca aactaaggcg 6120 agtcaggcac acgacttaac tgccaacatc aaacttggta ctaaggttgt ttcggtacat 6180 ctgaacgcca cagacattct tgtaaccgat gatggtgtgg gcgtaggtca gtaccaatac 6240 aaattggatg ctaacgggat cgctaaatta cgtcaggcat caggtgataa ttaccaattt 6300 gatgccaaag tcttggcggg attgactggt acgattacaa tcaaaccggt taccggtgcg 6360 gtgacagtta atgacacatc ttttgtttat gatggtcata ctaaagcaag tgctgccgcg 6420 ggattacagg caagtcttta cctgccgcaa gccgaggcca aagcaacgat acaactgaca 6480 cgggaagata tccttgtgac aaatgacggc acagcagcag gtacgtatcg ttatcggttg 6540 agccaaaccg gtatcgccaa gttacagaag gctgttggca agaactacga gttagatcaa 6600 gatgaattgg cgggattgac cggcaccatt acgattacgc cgctgacggt gaatgccaca 6660 gttaatcatg gtcagttcca atacaacggt gtcactcgtg caagtcaagc aggcggatta 6720 gcgataactg tccaactgcc agaaaagtct caaaagatcg ccttgacgaa cacagatatt 6780 gcagttgaaa acgacagcgt caatgtcggg acgtacacgt atcatttgac agcaagcggg 6840 ctggctaaat tggccgtagc gattggtcct aattatcagg ttactgatca aacgttcagc 6900 ggcaccatca ccattacacc agcgcctata tctgcaacgc tcagtggtct tcaaaagaaa 6960 acttacgatg gccagccagg cgctttgaat gacgactatt atcggttagt tttgggtgac 7020 ggaactgaaa ttcagcttca agccggcgat ctgatctttg tagacggtca agctcctgtt 7080 aatccgggaa gctatgcggt agctctcagc acatctggcc tgcaacgaat caaggcgtcg 7140 ttgccaaata atctgttgaa aaatgttaac acgcagcagg ctatttttga gattgttgcc 7200 ttgccaagtc ctgatcccgg gaccggaaca acgccggata cgccggatca tcacttgccg 7260 aatacaggta ctggcaccca acagtccgag atttccacgc ataatggaac gaaacatcga 7320 cttccacaaa caggcgatac ccagtcacaa acactaagcc tcatgggatt gttgctggca 7380 acgatgagcg gcttattcgg attagctggc cggaaacgga aagcgcaccg ttaaacgttt 7440 tgttagaaat gtagtgatta aaaagatcct atcacgatga gttctgctca tgtggtggga 7500 tcttttgtta tggcaaaaac taggcgcaaa agcttacagt ggtaccgctg cgccttgggt 7560 taaccctgat ttgattttgg caaaagccgg gtctgttagg aaagcactga tgagttgccg 7620 catattgatg ttactatcct gaatctccgg catgtttggc gtaatgcttg tgcctgtcac 7680 agtaagattg tactggctgg cgagactggt gatagcttgc ttggactgat acatgttgta 7740 gagtttaacg gtttc 7755 27 4645 DNA Lactobacillus rhamnosus 27 tagggggtca aaaatgggaa ccaaaatagc cgttaaaatc aacaagtggc aagtgtagct 60 caagccagca gcagtgcgag cgatggtcaa gccaaagcaa gcaggggcta atgtggcaac 120 gaccactaat agtaaaattg gcggcagtca aagtagtgcc aaggcagcca gtgcgtttaa 180 aagtagtgct agcgttgaaa gtagtggcca gatcaaaagc actagtttag ccagtgctgg 240 cagtaacggc gaaaaagcga ccagcgctct aagcagtagt gcagttgatg ccagcgatgg 300 tcgtgcgagt cagggtgttg gcggcacgtc aagtggtagt tcagatacta cgagtcaggc 360 aaatgaaggc aacagcgccg ccagtgtaac aagtgcaagc gccaatagtg cctctgcaac 420 aaatacatct gaaggtcaaa ctccagttaa tgaagcggta tcaaacgatg cttctagcgc 480 cgatgtcagc accgcgtcag agtttgatgc agccatggcc gattcaacgg taagtgtcat 540 caacgtacag tccgactttg ttatggatgt tagtggtgat cgccaatcgt atgcttatcg 600 gccaaaccta attattaatg gcaataacca cacaattgat tttcaaaaga agtatttcga 660 agctgatcct acaagtagtc agaatgaatc atttaccatc aacgatttaa atatgtacgg 720 ttacagttgg tggggcccgg ttactatcaa gggcagtaag ccgaaagacg gcatcgatca 780 ttcggtagtg ttcaataatg tcacatacac aggtgcacaa ctgatgtatg gcatttatac 840 aaaagccttt attaagggga atacaaagat tcagtcagtg ggcagttatg tttccccgct 900 ggacggatca acccagacaa cccaaggctt aggcaaccag caaaactttc aaattagtta 960 tttagaggtt ttgcctggcg ctacttacac ggggacaact actggtggga ctaacgttga 1020 agtatatgat ggcggttcat ttattgttga caagggagca accgttaact tacaacgcac 1080 ggatgcaagc aaatcgaatg aacgtggtac gaatgcattg attgatacac agggaggtaa 1140 cgttgagttt aaggatggat caaccgttat ccttaataaa aatgcacttg tgaaagatgg 1200 ctttgcacca atctatattg aagacggtgg taatctaacc gttgataaga atgcaacggt 1260 atccattacc ggtgcaactg gaaacatccc ggtaagaatt gacggtaccg gaactgtcaa 1320 cctcaacgaa ggatcgcaca tgacgatcac tcaaaatggt gcgcctaaac ttggctatgg 1380 ctttatcaat attaaaggta ccggaggctt cttcgttgca agtggcagca ctttggatct 1440 taatgtaacg ggtacaggga caaagagtgt caatgcaatt aatgtagcaa atgacggtca 1500 actgagtttt gcacaggatg ctacggccaa cttaaccatt gacggtggca cgggcgaagc 1560 gcatttgttg aaagtcggtg acgatgccaa cattaacatc tatatgccga aatccgttct 1620 ttttaagatt accgataacg atgacgcaga cagcagttta tttaaagtca gtggtaccgg 1680 cacgctaaca ggtcaatatg tgaaaatcat tccggatgac gggaatgcct atgggccata 1740 taagtccgct atctatacac taaaagggaa tggctcttct tcagataccg ctacggttga 1800 aggtgagaca gcagaagatg aacaatccgg gaaagcactt gccgacacgt ttgcgactga 1860 caaaagcttg gagttcgtca gtgccagtga taattttatt aaggtaaatc cagttactga 1920 tgaaaccaca acgcttacag gtaaaaccac tgccggagcc tatgtaacga tttcaggttt 1980 aaaggggatt ccagaaggca gcttaactgc gaattcctat gatagtacaa aatatttggt 2040 acaggcggac aaggacggta attggagtta cgaactgccg actggggttt cgttacctgc 2100 caatgcttca tttgaagtta tttcgagtgc tggattcatt gtgaaaacag cgacggtagt 2160 gatcaacgat gccgaaacgc caaagcaggc atccagtgca gctggcagct taatcaacgc 2220 caatagtgct gctgatgtca cagcttcaca ggcaaaggct acaagtgctg ctgctagtga 2280 tgcggcgagt tatgcaagtg aagcgcaatc gattgctggc agtcatgctg ataatatgga 2340 aatcaagtct ctcgccagtg atgctgagaa gcaatcgcaa attgctttgg cagctagcaa 2400 gtctgctgcg gctagttcca gtgcggcagc gtccgcagca atcgtggcaa gtagcgcggc 2460 tagtgaagcg tcatctgcag ctgctgccgt aagtaacgct gatgcatcag caaactctgc 2520 agccgctgct tatgattcct acgcttctga ggccagtgcc gcttctgctg ctaatgatag 2580 ttcgggatat gccactgcat catttgcagc aagttccgct gcggctgcca tgagcgcagc 2640

gttatcgaca gcgcaagttg ctgccaaggt tgcagtgagt gatgcagcag cagcgggtag 2700 tgcagctgct gttgctagtg cagctcaaag cgactccaag aataaacaag cgactgcagc 2760 tacagcaaga agtcaagcac ttgatgattt gaataagatc aagtctctaa ctgattacgc 2820 aagtggcgca agctccagtg ccagcgaagc gggtcaagca tcgactgcaa catctgcgta 2880 tgctagtgct gcaagttcga gtgccagtga agccggttca tatgctcatc aggcaggctc 2940 cagcgccagt gacgctgtcg gtcagtccgg cagtgcagcc caacatgcca gcaccgctgc 3000 gagtgcggca tccagctatc cgaaggatag tgggattcag tcactagcca gtcaggctgc 3060 aagcgaggca gcaaaggcaa gcagtaacgc gagtgccgca accagcgccg cggccgttgg 3120 tttcagtgct gccagtgatg caagtgaaca ggcgaagacg gctgcaagtg ccgatgtggt 3180 ggcaagcagt gcggccagca cggctaacag taatgcgagt gccgcagcca gtgcgaccaa 3240 ggctggtgat agcaaagccg cagcaggatt ctcgagtgca gcgagtgctg cagcaagcag 3300 tgccaagggt gcagaagcag ttgccagcga agcggcgagt gccgcggcat ccgatgactc 3360 ggtagcttct agtgccgcca gtgcggctgc aggctttgac aaagctgcca gcgctgcgga 3420 aggcgcagct tcaagtgccg cgagcgcggc tgctagttca gcggcagctc aaggcacacg 3480 aggtggcgca agctccagtg ccagcgaagc gggtcaagca tcaaccgcaa catctgtgta 3540 tgctagtgct gcaagttcga gtgccagtga agccggttca tatgctcatc aggcaggctc 3600 cagtgccagt gaagcgactg gccatgcaag tagtgctaca agtcaagcaa gtgccgcatc 3660 cagtgctgcg tccaggtacc caagtgatag tgggatccag tcagatgtaa gtattgcgtc 3720 cagtgcagca agtactgcat ccagtgccgc tagtgccgca caaagtgagg cttcgacggc 3780 atcgtcggct gcaagtcatg ctagtgaaca agcaagtatt gcttccagtg aggatgttgt 3840 atcaagcagt gctgcgagtg tcgcgtccag cgcggccagt gccgcatcca gtgctgcaaa 3900 ggctggtaac agtagtgctg cgggtatata ctctcatgca gcaagtgcag ctgcaagcag 3960 tgctaagagc gctgaaagtc aagcaagcag tgccgccagt gctgctgctt ctgatgattc 4020 ggtagcttct agcgctgcca gtgccgcttt gtctgacgat gctaaggcaa gtagcgccgc 4080 cgatgtagca tccagcgcta caactgctgc cattagttcc gccacatcct tggctgatca 4140 gagtgccaca gggtcaaccg ctggctccca tattttgcca agtactggtg gagagacgac 4200 aggtagtata ccatcgggtc agacgccaac acagacgaag ccaacacaga cgaagccaac 4260 acaaacgaag ccaacacaag ccggtcaaac aacccagaca ggttcattac cgcaaacgga 4320 tcatgcaggg aggcatatgc taccgcagac cggtgatgat gctgaaagcg gtacttctgt 4380 tttgggtttg ctgattgtta gtctgatggg attgtttggt cttgcgggaa ccagacatca 4440 gaaggacaat aagccatcaa agtaatattg gatcactaat gtcgcccata cactggtgat 4500 aaaccaaaat ctgatggaaa tagctagtgg tgtaagagat gattattctc ttgcaccact 4560 tttttgttaa gcacgttttt ttatggattc tgtgtgccaa atgtttgaaa ttgatgtggt 4620 taaatttggt tttgcgggta atcta 4645 28 7639 DNA Lactobacillus rhamnosus 28 ctgcttaatg gtcacccatt ccttgtcaag cagaaaacta atgatttcgt agtgcttgag 60 caggctactt tccaatagtt cttccataaa cttacctccc caagtaggtt gttactatca 120 aaacttgcct aacgttaggc aagctttgaa ctagaaccaa tcattgattt atttatacta 180 atgacatatt gcataagcat tgcttggttc accataaatt ataaagtgat aatgcttgtt 240 gtttcaatta ttaagaactc gcctttcaaa atgtaataat ttatatcaaa tattttgaga 300 atgggtaggg ttaacttaat tgtttgctgt tttgggttca ataaaaggga ggcatgttga 360 agtgaaaaag gggagactga tattactatt agccacggga ctgatttcaa ttggtctttg 420 ggattcaagc ggtgtcgtat tggcagcgaa taagccccag gctggtgata tccatttggg 480 tggtgccgat ggttcgagct ataggaagct tataaatagc atcacattcc aatatagcaa 540 cgacgccgtg gtatatgacg aaggtacgga taccttcaaa attccaattc ggttcggctc 600 gcttgaatca gatggcttgg atcggtattt ggagtttggg tattcgttta acgatgcctt 660 agaaggaaaa atcaagcggg ttgtgatttc acctgatggg ctggtcccag cggttattac 720 aagtcttaac aagaacagag aatttgcacg gcgctgggat ggtagtgatg gtaaaagcgt 780 tagtcatcaa ctaggtggac gagcagatgc cgtcatctac atgcaggcgc ataagattat 840 gcccgaggat tggattgctg ttcggatgga aaccaatcgg attgaaggga aacaccctat 900 tcatccagca tttcgatcca ctcgcattct tgagtacaac gattttggtc ctgcactcaa 960 cgccaaactt ttagaagcca tgaagaaaaa ggcgattgat gacacggcca aggatcctaa 1020 accggttcaa gaagaagtta aagaaaaagt cgacccaatc acggttgacg aggactttga 1080 caagctcatt caggaaatcg ttttaaacgc gcataaggaa caggctaaac gagatattga 1140 tgccgaagcc gccaaagtca gcgctgaaat tgagcaggat ccgactttaa cggcaacgga 1200 aaaggcaaag caaaaagatg gcgttgcagc cgaagcaacc aaggccaagg cggcaatcga 1260 ccaagcgcaa accgaaacag gggttcagca ggcgcgagat gccggcattg cagcaatcga 1320 tgcccaacat cagcctggaa ccggactcaa cgtgcgccga gaagaagcta agcaggcgat 1380 tgatgccgaa gcggctaaag tgactgctga gattgagcag gattcaacct tagctactag 1440 cgaaaaagcg gcccaaaagc aaggagttgc tgatgaagcc gcgaaagcca agacggcgat 1500 tgatcaggcc caaacgattg aagccatcga taaagctaaa gatgatggga ttaaagcaat 1560 tgatgcccaa cacaagcaag gcgctgactt cgatacgcgt aaagctcaag ctaaagacgc 1620 aattgatgcc gaagcggcca aagtcaagga tgctattgat caagacccga ctctgacggc 1680 caaagacaag acggcccaga agcaaggcgt tggtgatgaa gcgaccaaag ctaagactgc 1740 cattgatcaa gcgaagacca ttgatggggt gatccaagcg aaagatgatg gcatcaaggc 1800 aattgatgcc caacatcagg caggtaccga tttggcgacc cgcaaagata gtgctaaaca 1860 agcgatcgat gccgaagcgg ccaaaataac cgatgccatc aaccaagatg acacgctaac 1920 cagtaccgaa aaggacgccc agaagcaggc agtagctgac gaagcggcta aagccaaagc 1980 agcgattgac caggctcaaa acgcagatgc cattcttcag gcccaagctg atgggattaa 2040 agccattgat gcgaaacatc aaattggtgc agatttagat acccagaaaa ccaaggctaa 2100 gcaggcaatt gacaaggaag ccgccaaagt tttaacggca attgagcaag atccgacttt 2160 gaccagtgct gaaaaaaagg cgcaaaagca aggcgttgcc gatgaaactg ctaaagccaa 2220 gaccgcaatt gattcggcgc ggaatgctga tgaaatcgcc aaagcgcaag cagatgggat 2280 taaagccatc gatgcgcaac atcggctggg aatggattta gctaagcgta aaactgatgc 2340 acaagcggcc attgacgctg aagctgccaa agttggcgaa gcgattgatc aagatcctac 2400 tttaacgagc caagaaaagg cggcccaaaa gcagaccttt gctgctgaag caaccaaggc 2460 taaagatacc atcgccaaag cgcaggatgc cgatggtgtt attcaggctg aaaaagcagg 2520 cattcaagcc attgacgatg ggcatcaatc aggtgcactt ttagatacgc gcaaagttga 2580 tgctaaaaaa gccattgatg ccgaagctgc taaaattaat gacgccattg accaagatgt 2640 cacgttaacc agcgctgaga aagccactca gaagcaaaaa gttacggatg aagcagtcaa 2700 agccaagaca gcgattgacg cagctaaaaa tgcggacacc gttgatcagg ctaaagcatc 2760 aggcatccaa gccattgatg ccgtccatca aagcggcacg cttttagaca ctcgcaaaca 2820 agatgccaaa aaggcgattg atgcggaagc agttaaagtc attgcagcta ttggccaaga 2880 tgtgaccttg acgcaagcgg aaaaactaac gcaacagcaa gcagtcgctg atgcagcaac 2940 gcaagctaag gctgctattg atgctgccaa gaatgccgat gcggtggacc aagccaaagc 3000 ggatggtatc aaggcgattg atgcccaaca ccaagccggg ttggcgttga acgaacgcaa 3060 agaagcagcc aaaaagctaa ttgcggaaac cgctgataag gtgcaggctg cgattggtca 3120 ggatgtgacg ctgactgcga cccagaaagc agtgcaaaga caggcgatta ccgtggaagt 3180 cactaaagcc aatcaagcca ttgatgcggc tggcaatgct gacgcggtcg atcaagctaa 3240 aaatgcggga gttaaagcaa tttatgacca gcatcaatcc ggtcaggcac tcgcagatcg 3300 gaagcgtgat gccaaacagg cgattgatgc cgaggcggca aaagaaacag ctgccattga 3360 tcaggatgca actttaaccg cgaatgaaaa ggcaagccaa aaacaggcgg ttgccgatga 3420 agcgactaaa gccaaagaag cgattgatgc ggctaagcag gctgatgcag tcgaccaggc 3480 caagaatgac gggatcagag cgattgacgc ccaacatcac gctggccaag cagttgccga 3540 tcgtaaagcc gctgctaagc aagccattga tgccgaagcg gctaaagtaa cgggcaacat 3600 tgatcaagat gaaaccctca cagcgacaga aaaagcggcg caaaaacagg cagttgcaac 3660 cgaagccgat aacgcgaagc aagcgatcga caaagggcaa aatgctgacg ccgtcgacaa 3720 agctaaaaca ggcggcatca aagcgattga cgctcagcac cagtctgggc aggcaattaa 3780 agcgcgccaa aatgacgcca agcaggctat tgatgctgaa gccgcaaaag taaccaaagc 3840 gattgaccaa gatccaactt taaccgccgc tgaaaaaaag gcacagaagc aagcagtcac 3900 agatgcggaa actaaagcta aagctgctat tgatgctacg ttagtggccg atgcgattga 3960 ccaagctctg gctgacggga ttaaaaccat cgatgcccaa taccaaactg gtatagcatt 4020 ggataagcaa aaggcggcgg ccaaacaaac aattgatgcc gaagcagcca aggttagtga 4080 agcaattgat caggatgtca ctttgacagc cgaccaaaag gctacacaaa agcaggcagt 4140 ggcagatgaa gcaacgaaag caaaagcggc cattgaccaa gcctctgacg ccgatgcggt 4200 gattcaagca acaattgatg gtattgaagc tattgacgcg caacaccagt ccgcaacggc 4260 acttgacaag caaaagcagc aagcaaaaca ggccattgat gctgaagcgg ccaaagtaag 4320 taaggcgatc gatcaagatg tgacgttaac ggcaacgcaa aaagctgacc agaagcaggc 4380 tgtgatcgct gaagcagaca aagccaaaaa gcttatcgat gcagctggca atgctgatgg 4440 tatcaagcaa gctgaaagtg atgggatcaa agcaatcgac gctcagcatc aatccagtca 4500 ggcactcgca gatcggaagc gtgatgctaa aactgccatt gatgccgaag cggcaaaaga 4560 aacagctgct attgatcacg atgccacctt aaccgcgaat gaaaaggcaa gccagaaaca 4620 ggcggttacg gatgaagcaa ctaaagccaa aaaagcgatt gatgcggcta agcaggctga 4680 tgcagtcgac caggccaaga ctgacgggat caaagcgatt gacgcccaac atcactccgg 4740 gcaagctctt gacgatcgta aagccgatgc caagcaggtc attgatgctg aagcagccaa 4800 ggtgacggca gcgattgatc aggataacac gttgaccaaa gcccaaaaag ctgcccagaa 4860 acaaggggtt gcgacagaag ccgacaaagc taagcaagcc attgatgctg ccggggatgc 4920 cgatgctgta gatcaagcaa agacagccgg gattcaagcc atcgatgctc agcacaaagc 4980 cggtaaaacc attgatagcc gtcatgatga cgctaagcaa gcgattgatg aagaagcggc 5040 taaggtgatt aaagcgattg accaggatcc aactctgacc gctgcccaaa aagaagcaca 5100 aaagcaagcg gtagcaactg aagccgataa agctaaaaaa gcaattgacg ctgcaggcga 5160 tgcggatgct gtagatcagg caaaaacagc cggcatcaag gctatcgatg agcaacacaa 5220 gtcaggacaa acagttgatg cacgaaaaga agatgccaaa aaggccattg atgctgaagc 5280 cggtaaagtt actgatgcaa ttgatcacga cgccactttg acggctgctc aaaaagaagc 5340 gcagaagcag gcagttgctg atgaggctga taaagctaaa aaagcgattg atgcagctgg 5400 aaatgcggat gctattgatc aggcaaaatc tgctggtatc aaggcaattg acgaacaaca 5460 caagtcagga caaagcatcg atactcgtaa agatgacgct aagaaagcta ttgatggaga 5520 agttgctaag ataactgatg cgatcgatca tgacccaaca ctgaccgatg ctgaaaaggc 5580 aacacaaaag caggccgtca tcgctgaagc tgacaaggcc aagaaggcaa ttgatgcagc 5640 cggtgatgct gatgccgttg accaggcaca aaaggctggc atcaaggcga tcgaccagca 5700 acacaaatcc gggcaagcac tagcaatccg gaaagatgct gctaagaaag ccattgatga 5760 agaagctgct aaagtaagcg aagccattga tcatgatgta acgttgacgg acagcgaaaa 5820 gggcactcag aagcaagctg ttgctgacga ggccaagaaa gctaagcagg cgattgatac 5880 tgccgacaat gctgatggcg ttgatcaagc agtgaccaaa ggcattcaga tcattgacgc 5940 gcagcaccag tccggccaag cgctcaccga tcgtaaggct gctgcgaaaa aagccattga 6000 tgccgaagct gcaaaggtag gccaagctat tgagcaggat ccaacactga cggcaacaga 6060 aaagaagcgt caaaaacaag ccgttgcaga cgaagcaaca aaggccaaag cggcgattga 6120 tactgctgct aatgcttcag cggttgacca agcaaaaaat gccggtatta aggccattga 6180 tgctcaacac gtctctggta aagcttttga cttaagcaag gacgaagcca agaaagcgat 6240 tgatgctgaa gctaccaaag ttcaaggtga aattgatcag gacccgactc tgaccgctac 6300 tgccaagaaa cagcaaaaag aagcagtgcc gacagaagcc ggtaaagcaa aacaggcatt 6360 tgatcaggct aaaaatatcg aggaggtacg accgccaaag acgaaggcat caaagcgatt 6420 gatgcgcaac atcagtcagg acaagcagtt gcacacgtaa agacgatgca aagaaagcaa 6480 tcgacgacga agctgctaaa gtgaccgaag caattgatca tgattcgtca ttgactgatg 6540 ctgaaaagaa ggctcagaaa caaggcgttg taacagaagc tgacaaagcg aagaaagcga 6600 ttgatgcagc tggcagtgcc gatgcagtcg atcaggccaa agatgcaggc atcaaggcca 6660 tcgacgcgca acatcagtca ggacaagcag ttgcaacacg taaagacgat gcaaagaaag 6720 cgattgacga cgaagctgct aaagtcatca aggcaattga tcaagatccc aacattgact 6780 gacgcagaaa aaacggcgca aaagcaagca gttgcaacag aagctgacaa agcgaaaaaa 6840 gccattgatg cggcaaaagg tgccgatgca gtagacaaag ccaaagcagc tggtatcaag 6900 gcaattgatg cccagcaccg ctccggtcaa accatcgcgg cgcaaaaaga tgcggccaaa 6960 aaggcaattg acgacgaagc tgctaaagtc atcaaggcaa ttgatcaaga tccaacattg 7020 actgatgcag aaaaggcagc gcaaaagcaa gcagttgccg cagaagctga taaagcaaag 7080 aaagcgattg acgcagctgg taacgctgat gcggtgaacc aagccaaagt agctggcatt 7140 aaggcaatta acgaccaaca tcgtgccggc aagggacaaa aggtcaccaa agcaacacct 7200 ctgccaacga ctaaggcacc tgagacgcct gcagcaccta aaacaaaagt tatcacctca 7260 tcagaaggca accttccgaa aacaggggag caacaatctc tgtggatggt ggtcctaggc 7320 gctttgttga gtctgttctc aggattgtgg ttcgccaaaa agaaagcgtc acattaggcg 7380 ttgagatcaa gattcttaag ctcaaaaagt tgcagttatg aatggtaggg aaacctcatc 7440 atagaaagct gatttttcgg aaactgacag ccggcaagtg agacgtttta tctcatttgt 7500 cggctgtttt tctggctata cctgttgatg atttttaaat atttgattca tttttaaatt 7560 cagcggtcca gttgattgac atggtatagc ccaaccgcta cgcttaaagc atgacaaaga 7620 agggtgtgag cttatggca 7639 29 1257 DNA Lactobacillus rhamnosus 29 atgtgttatc agcgtgaccg tttcctttca aaccggtcag caaaaccgtc acgttctcat 60 cattttctcg cccttttctt ttgtcattta tggtagaata caacagttgt gaattgtata 120 tttcgtagga ggatatctac atgccattag ttaacgctgc agagcttgta aaagctgcac 180 ataaaggtca ctactgtatc ggtgccttca acaccaacaa cttggaatgg actcgtgcca 240 ttctcgccgg cgctcaagaa ttgaacgttc cggttatcat ccagacttcc atgggtgctg 300 ctaagtacat gggtggctat gaattctgcc aaaccatgat cgaagctgcc gttaaagcca 360 tggacatcac cgttcctgtt gtgattcact tggaccacgg taactatgaa gcagccaagg 420 aagctattgc tgctggctac aactcagtta tgtttgacgg ccacgacctc gactttgaag 480 ataacttgga aaagaccaag gaaatcgtta agctggccca cgccaagggc atttccgttg 540 aagctgaagt tggttccatc ggcggtgaag aagacggtgt tgtcggcgaa ggtgaattag 600 ctgacgttga agaagccaag actttggcag ctaccgggat cgacttcctg gcagccggca 660 ttggtaacat ccacggccaa tatccagaca actggaaagg cctgcacttc gaccgcttac 720 aagaattgaa cgacgctgtt aagatgccgc tcgttctcca cggtggttcc ggtatccctc 780 aagaacaagt tcaaaaggcg atcaccatgg gcatttccaa gttgaacatc aacaccgaat 840 gccaacttgc ctttgctaag gcaacacgtg aatacatcga agctggtaag gatcaacaag 900 gcaagggctt tgaccctcgt aagatgctca agccaggcac cgatgcgatc accgatacct 960 tcaaggaaat caccggctgg attggcaaca agccagttaa gatggttcct gaagcacttt 1020 aattttttaa tcaaagacca tttaaagaac ccactcgctg aaattgcgag tgggttcttt 1080 tcgtctctcg tacttaagct gttaaggata agcgctgccg ctgtgactga atttaggatg 1140 acgtacgctt agtcctctac ctcatcccat gctcggtctt catcagtcac agcatctctg 1200 aatccttgcc aatcagcggc agtggcaaat aaatcagatc gcagcggtgt cagcaca 1257 30 1153 DNA Lactobacillus rhamnosus 30 ccttcgtaca caaagtaatg gatattcgcc aaaggttgac agcactgtca aaacaccatc 60 acctaactgc acgatggaaa catcaaatgt gccgtcgaca aagtcgtaaa ccaaatcttt 120 tctctttgtc gcctttatcc aaaccatatg ccaaggctga cgcggttggt tcgttgataa 180 tccgttgaac attcaaacca gcgatcttac cggcatcctt gtttgcctga cgctcactgt 240 cattaaagta aaccggaact gtgataaccg catctttaac cggttcgccc agatagtctt 300 cagaaaattt tttgatgtac tgtaaaatca tcgctgaaat ttcttgcggg gtgtattctt 360 tatcgccaac cttaacttta tagttagctt cgcccatgtg acgcttaatt gacacgatgg 420 tatccggatt agtgatcgcc tggcgttttg ccacttcacc aacttggatt tcaccatctt 480 taaatgcgac aacagatggc gtggtgcgat tgccttccgg gttggtgatg atttttggct 540 gattgccttc caaaaccgca actgcagagt tggtggttcc taagtcaata ccaataactt 600 tactcatatt tttatacctt ctttatttca gattaattat ttagcgacaa cgaccatagc 660 agggcgcaga acccgatcct tgagataata ccctttttgt aacacctgcg cgaccgtgtc 720 agcgggatgt ttgtcgtccg ccgccacggt ttgtactgcc tgttgggtat tcggatcaaa 780 cttgtcgcca gcaccatcaa tcgcagtgat gccattttcc ttcaaggcgc gttccagatg 840 atcgtaaacc atctgcacac cttttttgag tgaggccgca ctgtcatctt tggcttcggt 900 tgcaagcgca cgctctagat tgtcaactac cggcaaaatc gccttggcta acttctggcc 960 gtcatatttc aacatttttt gctgctcttt ttcgaaccgc gcattcatgt tttgaatctc 1020 tgcagctgcg cgcaaatact tgtcttcgaa tgcatcacgc tcttgcttca gttgttcacc 1080 atcatgcttg ctggttttca attgctcatt aagatcagca atgctttcct gcagcccggg 1140 ggatccacta gtt 1153 31 1724 DNA Lactobacillus rhamnosus 31 tgcaaattgc cacggatacc cagacacaag tcattgcaga cggcgttgtt accaagtata 60 cgccagccaa tgccatgatc gttgccactc atcggcacac agccaaacag ttgctggccg 120 cagcaggaat accagttgca cgtggggcta agtttactaa atggccggat gccaaagcag 180 cttttgagca cagctttgcg cataaaagta ttgtggtgaa acccgaggca cgcagccaag 240 gcaaagcggt tgagcagttt tcgataccac cgactgaaaa gcagtttgac cgagcctttc 300 atgaagccaa tcgccatcat ggggtgctca ttgaaatgat ggcacgcggc acgacctacc 360 attttaccat catcgggcaa caagtgctca gcgtcttgga aacagcagca gctaatgttg 420 taggcgatgg gcgcaaagcc attaaggaat tgatcgcctt gaaaaatggt caccgcgcga 480 cttcccggca attgcagctt gacgccagtg cacggcgtca gttaaaggct caagcgttaa 540 cacccgagac tgtgcttcaa cgcgggcagc aggttttctt aaccactgcc gcgcatccgc 600 aaaccggtgg cgatttgtat gacgtgacgg acgagattga tgacagttac aagcaactgg 660 cgctaaaagc tgctgccacg cttgatttgc cggtagcagc tgtcgacatt gtgattgata 720 atctgtatgc accgtatgat ccggaggcag atgggcaggc aatcgtgatt agcctcaatc 780 cggtaccgga tctcgctgtg ccgttgcatc cggacatggg cgaatcacgc gcacttgccc 840 cggcattgct aaactggctg tttgctgtga gataagtaaa cgaggtcata ttaaaaccga 900 cctcagcatg gtaaatttgc tctaaggtcg gttggttaca ccgttcatga tcatgcttct 960 gcgcgttacg gtcacgatgc tgacatttag gtgcggccac actccattat attggttaag 1020 ttgcgccaaa cgtctttagc ggttgcttag ataggttaaa accacttttt cttaggcttt 1080 tcttgcgtgt catcaagtgg cggtaaggtg atgttagcct gattgatggc agtggctgcc 1140 acaataagta gccctggcgc ggtatcggca gtttgcgccg tttcgttagc aaccaatgta 1200 aatggcacat tggcatcggt gaggagcttc atgtaaggac cggtaatggc attatcaagt 1260 ttgccgttga gtagggcttt atagttgcgg tcatggaaat cttttaataa tggggcaacc 1320 tgatgctgtc gtttgggatc agccagttcc tgattgctga tacataaagc gacccgttca 1380 cgtaacgagc ccatgtactt gcggcgttcg tcgggtttgg tttgcggtgg gccgtatagt 1440 gcactgttga gatgttcctg catattgtct tctgccatga tgaaaagcct ccttatgatg 1500 ggtttgatca aataacgatt taacgatcct tggtgaaccg tcttgttgtg tgaacgcgag 1560 tcgtaatgtt gaaacctgac aacgcgttgc aatatgacct cattgtaaca tgttctagcg 1620 taaagaaagg aatgacgaaa gggtgtttac cagtaacgac tttgcggttt ttgctgcgcc 1680 aacgctaagt gcgcggatgg ccttgatccg gcaacagttg gatc 1724 32 1000 DNA Lactobacillus rhamnosus 32 gcgtggtgta agattcggta aggctagagc aaagcggttg tgtgaagtgt gaatccagca 60 agctgaattc ctgaattgat gaaaggaaga cggatatgta tcgagatctg aatggtaagg 120 ttgcagtcgt gactggtggc tccaaaggca ttggcgcggg cattgcagaa cggtttggcc 180 aagagcatat ggccgttgtg attaattatt taggtgatca cgaaggcgcg cgaaaaacag 240 ccgatacagt gatcaaaaat ggcggtcagg cagtcagtat tcatgcagat gtttcgacag 300 aagcggggat agcgagtttg gttaaaactg ccgagtccga atttggccgc cttgatgtct 360 gggtcaataa tgcaggcatg gaaattaaag caccgacgca tgaagtgtct ctggatgact 420 ggaataaagt cattgcgatt aatcaaaccg gggtcttttt aggcgcccgg gctgctttga 480 attattttct cgaccatcac cagccaggca atattattaa catctcatcg gtccatgaac 540 agattccctg gccaacgttt gccagttatg ctgcagctaa agggtcggtt aagcttttca 600 cggagacgat tgcgatggaa tacgctaacc gcggaattcg ggtcaacgct atcggccccg 660 gtgccattga gacgccgatt aatgcggaaa agtttgctga taaggcgcag tatgaccaaa 720 cagtcgccat gattccccaa ggacggctag gcaaaccgga agatgttgcc gccggagcag 780 cctggctggc atcgacagag tcaagttacg tcactggcac gaccctattt attgacggcg 840 ggatgacatt atatcctgcg tttaaagacg gacagggctg atcaatgttg cgaagatgca 900 aaaagtcgcc atctcgatta tgaaatggcg actttttgtg tacgggttag aattcgcgtt 960

ttttatacag cacggtgctt aaccaccaag agaagatgaa 1000 33 1191 DNA Lactobacillus rhamnosus 33 atggcaaaga ttctcgcagt caatgcaggt agttcgaccc tgaagtggaa gctttttgat 60 atgccggctg aagtgcagtt ggctgagggg ttggtcgatc gattgggcca gccgcaatcg 120 aaggttaaaa ttaaatatgg cgacggtcag aagtacgaga gcgatacccc aattgcaaac 180 tatcaagaag cagttgccag cttgatgggt aatattaagg cgctagggtt agtggagcat 240 ttgcacgaga ttatcggggt cggccatcga gtggttgctg gcggcgaaat ttttgccgaa 300 tcagttgttg ttgatgatga gacgttgctg cagattcaga atctgcgcga ctatgcaccg 360 ttgcataatc ccgttgaagc ggactatatt tcggtttttc ggaaaatgat gccttgggcg 420 aatgaagtgg cagtttttga cacggctttc caccaaacaa tgcaaccgga gaacttttta 480 tatagcattc catacgaata ttatgagcaa tatggtgcgc ggaagtatgg tgcgcatgga 540 acaagtgtcc gttatgtgag cgctcgtgct gctgaaatgt tgggcaagcc gctagaagat 600 ctacgtatga ttgtcatgca cttagggtct ggctctagca tcaccgcggt tcaaggcgga 660 cagtcaattg atacgtccat gggctttacg ccattagcag gtgtcaccat gggcacgcga 720 tcaggtgata ttgatccgtc attggtaggc tatctcatga agaagttggc gataccggat 780 gttggccaaa tgattcatat tctcaacaac gattccggtc tgctaggtat ctccggactc 840 agcaatgata tgcgtgactt ggaagccgcc gaggacacca atacacgcgc taagctggca 900 ctggatattt ttgtgaaccg cgttgtgaaa tacgttggct cttacgttgc tttaatggat 960 ggcgtcgacg tgctggtctt caccgctggc attggcgaaa acggtgacga gatccgtgat 1020 aagattatgc ggtcgcttga ttacctcggc gccaaaatcg acaatgatct gaattacaag 1080 tcacatggcg ttgaagcaga tctaagcacg gcagattcaa ccgtgaaaac gctgctggta 1140 ccgacaaatg aagaacttat gattgtacgc gatgtgatgg cactgagcta a 1191 34 33 DNA Artificial Sequence Made in the lab 34 ccgccgccgg gatccaccag cgcatcatct gac 33 35 36 DNA Artificial Sequence Made in the lab 35 ccgccgccgg aattcttact tggtggttaa atcggt 36 36 39 DNA Artificial Sequence Made in the lab 36 ccgccgccgg gatccctaag cagtagtgca gttgatgcc 39 37 39 DNA Artificial Sequence Made in the lab 37 ccgccgccgc tcgagttaat cgttgatcac taccgtcgc 39 38 35 DNA Artificial Sequence Made in the lab 38 ccgccgccgg aattcccttt gggattcaag cggtg 35 39 41 DNA Artificial Sequence Made in the lab 39 ccgccgccgg cggccgctca attcttggca gcatcaatag c 41 40 37 DNA Artificial Sequence Made in the lab 40 ccgccgccgg gatcccattc gttgacgttg gacaatc 37 41 42 DNA Artificial Sequence Made in the lab 41 ccgccgccgg aattcttaac ctagtaacgc ttgtaaacga gc 42 42 632 PRT Lactobacillus rhamnosus 42 Met Thr Leu Pro Arg Ile Gln Asp Asp Leu Tyr Leu Ala Val Asn Gly 1 5 10 15 Glu Trp Gln Ala Lys Thr Pro Ile Pro Pro Asp Lys Ser Val Val Ser 20 25 30 Ala Asp Ser Asn Leu Thr Asp Asp Ile Arg Gln Lys Leu Val Ala Asp 35 40 45 Leu Ser Thr Met Thr Lys Thr Ala Lys Thr Leu Pro Leu Gln Tyr Ala 50 55 60 Ala Arg Leu Phe Ala Lys Ala Asn Asp Gln Thr Arg Arg Gln Gln Leu 65 70 75 80 Gly Ile Glu Pro Val Arg Asp Arg Ile Ser Phe Leu Met Ala Leu Thr 85 90 95 Thr Leu Asp Gln Phe Arg Ser Ala Met Pro Lys Leu Val Ala Asp Gln 100 105 110 Tyr Val Leu Pro Ile Ser Pro Tyr Val Asp Ala Asp Met His Asp Ala 115 120 125 Glu His Asn Ile Leu Asn Leu Gly Gly Pro Asp Thr Ile Leu Pro Asp 130 135 140 Ala Ala Met Tyr Gln His Glu Asp Ala Glu Asn Ala Ala Asp Leu Ala 145 150 155 160 Ala Trp Ser Gln Met Ala Ala Ala Met Leu Ala Ala Val Gly Phe Ser 165 170 175 Gln Thr Asp Gln Thr Ala Tyr Val Glu Ala Ala Lys Arg Phe Asp Arg 180 185 190 Arg Leu Ala Asp Tyr Val Pro Ala Asn Val Asp Leu Ala Val Asp Ser 195 200 205 Thr Tyr Asp Asn Pro Leu Ser Trp Gln Ala Phe Glu Asp Ala Ala Gly 210 215 220 Tyr Leu Gly Ile Pro Gln Ala Phe Ala Thr Tyr Met Pro Gln Thr Pro 225 230 235 240 Ala Lys Val Asn Ala Val Val Pro Ala Tyr Leu Pro His Leu Ser Lys 245 250 255 Leu Leu Thr Pro Asp Asn Tyr Ser Glu Trp His Ala Trp Met Val Ile 260 265 270 Asn Glu Leu Leu Thr Cys Ala Thr Tyr Leu Ser Asp Asp Leu Arg Gln 275 280 285 Leu Ala Gly Gln Tyr Asp Arg Phe Leu Ala Gly Gln Pro Glu Ala Ser 290 295 300 Ser Trp Thr Lys His Ala Phe Gly Ile Ala Asn Glu Tyr Phe Asp Asp 305 310 315 320 Val Ile Gly Gln Tyr Tyr Gly Gln Thr Tyr Phe Gly Ala Asp Ala Lys 325 330 335 Ala Asp Val Thr Ala Met Val Lys Gln Ile Leu Ala Gln Tyr Arg Val 340 345 350 Gln Leu Glu Asn Asn Thr Trp Leu Ser Pro Ala Thr Lys Gln Lys Ala 355 360 365 Met Arg Lys Leu Ala Thr Met Gln Val Lys Met Gly Tyr Pro Glu Arg 370 375 380 Leu Phe Ser Leu Tyr Asp His Leu Ser Val Asp Val Asp Asp Asp Leu 385 390 395 400 Leu Thr Ala Ile Leu Lys Leu Ser Ala Gln Thr Gln Ala Phe Trp Phe 405 410 415 Lys Gln Leu Gly Gln Thr Val Asp Arg Asn Gln Trp Asn Met Pro Gly 420 425 430 His Leu Val Asn Ala Ser Tyr Asp Pro Leu Lys Asn Asp Ile Thr Phe 435 440 445 Pro Ala Gly Ile Leu Gln Pro Pro Tyr Tyr Ser Leu Lys Trp Thr Arg 450 455 460 Ala Glu Asn Leu Gly Gly Thr Gly Ala Thr Ile Gly His Glu Ile Ser 465 470 475 480 His Ser Phe Asp Asn Asn Gly Ala Leu Tyr Asp Glu Tyr Gly Asn Leu 485 490 495 His Asn Trp Trp Thr Pro Ala Asp Lys Gln Ala Phe Asp Gln Leu Val 500 505 510 Lys Ala Met Ala Ala Gln Phe Asp Gly Arg Asp Tyr Glu Gly Val Lys 515 520 525 Val Asn Gly Thr Leu Thr Val Ser Glu Asn Met Ala Asp Asn Ala Gly 530 535 540 Met Asp Val Ala Leu Ala Leu Leu Gly Asp Gln Pro Asp Val Lys Asp 545 550 555 560 Leu Gln Ala Phe Phe Ile Thr Tyr Ala Arg Ser Trp Ala Thr Lys Met 565 570 575 Arg Pro Glu Arg Ala Lys Thr Val Leu Arg Gln Asp Val His Ala Pro 580 585 590 Ala Thr Leu Arg Val Asn Val Pro Val Gln Asn Phe Pro Ala Trp Tyr 595 600 605 Gln Ala Phe Asn Val Gln Pro Gln Asp Gly Met Tyr Arg Gln Pro Gln 610 615 620 Lys Arg Leu Thr Ile Trp His Gln 625 630 43 242 PRT Lactobacillus rhamnosus 43 Met Ile His Met Ala Lys Lys Asp Phe Asn Gln Leu Ala Leu Asp Gln 1 5 10 15 Ala Lys Val Asn Gly Gly Lys Leu Ser Val Glu Pro Lys Val Pro Ile 20 25 30 Glu Thr Arg Asp Asp Leu Ser Ile Ala Tyr Thr Pro Gly Val Gly Ala 35 40 45 Val Ser Ser Ala Ile Ala Lys Asp Gln Ser Leu Val Tyr Asp Leu Thr 50 55 60 Thr Lys Lys Asn Thr Val Ala Val Val Ser Asp Gly Ser Ala Val Leu 65 70 75 80 Gly Leu Gly Asn Ile Gly Ala Glu Ala Ala Met Pro Val Met Glu Gly 85 90 95 Lys Ala Ala Leu Phe Lys Arg Phe Ala Lys Val Asp Ala Val Pro Ile 100 105 110 Val Leu Asp Thr Gln Asp Thr Glu Ala Ile Ile Ala Ala Val Lys Ala 115 120 125 Ile Ala Pro Thr Phe Gly Gly Ile Asn Leu Glu Asp Ile Ser Ala Pro 130 135 140 Arg Cys Phe Glu Ile Glu Ala Arg Leu Ile Asp Glu Leu Asn Ile Pro 145 150 155 160 Val Phe His Asp Asp Gln His Gly Thr Ala Ile Val Val Leu Ala Ala 165 170 175 Leu Tyr Asn Ala Leu Lys Val Ala Asp Lys Lys Ile Glu Asp Ile Arg 180 185 190 Val Val Val Asn Gly Gly Gly Ser Ala Gly Leu Ser Val Ala Arg Arg 195 200 205 Phe Leu Ala Ala Gly Val Lys His Val Met Val Val Asp Lys Val Gly 210 215 220 Ile Leu Ala Lys Lys Asn Ala Asp Gln Leu Pro Pro His Gln Ala Gly 225 230 235 240 Leu Pro 44 317 PRT Lactobacillus rhamnosus 44 Met Ala Asp Glu Glu Ala Met Leu Ala Lys Val Gln Ala Ser Trp Ala 1 5 10 15 Gln Thr Ala Ala Arg Asp Lys Ala Arg Tyr Ala Asp Glu Arg Val Pro 20 25 30 Glu Asp Val His Trp Glu Thr Glu Tyr Arg Tyr Glu Gln Ser Ala Asp 35 40 45 Pro Gln Gln Thr Leu Asn Leu Tyr Tyr Pro Ala Lys Arg Arg Asn Ala 50 55 60 Thr Met Pro Thr Val Ile Asp Ile His Gly Gly Gly Trp Phe Tyr Gly 65 70 75 80 Asp Arg Asn Leu Asn Arg Asn Tyr Cys Arg Tyr Leu Ala Ser Gln Gly 85 90 95 Tyr Ala Val Met Gly Met Gly Tyr Arg Leu Leu Pro Asp Val Asp Leu 100 105 110 Arg Gly Gln Ile Gln Asp Ile Phe Ala Ser Leu Arg Trp Leu Ser His 115 120 125 Phe Gly Pro Gln Arg Gly Phe Asp Leu Asp His Val Leu Leu Thr Gly 130 135 140 Asp Ser Ala Gly Gly His Leu Ala Ser Leu Val Ala Cys Ile Gln Gln 145 150 155 160 Ser Ala Glu Leu Gln Glu Leu Phe Gly Val Ser Arg Val Asn Phe Asn 165 170 175 Phe Thr Leu Val Ala Leu Val Cys Pro Val Ala Glu Pro Ser Lys Leu 180 185 190 Pro Glu Ala Ala Gly Asp Met Ser Asp Met Ala Ala Phe Tyr Leu Asp 195 200 205 Lys Leu Ser Gly Gly Asp Gln Ala Leu Ala Asp His Leu Asn Phe Ser 210 215 220 Gln Val Val Lys Gly Leu Asp Leu Pro Pro Phe Met Leu Ile Gly Gly 225 230 235 240 Gln Asn Asp Ser Phe Tyr Leu Gln Ser Gln Ala Leu Leu Lys Val Phe 245 250 255 Asp Ala Asn His Val Thr Tyr Thr Thr Lys Leu Trp Pro Ala Ser Ala 260 265 270 Gly Pro His Leu Lys His Val Phe Asn Val Gln His Trp Glu Trp Pro 275 280 285 Glu Ser Ile Glu Thr Asn Leu Glu Met Leu Arg Thr Phe Asp Ala Leu 290 295 300 Ser Lys Gln Gln Asp Gln Ala Glu Glu Asn Glu Phe Glu 305 310 315 45 88 PRT Lactobacillus rhamnosus 45 Met Glu Lys Arg Glu Phe Asn Ile Ile Ala Glu Thr Gly Ile His Ala 1 5 10 15 Arg Pro Ala Thr Leu Leu Val Gln Ala Ala Ser Lys Phe Asn Ser Asp 20 25 30 Ile Asn Leu Glu Tyr Lys Gly Lys Ser Val Asn Leu Lys Ser Ile Met 35 40 45 Gly Val Met Ser Leu Gly Val Gly Gln Gly Ala Asp Val Thr Ile Ser 50 55 60 Ala Glu Gly Ala Asp Glu Ala Asp Ala Ile Ala Ala Ile Thr Asp Thr 65 70 75 80 Met Lys Lys Glu Gly Leu Ala Glu 85 46 378 PRT Lactobacillus rhamnosus 46 Met Thr Gln Phe Asn Thr Lys Leu Val His Gly Pro Gln Leu Asn Val 1 5 10 15 Asp Gln Ala Gly Ala Ile Val Pro Pro Val Tyr Gln Ser Ala Met Phe 20 25 30 Arg Phe Ala Pro Asp Gly Gln Glu Thr His Trp Asp Tyr Ala Arg Ser 35 40 45 Gly Asn Pro Thr Arg Glu Tyr Leu Glu Arg Gln Ile Ala Thr Leu Glu 50 55 60 Asn Gly Asp Ala Gly Phe Ala Phe Ser Ser Gly Val Ala Ala Ile Ala 65 70 75 80 Thr Val Leu Ala Ile Phe Pro Asp His Ser His Phe Ile Ile Gly Asp 85 90 95 Ser Leu Tyr Ser Gly Thr Asp Arg Leu Ile Asn Gln Tyr Phe Ser Gln 100 105 110 His Gly Leu Thr Phe Thr Pro Val Asp Thr Arg Asp Leu Ala Ala Val 115 120 125 Glu Ala Ala Ile Arg Pro Glu Thr Lys Ala Ile Phe Phe Glu Thr Phe 130 135 140 Ser Asn Pro Leu Leu Lys Val Ser Ser Val Lys Ala Ile Ser Ala Leu 145 150 155 160 Ala Lys Thr His Asp Leu Leu Thr Ile Val Asp Asn Thr Phe Leu Thr 165 170 175 Pro Tyr Tyr Gln Arg Pro Leu Asp Leu Gly Ala Asp Ile Val Leu His 180 185 190 Ser Ala Thr Lys Tyr Leu Gly Gly His Gly Asp Leu Ile Ala Gly Leu 195 200 205 Val Val Ser Ala His Pro Asp Leu Ser Glu Lys Leu Ala Phe Leu Gln 210 215 220 Asn Thr Ile Gly Ala Ile Leu Ser Pro Leu Asp Cys Ser Leu Val Thr 225 230 235 240 Arg Gly Ile Ala Thr Leu Ser Val Arg Leu Asp Arg Glu Thr Ala Asn 245 250 255 Ala Gln Ala Val Ala Glu Phe Leu Ala Gln His Pro Asp Val Ala His 260 265 270 Val Tyr Tyr Pro Gly Leu Lys Asn Asp Pro Gly Tyr Ala Leu Ala Gln 275 280 285 Lys Glu Thr Thr Gly Ala Ser Gly Leu Leu Thr Ile Lys Leu Ala Asp 290 295 300 Asn Ile Asp Pro Leu Lys Phe Val Asn Ser Thr Lys Ile Phe Asp Phe 305 310 315 320 Ala Asp Ser Leu Gly Thr Val Ser Ser Leu Val Lys Leu Pro Trp Phe 325 330 335 Lys Leu Pro Glu Asp Lys Arg Ala Asp Phe Gly Leu Thr Pro Gln His 340 345 350 Val Arg Ile Ala Ile Gly Leu Glu Asp Gln Gln Asp Leu Ile Asp Asp 355 360 365 Leu Gln Gln Ala Leu Val Ala Ala Glu Lys 370 375 47 270 PRT Lactobacillus rhamnosus 47 Met Leu Lys Lys Lys Leu Trp Phe Leu Leu Pro Leu Val Ala Leu Val 1 5 10 15 Thr Phe Thr Leu Thr Ala Cys Thr Ser Ala Ser Ser Asp Thr Ser Lys 20 25 30 Asn Ser Asp Val Thr Ala Glu Leu Ile Asn Lys Asn Glu Leu Thr Ile 35 40 45 Gly Leu Glu Gly Thr Tyr Ala Pro Phe Ser Tyr Arg Lys Asp Gly Lys 50 55 60 Leu Glu Gly Phe Glu Val Glu Leu Gly Lys Ala Leu Ala Lys Lys Ile 65 70 75 80 Gly Val Lys Ala Lys Phe Val Pro Thr Gln Trp Asp Ser Leu Ile Ala 85 90 95 Gly Leu Gly Ser Gln Lys Phe Asp Leu Val Leu Asn Asp Ile Ser Glu 100 105 110 Thr Pro Ala Arg Lys Lys Val Tyr Asn Phe Thr Thr Pro Tyr Met Tyr 115 120 125 Ser Arg Tyr Ala Leu Ile Thr Arg Ser Asp Asn Thr Thr Ile Lys Ser 130 135 140 Leu Ala Asp Ile Lys Gly Lys Thr Phe Val Glu Gly Thr Gly Thr Pro 145 150 155 160 Asn Ala Ala Leu Ala Lys Lys Tyr Gly Ala Lys Ile Thr Pro Ser Gly 165 170 175 Asp Phe Thr Val Ser Leu Ser Leu Val Lys Glu Lys Arg Ala Asp Gly 180 185 190 Thr Ile Asn Ala Ser Ala Ala Trp Tyr Ala Phe Ala Lys Asn Asn Ser 195 200 205 Thr Ala Gly Leu Lys Ser Gln Thr Leu Lys Asp Ser Val Val Lys Pro 210 215 220 Asp Glu Val Ala Gly Met Val Ser Lys Lys Ser Pro Lys Leu Gln Ala 225 230 235 240 Ala Leu Ser Lys Gly Ile Gln Glu Leu Arg Lys Asp Gly Thr Leu Lys 245 250 255 Lys Leu Ser Gln Lys Tyr Phe Gly Thr Asp Leu Thr Thr Lys 260 265 270 48 221 PRT Lactobacillus rhamnosus 48 Met Pro Asp Val Arg Phe His Ser Val Phe Asp Ile Ile Gly Pro Val 1 5 10 15 Met Val Gly Pro Ser Ser Ser His Thr Ala Gly Ala Ala Arg Ile Gly 20 25 30 Lys Val Val Arg Asp Ile Phe Gly Glu Pro Pro Glu Thr Ile Thr Ile 35 40 45 Tyr Leu Tyr Glu Ser Phe Ala Lys Thr Tyr Arg Gly His Gly Thr Asp 50 55 60 Val Ala Leu Val Ala Gly Leu Leu Gly Met Ala Pro Asp Asp Pro Arg 65 70 75 80 Leu Pro Glu Ser Leu Lys Leu Ala Tyr Asp Gln Gly Ile Lys Val Ser 85 90 95 Phe Val Pro Lys Ser Asp Lys Val Asp His Pro Asn Thr Ala His Ile 100 105 110 Val Leu Gln Ala Gly Asp His Arg Leu Ala Val Thr Gly Val Ser Ile 115 120 125 Gly Gly Gly Asn Ile Gln Ile Thr Glu Ile Asn Gly Phe Lys Ile Ser 130 135 140 Leu Ser Met Gly Gln Pro Thr Tyr Ile Thr Ile His

Asp Asp Val Pro 145 150 155 160 Gly Met Ile Ala Gln Val Thr Lys Ile Phe Ser Asp Ala Gly Ile Asn 165 170 175 Ile Gly Thr Met Thr Val Thr Arg Thr Ala Lys Gly Glu Gln Ala Ile 180 185 190 Met Ile Ile Glu Thr Asp Asp Tyr His Asp Asp Ile Leu Ala Lys Leu 195 200 205 Lys Leu Leu Pro His Met Arg Asn Val Thr Tyr Phe Glu 210 215 220 49 289 PRT Lactobacillus rhamnosus 49 Met Phe Tyr Thr Val Lys Glu Leu Val Glu Gln Ser His Ala Phe Ser 1 5 10 15 Ser Val Ala Glu Leu Met Val His Thr Glu Val Glu Asn Ser Thr Arg 20 25 30 Thr Glu Ala Gln Ile Arg His Leu Met Ser Arg Asn Leu Glu Val Met 35 40 45 Glu Arg Ser Val Lys Glu Gly Ile Ala Gly Val Lys Ser Val Thr Gly 50 55 60 Leu Thr Gly Gly Glu Ala Lys Lys Leu Asn His Tyr Ile Ala Asp Asp 65 70 75 80 Arg Phe Met Ser Gly Lys Pro Ile Met Glu Ala Val Arg Asn Ala Val 85 90 95 Ala Val Asn Glu Val Asn Ala Lys Met Gly Leu Ile Cys Ala Thr Pro 100 105 110 Thr Ala Gly Ser Ala Gly Val Leu Ala Gly Val Leu Leu Ala Met Arg 115 120 125 Asp Arg Leu His Leu Thr His Asp Gln Gln Leu Asp Phe Leu Phe Thr 130 135 140 Ala Gly Ala Phe Gly Leu Val Ile Ala Asn Asn Ala Gly Ile Ala Gly 145 150 155 160 Ala Glu Gly Gly Cys Gln Glu Glu Val Gly Ser Ala Ser Ala Met Ala 165 170 175 Ala Ala Ala Leu Val Cys Ala Asn Gly Gly Ser Ala Glu Gln Ala Ala 180 185 190 Thr Ala Val Ala Ile Thr Leu Gln Asn Met Leu Gly Leu Val Cys Asp 195 200 205 Pro Val Ala Gly Leu Val Glu Val Pro Cys Val Lys Arg Asn Ala Leu 210 215 220 Gly Ala Ser Gln Ala Met Ile Ser Ala Asp Met Ala Leu Ala Gly Cys 225 230 235 240 Ile Ser Val Ile Pro Ala Asp Glu Val Ile Glu Ala Val Asn Arg Val 245 250 255 Gly Met Gln Leu Pro Ala Thr Leu Arg Glu Thr Gly Glu Gly Gly Leu 260 265 270 Ala Thr Thr Pro Thr Gly Leu Arg Leu Lys Glu Gln Ile Phe Gly Lys 275 280 285 Lys 50 368 PRT Lactobacillus rhamnosus 50 Met Phe Lys Pro Thr Ile His Gln Leu His Pro Tyr Thr Pro Glu Lys 1 5 10 15 Pro Leu Ala Val Leu Lys Glu Glu Leu Gly Leu Pro Gln Leu Val Arg 20 25 30 Met Ser Ala Asn Glu Asn Pro Phe Gly Thr Ser Val Lys Val Gln Gln 35 40 45 Ala Val Thr Asn Trp Asn Phe Thr Gln Ser Arg Asp Tyr Pro Asp Gly 50 55 60 Tyr Ala Ser Gln Leu Arg Thr Ala Val Ala Lys His Leu Asp Val Ala 65 70 75 80 Ala Glu Gln Leu Val Phe Gly Asn Gly Leu Asp Glu Val Ile Ala Leu 85 90 95 Ile Ala Arg Thr Phe Leu Ser Pro Gly Asp Glu Val Ile Glu Pro Trp 100 105 110 Pro Thr Phe Ser Glu Tyr Arg Leu His Ala Gln Ile Glu Gly Ala Thr 115 120 125 Val Ile Asp Val Pro Val Thr Glu Thr Gly Asn Phe Asp Leu Ser Ala 130 135 140 Met Ala Gln Ala Leu Thr Ala Lys Thr Lys Leu Ile Trp Val Cys Asn 145 150 155 160 Pro Asn Asn Pro Thr Gly Thr Leu Leu Ser Ile Ala Thr Leu Thr Glu 165 170 175 Trp Leu Arg Gln Ile Pro Lys Asp Val Leu Val Leu Met Asp Glu Ala 180 185 190 Tyr Ile Glu Phe Thr Asp Asp Tyr Pro Ala Thr Ser Ala Ile Ser Leu 195 200 205 Leu Ser Lys Phe Pro Asn Leu Val Val Leu Arg Thr Phe Ser Lys Ile 210 215 220 Tyr Gly Leu Ala Asn Phe Arg Val Gly Phe Gly Val Phe Pro Lys Gln 225 230 235 240 Leu Val Asn Tyr Leu Gln Thr Val Arg Leu Pro Tyr Asn Leu Ser Ser 245 250 255 Ile Ala Gln Val Ser Ala Gln Ala Ala Leu Ala Asp Gln Asp Phe Val 260 265 270 Ala Met Thr Arg Lys Arg Val Gln Gln Ala Arg Asp Ser Trp Glu Arg 275 280 285 Phe Leu Thr Gln Thr Gly Leu Pro His Thr Arg Ser Gln Thr Asn Phe 290 295 300 Gln Phe Phe Gln Ala Pro Lys Met Gln Ala Ser Ala Leu Lys Lys Arg 305 310 315 320 Leu Leu Gln Gln Gly Phe Leu Val Arg Asp Gly Leu Lys Pro Gly Trp 325 330 335 Leu Arg Val Thr Phe Gly Thr Glu Val Gln Asn Thr Ala Val Gln Arg 340 345 350 Ile Ile Glu Thr Phe Gln Ala Glu Leu Thr Gly Pro Asn Ala Leu Lys 355 360 365 51 301 PRT Lactobacillus rhamnosus 51 Leu Ala Arg Thr Ile Gly Ile Ile Gly Ile Gly His Val Gly Val Thr 1 5 10 15 Thr Ala Phe Asn Leu Val Ser Lys Gly Ile Ala Asp Arg Leu Val Leu 20 25 30 Ile Asp Gln Lys Ala Asp Leu Ala Glu Gly Glu Ser Tyr Asp Leu Lys 35 40 45 Asp Ala Leu Gly Gly Leu Pro Thr Tyr Thr Glu Ile Ile Val Asn Asp 50 55 60 Tyr Asp Ala Leu Lys Asp Ala Asp Val Val Ile Ser Ala Val Gly Asn 65 70 75 80 Ile Gly Ala Ile Ser Asn Gly Asp Arg Ile Gly Glu Thr Gln Thr Ser 85 90 95 Lys Gln Ala Leu Asp Asp Val Ala Pro Lys Leu Lys Ala Ser Gly Phe 100 105 110 His Gly Val Leu Leu Asp Ile Thr Asn Pro Cys Asp Ala Val Thr Ser 115 120 125 Tyr Trp Gln Tyr Leu Leu Asp Leu Pro Lys Ser Gln Ile Ile Gly Thr 130 135 140 Gly Thr Ser Leu Asp Thr Tyr Arg Met Arg Arg Ala Val Ala Glu Ser 145 150 155 160 Leu Asn Val Asn Val Ala Asp Val Arg Gly Tyr Asn Met Gly Glu His 165 170 175 Gly Glu Ser Gln Phe Thr Ala Trp Ser Thr Val Arg Val Asn Asn Glu 180 185 190 Pro Ile Thr Asp Tyr Ala Gln Val Asp Tyr Asp Gln Leu Ala Asp Ala 195 200 205 Ala Arg Ala Gly Gly Trp Lys Ile Tyr Gln Ala Lys His Tyr Thr Ser 210 215 220 Tyr Gly Ile Ala Thr Ile Ala Thr Glu Met Thr Gln Ala Ile Ile Ser 225 230 235 240 Asp Ala Lys Arg Ile Phe Pro Cys Ala Asn Tyr Asp Pro Glu Phe Gly 245 250 255 Ile Ala Ile Gly His Pro Ala Thr Ile Gly Lys Leu Gly Val Val Asn 260 265 270 Thr Pro Lys Leu Lys Leu Thr Asp Glu Glu Arg Ala Lys Tyr Val His 275 280 285 Ser Ala Gly Ile Ile Lys Ala Thr Val Glu Lys Met Lys 290 295 300 52 495 PRT Lactobacillus rhamnosus 52 Leu Asp His Asp Leu Leu Lys Ala Ile Ala Gln Ser Gly Phe Glu Glu 1 5 10 15 Ala Thr Pro Ile Gln Ala Glu Thr Ile Pro Leu Val Leu Glu Gly Lys 20 25 30 Asp Val Ile Gly Gln Ala Gln Thr Gly Thr Gly Lys Thr Ala Ala Phe 35 40 45 Gly Leu Pro Ile Leu Gln His Ile Asp Lys Ala Asp Arg Ser Ile Gln 50 55 60 Ala Leu Val Ile Ser Pro Thr Arg Glu Leu Ala Ile Gln Thr Gln Glu 65 70 75 80 Glu Leu Tyr Arg Leu Gly Arg Asp Lys Lys Ile Lys Val Gln Ala Val 85 90 95 Tyr Gly Gly Ala Asp Ile Arg Arg Gln Ile Arg Gln Leu Ala Asp His 100 105 110 Pro Gln Ile Val Val Gly Thr Pro Gly Arg Ile Leu Asp His Ile Gly 115 120 125 Arg His Thr Leu Lys Leu Glu His Leu Asp Thr Leu Val Leu Asp Glu 130 135 140 Ala Asp Glu Met Leu Asp Met Gly Phe Ile Asp Asp Ile Glu Lys Ile 145 150 155 160 Val Glu Gln Met Pro Thr Glu Arg Gln Thr Leu Leu Phe Ser Ala Thr 165 170 175 Met Pro Ala Ala Ile Met Arg Leu Thr Asn Lys Phe Met Lys Glu Pro 180 185 190 Val Ile Val Lys Ile Lys Ala Lys Glu Leu Thr Ala Asp Thr Val Glu 195 200 205 Gln Tyr Tyr Val Arg Ala Lys Asp Tyr Glu Lys Phe Asp Val Met Thr 210 215 220 Arg Leu Phe Asp Val Gln Asp Pro Asp Leu Ala Leu Ile Phe Gly Arg 225 230 235 240 Thr Lys Arg Arg Val Asp Glu Leu Thr Arg Gly Leu Lys Ala Arg Gly 245 250 255 Tyr Arg Ala Glu Gly Ile His Gly Asp Leu Thr Gln Gln Lys Arg Met 260 265 270 Ser Val Leu Arg Gln Phe Lys Ser Gly Gln Leu Asp Phe Leu Val Ala 275 280 285 Thr Asp Val Ala Ala Arg Gly Leu Asp Ile Ser Gly Val Thr His Val 290 295 300 Tyr Asn Tyr Asp Ile Pro Gln Asp Pro Asp Ser Tyr Val His Arg Ile 305 310 315 320 Gly Arg Thr Gly Arg Ala Gly His Lys Gly Val Ser Val Thr Phe Val 325 330 335 Thr Pro Asn Glu Ile Glu Tyr Leu His Thr Ile Glu Asp Leu Thr Lys 340 345 350 Lys Arg Met Leu Pro Met Lys Pro Pro Thr Ala Glu Glu Ala Leu Met 355 360 365 Gly Gln Ile Ser Ser Gly Leu Ala Thr Ile Lys Glu Gln Val Glu Ala 370 375 380 Asn Asp Thr Glu Lys Tyr Glu Ala Met Ala Glu Thr Leu Leu Glu Asn 385 390 395 400 Tyr Thr Pro Leu Gln Leu Val Ser Ala Tyr Leu Lys Ala Val Ser Pro 405 410 415 Asp Asp Ala Ser Ala Val Pro Val Lys Ile Thr Pro Glu Arg Pro Leu 420 425 430 Pro Arg Arg Gly Arg Asn Asn His Gly His Gly Asn Asn Arg Gly Gly 435 440 445 Tyr Lys Gly Gly Tyr Lys Gly Lys Arg Arg Asp Gly Gly Tyr Gln Gly 450 455 460 Asn Arg Asp Gly Lys Arg Ser Tyr Asp Lys Lys Arg Asn Phe Gly Asp 465 470 475 480 Lys Arg Lys Asn Val Lys Arg Asn Phe Lys Ile Arg Thr Gly Glu 485 490 495 53 390 PRT Lactobacillus rhamnosus 53 Met Thr Leu Gln Pro Leu Asn Glu Gln Leu Pro Ala Ile Glu Val Ser 1 5 10 15 Glu Ile Arg Gln Phe Asp Glu Ser Val Ser Asp Ile Pro Gly Ile Leu 20 25 30 Lys Leu Thr Leu Gly Glu Pro Asp Phe Asn Thr Pro Glu His Val Lys 35 40 45 Gln Ala Gly Ile Lys Ala Ile Gln Glu Asn Tyr Ser His Tyr Thr Gly 50 55 60 Met Val Gly Asp Pro Glu Leu Arg Glu Ala Ala Gln His Phe Phe Lys 65 70 75 80 Thr Lys Tyr Ala Thr Asp Tyr Arg Ala Thr Asp Glu Ile Leu Val Thr 85 90 95 Val Gly Ala Thr Glu Ala Leu Ala Thr Ala Ile Thr Thr Ile Ser Asp 100 105 110 Pro Gly Asp Ala Met Leu Val Pro Ser Pro Ile Tyr Pro Gly Tyr Ile 115 120 125 Pro Leu Leu Thr Leu Asn His Val Thr Pro Leu Tyr Met Asp Thr Ser 130 135 140 Lys Thr Asp Phe Val Leu Thr Pro Glu Leu Ile Glu Ala Thr Ile Thr 145 150 155 160 Ala Asn Pro Asp Ala Lys Ile Lys Gly Ile Ile Leu Asn Tyr Pro Ser 165 170 175 Asn Pro Thr Gly Val Thr Tyr Arg Ala Ala Glu Val Lys Ala Ile Ala 180 185 190 Asp Ile Ala Ala Lys His Asn Leu Tyr Ile Ile Cys Asp Glu Ile Tyr 195 200 205 Ser Glu Leu Thr Tyr Gly Glu Pro His Val Ser Met Gly Gln Phe Ala 210 215 220 Tyr Asp Arg Thr Phe Ile Val Asn Gly Leu Ser Lys Ser His Ala Met 225 230 235 240 Thr Gly Trp Arg Ile Gly Phe Leu Met Gly Pro Gln Gln Leu Ile Ala 245 250 255 Gln Ala Lys Lys Val His Gln Tyr Leu Val Thr Ala Ala Thr Thr Ile 260 265 270 Ala Gln Arg Ala Gly Ile Glu Ala Leu Thr Asn Gly Ala Asp Asp Ala 275 280 285 Gln Val Met Lys Ala Ala Tyr Val Lys Arg Arg Asp Phe Val Tyr Ala 290 295 300 Ala Leu Ile Asp Met Gly Phe Ser Val Ala Arg Pro Asp Gly Ala Phe 305 310 315 320 Tyr Leu Phe Ala Lys Ile Pro Thr Gln Leu His Leu Ser Ser Arg Glu 325 330 335 Phe Thr His Ala Leu Ala His Glu Gln Lys Leu Ala Leu Ile Ser Gly 340 345 350 Thr Ala Phe Gly Pro Gly Gly Glu Gly Tyr Ile Arg Ile Ser Tyr Ala 355 360 365 Ala Ser Met Thr Asp Leu Gln Glu Ala Val Lys Arg Leu Arg Ala Phe 370 375 380 Met Ala Ser His Ile Gly 385 390 54 391 PRT Lactobacillus rhamnosus 54 Val His Leu Ala Lys Arg Ile Leu Asn Val Ala Pro Ser Ala Thr Leu 1 5 10 15 Ala Leu Ser Asn Gln Thr Lys Asp Leu Lys Ala Lys Gly Ala Asp Val 20 25 30 Ile Asp Leu Ser Ile Gly Gln Pro Asp Phe Ser Thr Pro Lys Ala Ile 35 40 45 Asp Asp Ala Ala Ile Ala Ala Ile Gln Ala Gly Asn Ala Ser Phe Tyr 50 55 60 Thr Ala Ala Thr Gly Ile Pro Glu Leu Lys Gln Ala Ile Ser Asp Arg 65 70 75 80 Ile Phe Ala Gln Asp Gly Ile Arg Tyr Asp His Arg Gln Ile Val Ala 85 90 95 Thr Thr Gly Ala Lys Phe Ala Leu Tyr Ala Leu Phe Gln Val Phe Leu 100 105 110 Asn Pro Gly Asp Glu Val Leu Ile Pro Val Pro Tyr Trp Val Ser Tyr 115 120 125 Glu Glu Gln Ile Lys Leu Ala Ser Gly Val Pro His Leu Val Met Pro 130 135 140 Ala Val Gly His Lys Val Ser Val Asp Asp Leu Glu Ala Ala Arg Thr 145 150 155 160 Asp Lys Thr Arg Ala Leu Ile Ile Asn Ser Pro Gln Asn Pro Ser Gly 165 170 175 Val Val Tyr Asp Arg Thr Glu Leu Thr Leu Ile Gly Asn Trp Ala Leu 180 185 190 Lys His His Ile Leu Val Val Thr Asp Asp Ile Tyr Arg Asp Leu Ile 195 200 205 Tyr Asn Gly Thr Thr Tyr Thr Ser Met Ile Ser Ile Asp Pro Asp Ile 210 215 220 Ala Ala Asn Thr Val Leu Ile Ser Gly Val Ser Lys Ser Tyr Ala Met 225 230 235 240 Thr Gly Trp Arg Ile Gly Tyr Ala Ala Gly Pro Glu Lys Leu Ile Gln 245 250 255 Ala Met Ala Thr Phe Ile Ser His Thr Thr Ser Asn Pro Ala Ala Val 260 265 270 Ser Glu Tyr Ala Ala Val Ala Ala Leu Thr Gly Asp Gln Gln Val Val 275 280 285 Glu Lys Met Arg Arg Ala Phe Glu Glu Arg Leu Asn Leu Phe Tyr Asp 290 295 300 Leu Leu Ala Asp Ile Pro Gly Phe Asp Met Gly Asp Lys Pro Gln Gly 305 310 315 320 Ala Phe Tyr Leu Phe Pro Asn Ile Lys Arg Ala Ala Gln Leu Ser His 325 330 335 Tyr Gly Thr Val Asp Asp Phe Ile Ser Ala Leu Leu Thr Glu Thr Gly 340 345 350 Val Ala Ile Val Pro Gly Arg Ala Phe Gly Met Pro Asp His Ala Arg 355 360 365 Ile Ser Tyr Cys Lys Asp Leu Ala Ser Leu Lys Glu Ala Ala Arg Arg 370 375 380 Ile Arg Glu Phe Val Gly Lys 385 390 55 301 PRT Lactobacillus rhamnosus 55 Met Gln Arg Ala Glu Leu Ile Thr Ala Ile Val Thr Pro Phe Asn Asp 1 5 10 15 Arg Asp Glu Ile Asp Tyr Asp Ser Met Gln Arg Leu Val Asp His Leu 20 25 30 Ile Asp Gln Gly Thr Asp Gly Phe Val Val Gly Ala Thr Thr Gly Glu 35 40 45 Gly Pro Thr Leu Ser His Asp Glu Lys Ile Thr Leu Tyr Thr Arg Phe 50 55 60 Val Ala Met Val His Gly Arg Ala Leu Val Ile Ala Asn Ser Gly Ser 65 70 75 80 Asn Asn Thr Arg Glu Thr Thr Asp Phe Thr His Glu Val Gly Gly Ile 85 90 95 Ala Gly Ile Asp Ala Thr Leu Val Val Val Pro Tyr Tyr Asn Lys Pro 100 105 110 Asp Gln Asp Gly Met Ile

Ala His Tyr Thr Thr Val Ala Ala Ser Ala 115 120 125 Gln Lys Pro Ile Ile Ile Tyr Asn Ile Pro Gly Arg Thr Gly Val Asn 130 135 140 Met Leu Pro Glu Thr Val Ala Thr Leu Ala Gln Asn Pro Met Ile Gln 145 150 155 160 Gly Ile Lys Gln Cys Gly Ser Leu Ala Ala Leu Ser Asp Ile Ile Asp 165 170 175 Arg Thr Lys His Asp Ala Phe Asn Val Trp Thr Gly Glu Asp Ala Gln 180 185 190 Ala Leu Thr Ile Lys Thr Leu Gly Gly Met Gly Val Ile Ser Val Ala 195 200 205 Ser His Leu Tyr Ala His Ser Ile Arg Glu Met Tyr Arg Ala Leu Asp 210 215 220 Arg Gly Asp Ile Thr Thr Val Ala Ala Leu Gln Arg Gln Leu Leu Pro 225 230 235 240 Lys Met Ala Ala Leu Phe His Phe Pro Ser Pro Ala Pro Thr Lys Ala 245 250 255 Ala Leu Asn Ala Leu Gly Phe Lys Val Gly Ser Pro Arg Leu Pro Leu 260 265 270 Leu Pro Leu Thr Ala Ala Gln Gln Gln Glu Leu Ala His Leu Leu Gly 275 280 285 Val Ser Glu Leu Ser Ala Ile Glu Ala Glu Val Leu Ala 290 295 300 56 255 PRT Lactobacillus rhamnosus 56 Met Ile His Val Leu Val Ala Gly Phe Arg Gly Ala Met Gly Gln Lys 1 5 10 15 Thr Val Lys Met Val Gln Ser Gln Lys Asp Phe Ala Leu Ser Ala Val 20 25 30 Phe Asp Pro Lys Ala Thr Ala Ala Asp Ala Gln Lys Tyr Gly Leu Pro 35 40 45 Ala Asp Thr Lys Val Leu Thr Ser Tyr Asp Gln Leu Asn Pro Asp Ile 50 55 60 Ala Asp Val Trp Val Asp Phe Thr Asn Pro Thr Ala Val Ala Ala Asn 65 70 75 80 Ile Glu Ala Ala Ile Lys Ala Gly Ile His Pro Val Val Gly Thr Ser 85 90 95 Gly Met Thr Gln Ala Asp Gln Asn Arg Leu Ile Glu Leu Ala Gln Ala 100 105 110 Arg His Ile Gly Gly Leu Ile Ala Pro Asn Phe Gly Leu Ser Ala Val 115 120 125 Leu Leu Met Lys Phe Ala Gln Glu Ala Ala Ala Tyr Phe Pro Asp Ala 130 135 140 Glu Ile Ile Glu Met His His Gln Asp Lys Ala Asp Ala Pro Ser Gly 145 150 155 160 Thr Ala Ile Ala Thr Ala His Lys Ile Ala Ala Gly Arg Thr Gln Lys 165 170 175 Pro Leu Ser Thr Ile Asp Asn Asp Ala Arg Gly Gln Arg Ile Asp Asp 180 185 190 Val Pro Val His Ala Val Arg Leu Pro Gly Tyr Ile Ala His Glu Gln 195 200 205 Val Leu Phe Gly Gly Pro Gly Glu Ala Leu Thr Ile Arg Gln Asp Ser 210 215 220 Phe Asp Arg Gln Ser Phe Met Gln Gly Val Ala Val Ala Ile Arg Lys 225 230 235 240 Val Gln Ala Ala Asp His Leu Val Val Gly Leu Glu Asn Phe Leu 245 250 255 57 334 PRT Lactobacillus rhamnosus 57 Met Tyr His Ala Ala Ala Asp Arg Tyr Glu Lys Met Pro Val Arg His 1 5 10 15 Ala Gly Lys Thr Gly Leu Met Leu Pro Val Ile Ser Leu Gly Leu Trp 20 25 30 Gln His Tyr Gly Asn Leu Asp Pro Phe Gly Pro Arg Arg Ser Val Ile 35 40 45 Leu Asp Ala Phe Asp Arg Gly Val Phe His Phe Asp Val Ala Asn His 50 55 60 Tyr Gly Asn Gly Asp Arg Glu Pro Gly Phe Gly Ser Ser Glu Arg Leu 65 70 75 80 Leu Gly Gln Ile Leu Ala Thr Asp Leu Lys Pro Tyr Arg Asp Glu Leu 85 90 95 Val Ile Ser Thr Lys Val Gly Tyr Glu Ile His Pro Gly Pro Tyr Gly 100 105 110 Val Gly Thr Ser Arg Lys Ala Val Ile Gln Gly Leu Asn Asp Ser Leu 115 120 125 Lys Arg Leu Gln Leu Asp Tyr Val Asp Ile Tyr Tyr Ala His Arg Phe 130 135 140 Asp Asp Thr Val Ala Leu Glu Glu Thr Val Asn Ala Leu Asp Gln Thr 145 150 155 160 Val Arg Asp Gly Lys Ala Leu Tyr Ile Gly Ile Ser Asn Tyr Asp Thr 165 170 175 Lys Gln Thr Lys Glu Ala Ile Ala Met Phe Lys Asp Leu His Thr Pro 180 185 190 Phe Val Leu Asn Gln Tyr Ser Tyr Asn Met Phe Asn Arg Thr Ala Glu 195 200 205 Thr Ser Gly Leu Ile Asp Ala Leu Lys Ala Asp Gly Ala Gly Leu Ile 210 215 220 Ala Tyr Gly Pro Leu Ser Glu Gly Leu Leu Ser Asp Arg Tyr Leu Lys 225 230 235 240 Gly Ile Pro Asp Thr Phe Lys Ile His Pro Thr Asn Lys Ala Thr Phe 245 250 255 Ala Lys Gly Lys Glu Ala Val Val Lys Gln Leu Asn Ala Leu Asn Glu 260 265 270 Ile Ala His Asp Arg Asp Gln Thr Leu Ser Gln Met Ala Leu Ala Trp 275 280 285 Leu Leu Arg Asp Pro Val Val Thr Ser Val Ile Ile Gly Thr Thr Ser 290 295 300 Val Glu His Leu Gln Asp Asn Leu Lys Ala Thr Glu His Leu Thr Phe 305 310 315 320 Thr Ala Glu Glu Ile Gln Gln Ile Asp Asp Ile Leu Asn Ala 325 330 58 274 PRT Lactobacillus rhamnosus 58 Met Ala Lys Met Trp Lys Arg Met Leu Leu Pro Leu Val Leu Leu Leu 1 5 10 15 Leu Met Ile Pro Leu Ser Ser Cys Gly Lys Ser Val Ala Asp Arg Asp 20 25 30 Ile Leu Ala Asn Ala Lys Ala Thr Asn Thr Ile Ile Trp Gly Val Lys 35 40 45 Ala Asp Thr Arg Leu Phe Gly Leu Met Asn Ile Lys Thr Gly Lys Ile 50 55 60 Glu Gly Phe Asp Val Asp Met Ala Lys Ala Ile Thr Lys Gln Ile Leu 65 70 75 80 Gly Lys Lys Gly Asn Ala Gln Leu Val Gln Val Thr Ser Asp Thr Arg 85 90 95 Val Pro Met Ile Lys Gly Gly Asn Leu Asp Ala Val Ile Ala Thr Met 100 105 110 Thr Ile Thr Pro Glu Arg Gln Lys Ile Leu Asp Phe Ser Asp Val Tyr 115 120 125 Phe Asn Ala Gly Gln Ser Leu Leu Val Lys Lys Gly Ser Pro Ile Lys 130 135 140 Ser Val Lys Asp Leu Lys Lys Gly Thr Lys Val Ile Gly Val Gln Gly 145 150 155 160 Ser Asn Ser Val Asp Asn Val Lys Lys Ala Ala Pro Asp Thr Thr Val 165 170 175 Leu Gln Leu Ala Asp Tyr Ala Gln Ala Phe Thr Ala Leu Lys Ser Gly 180 185 190 Gln Gly Asp Ala Leu Thr Thr Asp Asn Gly Ile Leu Tyr Gly Met Ser 195 200 205 Glu Gln Asp Lys Asn Tyr Ile Val Thr Gly Gly Thr Phe Thr Lys Glu 210 215 220 Pro Tyr Gly Ile Ala Ile Asn Lys Gly Gln Lys Pro Phe Val Asn Ala 225 230 235 240 Val Asn Lys Ala Ile Lys Gln Leu Lys Gln Asn Gly Thr Tyr Ala Lys 245 250 255 Leu Ile Lys Lys Trp Phe Gly Asp Val Pro Gly Phe Ser Leu Lys Glu 260 265 270 Val Glu 59 390 PRT Lactobacillus rhamnosus 59 Met Lys Leu Thr Ile Tyr Asp Phe Asp His Val Ile Asp Arg Arg Gly 1 5 10 15 Thr Phe Ser Thr Gln Trp Asp Tyr Ile Ala Asp Arg Phe Gly Arg Asn 20 25 30 Asp Ile Leu Pro Phe Ser Ile Ser Asp Thr Asp Phe Pro Val Pro Val 35 40 45 Glu Val Gln Asp Ala Leu Lys Glu Arg Leu Thr His Pro Ile Tyr Gly 50 55 60 Tyr Thr Arg Trp Asn His Ala Thr Tyr Lys Asp Ser Ile Val His Trp 65 70 75 80 Phe Glu Arg Asp Gly His Thr Lys Ile Asn Pro Asp Trp Ile Val Tyr 85 90 95 Ser Pro Ser Val Val Phe Thr Ile Ala Thr Leu Ile Arg Met Lys Ser 100 105 110 Asp Pro Gly Asp Gly Val Ala Val Phe Thr Pro Met Tyr Asp Ala Phe 115 120 125 Tyr Gly Thr Ile Lys Gln Asn Asp Arg Val Leu Ile Pro Ile Arg Leu 130 135 140 Ala Ala Ala Asp Glu Gly Tyr Val Ile Asp Trp Asp Ser Leu Ala Thr 145 150 155 160 Val Leu Ala Glu Lys Gln Thr Lys Ile Phe Leu Leu Thr Asn Pro His 165 170 175 Asn Pro Thr Gly His Val Phe Thr Lys Ser Glu Leu Ala Arg Leu Tyr 180 185 190 Asp Leu Cys Gln Ala Ala His Val Phe Leu Ile Ser Asp Asp Ile His 195 200 205 Arg Asp Ile Val Tyr Pro Gly His Ser Tyr Glu Pro Met Thr Asn Val 210 215 220 Gly Thr Ser Asp Val Ala Leu Cys Cys Ser Gly Ser Lys Thr Phe Asn 225 230 235 240 Thr Pro Gly Leu Ile Gly Ser Tyr Ala Phe Leu Pro Asp His Asp Val 245 250 255 Arg Ala Gln Phe Leu Thr Glu Leu Lys Gln Lys Asn Ala Leu Ser Ser 260 265 270 Val Ser Ile Phe Gly Met Leu Ala Gln Ile Ala Ala Tyr Asn Gly Ser 275 280 285 Glu Asp Tyr Val Glu Gln Leu Thr Ala Tyr Thr Lys Asn Asn Met Glu 290 295 300 Leu Val Ala Ser Tyr Leu Glu Glu Asn Leu Pro Glu Leu Gln Phe Ser 305 310 315 320 Leu Pro Asp Ala Thr Tyr Leu Ala Trp Ile Asn Val Ser Lys Leu Arg 325 330 335 Leu Thr Ser Glu Glu Leu Gln His Arg Leu Val Asn Gly Gly His Val 340 345 350 Gly Ile Met Ala Gly Lys Thr Tyr Gly Asp Thr Arg Tyr Leu Arg Met 355 360 365 Asn Ile Ala Cys Pro Lys Lys Lys Leu Val Met Gly Leu Glu Arg Leu 370 375 380 Lys Lys Gly Ile Arg Gly 385 390 60 416 PRT Lactobacillus rhamnosus 60 Met Arg Thr Met Thr Thr Lys Ala Arg Lys Gln Gly Ser Leu Met Glu 1 5 10 15 Asp Leu Pro Thr Asp Ile Ala Thr Phe Val Asp Thr His Leu Val Asp 20 25 30 Arg His Asn Ser Asn Ala Val Lys Trp Asp Gly Leu Lys Glu Glu Phe 35 40 45 Gly Arg Ala Asp Leu Leu Pro Met Trp Ile Ala Asp Thr Glu Phe Lys 50 55 60 Ala Pro Gln Ala Val Leu Asp Ala Leu Thr Val Arg Val Lys Glu Gly 65 70 75 80 Thr Phe Gly Tyr Ser Ile Arg Pro Gln Ser Tyr Tyr Glu Ala Phe Ile 85 90 95 Asn Trp Gln Lys Glu Arg His Gly Ile Thr Val Glu Pro Glu Trp Met 100 105 110 Arg Phe Gly Val Gly Val Val Lys Ser Leu Tyr Ala Met Val Asn Trp 115 120 125 Leu Thr Glu Pro Gly Asp Pro Val Leu Ile Met Gln Pro Val Tyr Tyr 130 135 140 Pro Phe Met Asn Ala Ile Asn Asp Leu Gly Arg Lys Val Val Ser Val 145 150 155 160 Asp Leu Gln Leu Thr Ala Asp Gly Trp Arg Met Asp Phe Asp Gln Leu 165 170 175 Glu Lys Thr Leu Ala Ala Asn Glu Ile Lys Ala Met Ile Leu Cys Ser 180 185 190 Pro His Asn Pro Val Gly Arg Ile Trp Thr Arg Asp Glu Leu Glu Gln 195 200 205 Leu Phe Ala Ile Thr Ser Arg Tyr Asp Val Thr Val Val Ser Asp Glu 210 215 220 Ile His Gly Asp Leu Glu Val Ser Gly Pro Lys Phe Thr Ser Ala Leu 225 230 235 240 Gln Val Ala Glu Gly Lys Ala Arg Lys Lys Leu Val Val Leu Asn Ala 245 250 255 Pro Ser Lys Thr Phe Asn Leu Ala Ala Leu Leu Asn Ser His Ile Ile 260 265 270 Ile Pro Asp Gln Ala Leu Arg Thr Ser Tyr Asp Ala Phe Ile Lys Gln 275 280 285 Leu His Pro Val Asp Thr Ser Leu Met Gly Gln Val Ala Gly Glu Ala 290 295 300 Ala Tyr Arg His Gly Ala Ala Trp Leu Asp Gln Val Leu Gln Val Val 305 310 315 320 Arg Tyr Asn Tyr Arg Gln Leu Gln Ala Gly Leu Ala Ala Ala Ala Pro 325 330 335 Gln Ala Thr Leu Ala Asp Leu Gln Gly Thr Tyr Leu Ala Tyr Val Asp 340 345 350 Ile Gly Ala Tyr Val Ala Pro Ser Gln Ile Lys Asp Phe Val Glu Gly 355 360 365 Val Cys Gly Leu Ala Val Asp Tyr Gly Ala Trp Phe Ser Pro Gln Thr 370 375 380 Ala Thr Tyr Ile Arg Leu Asn Leu Ala Thr Asp Pro Lys Leu Val Ala 385 390 395 400 Glu Ala Ile Asn Arg Leu Thr Thr His Leu Ala Gln Gln Pro Gln Arg 405 410 415 61 332 PRT Lactobacillus rhamnosus 61 Met Ser Val Lys Leu Thr Ala Gly Gln Leu Glu His Leu Lys Gln Leu 1 5 10 15 Ser Asn Asp Asn Asn Val Ile Ser Ala Leu Ala Ile Asp Gln Arg Gly 20 25 30 Ser Leu Lys Lys Met Leu Ala Ala Ala Ala Asn Lys Pro Ala Asp Glu 35 40 45 Thr Thr Ile Val Asp Phe Lys Lys Ala Val Ser Glu Glu Leu Thr Lys 50 55 60 Tyr Ala Ser Ala Ile Leu Leu Asp Pro Glu Tyr Gly Leu Pro Ala Ala 65 70 75 80 Lys Val Arg Asp Pro Lys Ser Gly Leu Leu Leu Ser Tyr Glu Lys Thr 85 90 95 Gly Tyr Asp Ala Thr Glu Pro Gly Arg Phe Pro Asp Leu Ile Asp Asn 100 105 110 Gln Ser Ala Leu Arg Ile Lys Asn Glu Gly Gly Asp Ala Val Lys Phe 115 120 125 Leu Leu Tyr Ile Asp Pro Asp Glu Pro Asp Ser Ile Asn Asp Arg Lys 130 135 140 Tyr Ala Phe Val Glu Arg Val Gly Ala Glu Ala Lys Ala Asn Asp Leu 145 150 155 160 Pro Leu Phe Leu Glu Leu Val Ser Tyr Asp Gly Lys Thr Asn Glu Thr 165 170 175 Gly Thr Ala Ala Trp Ala Lys Ala Lys Pro Glu Lys Val Ile Lys Ile 180 185 190 Thr Lys Glu Phe Ser Lys Ala Gln Tyr Asn Val Ser Val Leu Lys Leu 195 200 205 Glu Val Pro Val Asp Gln Lys Phe Val Glu Gly Tyr Thr Asp Glu Gly 210 215 220 Val Thr Pro Val Tyr Ser Lys Glu Glu Ala Ala Lys Tyr Tyr Lys Ala 225 230 235 240 Gln Ser Asp Ala Thr Asp Leu Pro Phe Ile Phe Leu Ser Ala Gly Val 245 250 255 Ser Asn Glu Leu Phe Leu Glu Glu Leu Lys Phe Ala Lys Glu Ala Gly 260 265 270 Ser Thr Phe Asn Gly Val Leu Cys Gly Arg Ala Thr Trp Lys Pro Gly 275 280 285 Val Lys Pro Phe Ala Ala Glu Gly Glu Ala Ala Gly Lys Lys Trp Leu 290 295 300 Gln Thr Glu Gly Lys Ala Asn Ile Asp Arg Leu Asn Lys Val Leu Ala 305 310 315 320 Asp Thr Ala Thr Pro Trp Thr Asp Lys Val Glu Gly 325 330 62 434 PRT Lactobacillus rhamnosus 62 Met Ser Ile Ile Thr Asp Val Leu Ala Arg Glu Val Leu Asp Ser Arg 1 5 10 15 Gly Asn Pro Thr Val Glu Val Glu Leu Tyr Thr Glu Asp Gly Gly Phe 20 25 30 Gly Arg Ala Leu Val Pro Ser Gly Ala Ser Thr Gly Glu His Glu Ala 35 40 45 Val Glu Leu Arg Asp Gly Asp Lys Asp Arg Phe Gly Gly Lys Gly Val 50 55 60 Leu Lys Ala Val Asp His Val Asn Asn Glu Ile Ala Lys Ala Val Ile 65 70 75 80 Gly Leu Asp Val Thr Glu Gln Arg Leu Ile Asp Gln Thr Met Ile Asp 85 90 95 Leu Asp Gly Thr Pro Asn Lys Gly Lys Leu Gly Ala Asn Ala Ile Leu 100 105 110 Gly Val Ser Leu Ala Ala Ala Arg Ala Ala Ala Asp Glu Val Gly Leu 115 120 125 Pro Leu Tyr Gln Tyr Leu Gly Gly Pro Asn Ala His Val Leu Pro Thr 130 135 140 Pro Met Met Asn Val Leu Asn Gly Gly Ala His Ser Thr Asn Thr Val 145 150 155 160 Asp Phe Gln Glu Phe Met Ile Met Pro Val Gly Ala Lys Ser Val Arg 165 170 175 Glu Ala Val Arg Met Gly Ser Glu Thr Phe His Ala Leu Gln Ala Leu 180 185 190 Leu Lys Ser Lys Gly Asp Ile Thr Ala Val Gly Asp Glu Gly Gly Phe 195 200 205 Ala Pro Asn Leu Lys Asp Asn Glu Glu Ala Phe Glu Leu Leu Val Glu 210 215 220 Ala Ile Lys Lys Ala Gly Tyr Lys Pro Gly Asp Asp Ile Ala Leu Ala

225 230 235 240 Phe Asp Val Ala Ala Ser Glu Met Tyr Asp Ala Asp Thr Lys Thr Tyr 245 250 255 Thr Thr Lys Trp Ser Asn Pro Asp Lys Lys Tyr Thr Thr Glu Glu Trp 260 265 270 Thr Asn Met Ile Asp Gly Tyr Ile Asn Lys Tyr Pro Ile Val Ser Val 275 280 285 Glu Asp Pro Ile Asp Glu Asn Asp Trp Glu Gly Trp Gln Thr Phe Thr 290 295 300 Glu Lys Met Gly Asp Lys Val Gln Ile Val Gly Asp Asp Leu Phe Val 305 310 315 320 Thr Asn Thr Asp Tyr Leu Lys Lys Gly Ile Asp Met Gly Val Ala Asn 325 330 335 Ser Ile Leu Ile Lys Leu Asn Gln Ile Gly Thr Leu Thr Glu Thr Phe 340 345 350 Glu Ala Ile Glu Met Ala Lys Glu Ala Gly Tyr Thr Ala Val Val Ser 355 360 365 His Arg Ser Gly Glu Thr Glu Asp Thr Thr Ile Ala Asp Leu Val Val 370 375 380 Ala Thr Asn Ala Gly Glu Ile Lys Thr Gly Ser Met Ser Arg Thr Asp 385 390 395 400 Arg Ile Ala Lys Tyr Asn Gln Leu Met Arg Ile Glu Asp Gln Leu Gly 405 410 415 Ala Gln Ser Gln Tyr Lys Gly Arg Lys Ser Phe Tyr Asn Val Lys Ala 420 425 430 Ile Asp 63 251 PRT Lactobacillus rhamnosus 63 Met Arg Thr Pro Phe Ile Ala Gly Asn Trp Lys Met Asn Lys Asn Pro 1 5 10 15 Lys Glu Thr Gln Ala Phe Leu Asp Ala Val Lys Gly Lys Leu Pro Asp 20 25 30 Ala Ser Lys Val Glu Thr Val Ile Gly Ala Pro Ala Ile Asp Leu Thr 35 40 45 Thr Leu Val Ala Gly Ala Glu Gly Thr Pro Leu Lys Thr Ala Ala Glu 50 55 60 Asn Cys Tyr Phe Glu Asp Glu Gly Ala Phe Thr Gly Glu Thr Ser Pro 65 70 75 80 Lys Ala Leu Lys Glu Met Gly Val Asp Tyr Val Ile Ile Gly His Ser 85 90 95 Glu Arg Arg Gly Tyr Phe His Glu Thr Asp Glu Asp Ile Asn Lys Lys 100 105 110 Ala Lys Ala Ile Phe Lys Asn Asn Leu Leu Pro Ile Ile Cys Cys Gly 115 120 125 Glu Ser Leu Ala Gln Arg Glu Ala Gly Gln Thr Glu Asp Trp Val Ala 130 135 140 Ser Gln Ile Glu Ala Ala Leu Ala Gly Leu Ser Ala Asp Gln Val Lys 145 150 155 160 Val Ser Val Leu Ala Tyr Glu Pro Ile Trp Ala Ile Gly Thr Gly Lys 165 170 175 Thr Ala Thr Ala Asp Gln Ala Gln Glu Val Val Ala His Ile Arg Ala 180 185 190 Thr Val Glu Lys Leu Tyr Asn Lys Asp Thr Ala Asp Ala Val Arg Ile 195 200 205 Leu Tyr Gly Gly Ser Val Lys Pro Ala Asn Val Lys Glu Leu Met Ala 210 215 220 Lys Pro Asp Ile Asp Gly Gly Leu Val Gly Gly Ala Ser Met Asp Pro 225 230 235 240 Asp Ser Phe Ile Ala Leu Ala Asn Tyr Gln Asp 245 250 64 396 PRT Lactobacillus rhamnosus 64 Leu Ala Lys Leu Ile Val Ser Asp Leu Asp Val Lys Asp Lys Lys Val 1 5 10 15 Leu Ile Arg Val Asp Phe Asn Val Pro Ile Lys Asp Gly Val Ile Gly 20 25 30 Asp Asp Asn Arg Ile Val Ala Ala Leu Pro Thr Ile Gln Tyr Val Ile 35 40 45 Asp His Gly Gly Lys Ala Ile Leu Leu Ser His Leu Gly Arg Val Lys 50 55 60 Thr Glu Glu Asp Lys Ala Lys Leu Thr Leu Lys Pro Val Ala Glu Arg 65 70 75 80 Leu Ser Glu Leu Leu Lys Lys Pro Val Thr Phe Val Pro Ala Thr Arg 85 90 95 Gly Lys Glu Leu Glu Asp Ala Ile Ala Lys Leu Asn Asp Gly Asp Val 100 105 110 Leu Leu Met Glu Asn Thr Arg Phe Glu Asp Leu Asp Gly Lys Lys Glu 115 120 125 Ser Gly Asn Asp Pro Glu Leu Gly Lys Tyr Trp Ala Ser Leu Gly Asp 130 135 140 Leu Phe Val Asn Asp Ala Phe Gly Thr Ala His Arg Lys His Ala Ser 145 150 155 160 Asn Val Gly Ile Ala Ser Asn Met Lys Gln Thr Ala Ala Gly Phe Leu 165 170 175 Met Glu Lys Glu Ile Lys Phe Leu Gly Asp Ala Val Asp Asn Pro Lys 180 185 190 His Pro Phe Ile Ala Ile Leu Gly Gly Ala Lys Val Ser Asp Lys Ile 195 200 205 Gly Val Ile Glu Asn Leu Val Pro Lys Ala Asp Lys Ile Leu Ile Gly 210 215 220 Gly Gly Met Thr Tyr Thr Phe Tyr Ala Ala Lys Gly Met Ser Ile Gly 225 230 235 240 Asn Ser Leu Val Glu Lys Asp Lys Ile Asp Leu Ala Lys Lys Ile Met 245 250 255 Asp Gln Ala Gly Asp Lys Leu Leu Leu Pro Val Asp Ser Val Val Ala 260 265 270 Pro Glu Phe Ser Asn Asp Ala Pro His Lys Val Val Glu Gly Asp Ile 275 280 285 Pro Asp Gly Tyr Met Ala Leu Asp Ile Gly Pro Lys Thr Ile Gln Glu 290 295 300 Phe Lys Asp Ala Leu Lys Gly Ala Lys Thr Val Val Trp Asn Gly Pro 305 310 315 320 Met Gly Val Phe Glu Met Ser Asn Tyr Ala Glu Gly Thr Leu Glu Val 325 330 335 Gly Arg Ala Leu Gly Asp Leu Lys Asp Ala Thr Thr Ile Ile Gly Gly 340 345 350 Gly Asp Ser Thr Ala Ala Ala Lys Gln Leu Gly Ile Ala Pro Lys Ile 355 360 365 Thr His Ile Ser Thr Gly Gly Gly Ala Ser Leu Glu Tyr Leu Glu Gly 370 375 380 Lys Thr Leu Pro Gly Ile Ala Ala Ile Ser Asp Lys 385 390 395 65 340 PRT Lactobacillus rhamnosus 65 Met Thr Val Lys Ile Gly Ile Asn Gly Phe Gly Arg Ile Gly Arg Leu 1 5 10 15 Ala Phe Arg Arg Ile Tyr Glu Leu Gly Ala Lys Ser Asn Asp Ile Gln 20 25 30 Val Val Ala Ile Asn Asp Leu Thr Ser Pro Thr Met Leu Ala His Leu 35 40 45 Leu Lys Tyr Asp Ser Thr His Gly Thr Phe Pro Gly Glu Val Ser Ala 50 55 60 Thr Asp Asn Gly Ile Val Val Asp Gly Lys Glu Tyr Arg Val Tyr Ala 65 70 75 80 Glu Pro Gln Ala Gln Asn Ile Pro Trp Val Lys Asn Asp Gly Val Asp 85 90 95 Tyr Val Leu Glu Cys Thr Gly Phe Tyr Thr Ser Ala Glu Lys Ser Gln 100 105 110 Ala His Leu Asp Ala Gly Ala Lys Arg Val Leu Ile Ser Ala Pro Ala 115 120 125 Gly Lys Ile Lys Thr Ile Val Tyr Asn Val Asn Asp Asp Thr Leu Asn 130 135 140 Ala Asp Asp Lys Ile Val Ser Ala Gly Ser Cys Thr Thr Asn Cys Leu 145 150 155 160 Ala Pro Met Ala Tyr Phe Leu Asn Gln Glu Phe Gly Ile Glu Val Gly 165 170 175 Thr Met Thr Thr Val His Ala Tyr Thr Ser Thr Gln Met Leu Leu Asp 180 185 190 Gly Pro Val Arg Gly Gly Asn Leu Arg Ala Ala Arg Ser Ala Ala Ala 195 200 205 Asn Thr Ile Pro His Ser Thr Gly Ala Ala Lys Ala Ile Gly Leu Val 210 215 220 Ile Pro Glu Leu Asn Gly Lys Leu Gln Gly His Ala Gln Arg Val Ser 225 230 235 240 Val Val Asp Gly Ser Leu Thr Glu Leu Val Ser Ile Leu Lys Thr Lys 245 250 255 Asn Val Thr Ala Asp Gln Val Asn Glu Ala Ile Lys Lys His Thr Glu 260 265 270 Asn Asn Pro Ser Phe Gly Trp Asn Glu Asp Glu Ile Val Ser Ser Asp 275 280 285 Val Ile Gly Thr Thr Tyr Gly Ser Ile Phe Asp Pro Thr Gln Thr Glu 290 295 300 Val Thr Thr Ala Gly Asp Tyr Gln Leu Val Lys Thr Val Ala Trp Tyr 305 310 315 320 Asp Asn Glu Tyr Gly Phe Thr Cys Gln Met Ile Arg Thr Leu Leu Lys 325 330 335 Phe Ala Thr Leu 340 66 318 PRT Lactobacillus rhamnosus 66 Met Ser Asn Leu Pro Lys Arg Tyr Asp Arg Ala Thr Leu Val Lys Ile 1 5 10 15 Ser Asp Leu Tyr Tyr Met His Gly Leu Thr Gln Gln Glu Ile Ser Asn 20 25 30 Ile Ala His Ile His Arg Thr Glu Ile Ser Arg Ile Leu Lys Ala Ala 35 40 45 Arg Asp Glu Gly Val Val Ser Ile Ala Ile Asn Pro Glu Thr Thr Ala 50 55 60 Val Ser Gln Leu Ile Asp Phe Phe Lys Gln Lys Tyr Asn Leu Arg Glu 65 70 75 80 Ala Val Ile Val Pro Ala Ser Glu Asn Gly Gly Asn Glu Leu Asn Ala 85 90 95 Leu Ser Val Tyr Ala Ser Met Phe Leu Ser Arg Ile Ile Lys Ser Gly 100 105 110 Asp Val Ile Gly Leu Ser Trp Gly Ser Thr Leu Ser Ser Val Ile Ser 115 120 125 Gln Phe Pro Thr Asp Lys Gly Leu Arg Asp Ile Lys Val Val Pro Leu 130 135 140 Val Gly Gly Pro Met Gly Arg Ile Pro Ser Asn Tyr His Val Ser Tyr 145 150 155 160 Leu Thr His Arg Leu Ala Asn Arg Leu Asn Gly Thr Ala Phe Val Leu 165 170 175 Asp Ser Pro Ala Phe Val Arg Ser Lys Ala Leu Arg Lys Glu Leu Leu 180 185 190 Ala Asn Pro Asn Thr Gln Glu Ile Leu Gly Leu Trp Asn Arg Val Asn 195 200 205 Ile Ala Ile Phe Gly Ile Gly Ser Ser Leu Ile Thr Asp Ser Pro Asp 210 215 220 Trp Gln Ala Phe Tyr Glu Asn Thr Asn Phe Lys Ser Tyr Phe Ser Ala 225 230 235 240 Asp Met Val Gly Asp Ile Leu Ser His Pro Phe Asp Lys Asp Gly Lys 245 250 255 Leu Ala Arg Asp Ile Asp Ser Ile Leu Val Ala Phe Pro Phe Ser Ala 260 265 270 Leu Arg Lys Val Pro His Ser Val Gly Ile Ala Phe Gly Glu Glu Lys 275 280 285 Val Asn Ala Ile Leu Ala Ala Leu Arg Gly Gly Leu Leu Asn Thr Leu 290 295 300 Ile Thr Thr Glu Ala Thr Ala Lys Ala Ile Lys Glu Leu Ser 305 310 315 67 282 PRT Lactobacillus rhamnosus 67 Met Pro Glu Leu Pro Glu Val Glu Thr Val Arg Arg Ser Leu Leu Pro 1 5 10 15 Leu Val Lys Asn Lys Lys Ile Thr Ala Ile Ser Thr Asn Trp Glu Lys 20 25 30 Ile Leu Ile Asn Gly Leu Ala Thr Phe Gln Lys Gln Val Val Gly Ala 35 40 45 Ala Val Asn Thr Ile Asp Arg Arg Gly Lys Tyr Leu Leu Ile Arg Leu 50 55 60 Asn Asn Gly Met Thr Ile Val Ser His Leu Arg Met Glu Gly Arg Tyr 65 70 75 80 Tyr Val Val Ser Asp Ala Lys Thr Pro Leu Asp Lys His Asp His Val 85 90 95 Thr Phe Thr Phe Gln Asp Gly Ser Gln Leu Arg Tyr Arg Asp Leu Arg 100 105 110 Lys Phe Gly Arg Met Arg Leu Ile His Thr Gly Gln Glu Gln Leu Val 115 120 125 Pro Ala Leu Ala Lys Leu Gly Pro Glu Pro Thr Ala Ala Thr Phe Ser 130 135 140 Glu Ser Asp Phe Ala Gln Lys Leu Lys Arg His His Lys Ala Ile Lys 145 150 155 160 Ser Val Leu Leu Asp Gln Thr Val Val Ala Gly Ile Gly Asn Ile Tyr 165 170 175 Ala Asp Glu Val Leu Trp Leu Ser Lys Leu Asn Pro Leu Gln Pro Ala 180 185 190 Asn Thr Leu Thr Lys Ala Glu Val His Thr Leu His Asp Ala Ile Ile 195 200 205 Lys Glu Leu Asp Asp Ala Ile Ala Ala Gly Gly Thr Ser Ala His Thr 210 215 220 Tyr Val Asp Ala Lys Gly Asn Arg Gly Ser Phe Gln Asp Ala Leu His 225 230 235 240 Val Tyr Asp Arg Glu Gly Thr Pro Cys Asp Arg Cys Gly Thr Thr Ile 245 250 255 Val Lys Ile Lys Val Gly Gln Arg Gly Thr His Tyr Cys Pro His Cys 260 265 270 Gln Pro Leu Arg Arg Arg Gly Gln Leu Ala 275 280 68 1741 PRT Lactobacillus rhamnosus 68 Met Pro Ala Lys Thr Gln Gly Phe Asn Phe Asp Trp Ser Leu Lys Gly 1 5 10 15 Gln Asp Gly Val Thr Tyr Thr Gly His Tyr Ile Val His Leu Asp Asp 20 25 30 Pro Val Ile Arg Ala His Asp Ile Ser Leu Phe Thr Gly Gln Val Trp 35 40 45 Lys Pro Glu Leu Asn Phe Glu Asn Ala Ile Lys Ser Asp Gly Thr Glu 50 55 60 Val Pro Leu Ser Glu Leu Thr Trp Ser Val Thr Asp Glu Lys Gly Asn 65 70 75 80 Val Val Ala Ser Lys Asp Lys Asn Gly Val Val Thr Gly His Val Asp 85 90 95 Asn Ser Gln Pro Thr Thr Tyr Val Val Thr Tyr Thr Tyr Gly Ala Glu 100 105 110 Ser Gly Ser Ala Lys Ile Asn Tyr Lys Gln Arg Leu Ala Ala Ser Tyr 115 120 125 Ala Leu Thr Gly Thr Gln Thr Val Thr Ala Thr Gly Ser Pro Ile Thr 130 135 140 Val Asp Val Ser Gln Phe Ala Leu Ser Leu Gly Asp Gly Phe Asp Ala 145 150 155 160 Gly Lys Leu Glu Leu Ser Asp Leu Asn Phe Phe Asp Ala Asp Gly Lys 165 170 175 Pro Val Ala Ala Asp Ala Leu Ile Lys Thr Gly Val Tyr Ser Val Glu 180 185 190 Leu Ser Glu Ala Ala Trp Ala Arg Ile Ala Lys Leu Thr Asn Asp Glu 195 200 205 Gly Gln Ser Ala Ala Gly Tyr Asp Phe Thr Gly Thr Ser Thr Ala Gln 210 215 220 Leu Ile Ile Gly Leu Thr Ala Thr Gly His Leu Ser Asp Ser Gly Phe 225 230 235 240 Val Tyr Asp Gly Lys Thr Thr Ala Ser Gln Ser Lys Asp Leu Ala Val 245 250 255 Thr Val Thr Leu Ser Asp Gly Thr Gln Lys Glu Met Asn Leu Thr Ser 260 265 270 Glu Asp Phe Ser Leu Val Glu Lys Asp Ser Ala Asn Val Gly Thr Tyr 275 280 285 His Tyr Leu Leu Asn Ser Val Gly Phe Ala Arg Leu Gln Ala Leu Leu 290 295 300 Gly Asp Thr Val Thr Ile Asp Gln Thr Ala Ile Asn Gln Asn Ser Gly 305 310 315 320 Lys Ile Thr Ile Thr Pro Ala Pro Ala Thr Val Asn Ser Asn Ser Thr 325 330 335 Asp Phe Glu Tyr Asp Gly Lys Thr Lys Ala Ser Glu Ala Lys Gly Ile 340 345 350 Gln Ala Thr Val Lys Leu Gly Glu Thr Gly Lys Thr Ile Asp Leu Thr 355 360 365 Ser Ala Asp Ile Val Val Glu Asn Asp Gly Val Asp Ala Gly Lys Tyr 370 375 380 Ser Tyr Glu Leu Ser Asp Ala Gly Lys Ala Lys Leu Gln Ala Ala Thr 385 390 395 400 Gly Asn Asn Tyr Gln Leu Thr Ala Asp Asp Leu Ala Lys Val Thr Gly 405 410 415 Ala Ile Thr Ile Thr Pro Ala Thr Thr Ser Val Asp Ser Asn Asp Val 420 425 430 Ser Phe Glu Tyr Asp Gly Lys Thr Lys Ala Ser Glu Ala Ala Gly Ile 435 440 445 Gln Ala Thr Ile Lys Leu Asp Thr Gly Lys Val Val Asp Leu Thr Ala 450 455 460 Ala Asp Ile Ile Val Thr Asn Asp Asp Val Asn Ala Gly Gln Tyr Ser 465 470 475 480 Tyr Gln Leu Ser Asp Ala Gly Lys Ala Lys Leu Gln Ala Ala Thr Gly 485 490 495 Asn Asn Tyr Gln Leu Thr Ala Asp Asp Leu Ala Lys Val Ala Gly Thr 500 505 510 Ile Thr Ile Thr Pro Ala Val Thr Thr Val Asp Ser Ser Asp Val Ser 515 520 525 Phe Glu Tyr Asp Gly Lys Thr Lys Ala Ser Glu Ala Lys Gly Ile Gln 530 535 540 Ala Thr Ile Lys Leu Asp Thr Gly Lys Val Val Asp Leu Thr Ala Ala 545 550 555 560 Asp Ile Ile Val Thr Asn Asp Asp Val Asn Ala Gly Gln Tyr Ser Tyr 565 570 575 Gln Leu Ser Asp Ala Gly Lys Ala Lys Leu Gln Ala Ala Thr Gly Asn 580 585 590 Asn Tyr Gln Leu Thr Ala Asp Asp Leu Ala Lys Val Met Gly Thr Ile 595 600 605 Thr Ile Thr Pro Ala Ala Val Thr Ala Asp Ser Asn Asp Leu Ser Phe 610 615 620 Glu Tyr Asp Gly Lys Thr Lys Ala Ser Glu Ala Lys Gly Ile Gln Ala

625 630 635 640 Met Val Lys Leu Gly Glu Thr Glu Lys Thr Val Asp Leu Thr Ser Ala 645 650 655 Asp Ile Val Val Ala Asn Asp Asp Val Asn Ala Gly Gln Tyr Ser Tyr 660 665 670 Gln Leu Ser Asp Ala Gly Lys Ala Lys Leu Gln Ala Ala Thr Gly Asn 675 680 685 Asn Tyr Gln Leu Thr Ala Asp Gly Leu Ala Lys Val Ala Gly Thr Ile 690 695 700 Thr Ile Thr Pro Ala Thr Thr Thr Ala Asp Ser Asn Asp Val Ser Phe 705 710 715 720 Glu Tyr Asp Gly Lys Thr Lys Ala Ser Glu Ala Lys Gly Ile Gln Ala 725 730 735 Thr Ile Lys Leu Gly Glu Ile Glu Lys Thr Val Asp Leu Ser Ser Ala 740 745 750 Asp Ile Ile Val Ala Asn Asp Gly Val Ile Val Gly Lys Tyr Thr Tyr 755 760 765 Ser Leu Ser Asp Ser Gly Lys Ser Lys Leu Gln Ala Ala Thr Gly Ser 770 775 780 Asn Tyr Gln Leu Thr Thr Glu Val Leu Asp Lys Val Ser Gly Ser Ile 785 790 795 800 Thr Ile Thr Pro Ala Gly Ala Ile Ala Thr Gly Lys Asp Ala His Phe 805 810 815 Glu Tyr Asp Gly Lys Thr Lys Ala Ser Glu Ala Lys Gly Ile Gln Ala 820 825 830 Ile Leu Thr Ile Asp Gly Thr Glu Lys Thr Val Asp Leu Thr Ala Ala 835 840 845 Asp Ile Val Val Ala Glu Asp Gly Val Asp Ala Gly Lys Tyr Ser Tyr 850 855 860 Arg Leu Ser Asp Ala Gly Lys Ser Lys Leu Gln Arg Glu Ala Gly Ser 865 870 875 880 Asp His Gln Leu Thr Ala Asp Asp Leu Ala Glu Val Thr Gly Thr Ile 885 890 895 Thr Ile Thr Pro Ala Ile Ala Thr Ala Asp Ser Asn Asp Val Ser Phe 900 905 910 Glu Tyr Asn Gly Lys Thr Lys Ala Ser Glu Ala Glu Gly Ile Gln Ala 915 920 925 Thr Val Met Leu Gly Glu Ser Gly Gln Val Val Ala Leu Thr Ser Ala 930 935 940 Asp Val Val Val Val Asn Asp Gly Val Asp Ala Gly Lys Tyr Ser Tyr 945 950 955 960 Gln Leu Ser Asp Ala Gly Lys Ala Lys Leu Gln Ala Ala Thr Gly Asn 965 970 975 Asn Tyr Gln Leu Thr Ala Asp Asp Leu Asp Lys Val Thr Gly Thr Ile 980 985 990 Thr Ile Thr Pro Ala Thr Thr Thr Val Asp Ser Asn Asp Val Ser Phe 995 1000 1005 Glu Tyr Asp Gly Lys Thr Lys Ala Gly Glu Ala Lys Gly Ile Gln Val 1010 1015 1020 Thr Val Lys Leu Gly Glu Thr Glu Lys Thr Val Asp Leu Thr Ser Ala 1025 1030 1035 1040 Asp Ile Val Val Ala Asn Asp Asp Val Asn Ala Gly Gln Tyr Ser Tyr 1045 1050 1055 Gln Leu Ser Asp Ala Gly Lys Ala Lys Leu Gln Ala Ala Thr Gly Asn 1060 1065 1070 Asn Tyr Gln Leu Thr Ala Asp Asp Leu Ala Lys Val Thr Gly Thr Ile 1075 1080 1085 Thr Ile Thr Pro Ala Val Thr Thr Ala Asp Ser Asn Asp Val Ser Phe 1090 1095 1100 Glu Tyr Asp Gly Lys Thr Lys Ala Ser Glu Ala Lys Gly Ile Gln Val 1105 1110 1115 1120 Ile Val Lys Leu Gly Glu Thr Glu Lys Thr Val Asp Leu Thr Ser Ala 1125 1130 1135 Asp Ile Val Val Ala Asn Asp Asp Val Asn Ala Gly His Tyr Ser Tyr 1140 1145 1150 Gln Leu Ser Asp Ala Gly Lys Ala Lys Leu Gln Ala Ala Thr Gly Asn 1155 1160 1165 Asn Tyr Gln Leu Thr Ala Asp Asp Leu Ala Lys Ile Thr Gly Thr Ile 1170 1175 1180 Thr Ile Thr Pro Ala Val Ala Thr Ala Asp Ser Asn Asn Val Ser Phe 1185 1190 1195 1200 Glu Tyr Asn Gly Lys Thr Lys Ala Ser Glu Ala Arg Gly Ile Gln Ala 1205 1210 1215 Thr Val Lys Leu Gly Glu Asn Gly Lys Thr Val Ala Leu Thr Ala Ala 1220 1225 1230 Asp Ile Val Val Val Asn Asp Gly Val Asn Ala Gly Gln Tyr Asp Tyr 1235 1240 1245 Lys Leu Ser Ala Ala Gly Met Thr Lys Leu Arg Gln Ala Thr Gly Thr 1250 1255 1260 Asn Tyr Gln Phe Lys Lys Glu Asp Leu Thr Lys Leu Gly Gly Thr Val 1265 1270 1275 1280 Thr Ile Thr Pro Ala Thr Ala Leu Ala Asp Leu Asn Asp Val Ser Phe 1285 1290 1295 Ser Tyr Asp Gly Gln Thr Lys Ala Ser Gln Ala His Asp Leu Thr Ala 1300 1305 1310 Asn Ile Lys Leu Gly Thr Lys Val Val Ser Val His Leu Asn Ala Thr 1315 1320 1325 Asp Ile Leu Val Thr Asp Asp Gly Val Gly Val Gly Gln Tyr Gln Tyr 1330 1335 1340 Lys Leu Asp Ala Asn Gly Ile Ala Lys Leu Arg Gln Ala Ser Gly Asp 1345 1350 1355 1360 Asn Tyr Gln Phe Asp Ala Lys Val Leu Ala Gly Leu Thr Gly Thr Ile 1365 1370 1375 Thr Ile Lys Pro Val Thr Gly Ala Val Thr Val Asn Asp Thr Ser Phe 1380 1385 1390 Val Tyr Asp Gly His Thr Lys Ala Ser Ala Ala Ala Gly Leu Gln Ala 1395 1400 1405 Ser Leu Tyr Leu Pro Gln Ala Glu Ala Lys Ala Thr Ile Gln Leu Thr 1410 1415 1420 Arg Glu Asp Ile Leu Val Thr Asn Asp Gly Thr Ala Ala Gly Thr Tyr 1425 1430 1435 1440 Arg Tyr Arg Leu Ser Gln Thr Gly Ile Ala Lys Leu Gln Lys Ala Val 1445 1450 1455 Gly Lys Asn Tyr Glu Leu Asp Gln Asp Glu Leu Ala Gly Leu Thr Gly 1460 1465 1470 Thr Ile Thr Ile Thr Pro Leu Thr Val Asn Ala Thr Val Asn His Gly 1475 1480 1485 Gln Phe Gln Tyr Asn Gly Val Thr Arg Ala Ser Gln Ala Gly Gly Leu 1490 1495 1500 Ala Ile Thr Val Gln Leu Pro Glu Lys Ser Gln Lys Ile Ala Leu Thr 1505 1510 1515 1520 Asn Thr Asp Ile Ala Val Glu Asn Asp Ser Val Asn Val Gly Thr Tyr 1525 1530 1535 Thr Tyr His Leu Thr Ala Ser Gly Leu Ala Lys Leu Ala Val Ala Ile 1540 1545 1550 Gly Pro Asn Tyr Gln Val Thr Asp Gln Thr Phe Ser Gly Thr Ile Thr 1555 1560 1565 Ile Thr Pro Ala Pro Ile Ser Ala Thr Leu Ser Gly Leu Gln Lys Lys 1570 1575 1580 Thr Tyr Asp Gly Gln Pro Gly Ala Leu Asn Asp Asp Tyr Tyr Arg Leu 1585 1590 1595 1600 Val Leu Gly Asp Gly Thr Glu Ile Gln Leu Gln Ala Gly Asp Leu Ile 1605 1610 1615 Phe Val Asp Gly Gln Ala Pro Val Asn Pro Gly Ser Tyr Ala Val Ala 1620 1625 1630 Leu Ser Thr Ser Gly Leu Gln Arg Ile Lys Ala Ser Leu Pro Asn Asn 1635 1640 1645 Leu Leu Lys Asn Val Asn Thr Gln Gln Ala Ile Phe Glu Ile Val Ala 1650 1655 1660 Leu Pro Ser Pro Asp Pro Gly Thr Gly Thr Thr Pro Asp Thr Pro Asp 1665 1670 1675 1680 His His Leu Pro Asn Thr Gly Thr Gly Thr Gln Gln Ser Glu Ile Ser 1685 1690 1695 Thr His Asn Gly Thr Lys His Arg Leu Pro Gln Thr Gly Asp Thr Gln 1700 1705 1710 Ser Gln Thr Leu Ser Leu Met Gly Leu Leu Leu Ala Thr Met Ser Gly 1715 1720 1725 Leu Phe Gly Leu Ala Gly Arg Lys Arg Lys Ala His Arg 1730 1735 1740 69 1463 PRT Lactobacillus rhamnosus 69 Val Arg Ala Met Val Lys Pro Lys Gln Ala Gly Ala Asn Val Ala Thr 1 5 10 15 Thr Thr Asn Ser Lys Ile Gly Gly Ser Gln Ser Ser Ala Lys Ala Ala 20 25 30 Ser Ala Phe Lys Ser Ser Ala Ser Val Glu Ser Ser Gly Gln Ile Lys 35 40 45 Ser Thr Ser Leu Ala Ser Ala Gly Ser Asn Gly Glu Lys Ala Thr Ser 50 55 60 Ala Leu Ser Ser Ser Ala Val Asp Ala Ser Asp Gly Arg Ala Ser Gln 65 70 75 80 Gly Val Gly Gly Thr Ser Ser Gly Ser Ser Asp Thr Thr Ser Gln Ala 85 90 95 Asn Glu Gly Asn Ser Ala Ala Ser Val Thr Ser Ala Ser Ala Asn Ser 100 105 110 Ala Ser Ala Thr Asn Thr Ser Glu Gly Gln Thr Pro Val Asn Glu Ala 115 120 125 Val Ser Asn Asp Ala Ser Ser Ala Asp Val Ser Thr Ala Ser Glu Phe 130 135 140 Asp Ala Ala Met Ala Asp Ser Thr Val Ser Val Ile Asn Val Gln Ser 145 150 155 160 Asp Phe Val Met Asp Val Ser Gly Asp Arg Gln Ser Tyr Ala Tyr Arg 165 170 175 Pro Asn Leu Ile Ile Asn Gly Asn Asn His Thr Ile Asp Phe Gln Lys 180 185 190 Lys Tyr Phe Glu Ala Asp Pro Thr Ser Ser Gln Asn Glu Ser Phe Thr 195 200 205 Ile Asn Asp Leu Asn Met Tyr Gly Tyr Ser Trp Trp Gly Pro Val Thr 210 215 220 Ile Lys Gly Ser Lys Pro Lys Asp Gly Ile Asp His Ser Val Val Phe 225 230 235 240 Asn Asn Val Thr Tyr Thr Gly Ala Gln Leu Met Tyr Gly Ile Tyr Thr 245 250 255 Lys Ala Phe Ile Lys Gly Asn Thr Lys Ile Gln Ser Val Gly Ser Tyr 260 265 270 Val Ser Pro Leu Asp Gly Ser Thr Gln Thr Thr Gln Gly Leu Gly Asn 275 280 285 Gln Gln Asn Phe Gln Ile Ser Tyr Leu Glu Val Leu Pro Gly Ala Thr 290 295 300 Tyr Thr Gly Thr Thr Thr Gly Gly Thr Asn Val Glu Val Tyr Asp Gly 305 310 315 320 Gly Ser Phe Ile Val Asp Lys Gly Ala Thr Val Asn Leu Gln Arg Thr 325 330 335 Asp Ala Ser Lys Ser Asn Glu Arg Gly Thr Asn Ala Leu Ile Asp Thr 340 345 350 Gln Gly Gly Asn Val Glu Phe Lys Asp Gly Ser Thr Val Ile Leu Asn 355 360 365 Lys Asn Ala Leu Val Lys Asp Gly Phe Ala Pro Ile Tyr Ile Glu Asp 370 375 380 Gly Gly Asn Leu Thr Val Asp Lys Asn Ala Thr Val Ser Ile Thr Gly 385 390 395 400 Ala Thr Gly Asn Ile Pro Val Arg Ile Asp Gly Thr Gly Thr Val Asn 405 410 415 Leu Asn Glu Gly Ser His Met Thr Ile Thr Gln Asn Gly Ala Pro Lys 420 425 430 Leu Gly Tyr Gly Phe Ile Asn Ile Lys Gly Thr Gly Gly Phe Phe Val 435 440 445 Ala Ser Gly Ser Thr Leu Asp Leu Asn Val Thr Gly Thr Gly Thr Lys 450 455 460 Ser Val Asn Ala Ile Asn Val Ala Asn Asp Gly Gln Leu Ser Phe Ala 465 470 475 480 Gln Asp Ala Thr Ala Asn Leu Thr Ile Asp Gly Gly Thr Gly Glu Ala 485 490 495 His Leu Leu Lys Val Gly Asp Asp Ala Asn Ile Asn Ile Tyr Met Pro 500 505 510 Lys Ser Val Leu Phe Lys Ile Thr Asp Asn Asp Asp Ala Asp Ser Ser 515 520 525 Leu Phe Lys Val Ser Gly Thr Gly Thr Leu Thr Gly Gln Tyr Val Lys 530 535 540 Ile Ile Pro Asp Asp Gly Asn Ala Tyr Gly Pro Tyr Lys Ser Ala Ile 545 550 555 560 Tyr Thr Leu Lys Gly Asn Gly Ser Ser Ser Asp Thr Ala Thr Val Glu 565 570 575 Gly Glu Thr Ala Glu Asp Glu Gln Ser Gly Lys Ala Leu Ala Asp Thr 580 585 590 Phe Ala Thr Asp Lys Ser Leu Glu Phe Val Ser Ala Ser Asp Asn Phe 595 600 605 Ile Lys Val Asn Pro Val Thr Asp Glu Thr Thr Thr Leu Thr Gly Lys 610 615 620 Thr Thr Ala Gly Ala Tyr Val Thr Ile Ser Gly Leu Lys Gly Ile Pro 625 630 635 640 Glu Gly Ser Leu Thr Ala Asn Ser Tyr Asp Ser Thr Lys Tyr Leu Val 645 650 655 Gln Ala Asp Lys Asp Gly Asn Trp Ser Tyr Glu Leu Pro Thr Gly Val 660 665 670 Ser Leu Pro Ala Asn Ala Ser Phe Glu Val Ile Ser Ser Ala Gly Phe 675 680 685 Ile Val Lys Thr Ala Thr Val Val Ile Asn Asp Ala Glu Thr Pro Lys 690 695 700 Gln Ala Ser Ser Ala Ala Gly Ser Leu Ile Asn Ala Asn Ser Ala Ala 705 710 715 720 Asp Val Thr Ala Ser Gln Ala Lys Ala Thr Ser Ala Ala Ala Ser Asp 725 730 735 Ala Ala Ser Tyr Ala Ser Glu Ala Gln Ser Ile Ala Gly Ser His Ala 740 745 750 Asp Asn Met Glu Ile Lys Ser Leu Ala Ser Asp Ala Glu Lys Gln Ser 755 760 765 Gln Ile Ala Leu Ala Ala Ser Lys Ser Ala Ala Ala Ser Ser Ser Ala 770 775 780 Ala Ala Ser Ala Ala Ile Val Ala Ser Ser Ala Ala Ser Glu Ala Ser 785 790 795 800 Ser Ala Ala Ala Ala Val Ser Asn Ala Asp Ala Ser Ala Asn Ser Ala 805 810 815 Ala Ala Ala Tyr Asp Ser Tyr Ala Ser Glu Ala Ser Ala Ala Ser Ala 820 825 830 Ala Asn Asp Ser Ser Gly Tyr Ala Thr Ala Ser Phe Ala Ala Ser Ser 835 840 845 Ala Ala Ala Ala Met Ser Ala Ala Leu Ser Thr Ala Gln Val Ala Ala 850 855 860 Lys Val Ala Val Ser Asp Ala Ala Ala Ala Gly Ser Ala Ala Ala Val 865 870 875 880 Ala Ser Ala Ala Gln Ser Asp Ser Lys Asn Lys Gln Ala Thr Ala Ala 885 890 895 Thr Ala Arg Ser Gln Ala Leu Asp Asp Leu Asn Lys Ile Lys Ser Leu 900 905 910 Thr Asp Tyr Ala Ser Gly Ala Ser Ser Ser Ala Ser Glu Ala Gly Gln 915 920 925 Ala Ser Thr Ala Thr Ser Ala Tyr Ala Ser Ala Ala Ser Ser Ser Ala 930 935 940 Ser Glu Ala Gly Ser Tyr Ala His Gln Ala Gly Ser Ser Ala Ser Asp 945 950 955 960 Ala Val Gly Gln Ser Gly Ser Ala Ala Gln His Ala Ser Thr Ala Ala 965 970 975 Ser Ala Ala Ser Ser Tyr Pro Lys Asp Ser Gly Ile Gln Ser Leu Ala 980 985 990 Ser Gln Ala Ala Ser Glu Ala Ala Lys Ala Ser Ser Asn Ala Ser Ala 995 1000 1005 Ala Thr Ser Ala Ala Ala Val Gly Phe Ser Ala Ala Ser Asp Ala Ser 1010 1015 1020 Glu Gln Ala Lys Thr Ala Ala Ser Ala Asp Val Val Ala Ser Ser Ala 1025 1030 1035 1040 Ala Ser Thr Ala Asn Ser Asn Ala Ser Ala Ala Ala Ser Ala Thr Lys 1045 1050 1055 Ala Gly Asp Ser Lys Ala Ala Ala Gly Phe Ser Ser Ala Ala Ser Ala 1060 1065 1070 Ala Ala Ser Ser Ala Lys Gly Ala Glu Ala Val Ala Ser Glu Ala Ala 1075 1080 1085 Ser Ala Ala Ala Ser Asp Asp Ser Val Ala Ser Ser Ala Ala Ser Ala 1090 1095 1100 Ala Ala Gly Phe Asp Lys Ala Ala Ser Ala Ala Glu Gly Ala Ala Ser 1105 1110 1115 1120 Ser Ala Ala Ser Ala Ala Ala Ser Ser Ala Ala Ala Gln Gly Thr Arg 1125 1130 1135 Gly Gly Ala Ser Ser Ser Ala Ser Glu Ala Gly Gln Ala Ser Thr Ala 1140 1145 1150 Thr Ser Val Tyr Ala Ser Ala Ala Ser Ser Ser Ala Ser Glu Ala Gly 1155 1160 1165 Ser Tyr Ala His Gln Ala Gly Ser Ser Ala Ser Glu Ala Thr Gly His 1170 1175 1180 Ala Ser Ser Ala Thr Ser Gln Ala Ser Ala Ala Ser Ser Ala Ala Ser 1185 1190 1195 1200 Arg Tyr Pro Ser Asp Ser Gly Ile Gln Ser Asp Val Ser Ile Ala Ser 1205 1210 1215 Ser Ala Ala Ser Thr Ala Ser Ser Ala Ala Ser Ala Ala Gln Ser Glu 1220 1225 1230 Ala Ser Thr Ala Ser Ser Ala Ala Ser His Ala Ser Glu Gln Ala Ser 1235 1240 1245 Ile Ala Ser Ser Glu Asp Val Val Ser Ser Ser Ala Ala Ser Val Ala 1250 1255 1260 Ser Ser Ala Ala Ser Ala Ala Ser Ser Ala Ala Lys Ala Gly Asn Ser 1265 1270 1275 1280 Ser Ala Ala Gly Ile Tyr Ser His Ala Ala Ser Ala Ala Ala Ser Ser 1285 1290 1295 Ala Lys Ser Ala Glu Ser Gln Ala Ser Ser Ala Ala Ser Ala Ala Ala 1300 1305 1310 Ser Asp Asp Ser Val Ala Ser Ser

Ala Ala Ser Ala Ala Leu Ser Asp 1315 1320 1325 Asp Ala Lys Ala Ser Ser Ala Ala Asp Val Ala Ser Ser Ala Thr Thr 1330 1335 1340 Ala Ala Ile Ser Ser Ala Thr Ser Leu Ala Asp Gln Ser Ala Thr Gly 1345 1350 1355 1360 Ser Thr Ala Gly Ser His Ile Leu Pro Ser Thr Gly Gly Glu Thr Thr 1365 1370 1375 Gly Ser Ile Pro Ser Gly Gln Thr Pro Thr Gln Thr Lys Pro Thr Gln 1380 1385 1390 Thr Lys Pro Thr Gln Thr Lys Pro Thr Gln Ala Gly Gln Thr Thr Gln 1395 1400 1405 Thr Gly Ser Leu Pro Gln Thr Asp His Ala Gly Arg His Met Leu Pro 1410 1415 1420 Gln Thr Gly Asp Asp Ala Glu Ser Gly Thr Ser Val Leu Gly Leu Leu 1425 1430 1435 1440 Ile Val Ser Leu Met Gly Leu Phe Gly Leu Ala Gly Thr Arg His Gln 1445 1450 1455 Lys Asp Asn Lys Pro Ser Lys 1460 70 1879 PRT Lactobacillus rhamnosus 70 Met Gln Ala His Lys Ile Met Pro Glu Asp Trp Ile Ala Val Arg Met 1 5 10 15 Glu Thr Asn Arg Ile Glu Gly Lys His Pro Ile His Pro Ala Phe Arg 20 25 30 Ser Thr Arg Ile Leu Glu Tyr Asn Asp Phe Gly Pro Ala Leu Asn Ala 35 40 45 Lys Leu Leu Glu Ala Met Lys Lys Lys Ala Ile Asp Asp Thr Ala Lys 50 55 60 Asp Pro Lys Pro Val Gln Glu Glu Val Lys Glu Lys Val Asp Pro Ile 65 70 75 80 Thr Val Asp Glu Asp Phe Asp Lys Leu Ile Gln Glu Ile Val Leu Asn 85 90 95 Ala His Lys Glu Gln Ala Lys Arg Asp Ile Asp Ala Glu Ala Ala Lys 100 105 110 Val Ser Ala Glu Ile Glu Gln Asp Pro Thr Leu Thr Ala Thr Glu Lys 115 120 125 Ala Lys Gln Lys Asp Gly Val Ala Ala Glu Ala Thr Lys Ala Lys Ala 130 135 140 Ala Ile Asp Gln Ala Gln Thr Glu Thr Gly Val Gln Gln Ala Arg Asp 145 150 155 160 Ala Gly Ile Ala Ala Ile Asp Ala Gln His Gln Pro Gly Thr Gly Leu 165 170 175 Asn Val Arg Arg Glu Glu Ala Lys Gln Ala Ile Asp Ala Glu Ala Ala 180 185 190 Lys Val Thr Ala Glu Ile Glu Gln Asp Ser Thr Leu Ala Thr Ser Glu 195 200 205 Lys Ala Ala Gln Lys Gln Gly Val Ala Asp Glu Ala Ala Lys Ala Lys 210 215 220 Thr Ala Ile Asp Gln Ala Gln Thr Ile Glu Ala Ile Asp Lys Ala Lys 225 230 235 240 Asp Asp Gly Ile Lys Ala Ile Asp Ala Gln His Lys Gln Gly Ala Asp 245 250 255 Phe Asp Thr Arg Lys Ala Gln Ala Lys Asp Ala Ile Asp Ala Glu Ala 260 265 270 Ala Lys Val Lys Asp Ala Ile Asp Gln Asp Pro Thr Leu Thr Ala Lys 275 280 285 Asp Lys Thr Ala Gln Lys Gln Gly Val Gly Asp Glu Ala Thr Lys Ala 290 295 300 Lys Thr Ala Ile Asp Gln Ala Lys Thr Ile Asp Gly Val Ile Gln Ala 305 310 315 320 Lys Asp Asp Gly Ile Lys Ala Ile Asp Ala Gln His Gln Ala Gly Thr 325 330 335 Asp Leu Ala Thr Arg Lys Asp Ser Ala Lys Gln Ala Ile Asp Ala Glu 340 345 350 Ala Ala Lys Ile Thr Asp Ala Ile Asn Gln Asp Asp Thr Leu Thr Ser 355 360 365 Thr Glu Lys Asp Ala Gln Lys Gln Ala Val Ala Asp Glu Ala Ala Lys 370 375 380 Ala Lys Ala Ala Ile Asp Gln Ala Gln Asn Ala Asp Ala Ile Leu Gln 385 390 395 400 Ala Gln Ala Asp Gly Ile Lys Ala Ile Asp Ala Lys His Gln Ile Gly 405 410 415 Ala Asp Leu Asp Thr Gln Lys Thr Lys Ala Lys Gln Ala Ile Asp Lys 420 425 430 Glu Ala Ala Lys Val Leu Thr Ala Ile Glu Gln Asp Pro Thr Leu Thr 435 440 445 Ser Ala Glu Lys Lys Ala Gln Lys Gln Gly Val Ala Asp Glu Thr Ala 450 455 460 Lys Ala Lys Thr Ala Ile Asp Ser Ala Arg Asn Ala Asp Glu Ile Ala 465 470 475 480 Lys Ala Gln Ala Asp Gly Ile Lys Ala Ile Asp Ala Gln His Arg Leu 485 490 495 Gly Met Asp Leu Ala Lys Arg Lys Thr Asp Ala Gln Ala Ala Ile Asp 500 505 510 Ala Glu Ala Ala Lys Val Gly Glu Ala Ile Asp Gln Asp Pro Thr Leu 515 520 525 Thr Ser Gln Glu Lys Ala Ala Gln Lys Gln Thr Phe Ala Ala Glu Ala 530 535 540 Thr Lys Ala Lys Asp Thr Ile Ala Lys Ala Gln Asp Ala Asp Gly Val 545 550 555 560 Ile Gln Ala Glu Lys Ala Gly Ile Gln Ala Ile Asp Asp Gly His Gln 565 570 575 Ser Gly Ala Leu Leu Asp Thr Arg Lys Val Asp Ala Lys Lys Ala Ile 580 585 590 Asp Ala Glu Ala Ala Lys Ile Asn Asp Ala Ile Asp Gln Asp Val Thr 595 600 605 Leu Thr Ser Ala Glu Lys Ala Thr Gln Lys Gln Lys Val Thr Asp Glu 610 615 620 Ala Val Lys Ala Lys Thr Ala Ile Asp Ala Ala Lys Asn Ala Asp Thr 625 630 635 640 Val Asp Gln Ala Lys Ala Ser Gly Ile Gln Ala Ile Asp Ala Val His 645 650 655 Gln Ser Gly Thr Leu Leu Asp Thr Arg Lys Gln Asp Ala Lys Lys Ala 660 665 670 Ile Asp Ala Glu Ala Val Lys Val Ile Ala Ala Ile Gly Gln Asp Val 675 680 685 Thr Leu Thr Gln Ala Glu Lys Leu Thr Gln Gln Gln Ala Val Ala Asp 690 695 700 Ala Ala Thr Gln Ala Lys Ala Ala Ile Asp Ala Ala Lys Asn Ala Asp 705 710 715 720 Ala Val Asp Gln Ala Lys Ala Asp Gly Ile Lys Ala Ile Asp Ala Gln 725 730 735 His Gln Ala Gly Leu Ala Leu Asn Glu Arg Lys Glu Ala Ala Lys Lys 740 745 750 Leu Ile Ala Glu Thr Ala Asp Lys Val Gln Ala Ala Ile Gly Gln Asp 755 760 765 Val Thr Leu Thr Ala Thr Gln Lys Ala Val Gln Arg Gln Ala Ile Thr 770 775 780 Val Glu Val Thr Lys Ala Asn Gln Ala Ile Asp Ala Ala Gly Asn Ala 785 790 795 800 Asp Ala Val Asp Gln Ala Lys Asn Ala Gly Val Lys Ala Ile Tyr Asp 805 810 815 Gln His Gln Ser Gly Gln Ala Leu Ala Asp Arg Lys Arg Asp Ala Lys 820 825 830 Gln Ala Ile Asp Ala Glu Ala Ala Lys Glu Thr Ala Ala Ile Asp Gln 835 840 845 Asp Ala Thr Leu Thr Ala Asn Glu Lys Ala Ser Gln Lys Gln Ala Val 850 855 860 Ala Asp Glu Ala Thr Lys Ala Lys Glu Ala Ile Asp Ala Ala Lys Gln 865 870 875 880 Ala Asp Ala Val Asp Gln Ala Lys Asn Asp Gly Ile Arg Ala Ile Asp 885 890 895 Ala Gln His His Ala Gly Gln Ala Val Ala Asp Arg Lys Ala Ala Ala 900 905 910 Lys Gln Ala Ile Asp Ala Glu Ala Ala Lys Val Thr Gly Asn Ile Asp 915 920 925 Gln Asp Glu Thr Leu Thr Ala Thr Glu Lys Ala Ala Gln Lys Gln Ala 930 935 940 Val Ala Thr Glu Ala Asp Asn Ala Lys Gln Ala Ile Asp Lys Gly Gln 945 950 955 960 Asn Ala Asp Ala Val Asp Lys Ala Lys Thr Gly Gly Ile Lys Ala Ile 965 970 975 Asp Ala Gln His Gln Ser Gly Gln Ala Ile Lys Ala Arg Gln Asn Asp 980 985 990 Ala Lys Gln Ala Ile Asp Ala Glu Ala Ala Lys Val Thr Lys Ala Ile 995 1000 1005 Asp Gln Asp Pro Thr Leu Thr Ala Ala Glu Lys Lys Ala Gln Lys Gln 1010 1015 1020 Ala Val Thr Asp Ala Glu Thr Lys Ala Lys Ala Ala Ile Asp Ala Thr 1025 1030 1035 1040 Leu Val Ala Asp Ala Ile Asp Gln Ala Leu Ala Asp Gly Ile Lys Thr 1045 1050 1055 Ile Asp Ala Gln Tyr Gln Thr Gly Ile Ala Leu Asp Lys Gln Lys Ala 1060 1065 1070 Ala Ala Lys Gln Thr Ile Asp Ala Glu Ala Ala Lys Val Ser Glu Ala 1075 1080 1085 Ile Asp Gln Asp Val Thr Leu Thr Ala Asp Gln Lys Ala Thr Gln Lys 1090 1095 1100 Gln Ala Val Ala Asp Glu Ala Thr Lys Ala Lys Ala Ala Ile Asp Gln 1105 1110 1115 1120 Ala Ser Asp Ala Asp Ala Val Ile Gln Ala Thr Ile Asp Gly Ile Glu 1125 1130 1135 Ala Ile Asp Ala Gln His Gln Ser Ala Thr Ala Leu Asp Lys Gln Lys 1140 1145 1150 Gln Gln Ala Lys Gln Ala Ile Asp Ala Glu Ala Ala Lys Val Ser Lys 1155 1160 1165 Ala Ile Asp Gln Asp Val Thr Leu Thr Ala Thr Gln Lys Ala Asp Gln 1170 1175 1180 Lys Gln Ala Val Ile Ala Glu Ala Asp Lys Ala Lys Lys Leu Ile Asp 1185 1190 1195 1200 Ala Ala Gly Asn Ala Asp Gly Ile Lys Gln Ala Glu Ser Asp Gly Ile 1205 1210 1215 Lys Ala Ile Asp Ala Gln His Gln Ser Ser Gln Ala Leu Ala Asp Arg 1220 1225 1230 Lys Arg Asp Ala Lys Thr Ala Ile Asp Ala Glu Ala Ala Lys Glu Thr 1235 1240 1245 Ala Ala Ile Asp His Asp Ala Thr Leu Thr Ala Asn Glu Lys Ala Ser 1250 1255 1260 Gln Lys Gln Ala Val Thr Asp Glu Ala Thr Lys Ala Lys Lys Ala Ile 1265 1270 1275 1280 Asp Ala Ala Lys Gln Ala Asp Ala Val Asp Gln Ala Lys Thr Asp Gly 1285 1290 1295 Ile Lys Ala Ile Asp Ala Gln His His Ser Gly Gln Ala Leu Asp Asp 1300 1305 1310 Arg Lys Ala Asp Ala Lys Gln Val Ile Asp Ala Glu Ala Ala Lys Val 1315 1320 1325 Thr Ala Ala Ile Asp Gln Asp Asn Thr Leu Thr Lys Ala Gln Lys Ala 1330 1335 1340 Ala Gln Lys Gln Gly Val Ala Thr Glu Ala Asp Lys Ala Lys Gln Ala 1345 1350 1355 1360 Ile Asp Ala Ala Gly Asp Ala Asp Ala Val Asp Gln Ala Lys Thr Ala 1365 1370 1375 Gly Ile Gln Ala Ile Asp Ala Gln His Lys Ala Gly Lys Thr Ile Asp 1380 1385 1390 Ser Arg His Asp Asp Ala Lys Gln Ala Ile Asp Glu Glu Ala Ala Lys 1395 1400 1405 Val Ile Lys Ala Ile Asp Gln Asp Pro Thr Leu Thr Ala Ala Gln Lys 1410 1415 1420 Glu Ala Gln Lys Gln Ala Val Ala Thr Glu Ala Asp Lys Ala Lys Lys 1425 1430 1435 1440 Ala Ile Asp Ala Ala Gly Asp Ala Asp Ala Val Asp Gln Ala Lys Thr 1445 1450 1455 Ala Gly Ile Lys Ala Ile Asp Glu Gln His Lys Ser Gly Gln Thr Val 1460 1465 1470 Asp Ala Arg Lys Glu Asp Ala Lys Lys Ala Ile Asp Ala Glu Ala Gly 1475 1480 1485 Lys Val Thr Asp Ala Ile Asp His Asp Ala Thr Leu Thr Ala Ala Gln 1490 1495 1500 Lys Glu Ala Gln Lys Gln Ala Val Ala Asp Glu Ala Asp Lys Ala Lys 1505 1510 1515 1520 Lys Ala Ile Asp Ala Ala Gly Asn Ala Asp Ala Ile Asp Gln Ala Lys 1525 1530 1535 Ser Ala Gly Ile Lys Ala Ile Asp Glu Gln His Lys Ser Gly Gln Ser 1540 1545 1550 Ile Asp Thr Arg Lys Asp Asp Ala Lys Lys Ala Ile Asp Gly Glu Val 1555 1560 1565 Ala Lys Ile Thr Asp Ala Ile Asp His Asp Pro Thr Leu Thr Asp Ala 1570 1575 1580 Glu Lys Ala Thr Gln Lys Gln Ala Val Ile Ala Glu Ala Asp Lys Ala 1585 1590 1595 1600 Lys Lys Ala Ile Asp Ala Ala Gly Asp Ala Asp Ala Val Asp Gln Ala 1605 1610 1615 Gln Lys Ala Gly Ile Lys Ala Ile Asp Gln Gln His Lys Ser Gly Gln 1620 1625 1630 Ala Leu Ala Ile Arg Lys Asp Ala Ala Lys Lys Ala Ile Asp Glu Glu 1635 1640 1645 Ala Ala Lys Val Ser Glu Ala Ile Asp His Asp Val Thr Leu Thr Asp 1650 1655 1660 Ser Glu Lys Gly Thr Gln Lys Gln Ala Val Ala Asp Glu Ala Lys Lys 1665 1670 1675 1680 Ala Lys Gln Ala Ile Asp Thr Ala Asp Asn Ala Asp Gly Val Asp Gln 1685 1690 1695 Ala Val Thr Lys Gly Ile Gln Ile Ile Asp Ala Gln His Gln Ser Gly 1700 1705 1710 Gln Ala Leu Thr Asp Arg Lys Ala Ala Ala Lys Lys Ala Ile Asp Ala 1715 1720 1725 Glu Ala Ala Lys Val Gly Gln Ala Ile Glu Gln Asp Pro Thr Leu Thr 1730 1735 1740 Ala Thr Glu Lys Lys Arg Gln Lys Gln Ala Val Ala Asp Glu Ala Thr 1745 1750 1755 1760 Lys Ala Lys Ala Ala Ile Asp Thr Ala Ala Asn Ala Ser Ala Val Asp 1765 1770 1775 Gln Ala Lys Asn Ala Gly Ile Lys Ala Ile Asp Ala Gln His Val Ser 1780 1785 1790 Gly Lys Ala Phe Asp Leu Ser Lys Asp Glu Ala Lys Lys Ala Ile Asp 1795 1800 1805 Ala Glu Ala Thr Lys Val Gln Gly Glu Ile Asp Gln Asp Pro Thr Leu 1810 1815 1820 Thr Ala Thr Ala Lys Lys Gln Gln Lys Glu Ala Val Pro Thr Glu Ala 1825 1830 1835 1840 Gly Lys Ala Lys Gln Ala Phe Asp Gln Ala Lys Asn Ile Glu Glu Val 1845 1850 1855 Arg Pro Pro Lys Thr Lys Ala Ser Lys Arg Leu Met Arg Asn Ile Ser 1860 1865 1870 Gln Asp Lys Gln Leu His Thr 1875 71 293 PRT Lactobacillus rhamnosus 71 Met Pro Leu Val Asn Ala Ala Glu Leu Val Lys Ala Ala His Lys Gly 1 5 10 15 His Tyr Cys Ile Gly Ala Phe Asn Thr Asn Asn Leu Glu Trp Thr Arg 20 25 30 Ala Ile Leu Ala Gly Ala Gln Glu Leu Asn Val Pro Val Ile Ile Gln 35 40 45 Thr Ser Met Gly Ala Ala Lys Tyr Met Gly Gly Tyr Glu Phe Cys Gln 50 55 60 Thr Met Ile Glu Ala Ala Val Lys Ala Met Asp Ile Thr Val Pro Val 65 70 75 80 Val Ile His Leu Asp His Gly Asn Tyr Glu Ala Ala Lys Glu Ala Ile 85 90 95 Ala Ala Gly Tyr Asn Ser Val Met Phe Asp Gly His Asp Leu Asp Phe 100 105 110 Glu Asp Asn Leu Glu Lys Thr Lys Glu Ile Val Lys Leu Ala His Ala 115 120 125 Lys Gly Ile Ser Val Glu Ala Glu Val Gly Ser Ile Gly Gly Glu Glu 130 135 140 Asp Gly Val Val Gly Glu Gly Glu Leu Ala Asp Val Glu Glu Ala Lys 145 150 155 160 Thr Leu Ala Ala Thr Gly Ile Asp Phe Leu Ala Ala Gly Ile Gly Asn 165 170 175 Ile His Gly Gln Tyr Pro Asp Asn Trp Lys Gly Leu His Phe Asp Arg 180 185 190 Leu Gln Glu Leu Asn Asp Ala Val Lys Met Pro Leu Val Leu His Gly 195 200 205 Gly Ser Gly Ile Pro Gln Glu Gln Val Gln Lys Ala Ile Thr Met Gly 210 215 220 Ile Ser Lys Leu Asn Ile Asn Thr Glu Cys Gln Leu Ala Phe Ala Lys 225 230 235 240 Ala Thr Arg Glu Tyr Ile Glu Ala Gly Lys Asp Gln Gln Gly Lys Gly 245 250 255 Phe Asp Pro Arg Lys Met Leu Lys Pro Gly Thr Asp Ala Ile Thr Asp 260 265 270 Thr Phe Lys Glu Ile Thr Gly Trp Ile Gly Asn Lys Pro Val Lys Met 275 280 285 Val Pro Glu Ala Leu 290 72 174 PRT Lactobacillus rhamnosus 72 Met Ser Lys Val Ile Gly Ile Asp Leu Gly Thr Thr Asn Ser Ala Val 1 5 10 15 Ala Val Leu Glu Gly Asn Gln Pro Lys Ile Ile Thr Asn Pro Glu Gly 20 25 30 Asn Arg Thr Thr Pro Ser Val Val Ala Phe Lys Asp Gly Glu Ile Gln 35 40 45 Val Gly Glu Val Ala Lys Arg Gln Ala Ile Thr Asn Pro Asp Thr Ile 50 55 60 Val Ser Ile Lys Arg His Met Gly Glu Ala Asn Tyr Lys Val Lys Val 65 70 75 80 Gly Asp Lys Glu Tyr Thr Pro Gln Glu Ile Ser Ala Met Ile Leu Gln 85 90 95 Tyr Ile Lys Lys Phe Ser Glu Asp Tyr Leu Gly

Glu Pro Val Lys Asp 100 105 110 Ala Val Ile Thr Val Pro Val Tyr Phe Asn Asp Ser Glu Arg Gln Ala 115 120 125 Asn Lys Asp Ala Gly Lys Ile Ala Gly Leu Asn Val Gln Arg Ile Ile 130 135 140 Asn Glu Pro Thr Ala Ser Ala Leu Ala Tyr Gly Leu Asp Lys Gly Asp 145 150 155 160 Lys Glu Lys Arg Phe Gly Leu Arg Leu Cys Arg Arg His Ile 165 170 73 282 PRT Lactobacillus rhamnosus 73 Gln Val Ile Ala Asp Gly Val Val Thr Lys Tyr Thr Pro Ala Asn Ala 1 5 10 15 Met Ile Val Ala Thr His Arg His Thr Ala Lys Gln Leu Leu Ala Ala 20 25 30 Ala Gly Ile Pro Val Ala Arg Gly Ala Lys Phe Thr Lys Trp Pro Asp 35 40 45 Ala Lys Ala Ala Phe Glu His Ser Phe Ala His Lys Ser Ile Val Val 50 55 60 Lys Pro Glu Ala Arg Ser Gln Gly Lys Ala Val Glu Gln Phe Ser Ile 65 70 75 80 Pro Pro Thr Glu Lys Gln Phe Asp Arg Ala Phe His Glu Ala Asn Arg 85 90 95 His His Gly Val Leu Ile Glu Met Met Ala Arg Gly Thr Thr Tyr His 100 105 110 Phe Thr Ile Ile Gly Gln Gln Val Leu Ser Val Leu Glu Thr Ala Ala 115 120 125 Ala Asn Val Val Gly Asp Gly Arg Lys Ala Ile Lys Glu Leu Ile Ala 130 135 140 Leu Lys Asn Gly His Arg Ala Thr Ser Arg Gln Leu Gln Leu Asp Ala 145 150 155 160 Ser Ala Arg Arg Gln Leu Lys Ala Gln Ala Leu Thr Pro Glu Thr Val 165 170 175 Leu Gln Arg Gly Gln Gln Val Phe Leu Thr Thr Ala Ala His Pro Gln 180 185 190 Thr Gly Gly Asp Leu Tyr Asp Val Thr Asp Glu Ile Asp Asp Ser Tyr 195 200 205 Lys Gln Leu Ala Leu Lys Ala Ala Ala Thr Leu Asp Leu Pro Val Ala 210 215 220 Ala Val Asp Ile Val Ile Asp Asn Leu Tyr Ala Pro Tyr Asp Pro Glu 225 230 235 240 Ala Asp Gly Gln Ala Ile Val Ile Ser Leu Asn Pro Val Pro Asp Leu 245 250 255 Ala Val Pro Leu His Pro Asp Met Gly Glu Ser Arg Ala Leu Ala Pro 260 265 270 Ala Leu Leu Asn Trp Leu Phe Ala Val Arg 275 280 74 261 PRT Lactobacillus rhamnosus 74 Met Tyr Arg Asp Leu Asn Gly Lys Val Ala Val Val Thr Gly Gly Ser 1 5 10 15 Lys Gly Ile Gly Ala Gly Ile Ala Glu Arg Phe Gly Gln Glu His Met 20 25 30 Ala Val Val Ile Asn Tyr Leu Gly Asp His Glu Gly Ala Arg Lys Thr 35 40 45 Ala Asp Thr Val Ile Lys Asn Gly Gly Gln Ala Val Ser Ile His Ala 50 55 60 Asp Val Ser Thr Glu Ala Gly Ile Ala Ser Leu Val Lys Thr Ala Glu 65 70 75 80 Ser Glu Phe Gly Arg Leu Asp Val Trp Val Asn Asn Ala Gly Met Glu 85 90 95 Ile Lys Ala Pro Thr His Glu Val Ser Leu Asp Asp Trp Asn Lys Val 100 105 110 Ile Ala Ile Asn Gln Thr Gly Val Phe Leu Gly Ala Arg Ala Ala Leu 115 120 125 Asn Tyr Phe Leu Asp His His Gln Pro Gly Asn Ile Ile Asn Ile Ser 130 135 140 Ser Val His Glu Gln Ile Pro Trp Pro Thr Phe Ala Ser Tyr Ala Ala 145 150 155 160 Ala Lys Gly Ser Val Lys Leu Phe Thr Glu Thr Ile Ala Met Glu Tyr 165 170 175 Ala Asn Arg Gly Ile Arg Val Asn Ala Ile Gly Pro Gly Ala Ile Glu 180 185 190 Thr Pro Ile Asn Ala Glu Lys Phe Ala Asp Lys Ala Gln Tyr Asp Gln 195 200 205 Thr Val Ala Met Ile Pro Gln Gly Arg Leu Gly Lys Pro Glu Asp Val 210 215 220 Ala Ala Gly Ala Ala Trp Leu Ala Ser Thr Glu Ser Ser Tyr Val Thr 225 230 235 240 Gly Thr Thr Leu Phe Ile Asp Gly Gly Met Thr Leu Tyr Pro Ala Phe 245 250 255 Lys Asp Gly Gln Gly 260 75 396 PRT Lactobacillus rhamnosus 75 Met Ala Lys Ile Leu Ala Val Asn Ala Gly Ser Ser Thr Leu Lys Trp 1 5 10 15 Lys Leu Phe Asp Met Pro Ala Glu Val Gln Leu Ala Glu Gly Leu Val 20 25 30 Asp Arg Leu Gly Gln Pro Gln Ser Lys Val Lys Ile Lys Tyr Gly Asp 35 40 45 Gly Gln Lys Tyr Glu Ser Asp Thr Pro Ile Ala Asn Tyr Gln Glu Ala 50 55 60 Val Ala Ser Leu Met Gly Asn Ile Lys Ala Leu Gly Leu Val Glu His 65 70 75 80 Leu His Glu Ile Ile Gly Val Gly His Arg Val Val Ala Gly Gly Glu 85 90 95 Ile Phe Ala Glu Ser Val Val Val Asp Asp Glu Thr Leu Leu Gln Ile 100 105 110 Gln Asn Leu Arg Asp Tyr Ala Pro Leu His Asn Pro Val Glu Ala Asp 115 120 125 Tyr Ile Ser Val Phe Arg Lys Met Met Pro Trp Ala Asn Glu Val Ala 130 135 140 Val Phe Asp Thr Ala Phe His Gln Thr Met Gln Pro Glu Asn Phe Leu 145 150 155 160 Tyr Ser Ile Pro Tyr Glu Tyr Tyr Glu Gln Tyr Gly Ala Arg Lys Tyr 165 170 175 Gly Ala His Gly Thr Ser Val Arg Tyr Val Ser Ala Arg Ala Ala Glu 180 185 190 Met Leu Gly Lys Pro Leu Glu Asp Leu Arg Met Ile Val Met His Leu 195 200 205 Gly Ser Gly Ser Ser Ile Thr Ala Val Gln Gly Gly Gln Ser Ile Asp 210 215 220 Thr Ser Met Gly Phe Thr Pro Leu Ala Gly Val Thr Met Gly Thr Arg 225 230 235 240 Ser Gly Asp Ile Asp Pro Ser Leu Val Gly Tyr Leu Met Lys Lys Leu 245 250 255 Ala Ile Pro Asp Val Gly Gln Met Ile His Ile Leu Asn Asn Asp Ser 260 265 270 Gly Leu Leu Gly Ile Ser Gly Leu Ser Asn Asp Met Arg Asp Leu Glu 275 280 285 Ala Ala Glu Asp Thr Asn Thr Arg Ala Lys Leu Ala Leu Asp Ile Phe 290 295 300 Val Asn Arg Val Val Lys Tyr Val Gly Ser Tyr Val Ala Leu Met Asp 305 310 315 320 Gly Val Asp Val Leu Val Phe Thr Ala Gly Ile Gly Glu Asn Gly Asp 325 330 335 Glu Ile Arg Asp Lys Ile Met Arg Ser Leu Asp Tyr Leu Gly Ala Lys 340 345 350 Ile Asp Asn Asp Leu Asn Tyr Lys Ser His Gly Val Glu Ala Asp Leu 355 360 365 Ser Thr Ala Asp Ser Thr Val Lys Thr Leu Leu Val Pro Thr Asn Glu 370 375 380 Glu Leu Met Ile Val Arg Asp Val Met Ala Leu Ser 385 390 395 76 11 PRT Lactobacillus rhamnosus PEPTIDE (0)...(0) 76 Met Arg Thr Pro Phe Ile Ala Gly Asn Leu Lys 1 5 10 77 10 PRT Lactobacillus rhamnosus PEPTIDE (0)...(0) 77 Pro Leu Val Asn Ala Ala Glu Leu Val Lys 1 5 10 78 11 PRT Lactobacillus rhamnosus PEPTIDE (0)...(0) 78 Met Glu Lys Arg Glu Phe Asn Ile Ala Ala Glu 1 5 10 79 12 PRT Lactobacillus rhamnosus PEPTIDE (0)...(0) 79 Ser Lys Val Ile Gly Ile Asp Pro Gly Thr Gly Asn 1 5 10 80 12 PRT Lactobacillus rhamnosus PEPTIDE (0)...(0) 80 Thr Val Lys Ile Gly Ile Asn Gly Phe Gly Arg Ile 1 5 10 81 13 PRT Lactobacillus rhamnosus PEPTIDE (0)...(0) 81 Ser Val Lys Ile Thr Ala Gly Gln Leu Glu His Leu Lys 1 5 10 82 12 PRT Lactobacillus rhamnosus PEPTIDE (0)...(0) 82 Ala Lys Leu Ile Val Ser Asp Leu Asp Val Lys Asp 1 5 10 83 12 PRT Lactobacillus rhamnosus PEPTIDE (0)...(0) 83 Ser Ile Ile Thr Asp Val Leu Ala Arg Glu Val Leu 1 5 10

Claims

1. An isolated polynucleotide comprising a sequence selected from the group consisting of: SEQ ID NO: 1-33.

2. An isolated polynucleotide comprising a sequence selected from the group consisting of: (a) complements of SEQ ID NO: 1-33; (b) reverse complements of SEQ ID NO: 1-33; and (c) reverse sequences of SEQ ID NO: 1-33.

3. An isolated polynucleotide comprising a sequence selected from the group consisting of: (a) sequences having at least 75%, identity to a sequence of SEQ ID NO: 1-33; (b) sequences having at least 90% identity to a sequence of SEQ ID NO: 1-33; and (c) sequences having at least 95% identity to a sequence of SEQ ID NO: 1-33, wherein the polynucleotide encodes a polypeptide having substantially the same functional properties as a polypeptide encoded by SEQ ID NO: 1-33.

4. An isolated polynucleotide comprising a sequence selected from the group consisting of: (a) nucleotide sequences that are 200-mers of a sequence recited in SEQ ID NO: 1-33; (b) nucleotide sequences that are 100-mers of a sequence recited in SEQ ID NO: 1-33; (c) nucleotide sequences that are 40-mers of a sequence recited in SEQ ID NO: 1-33; and (d) nucleotide sequences that are 20-mers of a sequence recited in SEQ ID NO: 1-33;

5. An isolated oligonucleotide probe or primer comprising at least 10 contiguous residues complementary to 10 contiguous residues of a nucleotide sequence recited in any one of claims 1-3.

6. A kit comprising a plurality of oligonucleotide probes or primers of claim 5.

7. A genetic construct comprising a polynucleotide of any one of claims 1-3.

8. A transgenic host cell comprising a genetic construct according to claim 7.

9. A transgenic non-human organism comprising a transgenic host cell of claim 8.

10. The transgenic organism of claim 9, wherein the organism is selected from the group consisting of Lactobacillus species.

11. An isolated polynucleotide comprising a nucleotide sequence that differs from a nucleotide sequence recited in SEQ ID NO: 1-33 as a result of deletions and/or insertions totalling less than 15% of the total sequence length.

12. The isolated polynucleotide of claim 11, wherein the nucleotide sequence differs from a nucleotide sequence recited in SEQ ID NO: 1-33 as a result of substitutions, insertions, and/or deletions totalling less than 10% of the total sequence length.

13. A genetic construct comprising, in the 5'-3' direction: (a) a gene promoter sequence; and (b) a polynucleotide sequence comprising at least one of the following: (1) a polynucleotide coding for at least a functional portion of a polypeptide of SEQ ID NO: 42-75; and (2) a polynucleotide comprising a non-coding region of a polynucleotide of any one of claims 1-3.

14. The genetic construct of claim 13, wherein the polynucleotide is in a sense orientation.

15. The genetic construct of claim 13, wherein the polynucleotide is in an anti-sense orientation.

16. The genetic construct of claim 13, wherein the gene promoter sequence is functional in a prokaryote or eukaryote.

17. A transgenic host cell comprising a construct of claim 13.

18. A transgenic organism comprising a transgenic host cell according to claim 17, or progeny thereof.

19. The transgenic organism of claim 18, wherein the organism is selected from the group consisting of Lactobacillus species.

20. A method for modulating the activity of a polypeptide in an organism, comprising stably incorporating into the genome of the organism a polynucleotide of any one of claims 1-3.

21. The method of claim 20, wherein the organism is a microbe.

22. An isolated polypeptide comprising an amino acid sequence selected from the group consisting of: SEQ ID NO: 42-75.

23. An isolated polypeptide comprising an amino acid sequence selected from the group consisting of: (a) sequences having at least 75% identity to a sequence of SEQ ID NO: 42-75; (b) sequences having at least 90% identity to a sequence of SEQ ID NO: 42-75; and (c) sequences having at least 95% identity to a sequence of SEQ ID NO: 42-75, wherein the polypeptide has substantially the same functional properties as a polypeptide of SEQ ID NO: 42-75.

24. An isolated polypeptide encoded by a polynucleotide of any one of claims 1-3.

25. An isolated polynucleotide that encodes a polypeptide of any one of claims 22 and 23.

26. A fusion protein comprising at least one polypeptide according to any one of claims 22 and 23.

27. A composition comprising a polypeptide according to any one of claims 22 and 23 and at least one component selected from the group consisting of: physiologically acceptable carriers and immunostimulants.

28. A composition comprising a polynucleotide according to any one of claims 1-3 and at least one component selected from the group consisting of: physiologically acceptable carriers and immunostimulants.

29. A method for treating a disorder in a mammal, comprising administering a composition according to claim 27.

30. A method for treating a disorder in a mammal, comprising administering a composition according to claim 28.

31. A method for modifying a property of a microbe, comprising modulating the polynucleotide content or composition of the microbe by transforming the microbe with a polynucleotide of any one of claims 1-3.

32. The method of claim 31, wherein the microbe is used in the manufacture of a milk-derived product, food product, food additive, nutritional supplement, bioactive substance or probiotic supplement.

33. A method for modifying at least one property of a product, food, food additive, nutritional supplement or probiotic supplement, wherein the product, food, food additive, nutritional supplement or probiotic supplement is prepared from milk, the method comprising adding a polypeptide of any one of claims 22-24 to the milk.

34. The method of claim 33, wherein the property is selected from the group consisting of: flavor; aroma; texture; nutritional benefits; immune system modulation; and health benefits.

35. A food product comprising an isolated polypeptide of any one of claims 22 and 23.

36. The food product of claim 35, wherein the food product is derived from milk.

37. The food product of claim 36, wherein the food product is selected from the group consisting of: cheese; and yoghurt.

38. The food product of claim 35, wherein the food product has at least one modified property selected from the group consisting of: flavor; aroma; texture; nutritional benefits; immune system modulation; and health benefits.