Polynucleotides, materials incorporating them, and methods for using them

Abstract

Novel polynucleotides isolated from Lactobacillus rhamnosus, as well as oligonucleotide 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

TECHNICAL FIELD OF THE INVENTION

[0002] This invention relates to polynucleotides isolated from lactic acid bacteria as well as to probes and primers specific to the polynucleotides; 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.

BACKGROUND OF THE INVENTION

[0003] The present invention relates to polynucleotides 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.

[0004] 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° 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). 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. 211-253; 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). Beneficial health effects attributed to these bacteria include the following:

[0005] 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.

[0006] Aid in lactose digestion—due to lactose degradation by bacterial lactase enzymes (such as beta-galactosidase) that act in the small intestine.

[0007] 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.

[0008] Liver cancer reduction—due to aflatoxin detoxification and inhibition of mould growth.

[0009] Reduction of small bowel bacterial overgrowth—due to antibacterial activity; and decrease in toxic metabolite production from overgrowth flora.

[0010] 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.

[0011] Treatment of allergic responses to foods—due to prevention of antigen translocation into blood stream and modulation of allergenic factors in food.

[0012] Reduction of blood lipids and prevention of heart disease—due to assimilation of cholesterol by bacteria; hydrolysis of bile salts; and antioxidative effects.

[0013] Antihypertensive effect—bacterial protease or peptidase action on milk peptides produces antihypertensive peptides. Cell wall components act as ACE inhibitors

[0014] 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).

[0015] 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 and hydrogen peroxide and biosurfactants; and competitive exclusion.

[0016] Modulation of infective endocarditis—due to fibronectin receptor-mediated platelet aggregation associated with Lactobacillus sepsis.

[0017] Prevention and treatment of Helicobacter pylori infection—due to competitive colonization and antibacterial effect.

[0018] Prevention and treatment of hepatic encephalopathy—due to inhibition and/or exclusion of urease-producing gut flora.

[0019] Improved protein and carbohydrate utilisation and conversion—due to production of beneficial products by bacterial action on proteins and carbohydrates.

[0020] Other beneficial health effects associated 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.

[0021] 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 peptides 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.

[0022] 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:

[0023] Aminopeptidases—release a free amino acid from the N-terminus of a peptide chain;

[0024] dipeptidyl-peptidase (also known as dipeptidyl-aminopeptidases)—release a dipeptide from the N-terminus of a peptide chain;

[0025] tripeptidyl-peptidases (also known as tripeptidyl-aminopeptidases)—release a tripeptide from the N-terminus of a peptide chain);

[0026] carboxypeptidases—release a free amino acid from the C-terminus of a peptide chain;

[0027] peptidyl-dipeptidase—release a dipeptide from the C-terminus of a peptide chain;

[0028] dipeptidases—release two free amino acids from a dipeptide; and

[0029] tripeptidases—release a free amino acid and a dipeptide from a tripeptide.

[0030] 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).

[0031] 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, 2nd 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 specific characteristics and/or functions include the following:

[0032] 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.

[0033] 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 decarboxylase, acetolactate synthase, pyruvate decarboxylase, pyruvate formate lyase, diacetyl synthase, diacetyl reductase, alcohol decarboxylase, lactate dehydrogenase, pyruvate dehydrogenase, and aldehyde dehydrogenase.

[0034] Lipid degradation, modification or synthesis. Enzymes involved include lipases, esterases, phospholipases, serine hydrolases, desaturases, and linoleate isomerase.

[0035] 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.

[0036] Amino acid degradation. Enzymes include glutamate dehydrogenase, aminotransferases, amino acid decarboxylases, and enzymes involved in sulphur amino acid degradation including cystothione beta-lyase.

[0037] Sequencing of the genomes, or portions 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. Putative polypeptides may be identified based on polynucleotide sequences and further characterized. The sequencing data relating to polynucleotides thus represents valuable and useful information.

[0038] 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 putative 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 b e determined relative to polynucleotides and polypeptides having known functions.

[0039] 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

[0040] The present invention provides isolated polynucleotides comprising a sequence selected from the group consisting of: (a) sequences identified in the attached Sequence Listing as SEQ ID NOS: 1-121; (b) variants of those sequences; (c) extended sequences comprising the sequences set out in SEQ ID NOS: 1-121, and their variants; and (d) sequences comprising at least a specified number of contiguous residues of a sequence of SEQ ID NOS: 1-121 (x-mers). Oligonucleotide probes and primers corresponding to the sequences set out in SEQ ID NOS: 1-121, 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.”

[0041] The polynucleotide sequences identified as SEQ ID NOS: 1-121 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. 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° 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. 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.

[0042] Certain of the polynucleotide sequences disclosed herein are “partial” sequences in that they do not represent a full-length gene encoding a full-length polypeptide. Such partial sequences may be extended by analyzing and sequencing various DNA libraries using primers and/or probes and well-known hybridization and/or PCR techniques. The partial sequences disclosed herein may thus be extended until an open reading frame encoding a polypeptide, a full-length polynucleotide and/or gene capable of expressing a polypeptide, or another useful portion of the genome is identified. Such extended sequences, including full-length polynucleotides and genes, are described as “corresponding to” a sequence identified as one of the sequences of SEQ ID NOS: 1-121 or a variant thereof, or a portion of one of the sequences of SEQ ID NOS: 1-121 or a variant thereof, when the extended polynucleotide comprises an identified sequence or its variant, or an identified contiguous portion (x-mer) of one of the sequences of SEQ ID NOS: 1-121 or a variant thereof.

[0043] The polynucleotides identified as SEQ ID NOS: 1-121 were isolated from Lactobacillus rhamnosus genomic DNA clones and represent sequences that are present in the cells from which the DNA was prepared. The sequence information may be used to identify and isolate, or synthesize, DNA molecules such as promoters, DNA-binding elements, open reading frames or full-length genes, that then can be used as expressible or otherwise functional DNA in transgenic organisms. Similarly, 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 NOS: 1-121.

[0044] The present invention further provides isolated polypeptides encoded, or partially 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 sequences identified as SEQ ID NO: 122-253, 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.

[0045] Genetic constructs comprising the inventive polynucleotides are also provided, together with transgenic host cells comprising such constructs and transgenic organisms, such as microbes, comprising such cells.

[0046] The present invention also contemplates methods for modulating the polynucleotide and/or polypeptide content and composition of an organism, such methods involving stably incorporating into the genome of the organism a genetic construct comprising a polynucleotide of the present invention. 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 other closely microbial related species used in the dairy industry. In a related aspect, methods for producing a microbe having an altered genotype and/or phenotype is 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.

[0047] 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.

[0048] 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, better flavor and improved milk composition; in methods for the selection and production of better natural food bacteria for improved flavor, faster flavor development, better 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.

[0049] 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 NOS: 1-121, and their variants, may be used to design oligonucleotide probes and primers. Such 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 polymerase chain reaction (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.).

[0050] The polynucleotides of the present invention may also be used to tag or identify an organism or derived material or product therefrom. Such tagging may be accomplished, for example, by stably introducing a non-disruptive non-functional heterologous polynucleotide identifier into an organism, the polynucleotide comprising at least a portion of a polynucleotide of the present invention.

[0051] The polynucleotides of the present invention may also be used as promoters, gene regulators, origins of DNA replication, secretion signals, cell wall or membrane anchors for genetic tools (such as expression or integration vectors).

[0052] All references cited herein, including patent references and non-patent publications, are hereby incorporated by reference in their entireties.

DETAILED DESCRIPTION

[0053] 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. Cell wall, cell surface and secreted components of lactic acid bacteria are known to mediate immune modulation, cell adhesion and antibacterial activities, resulting in 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. These cell components include, but are not limited to, 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. 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 can be 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.

[0054] In order to function effectively as probiotic bacteria, L. rhamnosus HN001 must survive 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:

[0055] 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.

[0056] 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.

[0057] 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.

[0058] Acid resistance—lactobacilli naturally acidify their environment through t he excretion of lactic acid, mainly through the cit operon genes responsible for citrate uptake and utilization.

[0059] 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.

[0060] 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.

[0061] 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.

[0062] The isolated polynucleotides and polypeptides of the present invention have demonstrated similarity to polynucleotides and/or polypeptides of known function. The identity and functions of the inventive polynucleotides based on such similarities are shown below in Table 1.

TABLE 1
SEQ ID	SEQ ID
NO:	NO:
DNA	PROT	Category	Description
1	122	Construction of genetic vectors for	Homologue of purL, encoding a
		controlled expression of RNA and/or	phosphoribosylformylglycinamidine
		protein, fusion protein production,	(FGAM) synthetase (EC 6.3.5.3). PurL
		genetic modification, mutagenesis	catalyzes the fourth step in the
		amplification of genetic material or	biosynthesis of purines. It is involved
		for other genetic or protein	in resistance environmental stress
		manipulations.	conditions and the stringent response
		Production of desirable flavors.	through the control of intracellular
		Modified flavor, aroma and/or texture	phosphate levels. Purines also play
		attributes.	essential roles in many other cellular
		Altered survival characteristics:	functions, including DNA replication,
		survival of industrial processes,	transcription, intra-and extra-cellular
		growth or storage in product formats,	signaling, energy metabolism, and as
		persistence in gut environment.	coenzymes for many biochemical
		Altered viability in response to stress	reactions.
		conditions.
		Altered metabolic properties or
		regulation of metabolic pathways.
		Altered probiotic attributes.
2	123	Construction of genetic vectors for	Homologue of 5′-Phosphoribosyl-5
		controlled expression of RNA and/or	aminoimidazole (AIR) carboxylase
		protein, fusion protein production,	(EC 4.1.1.21). AIR carboxylase is
		genetic modification, mutagenesis	responsible for CO2 fixation during
		amplification of genetic material or	purine biosynthesis. It catalyzes the
		for other genetic or protein	carboxylation of AIR to 5′-
		manipulations.	phosphoribosyl-5-aminoimidazole-4-
		Production of desirable flavors.	carboxylic acid, in the de novo
		Modified flavor, aroma and/or texture	biosynthesis of purine nucleotides.
		attributes.	AIR carboxylase is composed of two
		Altered survival characteristics:	nonidentical subunits, the catalytic
		survival of industrial processes,	subunit is encoded by the purE gene,
		growth or storage in product formats,	while the CO2-binding subunit is
		persistence in gut environment.	encoded by the purK gene. These two
		Altered viability in response to stress	genes form an operon in which the
		conditions.	termination codon of the purE gene
		Altered metabolic properties or	overlapped the initiation codon of the
		regulation of metabolic pathways.	purK gene. The purEK operon is
		Altered probiotic attributes.	regulated by the purR gene product,
			and a purR regulatory-protein-binding
			site related to the sequences found in
			other pur loci was identified in the
			purEK operon control region. It is
			involved in resistance environmental
			stress conditions and the stringent
			response through the control of
			intracellular phosphate levels. Purines
			also play essential roles in many other
			cellular functions, including DNA
			replication, transcription, intra- and
			extra-cellular signaling, energy
			metabolism, and as coenzymes for
			many biochemical reactions.
3	124	Construction of genetic vectors for	Homologue of amino acid antiporters
		controlled expression of RNA and/or	gadC, Xasa and acsA. Amino acid
		protein, fusion protein production,	antiporters are integral membrane
		genetic modification, mutagenesis	proteins involved in the transport of
		amplification of genetic material or	amino acids into the cell and in
		for other genetic or protein	extreme acid resistance. GadC is
		manipulations.	homologous to putative glutamate-
		Production of desirable flavors.	gamma-aminobutyrate antiporters of
		Modified flavor, aroma and/or texture	Escherichia coli and Shigella flexneri
		attributes,	and contains 12 putative membrane-
		Altered survival characteristics:	spanning domains. It belongs to the
		survival of industrial processes,	amino acid-polyamine-organocation
		growth or storage in product formats,	(APC) superfamily, and the Xasa
		persistence in gut environment.	family of transporters. It is involved in
		Altered viability in response to stress	glutamate-dependent acid resistance
		conditions.	and in antiport of glutamate and
		Altered amino acid metabolism.	glutamate-gamma-aminobutyrate
		Altered metabolic properties or	(GABA). The chloride-dependent
		regulation of metabolic pathways.	expression is activated by gadR. GadC
		Altered probiotic attributes.	is involved in tolerance to
			environmental stress conditions such
			as high salt and low pH.
4	125, 126	Construction of genetic vectors for	Homologue of the B-subunit of
		controlled expression of RNA and/or	phosphate-specific transporter (PstB).
		protein, fusion protein production,	PstB is an ATP binding cassette
		genetic modification, mutagenesis	(ABC) protein. Phosphate-specific
		amplification of genetic material or	transporters (Pst) in bacteria are
		for other genetic or protein	involved in phosphate transport. Pst is
		manipulations.	a multisubunit system and belongs to
		Production of desirable flavors,	the ABC superfamily of transporters.
		Modified flavor, aroma and/or texture	(TC# 3.A.1.7.1) (Novak et al., J
		attributes.	Bacteriol. 181: 1126-1133, 1999).
		Altered survival characteristics:	Utility as a controlled expression
		survival of industrial processes,	vector and in the control of
		growth or storage in product formats,	intracellular phosphate levels
		persistence in gut environment,	important for resistance to
		Altered phosphate metabolism,	environmental stress conditions and
		Altered viability in response to stress	induction of the stringent response.
		conditions.
		Altered metabolic properties or
		regulation of metabolic pathways.
		Altered probiotic attributes.
5, 106	127, 230	Construction of genetic vectors for	Homologue of PstA/PstC, which are
		controlled expression of RNA and/or	the two hydrophobic subunits of a
		protein, fusion protein production,	phosphate-specific transporter (PstB),
		genetic modification, mutagenesis	an ATP binding cassette (ABC)
		amplification of genetic material or	protein. Phosphate specific transporter
		for other genetic or protein	(Pst) in bacteria is involved in
		manipulations.	phosphate transport. Pst is a
		Production of desirable flavors.	multisubunit system and belongs to the
		Modified flavor, aroma and/or texture	ABC superfamily of transporters. (TC#
		attributes.	3.A.1.7.1) (Novak et al., J. Bacteriol.
		Altered survival characteristics:	181: 1126-1133, 1999). Utility as a
		survival of industrial processes,	controlled expression vector and in the
		growth or storage in product formats,	control of intracellular phosphate
		persistence in gut environment.	levels important for resistance to
		Altered phosphate metabolism.	environmental stress conditions and
		Altered viability in response to stress	induction of the stringent response.
		conditions.
		Altered metabolic properties or
		regulation of metabolic pathways.
		Altered probiotic attributes.
6-10	128, 130-133	Construction of genetic vectors for	Homologue of a response regulator
		controlled expression of RNA and/or	belonging to the family of 2-
		protein, fusion protein production,	component signal transduction proteins
		genetic modification, mutagenesis	phosphorylated by a specific sensor
		amplification of genetic material or	kinase (phoR). PhoR
		for other genetic or protein	activates/represses Pho regulon gene
		manipulations.	transcription in response to phosphate
		Production of desirable flavors.	starvation. The gene is involved in cell
		Modified flavor, aroma and/or texture	cycle control, polysaccharide synthesis
		attributes.	and intestinal adhesion, also
		Altered survival characteristics:	multistress resistance. It is part of a
		survival of industrial processes,	phosphate (PHO) regulon which is
		growth or storage in product formats,	regulated by extracellular phosphate
		persistence in gut environment.	and consists of 20 phosphate-regulated
		Altered phosphate metabolism.	promotors, 10 regulatory genes and 2
		Altered viability in response to stress	phosphate transport systems. Under
		conditions.	conditions of phosphate limitation, the
		Altered metabolic properties or	response regulator PhoB is
		regulation of metabolic pathways.	phosphorylated by the histidine kinase
		Altered probiotic attributes.	PhoR and binds to promoters that
			share a consensus PHO box. Under
			conditions of phosphate excess, PhoR,
			Pst, and PhoU downregulate the PHO
			regulon (Novak et al., J. Bacteriol.
			181: 1126-1133, 1999). Utility as a
			controlled expression vector and in the
			control of intracellular phosphate
			levels important for resistance to
			environmental stress conditions and
			induction of the stringent response.
6	129	Construction of genetic vectors for	Homologue of the response regulator
		controlled expression of RNA and/or	PnpR. PnpR is part of a two-
		protein, fusion protein production,	component regulatory system, PnpR-
		genetic modification, mutagenesis	PnpS, and a downstream ABC
		amplification of genetic material or	transporter, similar to the Pst system in
		for other genetic or protein	E. coli, including a gene encoding a
		manipulations.	PhoU protein. The E. coli Pst system
		Production of desirable flavors.	belongs to the superfamily of ABC
		Modified flavor, aroma and/or texture	transporters. It is part of a phosphate
		attributes.	(PHO) regulon which is regulated by
		Altered survival characteristics:	extracellular phosphate and consists of
		survival of industrial processes,	20 phosphate-regulated promotors, 10
		growth or storage in product formats,	regulatory genes and 2 phosphate
		persistence in gut environment.	transport systems. Under conditions of
		Altered phosphate metabolism.	phosphate limitation, the response
		Altered viability in response to stress	regulator PhoB is phosphorylated by
		conditions.	the histidine kinase PhoR and binds to
		Regulation of metabolic pathways.	promoters that share a consensus PHO
		Altered metabolic properties or	box. Under conditions of phosphate
		regulation of metabolic pathways.	excess, PhoR, Pst, and PhoU
		Altered probiotic attributes.	downregulate the PHO regulon (Novak
			et al., J. Bacteriol. 181: 1126-1133,
			1999). Utility in immune modulation,
			gut adhesion, cell wall synthesis and
			polysaccharide production, survival,
			controlled expression vector.
11	134	Construction of genetic vectors for	Homologue of the histidine kinase
		controlled expression of RNA and/or	PhoR, which is involved in the E. coli
		protein, fusion protein production,	Pst system. PhoR is part of a
		genetic modification, mutagenesis	phosphate (PHO) regulon and
		amplification of genetic material or	phosphorylates under conditions of
		for other genetic or protein	phosphate limitation the response
		manipulations.	regulator PhoB. Under conditions of
		Production of desirable flavors.	phosphate excess, PhoR, Pst, and
		Modified flavor, aroma and/or texture	PhoU down regulate the PHO regulon
		attributes.	(Novak et al., J. Bacteriol. 181: 1126-1133,
		Altered survival characteristics:	1999) which consists of 20
		survival of industrial processes,	phosphate-regulated promoters, 10
		growth or storage in product formats,	regulatory genes and 2 phosphate
		persistence in gut environment.	transport systems. Utility in immune
		Altered phosphate metabolism.	modulation, gut adhesion, cell wall
		Altered viability in response to stress	synthesis and polysaccharide
		conditions.	production, survival, controlled
		Regulation of metabolic pathways.	expression vector.
		Altered metabolic properties or
		regulation of metabolic pathways.
		Altered probiotic attributes.
12, 107	135, 231	Construction of genetic vectors for	Homologue of PnpS (which in turn is a
		controlled expression of RNA and/or	homologue of PhoR), which is part of
		protein, fusion protein production,	a two-component regulatory system,
		genetic modification, mutagenesis	PnpR-PnpS, and a downstream ATP-
		amplification of genetic material or	binding cassette (ABC) transporter,
		for other genetic or protein	similar to the Pst system in E. coli
		manipulations.	including a gene encoding a PhoU
		Production of desirable flavors.	protein. The E. coli Pst system belongs
		Modified flavor, aroma and/or texture	to the superfamily of ABC
		attributes.	transporters. It is part of a phosphate
		Altered survival characteristics:	(PHO) regulon which is regulated by
		survival of industrial processes,	extracellular phosphate and consists of
		growth or storage in product formats,	20 phosphate-regulated promoters, 10
		persistence in gut environment.	regulatory genes and 2 phosphate
		Altered phosphate metabolism.	transport systems. Under conditions of
		Altered viability in response to stress	phosphate limitation, the response
		conditions.	regulator PhoB is phosphorylated by
		Regulation of metabolic pathways.	the histidine kinase PhoR and binds to
		Altered metabolic properties or	promoters that share a consensus PHO
		regulation of metabolic pathways.	box. Under conditions of phosphate
		Altered probiotic attributes.	excess, PhoR, Pst, and PhoU
			downregulate the PHO regulon. PnpS
			(Novak et al., J. Bacteriol. 181: 1126-1133,
			1999). Utility in immune
			modulation, gut adhesion, cell wall
			synthesis and polysaccharide
			production, survival, controlled
			expression vector.
13, 14	136, 137	Altered cell wall or cell surface	Homologue of penicillin-binding
		characteristics, structures or	protein 1B (Pbp1b) or murein
		functions.	polymerase. Penicillin-binding
		Improved antimicrobial properties	proteins (PBPs), targets of beta-lactam
		Modified adhesion to human or	antibiotics, are membrane-bound
		animal cells or cell lines.	enzymes essential for the biosynthesis
		Production of desirable flavors.	of the bacterial cell wall. PBPs possess
		Modified flavor, aroma and/or texture	a penicillin-insensitive
		attributes.	transglycosylase N-terminal domain
		Construction of genetic vectors for	(formation of linear glycan strands)
		controlled expression of RNA and/or	and a penicillin-sensitive
		protein, fusion protein production,	transpeptidase C-terminal domain
		genetic modification, mutagenesis	(cross-linking of the peptide subunits)
		amplification of genetic material or	responsible for the final steps of the
		for other genetic or protein	bacterial cell wall polymerization and
		manipulations.	cross-linking, respectively (Zhao et al.,
		Altered survival characteristics:	Protein Expr. Purif. 16: 331-339,
		survival of industrial processes,	1999). Utility in immune modulation,
		growth or storage in product formats,	gut adhesion, cell wall synthesis and
		persistence in gut environment.	polysaccharide production.
		Altered metabolic properties.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health).
		Modified antibiotic resistance.
		Improved fermentation properties or
		other industrially useful processes.
15, 42,	138, 167,	Altered cell wall or cell surface	Homologue of penicillin-binding
108	232	characteristics, structures or	protein 5 (Pbp5) also known as
		functions.	muramoylpentapeptide
		Improved antimicrobial properties	carboxypeptidase (EC 3.4.17.8,
		Modified adhesion to human or	formerly EC 3.4.12.6). Pbp5 is a
		animal cells or cell lines.	bacterial enzyme that requires a
		Production of desirable flavors.	divalent cation for activity. Does not
		Modified flavor, aroma and/or texture	cleave the C-terminal D-alanine from
		attributes.	the reaction product, UDP-N-acetyl-
		Construction of genetic vectors for	muramoyl-L-alanyl-D-g-glutamyl-6-
		controlled expression of RNA and/or	carboxy-L-lysyl-D-alanine.
		protein, fusion protein production,	Competitively inhibited by penicillins
		genetic modification, mutagenesis	and cephalosporins. Penicillin-binding
		amplification of genetic material or	proteins (PBPs), targets of beta-lactam
		for other genetic or protein	antibiotics, are membrane-bound
		manipulations.	enzymes essential for the biosynthesis
		Altered survival characteristics:	of the bacterial cell wall. (Sifaoui et
		survival of industrial processes,	al., Antimicrob. Agents Chemother.
		growth or storage in product formats,	45: 2594-2597, 2001). Utility in
		persistence in gut environment.	immune modulation, gut adhesion, cell
		Altered metabolic properties.	wall synthesis and polysaccharide
		Altered probiotic attributes.	production.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health).
		Modified antibiotic resistance.
		Improved fermentation properties or
		other industrially useful processes.
16, 109	139, 233	Altered cell wall or cell surface	Homologue of the hydrophobic
		characteristics, structures or	transmembrane protein psaC. PsaC is a
		functions.	member of the of ABC superfamily,
		Modified adhesion to human or	involved in the transport of nutrients,
		animal cells or cell lines.	translocation of signal molecules and
		Production of desirable flavors.	chemotaxis (Janulczyk et al., Mol.
		Modified flavor, aroma and/or texture	Microbiol. 34: 596-606, 1999). May be
		attributes.	employed in immune modulation, gut
		Construction of genetic vectors for	adhesion, cell wall synthesis, survival,
		controlled expression of RNA and/or	and polysaccharide production.
		protein, fusion protein production,
		genetic modification, mutagenesis
		amplification of genetic material or
		for other genetic or protein
		manipulations.
		Altered survival characteristics:
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Altered metabolic properties.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
17	140	Production of desirable flavors.	Homologue of plnH. PlnH is the
		Modified flavor, aroma and/or texture	accessory factor for ABC transporter
		attributes.	plnG with strong similarities to the
		Construction of genetic vectors for	proposed transport proteins of several
		controlled expression of RNA and/or	other bacteriocins and to proteins
		protein, fusion protein production,	implicated in the signal-sequence-
		genetic modification, mutagenesis	independent export of E. coli
		amplification of genetic material or	hemolysin (Huhne et al., Microbiol.
		for other genetic or protein	142: 1437-1448, 1996). LcnD is an
		manipulations.	accessory protein of Lactococcus lactis
		Altered survival characteristics:	with similarities to other proteins
		survival of industrial processes,	involved in the secretion of various
		growth or storage in product formats,	polypeptides. They operate in
		persistence in gut environment.	conjunction with a protein from the
		Altered metabolic properties.	family of ABC1 transporters. The
		Altered probiotic attributes.	accessory proteins of Gram-negative
		Modified health properties (including	bacteria are proposed to form a family
		immunoregulatory, anticancer gut	of so-called membrane fusion proteins.
		health).	It is hypothesized that they connect the
		Modified antibiotic resistance.	inner and the outer membranes to
		Improved antimicrobial properties.	facilitate the passage of substrates.
			CvaA, a member of the membrane
			fusion protein family, involved in the
			secretion of colicin V, has been shown
			to interact with both a cytoplasmic
			membrane protein (the ABC
			transporter) and a protein present in the
			outer membrane (Franke et al., J. Biol.
			Chem. 274: 8484-8490, 1999). May be
			employed as an antibacterial for
			control of infection and food
			preservation.
18, 121	141, 252		Homologue of Glyceraldehyde 3-
			phosphate dehydrogenase (GAPDH)
			(EC 1.2.1.12) is a tetrameric NAD-
			binding enzyme common to both the
			glycolytic and gluconeogenic
			pathways that catalyzes reversibly the
			oxidative phosphorylation of D-
			glyceraldehyde 3-phosphate (G3P) to
			form 1,3-diphosphoglycerate (1,3-
			dPG) in the presence of NAD and
			inorganic phosphate.
			This enzyme is useful in manipulating
			alcohol dehydrogenation in vitro or in
			vivo, e.g. in fermentation processes or
			with transgenic bacteria with deleted,
			added or modified alcohol
			dehydrogenase gene. It can also be
			useful as a controlled expression
			vector.
19	142	Removal of undesirable flavor	Homologue of the histidine-containing
		characteristics.	protein ptsH, also known as the
		Production of desirable flavors.	phosphocarrier protein HPr. Hpr is a
		Modified flavor, aroma, or texture	component of the
		attributes.	phosphoenolpyruvate-dependent sugar
		Construction of genetic vectors for	phosphotransferase system (PTS), a
		controlled expression of RNA and/or	major carbohydrate active-transport
		protein, fusion protein production,	system. The phosphoryl group from
		genetic modification, mutagenesis	phosphoenolpyruvate (PEP) is
		amplification of genetic material or	transferred to the phosphoryl carrier
		for other genetic or protein	protein HPr by enzyme I. Phospho-
		manipulations.	HPr then transfers it to the permease
		Altered survival characteristics:	(enzymes II/III). HPr is common to all
		survival of industrial processes,	PTS and belongs to the HPr family.
		growth or storage in product formats,	The HPr family consists of bacterial
		persistence in gut environment.	proteins, all of which function as
		Modified carbohydrate levels or	phosphoryl transfer proteins. They are
		functional properties.	energy-coupling constituents of the
		Altered metabolic properties.	phosphotransferase system (PTS)
		Modified carbohydrate metabolism.	(TC # 4.A.1-4.A.6). which catalyzes sugar
		Altered probiotic attributes.	uptake via a group translocation
		Improved fermentation properties or	mechanism. The E. coli genome
		other industrially useful processes.	encodes five HPr paralogues that
		Organisms or materials with	function in PTS-related regulatory
		improved health properties (including	capacities. May be employed in
		immunoregulatory, anticancer, gut	survival and carbohydrate metabolism
		health, lactose tolerance)	and as a controlled expression vector.
20	143	Removal of undesirable flavor	Homologue of gamma (acyl carrier
		characteristics.	protein) subunit of citrate lyase. Citrate
		Production of desirable flavors.	lyase (EC 4.1.3.6.) is part of the citrate
		Modified flavor, aroma, or texture	metabolism pathway and catalyzes the
		attributes.	cleavage of citrate to oxaloacetate and
		Construction of genetic vectors for	acetate and is composed of three
		controlled expression of RNA and/or	subunits (alpha, beta, and gamma).
		protein, fusion protein production,	Lactobacillae contribute through the
		genetic modification, mutagenesis	citrate metabolism actively to the
		amplification of genetic material or	flavor development of fermented dairy
		for other genetic or protein	products (e.g., Dutch cheeses). It is
		manipulations.	also involved in citrate metabolism
		Altered survival characteristics:	pathway that results in lactic acid
		survival of industrial processes,	production and acid tolerance (Magni
		growth or storage in product formats,	et al., J. Bacteriol. 181: 1451-1457,
		persistence in gut environment.	1999) and may be employed in
		Modified carbohydrate levels or	survival and carbohydrate metabolism.
		functional properties.
		Altered metabolic properties.
		Modified citrate metabolism.
		Altered probiotic attributes.
		Improved fermentation properties or
		other industrially useful processes.
		Organisms or materials with
		improved health properties (including
		immunoregulatory, anticancer, gut
		health, lactose tolerance)
20	144	Removal of undesirable flavor	Homologue of beta (citryl-S-ACP
		characteristics.	lyase) subunit of citrate lyase. Citrate
		Production of desirable flavors.	lyase (EC 4.1.3.6.) is part of the citrate
		Modified flavor, aroma, or texture	metabolism and catalyzes the cleavage
		attributes.	of citrate to oxaloacetate and acetate
		Construction of genetic vectors for	and is composed of three subunits
		controlled expression of RNA and/or	(alpha, beta, and gamma).
		protein, fusion protein production,	Lactobacillae contribute through the
		genetic modification, mutagenesis	citrate metabolism actively to the
		amplification of genetic material or	flavor development of fermented dairy
		for other genetic or protein	products (e.g., Dutch cheeses). It is
		manipulations.	also involved in citrate metabolism
		Altered survival characteristics:	pathway that results in lactic acid
		survival of industrial processes,	production and acid tolerance (Magni
		growth or storage in product formats,	et al., J. Bacteriol. 181: 1451-1457,
		persistence in gut environment.	1999) and may be employed in
		Modified carbohydrate levels or	survival and carbohydrate metabolism.
		functional properties.
		Altered metabolic properties.
		Modified citrate metabolism.
		Altered probiotic attributes.
		Improved fermentation properties or
		other industrially useful processes.
		Organisms or materials with
		improved health properties (including
		immunoregulatory, anticancer, gut
		health, lactose tolerance).
20	145	Removal of undesirable flavor	Homologue of alpha subunit
		characteristics.	(citrate: acetyl-ACP transferase) of
		Production of desirable flavors.	citrate lyase. Citrate lyase (EC 4.1.3.6.)
		Modified flavor, aroma, or texture	is part of the citrate metabolism and
		attributes.	catalyzes the cleavage of citrate to
		Construction of genetic vectors for	oxaloacetate and acetate and is
		controlled expression of RNA and/or	composed of three subunits (alpha,
		protein, fusion protein production,	beta, and gamma). Lactobacillae
		genetic modification, mutagenesis	contribute through the citrate
		amplification of genetic material or	metabolism actively to the flavor
		for other genetic or protein	development of fermented dairy
		manipulations.	products (e.g., Dutch cheeses). It is
		Altered survival characteristics:	also involved in citrate metabolism
		survival of industrial processes,	pathway that results in lactic acid
		growth or storage in product formats,	production and acid tolerance (Magni
		persistence in gut environment.	et al., J. Bacteriol. 181: 1451-1457,
		Modified carbohydrate levels or	1999) and may be employed in
		functional properties.	survival and carbohydrate metabolism.
		Altered metabolic properties.
		Modified citrate metabolism.
		Altered probiotic attributes.
		Improved fermentation properties or
		other industrially useful processes.
		Organisms or materials with
		improved health properties (including
		immunoregulatory, anticancer, gut
		health, lactose tolerance).
21, 119	146, 243	Removal of undesirable flavor	Homologue of malic enzyme (EC
		characteristics.	1.1.1.39). Malic enzyme catalyzes L-
		Production of desirable flavors.	malate oxidative decarboxylation and
		Modified flavor, aroma, or texture	pyruvate reductive carboxylation and a
		attributes.	malate transport protein (similar to
		Construction of genetic vectors for	citP) involved in membrane potential
		controlled expression of RNA and/or	generation via malate/lactate exchange.
		protein, fusion protein production,	Because lactobacilli appear not to have
		genetic modification, mutagenesis	a functioning Krebs cycle, this enzyme
		amplification of genetic material or	may be involved in carbohydrate
		for other genetic or protein	metabolism, amino acid biosynthesis
		manipulations.	or L-malate utilization pathways.
		Altered survival characteristics:
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Modified carbohydrate levels or
		functional properties.
		Altered metabolic properties.
		Modified carbohydrate metabolism.
		Altered probiotic attributes.
		Improved fermentation properties or
		other industrially useful processes.
		Organisms or materials with
		improved health properties (including
		immunoregulatory, anticancer, gut
		health, lactose tolerance).
22	147	Construction of genetic vectors for	Homologue of otsA, encoding
		controlled expression of RNA and/or	trehalose-6-phosphate synthetase
		protein, fusion protein production,	(UDP forming) (EC 2.4.1.15). OtsA
		genetic modification, mutagenesis	combines two glucose molecules to
		amplification of genetic material or	trehalose. Trehalose plays a protective
		for other genetic or protein	role in the ability of many organisms
		manipulations.	to tolerate adverse environmental
		Production of desirable flavors.	conditions (Fernandes et al., Lett.
		Modified flavor, aroma and/or texture	Appl. Microbiol. 32: 42, 2001) and acts
		attributes.	as an osmoprotectant as well as a
		Altered survival characteristics:	carbon source (Rimmele and Boos, J.
		survival of industrial processes,	Bacteriol. 176: 5654-5664, 1994). May
		growth or storage in product formats,	be involved in carbohydrate and amino
		persistence in gut environment,	acid metabolism, survival and may
		Altered viability in response to stress	have utility as a controlled expression
		conditions.	vector.
		Increased resistance to high salt
		levels.
		Altered metabolic properties or
		regulation of metabolic pathways.
		Altered probiotic attributes.
23	148	Construction of genetic vectors for	Homologue of trehalose-6-phosphate
		controlled expression of RNA and/or	hydrolase (EC 3.2.1.93). Trehalose-6-
		protein, fusion protein production,	phosphate hydrolase is the key enzyme
		genetic modification, mutagenesis	of the phosphotransferase system and
		amplification of genetic material or	hydrolyzes trehalose-6-phosphate to
		for other genetic or protein	glucose and glucose 6-phosphate. The
		manipulations.	enzyme shows strong homology with
		Production of desirable flavors.	those of oligo-1,6- glucosidases.
		Modified flavor, aroma and/or texture	Trehalose plays a protective role in the
		attributes.	ability of many organisms to tolerate
		Altered survival characteristics:	adverse environmental conditions
		survival of industrial processes,	(Fernandes et al., Lett. Appl.
		growth or storage in product formats,	Microbiol. 32: 42, 2001) and acts as an
		persistence in gut environment.	osmoprotectant as well as a carbon
		Altered viability in response to stress	source (Rimmele and Boos, J.
		conditions.	Bacteriol. 176: 5654-5664, 1994). May
		Increased resistance to high salt	be involved in carbohydrate and amino
		levels.	acid metabolism, survival and may
		Altered metabolic properties or	have utility as a controlled expression
		regulation of metabolic pathways.	vector.
		Altered probiotic attributes.
24	149	Construction of genetic vectors for	Homologue of proV. ProV is a glycine
		controlled expression of RNA and/or	betaine/proline transporter that also
		protein, fusion protein production,	transports proline betaine, carnitine,
		genetic modification, mutagenesis	dimethyl proline, homobetaine, g-
		amplification of genetic material or	butyrobetaine and choline with low
		for other genetic or protein	affinity (TC-Number: 3.A.1.12.1).
		manipulations.	ProV belongs to the ABC substrate
		Production of desirable flavors.	binding protein-dependent transporter
		Modified flavor, aroma and/or texture	superfamily, May be involved in
		attributes.	carbohydrate and amino acid
		Altered survival characteristics:	metabolism, survival and may have
		survival of industrial processes,	utility as a controlled expression
		growth or storage in product formats,	vector.
		persistence in gut environment.
		Altered viability in response to stress
		conditions.
		Increased resistance to high salt
		levels.
		Altered metabolic properties or
		regulation of metabolic pathways.
		Altered probiotic attributes.
25	150	Altered cell wall or cell surface	Homologue of rgg which positively
		characteristics, structures or	regulates the expression of
		functions.	extracellular glucosyltransferase
		Modified adhesion to human or	(GTF). rgg-like determinants make up
		animal cells or cell lines.	a widely occurring gene family in
		Production of desirable flavors.	pathogenic and commensal bacterial
		Modified flavor, aroma and/or texture	species and appear to share positive
		attributes.	regulatory functions (Vickerman and
		Construction of genetic vectors for	Minick, Infect. Immun. 70: 1703-1714,
		controlled expression of RNA and/or	2002).
		protein, fusion protein production,
		genetic modification, mutagenesis
		amplification of genetic material or
		for other genetic or protein
		manipulations.
		Altered survival characteristics:
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Altered metabolic properties.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Regulation of polysaccharide
		production, adhesion, immune
		modulation.
26	151	Altered cell wall or cell surface	Homologue of Cps14D. Cps gene
		characteristics, structures or	products are involved in bacterial
		functions.	capsular polysaccharide (CP)
		Modified adhesion to human or	biosynthesis. Bacterial CPs are
		animal cells or cell lines.	generally composed of repeating
		Production of desirable flavors.	oligosaccharides and are involved in
		Modified flavor, aroma and/or texture	resistance to opsonophagocytosis,
		attributes.	avoidance of the immune system of the
		Construction of genetic vectors for	host and attachment. Cps genes are
		controlled expression of RNA and/or	normally clustered on the bacterial
		protein, fusion protein production,	chromosome and have a common
		genetic modification, mutagenesis	genetic organization involving three
		amplification of genetic material or	functional regions. Cps14D codes for a
		for other genetic or protein	protein involved in chain length
		manipulations.	determination and export of CP
		Altered survival characteristics:	(Kolkman et al., J. Biol. Chem.
		survival of industrial processes,	272: 19502-19508, 1997).
		growth or storage in product formats,
		persistence in gut environment.
		Altered metabolic properties.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Regulation of polysaccharide
		production, adhesion, immune
		modulation.
27	152	Altered cell wall or cell surface	Homologue of a Cps-like gene
		characteristics, structures or	product. Cps-like gene products are
		functions.	involved in bacterial capsular
		Modified adhesion to human or	polysaccharide (CP) biosynthesis.
		animal cells or cell lines.	Bacterial CPs are generally composed
		Production of desirable flavors.	of repeating oligosaccharides and are
		Modified flavor, aroma and/or texture	involved in resistance to
		attributes.	opsonophagocytosis, avoidance of the
		Construction of genetic vectors for	immune system of the host and
		controlled expression of RNA and/or	attachment. Cps genes are normally
		protein, fusion protein production,	clustered on the bacterial chromosome
		genetic modification, mutagenesis	and have a common genetic
		amplification of genetic material or	organization involving three functional
		for other genetic or protein	regions (Kolkman et al., J. Biol. Chem.
		manipulations.	272: 19502-19508, 1997). Cps14J
		Altered survival characteristics:	encodes a beta-1,4-
		survival of industrial processes,	galactosyltransferase that requires
		growth or storage in product formats,	beta-linked GlcNAc as an acceptor.
		persistence in gut environment.
		Altered metabolic properties.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Regulation of polysaccharide
		production, adhesion, immune
		modulation.
28	153	Altered cell wall or cell surface	Homologue of a Cps-like gene
		characteristics, structures or	product. Cps-like gene products are
		functions.	involved in bacterial capsular
		Modified adhesion to human or	polysaccharide (CP) biosynthesis.
		animal cells or cell lines.	Bacterial CPs are generally composed
		Production of desirable flavors.	of repeating oligosaccharides and are
		Modified flavor, aroma and/or texture	involved in resistance to
		attributes.	opsonophagocytosis, avoidance of the
		Construction of genetic vectors for	immune system of the host and
		controlled expression of RNA and/or	attachment. Cps genes are normally
		protein, fusion protein production,	clustered on the bacterial chromosome
		genetic modification, mutagenesis	and have a common genetic
		amplification of genetic material or	organization involving three functional
		for other genetic or protein	regions. (Kolkman et al., J. Biol.
		manipulations.	Chem. 272: 19502-19508, 1997).
		Altered survival characteristics:	Cps14L encodes a transporter for the
		survival of industrial processes,	repeating unit of the polysaccharide
		growth or storage in product formats,	(Kolkman et al. J. Biochem. 123: 937-945,
		persistence in gut environment.	1998).
		Altered metabolic properties.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Regulation of polysaccharide
		production, adhesion, immune
		modulation.
29, 30	154, 155	Altered cell wall or cell surface	Homologue of D-alanyl-D-alanine
		characteristics, structures or	carboxypeptidase (EC 3.4.17.8,
		functions.	formerly EC 3.4.12.6). D-alanyl-D-
		Modified adhesion to human or	alanine carboxypeptidase is a
		animal cells or cell lines.	periplasmic membrane-attached
		Production of desirable flavors.	protein involved in the construction
		Modified flavor, aroma and/or texture	and maintenance of the bacterial cell
		attributes.	walls and also a penicillin binding
		Construction of genetic vectors for	protein involved in the late stages of
		controlled expression of RNA and/or	murein synthesis. Peptidases are
		protein, fusion protein production,	important in the process of cheese
		genetic modification, mutagenesis	ripening and the development of
		amplification of genetic material or	cheese flavor. May have utility as a
		for other genetic or protein	controlled expression vector.
		manipulations.
		Altered survival characteristics:
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Altered metabolic properties.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Regulation of polysaccharide
		production, adhesion, immune
		modulation.
31	156	Altered cell wall or cell surface	Homologue of aggregation protein
		characteristics, structures or	aggH. Transgenic microbes with
		functions.	added, deleted or modified aggregation
		Modified adhesion to human or	protein gene can have a modified
		animal cells or cell lines.	aggregation response in vitro (useful in
		Production of desirable flavors.	bioprocessing with bacteria, e.g.
		Modified flavor, aroma and/or texture	fermentation, flocculation) or in vivo
		attributes.	(useful in enhancing/decreasing
		Construction of genetic vectors for	clumping of bacteria, e.g. in
		controlled expression of RNA and/or	gastrointestinal tract, as desired).
		protein, fusion protein production,	Aggregation protein gene can be used
		genetic modification, mutagenesis	also for production of protein as
		amplification of genetic material or	antigen to vaccinate mammals. Gene
		for other genetic or protein	can be used as vehicle for vaccination
		manipulations.	by fusing with an exogenous antigen
		Altered survival characteristics:	with it, transforming a bacterium and
		survival of industrial processes,	treating the mammal to be immunized
		growth or storage in product formats,	with killed or live bacteria for
		persistence in gut environment.	preventive or therapeutic vaccination
		Altered metabolic properties.	(see patent WO9947657-A2;
		Altered probiotic attributes.	Lactobacillus reuteri bacterial
		Modified health properties (including	aggregation protein). The aggregation
		immunoregulatory, anticancer, gut	protein is targeted for the bacterial
		health).	surface, so this ensures efficient
		Modified antibiotic resistance.	antigen presentation to the immune
		Improved antimicrobial properties.	system as the Lactobacillus or other
		Improved fermentation properties or	gastrointestinal bacteria adhere to
		other industrially useful processes.	epithelial cells. Finally, gene is useful
			for detecting Lactobacillus species
			using the DNA as detection probe.
32	157	Altered cell wall or cell surface	Homologue of exopolyphosphatase
		characteristics, structures or	(PPX) (EC 3.6.1.11). Polyphosphate is
		functions.	made by polyphosphate kinase PPK
		Modified adhesion to human or	(EC 2.7.4.1) and is broken down by
		animal cells or cell lines.	PPX.
		Production of desirable flavors.
		Modified flavor, aroma and/or texture
		attributes.
		Construction of genetic vectors for
		controlled expression of RNA and/or
		protein, fusion protein production,
		genetic modification, mutagenesis
		amplification of genetic material or
		for other genetic or protein
		manipulations.
		Altered survival characteristics:
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Altered metabolic properties.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
33	158	Altered cell wall or cell surface	Homologue of a peptidoglycan
		characteristics, structures or	(mureins) bound protein with an
		functions.	LPXTG motif similar to an adhesin.
		Modified adhesion to human or	Adhesins mediate attachment of cells
		animal cells or cell lines.	to collagen-containing substrata. Type
		Production of desirable flavors.	I membrane protein. Collagen binding
		Modified flavor, aroma and/or texture	is important property in attachment
		attributes.	and potential pathogenesis of various
		Construction of genetic vectors for	bacteria with mammalian hosts. The
		controlled expression of RNA and/or	gene can be used to screen bacteria
		protein, fusion protein production,	with DNA or protein probes/antibodies
		genetic modification, mutagenesis	for the presence of collagen adhesion
		amplification of genetic material or	gene in various pathogenic and non-
		for other genetic or protein	pathogenic bacteria, e.g. for selection
		manipulations.	of strains or for diagnostic purposes
		Altered survival characteristics:	(see e.g. patent WO9207002). It is
		survival of industrial processes,	known that expression of a collagen
		growth or storage in product formats,	adhesin is essential for the attachment
		persistence in gut environment.	of Staphylococcus aureus to cartilage,
		Altered metabolic properties.	which contains collagen (Switalski et
		Altered probiotic attributes.	al., Mol. Microbiol. 7: 99-107, 1993).
		Modified health properties (including	Deletion/addition or modification of
		immunoregulatory, anticancer, gut	the gene can alter collagen-binding
		health).	properties of cells to the desired effect
		Modified antibiotic resistance.	in bacteria-host interactions. Finally,
		Improved antimicrobial properties.	protein can be used as an administered
		Improved fermentation properties or	reagent in in vitro or in vivo collagen
		other industrially useful processes.	binding reactions.
34	159	Altered cell wall or cell surface	Homologue of a bacterial hemolysin.
		characteristics, structures or	Hemolysin is a bacterial toxin gene
		functions.	that can be used to develop vaccines
		Modified adhesion to human or	against pathogenic bacteria carrying
		animal cells or cell lines.	the gene/protein. Transgenic microbes
		Production of desirable flavors.	with added, deleted or modified
		Modified flavor, aroma and/or texture	hemolysin protein gene can have a
		attributes.	modified hemolytic activity in vitro
		Construction of genetic vectors for	(useful e.g. in bacteria-based assays) or
		controlled expression of RNA and/or	in vivo (useful in enhancing/decreasing
		protein, fusion protein production,	pathogenicity of bacteria, as desired
		genetic modification, mutagenesis	(see e.g. J. Biol. Chem. 267: 10902-10909,
		amplification of genetic material or	1992). Functional expression
		for other genetic or protein	of the alpha-hemolysin gene of
		manipulations.	Staphylococcus aureus in intact E. coli
		Altered survival characteristics:	and in cell lysates. Deletion of five C-
		survival of industrial processes,	terminal amino acids selectively
		growth or storage in product formats,	impairs hemolytic activity. The peptide
		persistence in gut environment.	itself can be used as a reagent e.g. in in
		Altered metabolic properties.	vitro assays of hemolytic activity.
		Altered probiotic attributes.	May be invovled in scavenging iron
		Modified health properties (including	from environment, and therefore is
		immunoregulatory, anticancer, gut	involved in cell survival and
		health).	metabolism, as well as restricting
		Modified antibiotic resistance.	growth of surrounding microbes.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
35	160	Altered cell wall or cell surface	Homologue of autoinducer 2 (AI-2).
		characteristics, structures or	AI-2 participates in quorum sensing in
		functions.	bacteria. Autoinducer is secreted by
		Modified adhesion to human or	bacteria and is used to communicate
		animal cells or cell lines.	both the cell density and the metabolic
		Production of desirable flavors.	potential of the environment. The gene
		Modified flavor, aroma and/or texture	can be used in DNA or protein assays
		attributes.	to detect presence of the DNA or
		Construction of genetic vectors for	protein in microbes. The deletion,
		controlled expression of RNA and/or	addition or modification of the gene
		protein, fusion protein production,	can change the intercellular signaling
		genetic modification, mutagenesis	of bacteria, affecting their growth
		amplification of genetic material or	mode, pathogenesis and survival. The
		for other genetic or protein	peptide can be used as a reagent to
		manipulations.	modify the bacterial communication in
		Altered survival characteristics:	vitro or in vivo.
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Altered metabolic properties.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
		Regulation of cell numbers and
		growth.
36	161	Altered cell wall or cell surface	Homologue of autolysin. Autolysins
		characteristics, structures or	control the lysis bacterial cells. It can
		functions.	be used for controlling lysis of food
		Modified adhesion to human or	fermenting bacteria, e.g. in cheese
		animal cells or cell lines.	production, as well as lysis of
		Production of desirable flavors.	pathogenic organisms with in vivo or
		Modified flavor, aroma and/or texture	in vitro administration of the peptide or
		attributes.	peptide-producing microorganisms.
		Construction of genetic vectors for	The deleted/added or modified gene in
		controlled expression of RNA and/or	transgenic bacteria can be used to
		protein, fusion protein production,	modify the lysis process as required.
		genetic modification, mutagenesis	The DNA and peptide can be used in
		amplification of genetic material or	developing and using various
		for other genetic or protein	screening assays to detect presence of
		manipulations.	hemolysin gene/protein and autolytic
		Altered survival characteristics:	activity.
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Altered metabolic properties.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
		Regulation of cell numbers and
		growth.
37-39	162-164	Altered cell wall or cell surface	Homologue of a bacterial hemolysin.
		characteristics, structures or	Hemolysin is a bacterial toxin gene
		functions.	that can be used to develop vaccines
		Modified adhesion to human or	against pathogenic bacteria carrying
		animal cells or cell lines.	the gene/protein. Transgenic microbes
		Production of desirable flavors.	with added, deleted or modified
		Modified flavor, aroma and/or texture	hemolysin protein gene can have a
		attributes.	modified hemolytic activity in vitro
		Construction of genetic vectors for	(useful e.g. in bacteria-based assays) or
		controlled expression of RNA and/or	in vivo (useful in enhancing/decreasing
		protein, fusion protein production,	pathogenicity of bacteria, as desired
		genetic modification, mutagenesis	(see e.g. J. Biol. Chem. 267: 10902-10909,
		amplification of genetic material or	1992). Functional expression
		for other genetic or protein	of the alpha-hemolysin gene of
		manipulations.	Staphylococcus aureus in intact E. coli
		Altered survival characteristics:	and in cell lysates. Deletion of five C-
		survival of industrial processes,	terminal amino acids selectively
		growth or storage in product formats,	impairs hemolytic activity. The peptide
		persistence in gut environment.	itself can be used as a reagent e.g. in in
		Altered metabolic properties.	vitro assays of hemolytic activity.
		Altered probiotic attributes.	May be invovled in scavenging iron
		Modified health properties (including	from environment, and therefore is
		immunoregulatory, anticancer, gut	involved in cell survival and
		health).	metabolism, as well as restricting
		Modified antibiotic resistance.	growth of surrounding microbes.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
		Regulation of cell numbers and
		growth.
40, 41	165, 166	Altered cell wall or cell surface	Homologue of penicillin-binding
		characteristics, structures or	proteins (PBPs). PBPs are enzymes
		functions.	involved in the final stages of
		Improved antimicrobial properties	peptidoglycan biosynthesis. The C-
		Modified adhesion to human or	terminal module binds penicillin and
		animal cells or cell lines.	catalyzes peptidoglycan cross-linking.
		Production of desirable flavors.	The N-terminal domain can have
		Modified flavor, aroma and/or texture	transglycosylase activity (class A
		attributes.	HMW PBPs). PBPs are the targets of
		Construction of genetic vectors for	beta-lactam antibiotics, which
		controlled expression of RNA and/or	covalently bind to these proteins,
		protein, fusion protein production,	inhibiting cell wall synthesis (Mariana
		genetic modification, mutagenesis	et al., J. Bacteriol. 182: 1074-1079,
		amplification of genetic material or	2000). Penicillin-binding protein gene
		for other genetic or protein	can be used for modifications in
		manipulations.	transgenic bacteria, which can change
		Altered survival characteristics:	their susceptibility to penicillin (see
		survival of industrial processes,	e.g. Smith and Klugman, Antimicrob.
		growth or storage in product formats,	Agents Chemother. 42: 1329-1333,
		persistence in gut environment.	1998). Alterations in PBP 1A
		Altered metabolic properties.	essential-for high-level penicillin
		Altered probiotic attributes.	resistance in Streptococcus
		Modified health properties (including	pneumoniae. The DNA or protein can
		immunoregulatory, anticancer, gut	be used in various assays to detect the
		health).	presence of the gene or protein in
		Modified antibiotic resistance.	various biological samples, where
		Improved fermentation properties or	penicillin binding is of interest.
		other industrially useful processes.
42	167	Altered cell wall or cell surface	Homologue of penicillin-binding
		characteristics, structures or	protein 5 (Pbp5) also known as
		functions.	muramoylpentapeptide
		Improved antimicrobial properties	carboxypeptidase (EC 3.4.17.8,
		Modified adhesion to human or	formerly EC 3.4.12.6). Ppb5 requires a
		animal cells or cell lines.	divalent cation for activity. Penicillin-
		Production of desirable flavors.	binding proteins (PBPs), targets of
		Modified flavor, aroma and/or texture	beta-lactam antibiotics, are membrane-
		attributes.	bound enzymes essential for the
		Construction of genetic vectors for	biosynthesis of the bacterial cell wall
		controlled expression of RNA and/or	(Sifaoui et al., Antimicrob. Agents
		protein, fusion protein production,	Chemother. 45: 2594-2597, 2001).
		genetic modification, mutagenesis	Penicillin-binding protein gene can be
		amplification of genetic material or	used for modifications in transgenic
		for other genetic or protein	bacteria, which can change their
		manipulations.	susceptibility to penicillin (see e.g.
		Altered survival characteristics:	Smith and Klugman, Antimicrob.
		survival of industrial processes,	Agents Chemother. 42:1329-1333,
		growth or storage in product formats,	1998). Alterations in PBP 1A
		persistence in gut environment.	essential-for high-level penicillin
		Altered metabolic properties.	resistance in Streptococcus
		Altered probiotic attributes.	pneumoniae. The DNA or protein can
		Modified health properties (including	be used in various assays to detect the
		immunoregulatory, anticancer, gut	presence of the gene or protein in
		health).	various biological samples, where
		Modified antibiotic resistance.	penicillin binding is of interest.
		Improved fermentation properties or
		other industrially useful processes.
43	168	Altered cell wall or cell surface	Homologue of penicillin-binding
		characteristics, structures or	protein 1B (Pbp1b) or murein
		functions.	polymerase. Penicillin-binding
		Improved antimicrobial properties	proteins (PBPs), targets of beta-lactam
		Modified adhesion to human or	antibiotics, are membrane-bound
		animal cells or cell lines.	enzymes essential for the biosynthesis
		Production of desirable flavors.	of the bacterial cell wall. PBPs possess
		Modified flavor, aroma and/or texture	a penicillin-insensitive
		attributes.	transglycosylase n-terminal domain
		Construction of genetic vectors for	(formation of linear glycan strands)
		controlled expression of RNA and/or	and a penicillin-sensitive
		protein, fusion protein production,	transpeptidase c-terminal domain
		genetic modification, mutagenesis	(cross-linking of the peptide subunits)
		amplification of genetic material or	responsible for the final steps of the
		for other genetic or protein	bacterial cell wall polymerization and
		manipulations.	cross-linking, respectively (Zhao et al.,
		Altered survival characteristics:	Protein Expr. Purif. 16: 331-339,
		survival of industrial processes,	1999). Penicillin-binding protein gene
		growth or storage in product formats,	can be used for modifications in
		persistence in gut environment.	transgenic bacteria, which can change
		Altered metabolic properties.	their susceptibility to penicillin (see
		Altered probiotic attributes.	e.g. Smith and Klugman, Antimicrob.
		Modified health properties (including	Agents Chemother. 42: 1329-1333,
		immunoregulatory, anticancer, gut	1998). Alterations in PBP 1A
		health).	essential-for high-level penicillin
		Modified antibiotic resistance.	resistance in Streptococcus
		Improved fermentation properties or	pneumoniae. The DNA or protein can
		other industrially useful processes.	be used in various assays to detect the
			presence of the gene or protein in
			various biological samples, where
			penicillin binding is of interest.
44, 110	169, 234	Production of desirable flavors.	Homologue of protein p60, encoded by
		Modified flavor, aroma and/or texture	the gene termed iap. p60 protein is a
		attributes.	major extracellular product secreted by
		Construction of genetic vectors for	all isolates of Listeria monocytogenes.
		controlled expression of RNA and/or	This protein has peptidoglycan
		protein, fusion protein production,	hydrolase activity but also influences
		genetic modification, mutagenesis	the uptake of L. monocytogenes by
		amplification of genetic material or	non-phagocytic cells. Proteins related
		for other genetic or protein	to p60 are found in all other Listeria
		manipulations.	species. It has been shown that p60
		Altered survival characteristics:	protein is among the strongest antigens
		survival of industrial processes,	in listeriae for B- and T-cell responses.
		growth or storage in product formats,	The protein p60 belongs to the E. coli
		persistence in gut environment.	nlpc/listeria p60 family. This gene
		Altered metabolic properties.	can be useful as a probe to detect the
		Altered probiotic attributes.	presence of the gene/protein in various
		Modified adhesion to human or	bacteria. Deletion, addition and
		animal cells or cell lines.	modification of the gene in transgenic
		Organisms or materials with	bacteria can alter their extracellular
		improved health properties (including	envelope structure, thereby altering
		immunoregulatory, anticancer, gut	their growth and pathogenicity
		health)	characteristics. See e.g. Bubert et al.,
		Altered resistance to antibiotics.	J. Bacteriol. 174: 8166-8171, 1992.
		Improved antimicrobial properties.
45	170	Altered cell wall or cell surface	Homologue of flotillin. Flotillins have
		characteristics, structures or	been found in mammalian, insect and
		functions.	bacterial cells and behave as resident
		Modified adhesion to human or	integral membrane protein components
		animal cells or cell lines.	of caveolae which are plasmalemmal
		Production of desirable flavors.	microdomains that are involved in
		Modified flavor, aroma and/or texture	vesicular trafficking and signal
		attributes.	transduction (Huang et al., Mol.
		Construction of genetic vectors for	Microbiol. 31: 361-371, 1999).
		controlled expression of RNA and/or	Flotillins (also known as epidermal
		protein, fusion protein production,	surface antigens (ESAs)) belong to the
		genetic modification, mutagenesis	family of caveolae-associated integral
		amplification of genetic material or	membrane proteins and may act as a
		for other genetic or protein	scaffolding protein within caveolar
		manipulations.	membranes. This gene is similar to an
		Altered survival characteristics:	epidermal surface antigen of Bacillus
		survival of industrial processes,	subtilis. It is useful as a vaccine
		growth or storage in product formats,	development target.
		persistence in gut environment.
		Altered metabolic properties.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
46	171	Altered cell wall or cell surface	Homologue of fimbria associated
		characteristics, structures or	protein. Fimbriae and pili are
		functions.	interchangeable terms used to
		Modified adhesion to human or	designate short, hair-like structures on
		animal cells or cell lines.	the surfaces of prokaryotic cells
		Production of desirable flavors.	composed of protein. Fimbriae are
		Modified flavor, aroma and/or texture	most often involved in adherence of
		attributes.	bacteria to surfaces, substrates and
		Construction of genetic vectors for	other cells in nature. This gene is
		controlled expression of RNA and/or	similar to sortase, which is involved in
		protein, fusion protein production,	covalent anchoring to the cell wall (see
		genetic modification, mutagenesis	Cossart and Jonquieres, Proc. Natl.
		amplification of genetic material or	Acad. Sci. USA 97: 5013-5015, 2000).
		for other genetic or protein	The gene is useful as a target for
		manipulations.	antibiotic development as the gene
		Altered survival characteristics:	performs a very important function in
		survival of industrial processes,	cell wall protein anchoring. The DNA
		growth or storage in product formats,	and protein can be used in vitro and in
		persistence in gut environment.	vivo assays and treatments as a
		Altered metabolic properties.	reagent. Transgenic bacteria with
		Altered probiotic attributes.	deleted, added or modified sortase
		Modified health properties (including	gene can have modified protein
		immunoregulatory, anticancer, gut	anchoring at the cell surface layer.
		health).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
47	172	Altered cell wall or cell surface	Homologue of a collagen binding
		characteristics, structures or	protein. Collagen binding is important
		functions.	property in attachment and potential
		Modified adhesion to human or	pathogenesis of various bacteria with
		animal cells or cell lines.	mammalian hosts. The gene can be
		Production of desirable flavors.	used to screen bacteria with DNA or
		Modified flavor, aroma and/or texture	protein probes/antibodies for the
		attributes.	presence of collagen adhesion gene in
		Construction of genetic vectors for	various pathogenic and non-pathogenic
		controlled expression of RNA and/or	bacteria, e.g. for selection of strains or
		protein, fusion protein production,	for diagnostic purposes (see e.g. patent
		genetic modification, mutagenesis	WO9207002). It is known that
		amplification of genetic material or	expression of a collagen adhesin is
		for other genetic or protein	essential for the attachment of
		manipulations.	Staphylococcus aureus to cartilage,
		Altered survival characteristics:	which contains collagen (Switalski et
		survival of industrial processes,	al., mol. Microbiol. 7, 99-107, 1993).
		growth or storage in product formats,	Deletion/addition or modification of
		persistence in gut environment.	the gene can alter collagen-binding
		Altered metabolic properties.	properties of cells to the desired effect
		Altered probiotic attributes.	in bacteria-host interactions. Finally,
		Modified health properties (including	protein can be used as an administered
		immunoregulatory, anticancer, gut	reagent in in vitro or in vivo collagen
		health).	binding reactions.
		Modified antibiotic resistance.
		Improved antimicrobial properties.
48	173	Altered cell wall or cell surface	Homologue of bacteriophage
		characteristics, structures or	immunity repressor IMMREP.
		functions.	IMMREP is involved in the regulation
		Modified adhesion to human or	of lysogeny in the temperate Bacillus
		animal cells or cell lines.	subtilis phage phi 105, which can
		Production of desirable flavors.	make B. subtilis immune to infection
		Modified flavor, aroma and/or texture	by phi 105 phage (see Cully and Garro,
		attributes.	Gene 38: 153-164, 1985). Can be used
		Construction of genetic vectors for	to manipulate bacteria as to their
		controlled expression of RNA and/or	susceptibility to phage invasion and
		protein, fusion protein production,	hence acquiring desired/undesired
		genetic modification, mutagenesis	genetic element carried by the phage.
		amplification of genetic material or
		for other genetic or protein
		manipulations.
		Altered survival characteristics:
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Altered metabolic properties.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health).
		Modified antimicrobial properties.
49	174	Altered cell wall or cell surface	Homologue of N-acetylmuramoyl-L-
		characteristics, structures or	alanine amidase (EC 3.5.1.28). N-
		functions.	acetylmuramoyl-L-alanine amidase
		Improved antimicrobial properties	hydrolyzes the link between N-
		Modified adhesion to human or	acetylmuramoyl residues and L-amino
		animal cells or cell lines.	acid residues in certain cell-wall
		Production of desirable flavors.	glycopeptides. N-acetylmuramoyl-L-
		Modified flavor, aroma and/or texture	alanine amidases contain a COOH-
		attributes.	terminal choline-binding domain and
		Construction of genetic vectors for	an NH2-terminal catalytic domain.
		controlled expression of RNA and/or	Useful for N-acetylmuramoyl-L-
		protein, fusion protein production,	alanine amidase activity using the
		genetic modification, mutagenesis	peptide in vitro or in vivo, or
		amplification of genetic material or	transgenic bacteria with the gene
		for other genetic or protein	expressed to effect the enzyme
		manipulations.	activity. The DNA or protein can be
		Altered survival characteristics:	used in assays to detect the presence of
		survival of industrial processes,	the gene or protein in various assays.
		growth or storage in product formats,	This enterotoxin related gene is also a
		persistence in gut environment.	vaccine development target for
		Altered metabolic properties.	pathogenic or other undesired bacteria,
		Altered probiotic attributes.	e.g. various Lactobacillus strains.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health).
		Modified antibiotic resistance.
		Improved fermentation properties or
		other industrially useful processes.
50	175	Removal of undesirable flavor	Homologue of hrdT. hrdT is a
		characteristics.	member of the multidrug resistance
		Production of desirable flavors.	exporter (MDR) family (TC#
		Modified flavor, aroma, or texture	3.A.1.201) in the ATP-binding
		attributes.	Cassette (ABC) Superfamily of
		Construction of genetic vectors for	transporters. ABC transporters
		controlled expression of RNA and/or	translocate a wide variety of substrates,
		protein, fusion protein production,	including amino acids, peptides, ions,
		genetic modification, mutagenesis	sugars, toxins, lipids, and drugs
		amplification of genetic material or
		for other genetic or protein
		manipulations.
		Altered survival characteristics:
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Modified carbohydrate levels or
		functional properties.
		Altered metabolic properties.
		Altered probiotic attributes.
		Improved fermentation properties or
		other industrially useful processes.
		Organisms or materials with
		improved health properties (including
		immunoregulatory, anticancer, gut
		health, lactose tolerance)
51	176	Altered cell wall or cell surface	Homologue of adhesin-involved-in-
		characteristics, structures or	diffuse-adherence (AIDA) a fimbrial
		functions.	adhesin and virG (icsA) protein. VirG
		Improved antimicrobial properties	and AIDA are precursor virulence
		Modified adhesion to human or	factors that transport themselves out of
		animal cells or cell lines.	the bacterial cell and are then usually
		Production of desirable flavors.	proteolytically digested to release a
		Modified flavor, aroma and/or texture	soluble protein that can promote
		attributes.	virulence. They are members of the
		Construction of genetic vectors for	autotransporter (AT) family of outer
		controlled expression of RNA and/or	membrane proteins and play an
		protein, fusion protein production,	important role in virulence. The gene
		genetic modification, mutagenesis	is useful as a target for vaccine
		amplification of genetic material or	development of bacteria having this
		for other genetic or protein	kind of gene, as well as manipulation
		manipulations.	of virulence by deletion, addition or
		Altered survival characteristics:	modification of the gene in transgenic
		survival of industrial processes,	bacteria.
		growth or storage in product formats,
		persistence in gut environment.
		Altered metabolic properties.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health).
		Modified antibiotic resistance.
		Improved fermentation properties or
		other industrially useful processes.
52	177	Altered cell wall or cell surface	Homologue of cyclopropane fatty acid
		characteristics, structures or	synthase (cfa). cfa is similar to the
		functions.	cyclopropane-fatty-acyl-phospholipid
		Modified adhesion to human or	synthase of bacteria, and catalyzes a
		animal cells or cell lines.	modification of the acyl chains of
		Production of desirable flavors.	phospholipid bilayers. This gene is
		Modified flavor, aroma and/or texture	useful in modifying the bacterial
		attributes.	phospholipid bilayers by altered
		Construction of genetic vectors for	enzyme activity, e.g. by deleted, added
		controlled expression of RNA and/or	or modified gene in transgenic bacteria
		protein, fusion protein production,	(see e.g. U.S. Pat. No. 5,573,915:
		genetic modification, mutagenesis	Determining the ability of a compound
		amplification of genetic material or	to inhibit the cyclopropanation of
		for other genetic or protein	mycolic acids in pathogenic
		manipulations.	mycobacteria).
		Altered survival characteristics:
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Altered metabolic properties.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health, apoptosis).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
53	178	Removal of undesirable flavor	Homologue of adhE. adhE encodes a
		characteristics.	multifunctional dehydrogenase that
		Production of desirable flavors.	catalyzes the conversion of acetyl-CoA
		Modified flavor, aroma, or texture	into ethanol and has acetaldehyde
		attributes.	dehydrogenase [acetylating] (EC
		Construction of genetic vectors for	1.2.1.10) (ACDH) and alcohol
		controlled expression of RNA and/or	dehydrogenase (ADH) (EC 1.1.1.1)
		protein, fusion protein production,	activities (Arnau et al., J. Bacteriol.
		genetic modification, mutagenesis	180: 3049-3055, 1998). This enzyme is
		amplification of genetic material or	useful in manipulating alcohol
		for other genetic or protein	dehydrogenation in vitro or in vivo,
		manipulations.	e.g. in fermentation processes or with
		Altered survival characteristics:	transgenic bacteria with deleted, added
		survival of industrial processes,	or modified alcohol dehydrogenase
		growth or storage in product formats,	gene.
		persistence in gut environment.
		Modified carbohydrate levels or
		functional properties.
		Altered metabolic properties.
		Modified carbohydrate metabolism.
		Altered probiotic attributes.
		Improved fermentation properties or
		other industrially useful processes.
		Organisms or materials with
		improved health properties (including
		immunoregulatory, anticancer, gut
		health, lactose tolerance).
54	179	Altered cell wall or cell surface	Homologue of biotin carboxylase (EC
		characteristics, structures or	6.3.4.14). Biotin carboxylase is one
		functions.	component of acetyl CoA carboxylase
		Modified adhesion to human or	which, in turn, catalyzes the regulated
		animal cells or cell lines.	step in long-chain fatty acid synthesis.
		Production of desirable flavors.	This enzyme is useful in manipulating
		Modified flavor, aroma and/or texture	biotin carboxylation in vitro or in vivo,
		attributes.	e.g. in transgenic plants with deleted,
		Construction of genetic vectors for	added or modified gene leading to
		controlled expression of RNA and/or	altered biotin metabolism, thus
		protein, fusion protein production,	affecting insect herbivores which
		genetic modification, mutagenesis	require plant-derived biotin; may also
		amplification of genetic material or	have utility in manipulation of
		for other genetic or protein	herbicide tolerance (see U.S. Pat. No. 5,910,626:
		manipulations.	Acetyl-CoA carboxylase
		Altered survival characteristics:	compositions and methods of use).
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Altered metabolic properties.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health, apoptosis).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
55	180	Removal of undesirable flavor	Homologue of the argE gene product
		characteristics.	of E. coli. argE is a N-acetyl-L-
		Production of desirable flavors.	ornithine deacetylase that can remove
		Modified flavor, aroma, or texture	the acetyl-group from N-
		attributes.	acetylphosphinothricin giving the
		Construction of genetic vectors for	cytotoxic compound L-
		controlled expression of RNA and/or	phosphinothricin (Pt, glufosinate).
		protein, fusion protein production,	This gene is useful in related
		genetic modification, mutagenesis	deacetylase reactions, in vitro or in
		amplification of genetic material or	vivo using the proteins as such, of
		for other genetic or protein	bacteria engineered to produce the
		manipulations.	enzyme activity.
		Altered survival characteristics:
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Modified carbohydrate levels or
		functional properties.
		Altered metabolic properties.
		Modified carbohydrate metabolism.
		Altered probiotic attributes.
		Improved fermentation properties or
		other industrially useful processes.
		Organisms or materials with
		improved health properties (including
		immunoregulatory, anticancer, gut
		health, lactose tolerance).
56	181	Production of bioactive or functional	Homology to serine proteases, which
		polypeptides.	break down milk proteins during the
		Removal of undesirable flavor	growth of the bacteria on milk.
		characteristics.	Contains the subtilase pattern of the
		Production of desirable flavors.	subtilase family(G-T-S-x-[SA]-x-P-
		Modified flavor, aroma and/or texture	x(2)-[STAVC]-[AG]). Subtilases are
		attributes.	an extensive family of serine proteases
		Construction of genetic vectors for	whose catalytic activity is provided by
		controlled expression of RNA and/or	a charge relay system similar to that of
		protein, fusion protein production,	the trypsin family of serine proteases
		genetic modification, mutagenesis	but which evolved by independent
		amplification of genetic material or	convergent evolution. The sequence
		for other genetic or protein	around the residues involved in the
		manipulations.	catalytic triad (aspartic acid, serine and
		Altered survival characteristics:	histidine) are completely different
		survival of industrial processes,	from that of the analogous residues in
		growth or storage in product formats,	the trypsin serine proteases and can be
		persistence in gut environment.	used as signatures specific to that
		Altered metabolic properties or	category of proteases. This enzyme is
		regulation of metabolic pathways.	similar to prochymosin, a protein used
		Altered probiotic attributes.	in cheese making. The gene is useful in
		Organisms or materials with	protease utilization in protein
		improved health properties (including	processing (see e.g. NL8701378; S.
		immunoregulatory, anticancer, gut	cremoris proteinase).
		health).
		Altered resistance to antibiotics.
57	182	Altered cell wall or cell surface	Homologoue of GABA permeases.
		characteristics, structures or	GABA permeases belong to the amino
		functions.	acid-polyamine-organocation (APC)
		Modified adhesion to human or	superfamily. This superfamily of
		animal cells or cell lines.	transport proteins includes members
		Production of desirable flavors.	that function as solute: cation
		Modified flavor, aroma and/or texture	symporters and solute: solute
		attributes.	antiporters. They occur in bacteria,
		Construction of genetic vectors for	archaea, yeast, fungi, unicellular
		controlled expression of RNA and/or	eukaryotic protists, slime molds, plants
		protein, fusion protein production,	and animals. This enzyme is similar to
		genetic modification, mutagenesis	linoleate isomerase (see e.g.
		amplification of genetic material or	WO9932604-A1). This gene is useful
		for other genetic or protein	in enzyme reactions similar to lineolate
		manipulations.	isomerase, either as a purified protein,
		Altered survival characteristics:	or in transgenic organisms containing
		survival of industrial processes,	the gene effecting the enzyme activity.
		growth or storage in product formats,
		persistence in gut environment.
		Altered metabolic properties.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health, apoptosis).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
58	183	Altered cell wall or cell surface	Homologue of iap. iap is a major
		characteristics, structures or	extracellular protein in Listeria, and
		functions.	seems to be required for adherence to
		Modified adhesion to human or	and invasion of 3T6 mouse fibroblasts.
		animal cells or cell lines.	This gene can be useful as a probe to
		Production of desirable flavors.	detect the presence of the gene/protein
		Modified flavor, aroma and/or texture	in various bacteria. Deletion, addition
		attributes.	and modification of the gene in
		Construction of genetic vectors for	transgenic bacteria can alter their
		controlled expression of RNA and/or	extracellular envelope structure,
		protein, fusion protein production,	thereby altering their growth and
		genetic modification, mutagenesis	pathogenicity characteristics. See e.g.
		amplification of genetic material or	Bubert et al., J. Bacteriol.
		for other genetic or protein	174(24): 8166-8171, 1992. Involved in
		manipulations.	the invasion of cells, could be
		Altered survival characteristics:	necessary for the export of invasion
		survival of industrial processes,	related determinants. iap mediates
		growth or storage in product formats,	adhesion to particular cell surfaces,
		persistence in gut environment.	therefore has utility in persistance in
		Altered metabolic properties.	the gut enviroment, probiotic effects
		Altered probiotic attributes.	and pathogen exclusion.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health, apoptosis).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
59	184	Altered cell wall or cell surface	Homologue of preprotein translocase
		characteristics, structures or	secY subunit. The sequence contains
		functions.	the protein secY signature 1 pattern
		Modified adhesion to human or	(SIFSMGVSPYITAQIVVQLL), the
		animal cells or cell lines.	protein secY signature 2 pattern
		Production of desirable flavors.	(WMGEQITDKGLGNGVSLLI) and
		Modified flavor, aroma and/or texture	C-5 cytosine-specific DNA methylases
		attributes.	C-terminal signature pattern
		Construction of genetic vectors for	(KGLGNGVSLLIFSGIVARL). The
		controlled expression of RNA and/or	eubacterial secY protein plays an
		protein, fusion protein production,	important role in protein export. It
		genetic modification, mutagenesis	interacts with the signal sequences of
		amplification of genetic material or	secretory proteins as well as with two
		for other genetic or protein	other components of the protein
		manipulations.	translocation system: secA and secE.
		Altered survival characteristics:	SecY is an integral plasma membrane
		survival of industrial processes,	protein of 419 to 492 amino acid
		growth or storage in product formats,	residues that apparently contains ten
		persistence in gut environment.	transmembrane segments. Such a
		Altered metabolic properties.	structure probably confers to secY a
		Altered probiotic attributes.	‘translocator’ function, providing a
		Modified health properties (including	channel for periplasmic and outer-
		immunoregulatory, anticancer, gut	membrane precursor proteins. This
		health, apoptosis).	gene is useful for enhancing
		Modified antibiotic resistance.	extracellular protein production by
		Improved antimicrobial properties.	improved transport from cell (see e.g.
		Improved fermentation properties or	JP5153979A2: Sec Y protein gene)
		other industrially useful processes.
60	185	Altered cell wall or cell surface	Homolougue of cationic amino acid
		characteristics, structures or	transport protein ctrA. As a cell
		functions.	surface protein, ctrA has been shown
		Modified adhesion to human or	to give a strong response as antigen
		animal cells or cell lines.	and could be used as a prominent
		Production of desirable flavors.	target for antibodies and diagnostic
		Modified flavor, aroma and/or texture	procedures or vaccine development
		attributes.	(surface location enhances its exposure
		Construction of genetic vectors for	to the immune system). Amino acid
		controlled expression of RNA and/or	acid metabolism plays a role not only
		protein, fusion protein production,	in metabolism and growth, but also in
		genetic modification, mutagenesis	the production of flavour and aroma
		amplification of genetic material or	compounds. Control over the import
		for other genetic or protein	of amino acids will modulate the
		manipulations.	production of these compounds.
		Altered survival characteristics:
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Altered amino acid metabolism.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health, apoptosis).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
61	186	Altered cell wall or cell surface	Homologue of lipoprotein plpB.
		characteristics, structures or	Bacterial surface lipoproteins give
		functions.	strong responses as antigens and could
		Modified adhesion to human or	be used as prominent targets for
		animal cells or cell lines.	antibodies and diagnostic procedures.
		Production of desirable flavors.	Thus, is useful in vaccine development
		Modified flavor, aroma and/or texture	(surface location enhances its exposure
		attributes.	to the immune system). May also have
		Construction of genetic vectors for	a role in solute binding and adhesion to
		controlled expression of RNA and/or	cell surfaces.
		Protein, fusion protein production,
		genetic modification, mutagenesis
		amplification of genetic material or
		for other genetic or protein
		manipulations.
		Altered survival characteristics:
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Altered metabolic properties.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health, apoptosis).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
		Vaccine development.
62	187	Altered cell wall or cell surface	Homologue of dihydrodipicolinate
		characteristics, structures or	synthase (EC 4.2.1.52).
		functions.	Dihydrodipicolinate synthase catalyzes
		Altered amino acid metabolism.	the first step in the biosynthesis of
		Removal of undesirable flavor	diaminopimelate and lysine from
		characteristics.	aspartate semialdehyde; L-aspartate 4-
		Production of desirable flavors.	semialdehyde and pyruvate to
		Modified flavor, aroma and/or texture	dihydrodipicolinate and water. It is
		attributes.	feedback-inhibited by lysine and
		Construction of genetic vectors for	belongs to the dihydrodipicolinate
		controlled expression of RNA and/or	synthetase (DHDPS) family. This
		protein, fusion protein production,	gene is involved in bacterial wall
		genetic modification, mutagenesis	synthesis, and is thus a target for
		amplification of genetic material or	antibiotic development, as its
		for other genetic or protein	inhibition would affect growth of the
		manipulations.	bacterium.
		Altered survival characteristics:
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Altered metabolic properties.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health).
		Modified antibiotic resistance.
63	188	Construction of genetic vectors for	Homologue of GroEL, a heat shock
		controlled expression of RNA and/or	protein, which makes up the GroE
		protein, fusion protein production,	chaperonin system in bacteria together
		genetic modification, mutagenesis	With GroE. It is involved in the
		amplification of genetic material or	folding and assembly of newly
		for other genetic or protein	synthesized polypeptide chains
		manipulations.	released from the translation
		Production of desirable flavors.	machinery and the refolding of stress-
		Modified flavor, aroma and/or texture	denatured proteins. GroEL, a member
		attributes.	of the hsp60 family is a highly
		Altered survival characteristics:	conserved heat-shock chaperonin
		survival of industrial processes,	protein and is an oligomer of 14
		growth or storage in product formats,	subunits composed of two stacked
		persistence in gut environment.	rings of 7 subunits. This gene is
		Altered viability in response to stress	similar to a gene used in mycobacterial
		conditions.	vaccine development, and is thus a
		Improved stress-response	target for antibiotic development, as its
		Altered probiotic attributes.	inhibition would affect growth of the
		Vaccine development.	bacterium (see e.g. WO9932634-A2:
			Compositions derived from
			Mycobacterium vaccae and methods
			for their use). Also noted as having a
			role in resistance to environmental
			stress conditions.
64	189	Altered cell wall or cell surface	Homologue of hyaluronan synthase.
		characteristics, structures or	Hyaluronan (or hyaluronic acid or
		functions.	hyaluronate; HA) is a polysaccharide
		Modified adhesion to human or	of the glycosaminoglycans class found
		animal cells or cell lines.	in the extracellular matrix of vertebrate
		Production of desirable texture.	tissues and in the surface coating of
		Modified flavor, aroma and/or texture	certain Streptococcus and Pasteurella
		attributes.	bacterial pathogens. It is a unique
		Construction of genetic vectors for	biopolymer found in all tissues and
		controlled expression of RNA and/or	body fluids in every mammalian
		protein, fusion protein production,	species as well as in microorganisms.
		genetic modification, mutagenesis	HA synthases (HASs) are the enzymes
		amplification of genetic material or	that polymerize HA using uridine
		for other genetic or protein	diphospho-sugar precursors. In all
		manipulations.	known cases, HA is secreted out of the
		Altered survival characteristics:	cell; therefore, HASs are normally
		survival of industrial processes,	found in the outer membranes of the
		growth or storage in product formats,	organism. They were the first class of
		persistence in gut environment.	glycosyltransferases identified in
		Altered metabolic properties.	which a single polypeptide species
		Altered probiotic attributes.	catalyzes the transfer of two different
		Modified health properties (including	monosaccharides; this finding is in
		immunoregulatory, anticancer, gut	contrast to the usual ‘single enzyme,
		health, apoptosis).	single sugar’ dogma of glycobiology.
		Modified antibiotic resistance.	Derivatizing and complexing
		Improved antimicrobial properties.	hyaluronan with other substances
		Improved fermentation properties or	makes it possible to create bioactive
		other industrially useful processes.	(e.g. anti-thrombogenic, anti-bacterial)
			surfaces. This gene is involved in
			pathogenesis with cell-cell
			interactions, differentiation, tissue
			repair. The gene is also similar to an
			Enterococcus antigen that is useful in
			vaccine development (see e.g.
			WO9850554-A2; Enterococcus
			faecalis antigenic polypeptide
			fragment EF017).
65, 111	190, 235	Altered cell wall or cell surface	Homologue of MurD. MurD encodes
		characteristics, structures or	UDP-N-acetylmuramoylalanine - D-
		functions.	glutamate ligase (EC 6.3.2.9) also
		Modified adhesion to human or	known as UDP-N-acetylmuramoyl-L-
		animal cells or cell lines.	alanyl-D-glutamate synthetase or D-
		Production of desirable flavors.	glutamic acid adding enzyme catalyzes
		Modified flavor, aroma and/or texture	the addition of D-glutamate to the
		attributes.	nucleotide precursor UDP-N-
		Construction of genetic vectors for	acetylmuramoyl-l-alanine (UMA)and
		controlled expression of RNA and/or	belongs to the cytoplasmic
		protein, fusion protein production,	peptidoglycan synthetases involved in
		genetic modification, mutagenesis	cell wall formation. Thus it is useful
		amplification of genetic material or	for antibiotic development to inhibit
		for other genetic or protein	bacterial cell wall synthesis.
		manipulations.
		Altered survival characteristics:
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Altered metabolic properties.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
66	191	Altered cell wall or cell surface	Homologue of transmembrane
		characteristics, structures or	glycoprotein involved in nephritis
		functions.	(inflammation of the kidney).
		Modified adhesion to human or
		animal cells or cell lines.
		Production of desirable texture.
		Modified flavor, aroma and/or texture
		attributes.
		Construction of genetic vectors for
		controlled expression of RNA and/or
		protein, fusion protein production,
		genetic modification, mutagenesis
		amplification of genetic material or
		for other genetic or protein
		manipulations.
		Altered survival characteristics:
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Altered metabolic properties.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health, apoptosis).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
67	192	Altered amino acid metabolism.	Homologue of glutamine transport
		Removal of undesirable flavor	ATP-binding protein glnQ (TC#
		characteristics.	3.A.1.3.2). glnQ belongs to the polar
		Production of desirable flavors.	amino acid uptake transporter (PAAT)
		Modified flavor, aroma and/or texture	family (TC# 3.A.1.3) of the ATP-
		attributes.	binding Cassette (ABC) superfamily of
		Construction of genetic vectors for	transporters. The enzymatic
		controlled expression of RNA and/or	degradation of amino acids in cheese
		protein, fusion protein production,	plays a major role in cheese flavor
		genetic modification, mutagenesis	development. Amino acid degradation
		amplification of genetic material or	products greatly contribute to flavor or
		for other genetic or protein	to off-flavors (Rijnen et al., Appl.
		manipulations.	Environ. Microbiol. 65: 4873-4880,
		Altered survival characteristics:	1999).
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Altered metabolic properties.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health).
68	193	Altered cell wall or cell surface	Homologue of fibronectin/fibrinogen-
		characteristics, structures or	binding protein like FBP54. FBP54 is
		functions.	a surface protein that reacts with both
		Modified adhesion to human or	fibronectin and fibrinogen and
		animal cells or cell lines.	therefore may participate in the
		Production of desirable texture.	adhesion of bacteria to host cells. This
		Modified flavor, aroma and/or texture	gene is involved in bacterial entry into
		attributes.	mammalian cells (see Joh et al., Matrix
		Construction of genetic vectors for	Biol. 18: 211-223, 1999). Thus this
		controlled expression of RNA and/or	gene is useful in manipulation of the
		protein, fusion protein production,	binding process to alter pathogenicity
		genetic modification, mutagenesis	through drugs interfering with the gene
		amplification of genetic material or	product.
		for other genetic or protein
		manipulations.
		Altered survival characteristics:
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Altered metabolic properties.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health, apoptosis).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
69	194	Altered cell wall or cell surface	Homologue of virulence factor mviM.
		characteristics, structures or	Bacteria that cause disease have
		functions.	special factors which are designated as
		Modified adhesion to human or	virulence factors. These factors
		animal cells or cell lines.	contribute to the virulence of the
		Production of desirable flavors.	microorganisms and to their survival in
		Modified flavor, aroma and/or texture	the hostile environment within the
		attributes.	body of their host. Various signals
		Construction of genetic vectors for	control the expression of the virulence
		controlled expression of RNA and/or	factors. Oxygen, temperature,
		protein, fusion protein production,	concentration of ions, and pH are some
		genetic modification, mutagenesis	of the known signals that change the
		amplification of genetic material or	bacterial virulence. The action of
		for other genetic or protein	virulence factors ranges from adhesion
		manipulations.	mediation to target cells to molecular
		Altered survival characteristics:	mimicry and mobility to pH buffering.
		survival of industrial processes,	The gene is useful as a target for
		growth or storage in product formats,	vaccine development of bacteria
		persistence in gut environment.	having this kind of gene, as well as
		Altered metabolic properties.	manipulation of virulence by deletion,
		Altered probiotic attributes.	addition or modification of the gene in
		Modified health properties (including	transgenic bacteria.
		immunoregulatory, anticancer, gut
		health, apoptosis).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
		Vaccine development.
70	195	Altered cell wall or cell surface	Homologue of the response regulator
		characteristics, structures or	cheY. Chemotactic receptors at the
		functions.	bacterial cell surface communicate
		Modified adhesion to human or	with flagellar basal structures to elicit
		animal cells or cell lines.	appropriate motor behavior in response
		Production of desirable flavors.	to extracellular stimuli. Genetic and
		Modified flavor, aroma and/or texture	physiological studies indicate that the
		attributes.	product of the cheY gene interacts
		Construction of genetic vectors for	directly with components of the
		controlled expression of RNA and/or	flagellar motor to control swimming
		protein, fusion protein production,	behavior. Response regulators are
		genetic modification, mutagenesis	involved in production of virulence
		amplification of genetic material or	factors, motility, antibiotic resistance
		for other genetic or protein	and cell replication. Inhibitors of these
		manipulations.	proteins would be useful in preventing
		Altered survival characteristics:	bacterium from progressing to
		survival of industrial processes,	pathogenesis, thus useful in medical
		growth or storage in product formats,	treatments against bacteria. May have
		persistence in gut environment.	utility as a controlled expression
		Regulation of metabolic processes.	vector.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health, apoptosis).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
71, 112	196, 236	Modified adhesion to human or	Homologue of the mycobacterial
		animal cells or cell lines.	RegX3 protein. RegX3 is a response
		Production of desirable flavors.	regulator, which together with the
		Modified flavor, aroma and/or texture	histidine kinase SenX3 forms a two-
		attributes.	component signal transduction system
		Construction of genetic vectors for	that is positively autoregulated
		controlled expression of RNA and/or	(Himpens et al., Microbiol. 146: 3091-3098,
		protein, fusion protein production,	2000). Response regulators in
		genetic modification, mutagenesis	bacteria are involved in the bacterium's
		amplification of genetic material or	ability to monitor its surroundings and
		for other genetic or protein	adapt to changes in its environment.
		manipulations.	Several of these bacterial regulators
		Altered survival characteristics:	are involved in virulence and bacterial
		survival of industrial processes,	pathogenesis within the host (see e.g.
		growth or storage in product formats,	U.S. Pat. No. 5,910,572) The response
		persistence in gut environment.	regulators are involved in production
		Regulation of metabolic processes.	of virulence factors, motility, antibiotic
		Altered probiotic attributes.	resistance and cell replication.
		Modified health properties (including	Inhibitors of these proteins would be
		immunoregulatory, anticancer, gut	useful in preventing bacterium from
		health, apoptosis).	progressing to pathogenesis, thus
		Modified antibiotic resistance.	useful in medical treatments against
		Improved antimicrobial properties.	bacteria. May have utility as a
		Improved fermentation properties or	controlled expression vector.
		other industrially useful processes.
72, 113	197, 237	Altered cell wall or cell surface	Homologue of spinosyn biosynthesis.
		characteristics, structures or	Spinosyns are macrolides with a 21-
		functions.	carbon, tetracyclic lactone backbone to
		Modified adhesion to human or	which the deoxysugars forosamine and
		animal cells or cell lines.	tri-O-methylrhamnose are attached.
		Production of desirable flavors.	Macrolides interfere with the
		Modified flavor, aroma and/or texture	peptidlytransfer function of the
		attributes.	ribosome. The macrolide antibiotics,
		Construction of genetic vectors for	which include erythromycin,
		controlled expression of RNA and/or	azithromycin, and the streptogramin
		protein, fusion protein production,	family among others, work by binding
		genetic modification, mutagenesis	the large ribosomal subunit. The
		amplification of genetic material or	molecular details of the binding site for
		for other genetic or protein	macrolides are not well understood.
		manipulations.	The spinosyns, a novel family of
		Altered survival characteristics:	insecticidal macrocyclic lactones, are
		survival of industrial processes,	active on a wide variety of insect pests,
		growth or storage in product formats,	especially lepidopterans and dipterans
		persistence in gut environment.	(see WO9946387-A1: Biosynthetic
		Regulation of metabolic processes.	genes for spinosyn insecticide
		Altered probiotic attributes.	production). This gene can be useful
		Modified health properties (including	in a related compound biosynthesis
		immunoregulatory, anticancer, gut	utilization for bioactive compounds.
		health, apoptosis).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
73	198	Altered cell wall or cell surface	Homologue of EpsK protein. EpsK is
		characteristics, structures or	involved in exopolysaccharide
		functions.	biosynthesis. A broad variety of
		Modified adhesion to human or	bacteria produce polysaccharides,
		animal cells or cell lines.	which can either be excreted into the
		Production of desirable texture.	environment as exopolysaccharides
		Modified flavor, aroma and/or texture	(EPSs), form a capsule around the cell
		attributes.	as capsular polysaccharides, or be
		Construction of genetic vectors for	attached to the cell membrane as the O
		controlled expression of RNA and/or	antigens of lipopolysaccharides. The
		protein, fusion protein production,	biosynthesis of polysaccharides that
		genetic modification, mutagenesis	consist of repeating units includes their
		amplification of genetic material or	assembly on a lipid carrier by
		for other genetic or protein	sequential transfer of monosaccharides
		manipulations.	from nucleotide sugars by
		Altered survival characteristics:	glycosyltransferases (GTFs) and the
		survival of industrial processes,	subsequent polymerization and export
		growth or storage in product formats,	of these repeating units. Secreted
		persistence in gut environment.	exopolysaccharides contribute to the
		Altered metabolic properties.	cell protection against environmental
		Altered probiotic attributes.	influences, attachment to surfaces,
		Modified health properties (including	nutrient gathering and to antigenicity.
		immunoregulatory, anticancer, gut	Due to the variation of
		health, apoptosis).	monosaccharide sequences,
		Modified antibiotic resistance.	condensation linkages and non-
		Improved antimicrobial properties.	carbohydrate decorations, an infinite
		Improved fermentation properties or	array of structures can be provided by
		other industrially useful processes.	these sugar polymers. Deletion,
			addition and modification of the gene
			in transgenic bacteria can alter their
			extracellular envelope structure,
			thereby altering their growth and
			pathogenicity characteristics.
74	199	Altered cell wall or cell surface	Homologue of CpxA protein. CpxA is
		characteristics, structures or	involved in several diverse cellular
		functions.	processes, such as the functioning of
		Modified adhesion to human or	acetohydroxyacid synthetase I, in the
		animal cells or cell lines.	biosynthesis of isoleucine and valine,
		Production of desirable flavors.	the traJ protein activation activity for
		Modified flavor, aroma and/or texture	tra gene expression in F plasmid, and
		attributes.	the synthesis, translocation, or stability
		Construction of genetic vectors for	of cell envelope proteins. It also
		controlled expression of RNA and/or	activates CpxR by phosphorylation.
		protein, fusion protein production,	The CpxA-CpxR two-component
		genetic modification, mutagenesis	signal transduction system regulates
		amplification of genetic material or	gene expression in adaptation to
		for other genetic or protein	adverse conditions. These include
		manipulations.	envelope protein distress, heat shock,
		Altered survival characteristics:	oxidative stress, high pH, and entry
		survival of industrial processes,	into stationary phase. This gene can be
		growth or storage in product formats,	useful in manipulation the sensory
		persistence in gut environment.	apparatus related functions by deletion,
		Regulation of metabolic processes.	addition or modification of the gene in
		Altered probiotic attributes.	transgenic bacteria, or as a drug target
		Modified health properties (including	to interfere with bacterial signaling
		immunoregulatory, anticancer, gut	systems. May have utility as a
		health, apoptosis).	controlled expression vector.
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
75	200	Altered cell wall or cell surface	Homologue of 1,4-dihydroxy-2-
		characteristics, structures or	naphthoate octaprenyltransferase. 1,4-
		functions.	dihydroxy-2-naphthoate
		Production of desirable flavors.	octaprenyltransferase is a membrane-
		Modified flavor, aroma and/or texture	associated enzyme that converts the
		attributes.	soluble bicyclic naphthalenoid
		Construction of genetic vectors for	compound 1,4-dihydroxy-2-naphthoic
		controlled expression of RNA and/or	acid (DHNA) to membrane-bound
		protein, fusion protein production,	demethylmenaquinone, a key step in
		genetic modification, mutagenesis	the menaquinone biosynthesis.
		amplification of genetic material or
		for other genetic or protein
		manipulations.
		Altered survival characteristics:
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Regulation of metabolic processes.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health, apoptosis).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
76	201	Production of desirable flavors.	Homologue of the bifunctional
		Modified flavor, aroma and/or texture	bacterial gene HpcE coding for 2-
		attributes.	hydroxyhepta-2,4-diene-1,7-
		Construction of genetic vectors for	dioateisomerase and 5-carboxymethyl-
		controlled expression of RNA and/or	2-oxo-hex-3-ene-1,7-
		protein, fusion protein production,	dioatedecarboxylase (EC 5.3.3.—).
		genetic modification, mutagenesis	HpcE produces 2-hydroxyhepta-2,4-
		amplification of genetic material or	diene, 1,7-dioate from 5-
		for other genetic or protein	carboxymethyl-2-oxo-hex-3-ene-1,5-
		manipulations.	dioate or 5-Carboxymethyl-2-
		Altered survival characteristics:	hydroxymuconate.
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Regulation of metabolic processes.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health, apoptosis).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
77	202	Altered cell wall or cell surface	Homologue of UbiX. UbiX codes for
		characteristics, structures or	3-octaprenyl-4-hydroxybenzoate
		functions.	carboxy-lyase (EC 4.1.1.—) and that
		Modified adhesion to human or	catalyzes the third reaction in
		animal cells or cell lines.	ubiquinone biosynthesis pathway, the
		Production of desirable flavors,	conversion of 3-octaprenyl-4-
		Modified flavor, aroma and/or texture	hydroxybenzoate to 2-octaprenyl
		attributes.	phenol, and normally functions in
		Construction of genetic vectors for	association with the cytoplasmic
		controlled expression of RNA and/or	membrane.
		protein, fusion protein production,
		genetic modification, mutagenesis
		amplification of genetic material or
		for other genetic or protein
		manipulations.
		Altered survival characteristics:
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Regulation of metabolic processes.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health, apoptosis).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
78, 114	203, 238	Removal of undesirable flavor	Homologue of lacG. LacG codes for
		characteristics.	the enzyme 6-phospho-beta-
		Modified flavor, aroma, texture	galactosidase (EC 3.2.1.85) that is part
		attributes.	of the lactose metabolism and
		Construction of genetic vectors for	hydrolyzes phospholactose, the
		controlled expression of RNA and/or	product of a phosphor-enolpyruvate-
		protein, fusion protein production,	dependent phosphotransferase system.
		genetic modification, mutagenesis	It belongs to the glycosidase family 1
		amplification of genetic material or	and contributes to bitter flavor.
		for other genetic or protein
		manipulations.
		Altered survival characteristics:
		(survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment).
		Modified carbohydrate levels or
		functional properties.
		Altered metabolic properties.
		Modified lactose metabolism.
		Altered probiotic attributes.
		Organisms or materials with
		improved health properties (including
		immunoregulatory, anticancer, gut
		health, lactose tolerance).
79, 115	204, 239	Altered cell wall or cell surface	Homologue of the dnrH, dpsA-dpsF
		characteristics, structures or	genes, which encode daunorubicin
		functions.	(DNR)-doxorubicin (DXR) polyketide
		Production of desirable flavors.	synthase (PKS). DNR and its C-14-
		Modified flavor, aroma and/or texture	hydroxylated derivative DXR are
		attributes.	among the most important antitumor
		Construction of genetic vectors for	antibiotics in current use. Both
		controlled expression of RNA and/or	antibiotics are produced by
		protein, fusion protein production,	Streptomyces peucetius through a
		genetic modification, mutagenesis	pathway involving a type II PKS,
		amplification of genetic material or	which executes the condensation of
		for other genetic or protein	propionyl coenzyme A (CoA), as the
		manipulations.	starter unit, and nine malonyl-CoA
		Altered survival characteristics:	extender units in the production of a
		survival of industrial processes,	21-carbon decaketide (Bao et al., J.
		growth or storage in product formats,	Bacteriol. 181: 4690-4695, 1999).
		persistence in gut environment.
		Regulation of metabolic processes.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health, apoptosis).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
80	205	Construction of genetic vectors for	Homologue of decaprenyl diphosphate
		controlled expression of RNA and/or	(decaprenyl-PP) synthase. Decaprenyl-
		protein, fusion protein production,	PP synthase catalyzes the consecutive
		genetic modification, mutagenesis	condensation of isopentenyl
		amplification of genetic material or	diphosphate with allylic diphosphates
		for other genetic or protein	to produce decaprenyl-PP, which is
		manipulations.	used for the side chain of ubiquinone
		Production of desirable flavors.	(Q)-10.
		Modified flavor, aroma and/or texture
		attributes.
		Altered survival characteristics:
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Altered phosphate metabolism.
		Altered viability in response to stress
		conditions.
		Altered metabolic properties or
		regulation of metabolic pathways.
		Altered probiotic attributes.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
81, 116	206, 240	Construction of genetic vectors for	Homologue of geranyltranstransferase
		controlled expression of RNA and/or	(EC 2.5.1.10) also known as farnesyl-
		protein, fusion protein production,	diphosphate synthase.
		genetic modification, mutagenesis	Geranyltranstransferase catalyzes the
		amplification of genetic material or	basic chain-elongation reaction in the
		for other genetic or protein	isoprene biosynthetic pathway, the
		manipulations.	condensation of isopentenyl
		Production of desirable flavors.	pyrophosphate with dimethylallyl
		Modified flavor, aroma and/or texture	pyrophosphate to give geranyl
		attributes.	pyrophosphate.
		Altered survival characteristics:
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Altered phosphate metabolism.
		Altered viability in response to stress
		conditions.
		Altered metabolic properties or
		regulation of metabolic pathways.
		Altered probiotic attributes.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
82	207	Construction of genetic vectors for	Homologue of heptaprenyl
		controlled expression of RNA and/or	diphosphate synthase. Heptaprenyl
		protein, fusion protein production,	diphosphate synthase catalyzes the
		genetic modification, mutagenesis	condensation of four molecules of
		amplification of genetic material or	isopentenyl diphosphate with farnesyl
		for other genetic or protein	diphosphate to give heptaprenyl
		manipulations.	diphosphate, which is involved in the
		Production of desirable flavors.	biosynthesis of the side chain of
		Modified flavor, aroma and/or texture	menaquinone-7 (Zhang et al., J.
		attributes.	Bacteriol. 179: 1417-1419, 1997)
		Altered survival characteristics:
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Altered phosphate metabolism.
		Altered viability in response to stress
		conditions.
		Altered metabolic properties or
		regulation of metabolic pathways.
		Altered probiotic attributes.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
83-85,	208-210,	Construction of genetic vectors for	Homologue of the ispE (formerly
117	241	controlled expression of RNA and/or	designated ychB) gene. IspE encodes
		protein, fusion protein production,	4-(cytidine 5′-diphospho)-2-C-methyl-
		genetic modification, mutagenesis	D-erythritol kinase also called 4-
		amplification of genetic material or	diphosphocytidyl-2-C-methyl-D-
		for other genetic or protein	erythritol kinase (EC 2.7.1.148) that
		manipulations.	belongs to the non-mevalonate
		Production of desirable flavors.	terpenoid biosynthesis pathway and
		Modified flavor, aroma and/or texture	catalyzes the phosphorylation of 4-
		attributes.	diphosphocytidyl-2-C-methyl-D-
		Altered survival characteristics:	erythritol yielding 4-diphosphocytidyl-
		survival of industrial processes,	2-C-methyl-D-erythritol 2-phosphate
		growth or storage in product formats,	(Rohdich et al., Proc. Natl. Acad. Sci.
		persistence in gut environment.	USA 97: 8251-8256, 2000).
		Altered phosphate metabolism.
		Altered viability in response to stress
		conditions.
		Altered metabolic properties or
		regulation of metabolic pathways.
		Altered probiotic attributes.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
86, 88	211, 213	Construction of genetic vectors for	Homologue of MIAA that encodes
		controlled expression of RNA and/or	tRNA delta(2)-
		protein, fusion protein production,	isopentenylpyrophosphate transferase
		genetic modification, mutagenesis	(EC 2.5.1.8), which catalyzes the first
		amplification of genetic material or	step in the biosynthesis of 2-
		for other genetic or protein	methylthio-n6-(delta(2)-isopentenyl)-
		manipulations.	adenosine (ms[2]i[6]a]) adjacent to the
		Production of desirable flavors.	anticodon of several tRNA species.
		Modified flavor, aroma and/or texture
		attributes.
		Altered survival characteristics:
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Altered phosphate metabolism.
		Altered viability in response to stress
		conditions.
		Altered metabolic properties or
		regulation of metabolic pathways.
		Altered probiotic attributes.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
87	212	Construction of genetic vectors for	Homologue of mvaD coding for
		controlled expression of RNA and/or	mevalonate pyrophosphate
		protein, fusion protein production,	decarboxylase (EC 4.1.1.33). MvaD is
		genetic modification, mutagenesis	part of the mevalonate pathway for the
		amplification of genetic material or	biosynthesis of the central isoprenoid
		for other genetic or protein	precursor, isopentenyl diphosphate by
		manipulations.	catalyzing the reaction of mevalonate
		Production of desirable flavors.	5-diphosphate (MVADP) with ATP to
		Modified flavor, aroma and/or texture	produce isopentenyl diphosphate,
		attributes.	ADP, CO2, and inorganic phosphate.
		Altered survival characteristics:
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Altered phosphate metabolism.
		Altered viability in response to stress
		conditions.
		Altered metabolic properties or
		regulation of metabolic pathways.
		Altered probiotic attributes.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
89, 90	214, 215	Altered cell wall or cell surface	Homologue of mraY, coding for
		characteristics, structures or	phospho-N-acetylmuramoyl-
		functions.	pentapeptide-transferase (EC 2.7.8.13)
		Modified adhesion to human or	also known as UDP-N-acetyl-
		animal cells or cell lines.	muramoyl-L-alanyl-D-gamma-
		Production of desirable flavors.	glutamyl-L-lysyl-D-alanyl-D-
		Modified flavor, aroma and/or texture	alanine: undecaprenoid-alcohol-
		attributes.	phosphate-phospho-N-
		Construction of genetic vectors for	acetylmuramoyl-pentapeptide-
		controlled expression of RNA and/or	transferase. mraY catalyzes the
		protein, fusion protein production,	formation of undecaprenyl-
		genetic modification, mutagenesis	pyrophosphoryl-N-acetylmuramoyl-
		amplification of genetic material or	pentapeptide from UDP-N-
		for other genetic or protein	acetylmuramoyl-pentapeptide and
		manipulations.	undecaprenyl-phosphate, the first step
		Altered survival characteristics:	in the lipid cycle reactions in
		survival of industrial processes,	biosynthesis of bacterial cell wall
		growth or storage in product formats,	peptidoglycans. Phospho-N-
		persistence in gut environment.	acetylmuramoyl-pentapeptide-
		Altered metabolic properties.	transferase is an integral membrane
		Altered probiotic attributes.	protein and belongs to the
		Modified health properties (including	glycosyltransferase family 4 mraY
		immunoregulatory, anticancer, gut	subfamily.
		health).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
91, 92	216, 217	Altered cell wall or cell surface	Homologue of UPPS, encoding
		characteristics, structures or	undecaprenyl pyrophosphate
		functions.	synthetase (EC 2.5.1.31). UPPS
		Modified adhesion to human or	catalyzes the Z-oligomerization of
		animal cells or cell lines.	isopentenyl units with farnesyl
		Production of desirable flavors.	pyrophosphate as a priming substrate
		Modified flavor, aroma and/or texture	to give C50 and C55 prenyl
		attributes.	pyrophosphates with Z,E mixed
		Construction of genetic vectors for	stereochemistry. Undecaprenyl
		controlled expression of RNA and/or	pyrophosphate synthetase is required
		protein, fusion protein production,	as a lipid carrier of glycosyl transfer in
		genetic modification, mutagenesis	the biosynthesis of a variety of cell
		amplification of genetic material or	wall polysaccharide components in
		for other genetic or protein	bacteria.
		manipulations.
		Altered survival characteristics:
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Altered metabolic properties.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
93, 94	218, 219	Altered cell wall or cell surface	Homologue of Cps-like gene products
		characteristics, structures or	are involved in bacterial capsular
		functions.	polysaccharide (CP) biosynthesis.
		Modified adhesion to human or	Bacterial CPs are generally composed
		animal cells or cell lines.	of repeating oligosaccharides and are
		Production of desirable flavors.	involved in resistance to
		Modified flavor, aroma and/or texture	opsonophagocytosis, avoidance of the
		attributes.	immune system of the host and
		Construction of genetic vectors for	attachment. Cps genes are normally
		controlled expression of RNA and/or	clustered on the bacterial chromosome
		protein, fusion protein production,	and have a common genetic
		genetic modification, mutagenesis	organization involving three functional
		amplification of genetic material or	regions. Cps14E codes for
		for other genetic or protein	undecaprenyl-phosphate Glc-1-
		manipulations.	phosphate transferase that links
		Altered survival characteristics:	glucose to an undecaprenylphosphate
		survival of industrial processes,	lipid carrier, the first step in the
		growth or storage in product formats,	biosynthesis of enterobacterial
		persistence in gut environment.	common antigen as well as of many O-
		Altered metabolic properties.	specific lipopolysaccharides (Kolkman
		Altered probiotic attributes.	et al., J. Biol. Chem. 272: 19502-19508,
		Modified health properties (including	1997).
		immunoregulatory, anticancer, gut
		health).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
95, 97	220, 221	Production of bioactive or functional	Homologue of pepV, encoding Xaa-
		polypeptides.	His dipeptidase (EC 3.4.13.3)
		Removal of undesirable flavor	(carnosinase). PepV is a
		characteristics.	metalloenzyme member of the
		Production of desirable flavors.	metallopeptidase families M20A or
		Modified flavor, aroma and/or texture	M25, with activity against beta-alanyl-
		attributes.	dipeptides. It hydrolyzes a broad range
		Construction of genetic vectors for	of dipeptides including carnosine
		controlled expression of RNA and/or	(beta-alanyl-histidine) but no tri-, tetra-,
		protein, fusion protein production,	or larger oligopeptides. PepV in
		genetic modification, mutagenesis	related lactic acid bacteria act as
		amplification of genetic material or	intracellular dipeptidases (Hellendorn
		for other genetic or protein	et al., J. Bacteriol. 179: 3410-3415)
		manipulations.	and are important in the final
		Altered survival characteristics:	breakdown of casein. PepV mutants
		survival of industrial processes,	exhibit slower growth rates in milk and
		growth or storage in product formats,	alter some flavor characteristics. The
		persistence in gut environment.	proteolytic system of lactic acid
		Altered metabolic properties or	bacteria is essential for bacterial
		regulation of metabolic pathways.	growth in milk but also for the
		Altered probiotic attributes.	development of the organoleptic
		Organisms or materials with	properties of dairy products. PepV is
		improved health properties (including	involved both in bacterial growth by
		immunoregulatory, anticancer, gut	supplying amino acids, and in the
		health).	development of flavor in dairy
		Altered resistance to antibiotics.	products, by hydrolyzing peptides
			(including bitter peptides) and
			liberating aromatic amino acids which
			are important precursors of aroma
			compounds (Fernandez-Espla and Rul,
			Eur. J. Biochem. 263: 502-510, 1999).
98	222	Altered cell wall or cell surface	Homologue of a 19 kDa secreted
		characteristics, structures or	immunogenic lipoprotein. The 19 kDa
		functions.	lipoprotein gives a strong response as
		Modified adhesion to human or	antigen and could be used as a
		animal cells or cell lines.	prominent target for antibodies and
		Production of desirable flavors.	diagnostic procedures. It is a secreted
		Modified flavor, aroma and/or texture	lipoprotein isolated from
		attributes.	Mycobacterium tuberculosis
		Construction of genetic vectors for	(Ashbridge et al. Nucleic. Acids Res.
		controlled expression of RNA and/or	17: 1249-1253, 1989). It is
		protein, fusion protein production,	immunogenic and stimulates TH1-type
		genetic modification, mutagenesis	T cell responses (Mohagheghpour et
		amplification of genetic material or	al., J. Immunol. 161: 2400-2406, 1998).
		for other genetic or protein
		manipulations.
		Altered survival characteristics:
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Altered metabolic properties.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
		Vaccine production.
99	223, 253	Altered cell wall or cell surface	Homologue of LecLA2-20, a lectin-
		characteristics, structures or	like protein LA2-20. Lectins are
		functions.	ubiquitous proteins, which exhibit a
		Modified adhesion to human or	specific and reversible sugar-binding
		animal cells or cell lines.	activity. They react with glycosylated
		Production of desirable flavors.	macromolecules and cells and may
		Modified flavor, aroma and/or texture	coaggragate them and lead to their
		attributes.	lysis or alterations (Gilboa-Garber and
		Construction of genetic vectors for	Garber, FEMS Microbiol. Rev. 5: 211-221,
		controlled expression of RNA and/or	1989). May have a role in
		protein, fusion protein production,	intestinal adhesion via mucin-binding
		genetic modification, mutagenesis	capability (Matsumura et al., J. Dairy
		amplification of genetic material or	Sci. 82: 2523-2529, 1999).
		for other genetic or protein
		manipulations.
		Altered survival characteristics:
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Altered metabolic properties.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
		Vaccine production.
100	224	Altered amino acid metabolism.	Homologue of ilvB that encodes
		Removal of undesirable flavor	acetolactate synthase (EC 4.1.3.18).
		characteristics.	IlvB catalyzes the first step common to
		Altered cell wall or cell surface	the biosynthesis of the branched-chain
		characteristics, structures or	amino acids (valine, leucine and
		functions.	isoleucine). The enzyme catalyzes two
		Production of desirable flavors.	parallel reactions: condensation of two
		Modified flavor, aroma and/or texture	molecules of pyruvate to give rise to
		attributes.	acetolactate and condensation of
		Construction of genetic vectors for	pyruvate and alpha-ketobutyrate to
		controlled expression of RNA and/or	yield acetohydroxybutyrate. The
		protein, fusion protein production,	enzyme is inhibited by the end
		genetic modification, mutagenesis	products of the pathway (Singh et al.,
		amplification of genetic material or	Proc. Natl. Acad. Sci. USA 88: 145 72-4576,
		for other genetic or protein	1991). Lactic acid bacteria are
		manipulations.	nutritionally demanding bacteria which
		Altered survival characteristics:	need amino acids for optimal growth.
		survival of industrial processes,	Therefore the branched-chain amino
		growth or storage in product formats,	acid (BCAA) biosynthesis pathway is
		persistence in gut environment.	an essential pathway for optimal
		Altered metabolic properties.	growth of lactic acid bacteria in milk.
		Altered probiotic attributes.	Branch chain amino acids impact on
		Modified health properties (including	cheese flavor (Yvon et al., Appl.
		immunoregulatory, anticancer, gut	Environ. Microbiol. 63: 414-419,
		health).	1997).
		Improved fermentation properties or
		other industrially useful processes.
101	225	Altered amino acid metabolism.	Homologue of ilvG (an isoenzyme of
		Removal of undesirable flavor	ilvB) that encodes acetolactate
		characteristics.	synthase (EC 4.1.3.18). IlvG catalyzes
		Altered cell wall or cell surface	the first step common to the
		characteristics, structures or	biosynthesis of the branched-chain
		functions.	amino acids (valine, leucine and
		production of desirable flavors.	isoleucine). The enzyme catalyzes two
		Modified flavor, aroma and/or texture	parallel reactions: condensation of two
		attributes.	molecules of pyruvate to give rise to
		Construction of genetic vectors for	acetolactate and condensation of
		controlled expression of RNA and/or	pyruvate and alpha-ketobutyrate to
		protein, fusion protein production,	yield acetohydroxybutyrate. The
		genetic modification, mutagenesis	enzyme is inhibited by the end
		amplification of genetic material or	products of the pathway (Singh et al.,
		for other genetic or protein	Proc. Natl. Acad. Sci. USA 88: 4572-4576,
		manipulations.	1991). Lactic acid bacteria are
		Altered survival characteristics:	nutritionally demanding bacteria which
		survival of industrial processes,	need amino acids for optimal growth.
		growth or storage in product formats,	Thus, the branched-chain amino acid
		persistence in gut environment.	(BCAA) biosynthesis pathway is an
		Atered metabolic properties.	essential pathway for optimal growth
		Altered probiotic attributes.	of lactic acid bacteria in milk and
		Modified health properties (including	impacts on cheese flavor (Yvon et al.,
		immunoregulatory, anticancer, gut	Appl. Environ. Microbiol. 63: 414-419,
		health).	1997).
		Improved fermentation properties or
		other industrially useful processes.
102	226	Altered cell wall or cell surface	Homologue of basic surface protein
		characteristics, structures or	BspA of Lactobacillus fermentum.
		functions.	BspA is involved in L-cysteine uptake.
		Modified adhesion to human or	BspA is believed to belong to the
		animal cells or cell lines.	family III of the bacterial solute-
		Production of desirable flavors.	binding proteins and does not contain a
		Modified flavor, aroma and/or texture	lipoprotein consensus sequence
		attributes.	(Turner et al., J. Bacteriol. 179: 3310-3316,
		Construction of genetic vectors for	1997). Members of the family III
		controlled expression of RNA and/or	solute binding proteins have been
		protein, fusion protein production,	shown to bind polar amino acids and
		genetic modification, mutagenesis	opines such as cystine, glutamine,
		amplification of genetic material or	arginine, histidine, lysine, octopine,
		for other genetic or protein	and nopaline. Implicated in response
		manipulations.	to oxidative stress (Turner et al., J.
		Altered survival characteristics:	Bacteriol. 181: 2192-2198, 1999).
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Altered amino acid metabolism.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health, apoptosis).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
103, 118	227, 242	Altered cell wall or cell surface	Homologue of outer membrane
		characteristics, structures or	lipoprotein gna1946, similar to HlpA
		functions.	of H. influenzae. H1pA belongs to the
		Modified adhesion to human or	N1pA family of lipoproteins like the
		animal cells or cell lines.	iap genes.
		Production of desirable flavors.
		Modified flavor, aroma and/or texture
		attributes.
		Construction of genetic vectors for
		controlled expression of RNA and/or
		protein, fusion protein production,
		genetic modification, mutagenesis
		amplification of genetic material or
		for other genetic or protein
		manipulations.
		Altered survival characteristics:
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Altered probiotic attributes.
		Modified health properties (including
		immunoregulatory, anticancer, gut
		health, apoptosis).
		Modified antibiotic resistance.
		Improved antimicrobial properties.
		Improved fermentation properties or
		other industrially useful processes.
104	228	Construction of genetic vectors for	Homologue of cold shock protein
		controlled expression of RNA and/or	cspB. CspB is involved in an adaptive
		protein, fusion protein production,	process required for cell viability at
		genetic modification, mutagenesis	low temperatures or may function as
		amplification of genetic material or	antifreeze protein. Several bacteria
		for other genetic or protein	react to a sudden downshift in
		manipulations.	temperature by the production of a set
		Production of desirable flavors.	of proteins, together forming the cold-
		Modified flavor, aroma and/or texture	shock stimulon, that includes small (7-
		attributes,	kDa) cold-shock proteins (CSPs). In a
		Altered survival characteristics:	variety of bacteria, families of CSPs,
		survival of industrial processes,	consisting of three to nine members,
		growth or storage in product formats,	have been described of which CspA in
		persistence in gut environment.	E. coli (CspAE) and CspB in Bacillus
		Altered viability in response to stress	subtilis (CspBB) are the best
		conditions.	characterized. CspAE and CspBB are
		Altered metabolic properties or	capable of binding to single-stranded
		regulation of metabolic pathways.	DNA and RNA, and based on these
		Altered probiotic attributes.	characteristics, several functions for
		Improved fermentation properties or	CSPs have been suggested, such as
		other industrially useful processes.	transcriptional activators, RNA
			chaperones that facilitate the initiation
			of translation, and freeze-protective
			proteins. Recently it has been shown
			that CSPs might regulate the
			expression of cold-induced genes as
			antiterminators. Regulation of csp
			genes takes place at several levels, and
			for CspAE it was shown that cold-
			shock induction is achieved at the
			transcriptional level as well as at the
			level of mRNA and protein stability
			(Wouters et al., Appl. Environ.
			Microbiol 67: 5171-5178, 2001).
105, 120	229, 244	Production of desirable flavors.	Homologue of fabF, beta-ketoacyl
		Modified flavor, aroma and/or texture	synthase (acyl carrier protein). FabF is
		attributes.	part of the fatty acid biosynthesis (fab)
		Construction of genetic vectors for	gene cluster (fabD-fabH-acpP-fabF)
		controlled expression of RNA and/or	involved in fatty acid biosynthesis.
		protein, fusion protein production,	FabF is the condensing enzyme
		genetic modification, mutagenesis	thought to be responsible for
		amplification of genetic material or	elongation of fatty acids. The fab
		for other genetic or protein	genes are important in the production
		manipulations.	of butyric acid, with important flavor
		Altered survival characteristics:	and health impacts. It also has
		survival of industrial processes,	antibiotic effects and may be
		growth or storage in product formats,	protective against colon cancer
		persistence in gut environment.	(Mortensen and Clausen, Scand. J.
		Altered metabolic properties.	Gastroenterol. Suppl. 216: 132-148,
		Modified lipid, glycolipid or free	1996).
		fatty acid levels or functional
		properties.
		Modified production of short chain
		fatty acids.
		Altered lipid metabolism.
		Altered probiotic attributes.
		Organisms or materials with
		improved health properties (including
		immunoregulatory, anticancer, gut
		health)
120	245	Production of desirable flavors.	Homologue of accA, which encodes
		Modified flavor, aroma and/or texture	the acetyl-CoA carboxylase alpha
		attributes.	subunit (EC 6.4.1.2). AccA is part of
		Construction of genetic vectors for	the acc operon. E. coli acetyl-CoA
		controlled expression of RNA and/or	carboxylase catalyzes the first
		protein, fusion protein production,	committed and rate-controlling step in
		genetic modification, mutagenesis	fatty acid biosynthesis. Fatty acids in
		amplification of genetic material or	gram-positive bacteria act as signaling
		for other genetic or protein	molecules that are important for cell
		manipulations.	differentiation (Marini et al., J.
		Altered survival characteristics:	Bacteriol. 177: 7003-7006, 1995).
		survival of industrial processes,
		growth or storage in product formats,
		persistence in gut environment.
		Altered metabolic properties.
		Modified lipid, glycolipid or free
		fatty acid levels or functional
		properties.
		Modified production of short chain
		fatty acids.
		Altered lipid metabolism.
		Altered probiotic attributes.
		Organisms or materials with
		improved health properties (including
		immunoregulatory, anticancer, gut
		health)
120	246	Production of desirable flavors.	Homologue of accB encoding biotin
		Modified flavor, aroma and/or texture	carboxyl carrier protein (BCCP), a part
		attributes.	of the acc operon. E. coli acetyl-CoA
		Construction of genetic vectors for	carboxylase catalyzes the first
		controlled expression of RNA and/or	committed and rate-controlling step in
		protein, fusion protein production,	fatty acid biosynthesis. The overall
		genetic modification, mutagenesis	reaction catalyzed by acetyl-CoA
		amplification of genetic material or	carboxylase proceeds via two half-
		for other genetic or protein	reactions. To carry out this two-step
		manipulations.	reaction acetyl-CoA carboxylase
		Altered survival characteristics:	requires three distinct components:
		survival of industrial processes,	biotin carboxylase, biotin carboxyl
		growth or storage in product formats,	carrier protein, and
		persistence in gut environment.	carboxyltransferase. The biotin
		Altered metabolic properties.	carboxylase component catalyzes the
		Modified lipid, glycolipid or free	first half-reaction, which is an ATP-
		fatty acid levels or functional	dependent carboxylation of the vitamin
		properties.	biotin. In vivo, biotin is covalently
		Modified production of short chain	attached to the biotin carboxyl carrier
		fatty acids.	protein designated as BCCP. (Janiyani
		Altered lipid metabolism.	et al., J. Biol. Chem. 276: 29864-29870,
		Altered probiotic attributes.	2001). Indications are that fatty
		Organisms or materials with	acids in gram-positive bacteria act as
		improved health properties (including	signaling molecules that are important
		immunoregulatory, anticancer, gut	for cell differentiation (Marini et al., J.
		health)	Bacteriol. 177: 7003-7006, 1995).
120	247	Production of desirable flavors.	Homologue of accC encoding the
		Modified flavor, aroma and/or texture	biotin carboxylase (EC 6.3.4.14), a
		attributes.	part of the acc operon. E. coli acetyl-
		Construction of genetic vectors for	CoA carboxylase catalyzes the first
		controlled expression of RNA and/or	committed and rate-controlling step in
		protein, fusion protein production,	fatty acid biosynthesis. The overall
		genetic modification, mutagenesis	reaction catalyzed by acetyl-CoA
		amplification of genetic material or	carboxylase proceeds via two half-
		for other genetic or protein	reactions. To carry out this two-step
		manipulations.	reaction acetyl-CoA carboxylase
		Altered survival characteristics:	requires three distinct components:
		survival of industrial processes,	biotin carboxylase, biotin carboxyl
		growth or storage in product formats,	carrier protein, and
		persistence in gut environment.	carboxyltransferase. The biotin
		Altered metabolic properties.	carboxylase component catalyzes the
		Modified lipid, glycolipid or free	first half-reaction, which is an ATP-
		fatty acid levels or functional	dependent carboxylation of the vitamin
		properties.	biotin. In vivo, biotin is covalently
		Modified production of short chain	attached to the biotin carboxyl carrier
		fatty acids.	protein designated as BCCP. The
		Altered lipid metabolism.	second half-reaction, the transfer of the
		Altered probiotic attributes.	carboxyl group from carboxybiotin to
		Organisms or materials with	acetyl-CoA to make malonyl-CoA, is
		improved health properties (including	catalyzed by the carboxyltransferase
		immunoregulatory, anticancer, gut	component. The chain length of newly
		health)	synthesized fatty acids depends on the
			concentration of malonyl-CoA
			(Janiyani et al., J. Biol. Chem.
			276: 29864-29870, 2001). Indications
			are that fatty acids in gram-positive
			bacteria act as signaling molecules that
			are important for cell differentiation
			(Marini et al., J. Bacteriol. 177: 7003-7006,
			1995).
120	248	Production of desirable flavors.	Homologue of accD encoding the
		Modified flavor, aroma and/or texture	acetyl-coA carboxylase carboxyl
		attributes.	transferase subunit beta (EC 6.4.1.2), a
		Construction of genetic vectors for	part of the acc operon. E. coli acetyl-
		controlled expression of RNA and/or	CoA carboxylase catalyzes the first
		protein, fusion protein production,	committed and rate-controlling step in
		genetic modification, mutagenesis	fatty acid biosynthesis. The overall
		amplification of genetic material or	reaction catalyzed by acetyl-CoA
		for other genetic or protein	carboxylase proceeds via two half-
		manipulations.	reactions. To carry out this two-step
		Altered survival characteristics:	reaction acetyl-CoA carboxylase
		survival of industrial processes,	requires three distinct components:
		growth or storage in product formats,	biotin carboxylase, biotin carboxyl
		persistence in gut environment.	carrier protein, and
		Altered metabolic properties.	carboxyltransferase. The biotin
		Modified lipid, glycolipid or free	carboxylase component catalyzesthe
		fatty acid levels or functional	first half-reaction, which is an ATP-
		properties.	dependent carboxylation of the vitamin
		Modified production of short chain	biotin. In vivo, biotin is covalently
		fatty acids.	attached to the biotin carboxyl carrier
		Altered lipid metabolism.	protein designated as BCCP. The
		Altered probiotic attributes.	second half-reaction, the transfer of the
		Organisms or materials with	carboxyl group from carboxybiotin to
		improved health properties (including	acetyl-CoA to make malonyl-CoA, is
		immunoregulatory, anticancer, gut	catalyzed by the carboxyltransferase
		health)	component. The chain length of newly
			synthesized fatty acids appears to
			depend on the concentration of
			malonyl-CoA (Janiyani et al., J. Biol.
			Chem. 276: 29864-29870, 2001).
			Indications are that fatty acids in gram-
			positive bacteria act as signaling
			molecules that are important for cell
			differentiation (Marini et al., J.
			Bacteriol. 177: 7003-7006, 1995).
120	249	Production of desirable flavors.	Homologue of fabD, malonyl
		Modified flavor, aroma and/or texture	coenzyme A-acyl carrier protein
		attributes.	transacylase, which is part of the fatty
		Construction of genetic vectors for	acid biosynthesis (fab) gene cluster
		controlled expression of RNA and/or	(fabD-fabH-acpP-fabF) involved in
		protein, fusion protein production,	fatty acid biosynthesis. FabD
		genetic modification, mutagenesis	overexpression leads to altered fatty
		amplification of genetic material or	acid composition in E. coli, with
		for other genetic or protein	increased amounts of cis-vaccenate
		manipulations.	incorporated into membrane
		Altered survival characteristics:	phospholipids. The fab genes are
		survival of industrial processes,	important in the production of butyric
		growth or storage in product formats,	acid, with important flavor and health
		persistence in gut environment.	impacts. It also has antibiotic effects
		Altered metabolic properties.	and may be protective against colon
		Modified lipid, glycolipid or free	cancer (Mortensen and Clausen,
		fatty acid levels or functional	Scand. J. Gastroenterol. Suppl.
		properties.	216: 132-148, 1996).
		Modified production of short chain
		fatty acids.
		Altered lipid metabolism.
		Altered probiotic attributes.
		Organisms or materials with
		improved health properties (including
		immunoregulatory, anticancer, gut
		health)
120	250	Production of desirable flavors.	Homologue of fox2, encoding
		Modified flavor, aroma and/or texture	peroxisomal hydratase-dehydrogenase-
		attributes.	epimerase (HDE) also known as
		Construction of genetic vectors for	multifunctional beta-oxidation protein
		controlled expression of RNA and/or	(MFP). Fox2 is the second
		protein, fusion protein production,	trifunctional enzyme acting on the
		genetic modification, mutagenesis	beta-oxidation (cellular fatty acid
		amplification of genetic material or	degradation) pathway for fatty acids,
		for other genetic or protein	possessing hydratase-dehydrogenase-
		manipulations.	epimerase activities. This enzyme
		Altered survival characteristics:	converts trans-2-enoyl-CoA via d-3-
		survival of industrial processes,	hydroxyacyl-CoA to 3-ketoacyl-CoA.
		growth or storage in product formats,
		persistence in gut environment.
		Altered metabolic properties.
		Modified lipid, glycolipid or free
		fatty acid levels or functional
		properties.
		Modified production of short chain
		fatty acids.
		Altered lipid metabolism.
		Altered probiotic attributes.
		Organisms or materials with
		improved health properties (including
		immunoregulatory, anticancer, gut
		health)
120	251	Production of desirable flavors.	Homologue of ncd2 gene, encoding 2-
		Modified flavor, aroma and/or texture	nitropropane dioxygenase (EC
		attributes.	1.13.11.32) also called nitroalkane
		Construction of genetic vectors for	oxidase. Ncd2 is a flavoprotein that
		controlled expression of RNA and/or	catalyzes the oxidation of nitroalkanes
		protein, fusion protein production,	to respective aldehydes or ketones with
		genetic modification, mutagenesis	production of nitrite and water.
		amplification of genetic material or	Nitroalkanes are widely used as
		for other genetic or protein	industrial solvents, chemical
		manipulations.	intermediates, explosives and fuels.
		Altered survival characteristics:	Several nitroalkanes are toxic and/or
		survival of industrial processes,	carcinogenic. Thus, an enzymatic
		growth or storage in product formats,	activity that converts nitroalkanes into
		persistence in gut environment.	less harmful species has significant
		Altered metabolic properties.	potential for bioremediation.
		Altered lipid metabolism.
		Altered probiotic attributes.
		Organisms or materials with
		improved health properties (including
		immunoregulatory, anticancer, gut
		health).
		Bioremediation of toxic, carcinogenic
		or otherwise harmful substances.

[0063] Isolated polynucleotides of the present invention include the polynucleotides identified herein as SEQ ID NOS: 1-121; isolated polynucleotides comprising a polynucleotide sequence selected from the group consisting of SEQ ID NOS: 1-121; isolated polynucleotides comprising at least a specified number of contiguous residues (x-mers) of any of the polynucleotides identified as SEQ ID NOS: 1-121; 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.

[0064] 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.

[0065] 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:

[0066] complement 3′ TCCTGG 5′

[0067] reverse complement 3′ GGTCCT 5′

[0068] reverse sequence 5′ CCAGGA 3′

[0069] 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.

[0070] The polynucleotides identified as SEQ ID NOS: 1-121 contain open reading frames (“ORFs”), or partial open reading frames, encoding polypeptides. Additionally, polynucleotides identified as SEQ ID NOS: 1-121 may contain non-coding sequences such as promoters and terminators that may be useful as control elements. Additionally, open reading frames encoding polypeptides may be identified in extended or full-length sequences corresponding to the sequences set out as SEQ ID NOS: 122-253. Open reading frames may be identified using techniques that are well known in the art. These techniques include, for example, analysis for the location of known start and stop codons, most likely reading frame identification based on codon frequencies, similarity to known bacterial expressed genes, etc. Tools and software suitable for ORF analysis include GeneWise (The Sanger Center, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom), Diogenes (Computational Biology Centers, University of Minnesota, Academic Health Center, UMHG Box 43 Minneapolis Minn. 55455), and GRAIL (Informatics Group, Oak Ridge National Laboratories, Oak Ridge, Tennessee, Tenn.). Open reading frames and portions of open reading frames may be identified in the polynucleotides of the present invention. Once a partial open reading frame is identified, the polynucleotide may be extended in the area of the partial open reading frame using techniques that are well known in the art until the polynucleotide for the full open reading frame is identified. Thus, polynucleotides and open reading frames encoding polypeptides may be identified using the polynucleotides of the present invention.

[0071] Once open reading frames are identified in the polynucleotides of the present invention, the open reading frames 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. Suitable host cells may include various prokaryotic and eukaryotic cells. In vitro expression of polypeptides is also possible, as well known in the art.

[0072] 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.

[0073] As used herein, the term “x-mer,” with reference to a specific value of “x,” refers to a polynucleotide comprising at least a specified number (“x”) of contiguous residues of any of the polynucleotides identified as SEQ ID NOS: 1-121. The value of x may be from about 20 to about 600, depending upon the specific sequence.

[0074] In another aspect, the present invention provides isolated polypeptides encoded, or partially encoded, by the above polynucleotides. In specific embodiments, such polypeptides comprise a sequence selected from the group consisting of SEQ ID NO: 122-253, and variants thereof. 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.

[0075] 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 polypeptide 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 a mammalian cell line such as COS or CHO. The polynucleotide(s) expressed in this manner may encode naturally occurring polypeptides, portions of naturally occurring polypeptides, or other variants thereof.

[0076] 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.

[0077] 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.

[0078] 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 mutagenesis (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.

[0079] 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.

[0080] 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 sequences preferably exhibit at least 60%, more preferably at least 75%, more preferably yet at least 90%, and most preferably at least 95% identity to a sequence of the present invention. Variant polypeptide sequences preferably exhibit at least 60%, more preferably at least 75%, more preferably yet at least 90%, and most preferably at least 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.

[0081] 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 2.0.4 [Feb. 24, 1998], Version 2.0.6 [Sep. 16, 1998] and 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 in the publication of Altschul, et al., Nucleic Acids Res. 25: 3389-3402, 1997.

[0082] The computer algorithm FASTA is available on the Internet and from the University of Virginia by contacting David Hudson, 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.

[0083] 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.

[0084] 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.

[0085] 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.

[0086] 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 when compared to the polynucleotide or polypeptide of the present invention. That is, a variant polynucleotide or polypeptide is any sequence that has at least a 99% probability of being the same as the polynucleotide or polypeptide of the present invention, measured as having an E value of 0.01 or less using the BLASTN, FASTA, or BLASTP algorithms set at parameters described above. According to a preferred embodiment, a variant polynucleotide is a sequence having the same number or fewer nucleic acids than a polynucleotide of the present invention that has at least a 99% probability of being the same as the polynucleotide of the present invention, measured as having an E value of 0.01 or less using the BLASTN or FASTA algorithms set at parameters described above. Similarly, according to a preferred embodiment, a variant polypeptide is a sequence having the same number or fewer amino acids than a polypeptide of the present invention that has at least a 99% probability of being the same as a polypeptide of the present invention, measured as having an E value of 0.01 or less using the BLASTP algorithm set at the parameters described above.

[0087] 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.

[0088] In addition to having a specified percentage identity to an inventive polynucleotide or polypeptide se quence, v ariant p olynucleotides a nd p olypeptides p referably h ave a dditional 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 as pecified degree of identity to, or capable o f 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.

[0089] Alternatively, variant polynucleotides of the present invention hybridize to the polynucleotide sequences recited in SEQ ID NOS: 1-121, 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×SSC, 0.2% SDS; hybridizing at 65° C., 6×SSC, 0.2% SDS overnight; followed by two washes of 30 minutes each in 1×SSC, 0.1% SDS at 65° C. and two washes of 30 minutes each in 0.2×SSC, 0.1% SDS at 65° C.

[0090] 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 NOS: 1-121, 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 10% 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.

[0091] 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.

[0092] Certain of the polynucleotides identified as SEQ ID NOS: 1-121 are generally referred to as “partial” sequences, in that they may not represent the full coding portion of a gene encoding a naturally occurring polypeptide. The partial polynucleotide sequences disclosed herein may be employed to obtain the corresponding full-length genes for various species and organisms by, for example, screening DNA expression libraries using hybridization probes based on the polynucleotides of the present invention, or using PCR amplification with primers based upon the polynucleotides of the present invention. In this way one can, using methods well known in the art, extend a polynucleotide of the present invention upstream and downstream of the corresponding DNA, as well as identify the corresponding MRNA and genomic DNA, including the promoter and enhancer regions, of the complete gene. The present invention thus comprehends isolated polynucleotides comprising a sequence identified in SEQ ID NOS: 1-121, or a variant of one of the specified sequences, that encode a functional polypeptide, including full-length genes. Such extended polynucleotides may have a length of from about 50 to about 4,000 nucleic acids or base pairs, and preferably have a length of less than about 4,000 nucleic acids or base pairs, more preferably yet a length of less than about 3,000 nucleic acids or base pairs, more preferably yet a length of less than about 2,000 nucleic acids or base pairs. Under some circumstances, extended polynucleotides of the present invention may have a length of less than about 1,800 nucleic acids or base pairs, preferably less than about 1,600 nucleic acids or base pairs, more preferably less than about 1,400 nucleic acids or base pairs, more preferably yet less than about 1,200 nucleic acids or base pairs, and most preferably less than about 1,000 nucleic acids or base pairs.

[0093] Polynucleotides of the present invention comprehend polynucleotides comprising at least a specified number of contiguous residues (x-mers) of any of the polynucleotides identified as SEQ ID NOS: 1-121 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 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 identified as SEQ ID NOS: 1-121 or a variant of one of the polynucleotides identified as SEQ ID NOS: 1-121.

[0094] Oligonucleotide probes and primers complementary to and/or corresponding to SEQ ID NOS: 1-121, 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 NOS: 1-121 or a variant, if the oligonucleotide probe or primer, or its complement, is contained within one of the sequences set out as SEQ ID NOS: 1-121 or a variant of one of the specified sequences.

[0095] 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° C., but are generally greater than about 22° C., more preferably greater than about 30° C. and most preferably greater than about 37° 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.

[0096] 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.

[0097] 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 for designing PCR primers, are 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.

[0098] 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 NOS: 1-121.

[0099] 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.

[0100] 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.

[0101] 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.

[0102] 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 mm2. Preferably each discrete area is less than about 10,000 mm2, more preferably less than about 100 mm2. In this manner, a multitude of oligonucleotide probes may be immobilized at predefined locations on the array.

[0103] 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.

[0104] 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 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.

[0105] The significance of such 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.

[0106] 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.

[0107] 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 NOS: 1-121, 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.

[0108] 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 NOS: 1-121. According to one embodiment, the storage medium includes a collection of at least 20, preferably at least 50, more preferably at least 100, and most preferably at least 200 of the polynucleotides of the present invention, preferably the polynucleotides identified as SEQ ID NOS: 1-121, including variants of those polynucleotides.

[0109] 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, and most preferably at least 50 different polynucleotides of the present invention, including polynucleotides selected from SEQ ID NOS: 1-121, and variants of these polynucleotides.

[0110] 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 an inventive polynucleotide 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.

[0111] 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.

[0112] 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 described in Example 1.

[0113] 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.

[0114] 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 and is most preferably selected from the group consisting of the following Lactobacillus species: 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 ruminis, Lactobacillus sake, Lactobacillus salivarius, Lactobacillus salivarius subsp. salicinius, Lactobacillus salivarius subsp. salivarius, Lactobacillus sanfranciscensis, Lactobacillus sharpeae, Lactobacillus thermophilus, Lactobacillus vaginalis, Lactobacillus vermiforme, and Lactobacillus zeae.

[0115] 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 including plants, such as monocotyledonous angiosperms (e.g., grasses, corn, grains, oat, wheat and barley); dicotyledonous angiosperms (e.g., Arabidopsis, tobacco, legumes, alfalfa, oaks, eucalyptus, maple); gymnosperms, (e.g., Scots pine (Aronen, Finnish Forest Res. Papers, Vol. 595, 1996); white spruce (Ellis et al., Biotechnology 11:84-89, 1993); larch (Huang et al., In Vitro Cell 27:201-207, 1991); and any kind of plant amenable to genetic engineering.

[0116] Thus, in yet another aspect, transgenic plant cells comprising the genetic constructs of the present invention are provided, together with plants comprising such transgenic cells, and fruits, seeds, products and progeny of such plants. Techniques for stably incorporating genetic constructs into the genome of target organisms, such as plants, are well known in the art and include Agrobacterium tumefaciens mediated introduction, electroporation, protoplast fusion, injection into reproductive organs, injection into immature embryos, high velocity projectile introduction and the like. The choice of technique will depend upon the target plant to be transformed. For example, dicotyledonous plants, and certain monocots and gymnosperms, may be transformed by Agrobacterium Ti plasmid technology, as described, for example by Bevan, Nucleic Acids Res. 12:8711-8721, 1984. Targets for the introduction of the genetic constructs include tissues, such as leaf tissue, disseminated cells, protoplasts, seeds, embryos, meristematic regions, cotyledons, hypocotyls, and the like.

[0117] 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. In the case of protoplasts, the cell wall is allowed to reform under appropriate osmotic conditions. In the case of seeds or embryos, an appropriate germination or callus initiation medium is employed. For explants, an appropriate regeneration medium is used. Regeneration of plants is well established for many species. For a review of regeneration of forest trees, see Dunstan et al., “Somatic embryogenesis in woody plants,” in Thorpe, T. A., ed., In vitro embryogenesis of plants, (Current Plant Science and Biotechnology in Agriculture), 20(12):471-540, 1995. Specific protocols for the regeneration of spruce are discussed by Roberts et al. (“Somatic embryogenesis of Spruce,” in Redenbaugh K., ed., Synseed. applications of synthetic seed to crop improvement, CRC Press: Ch.23:427-449, 1993). The resulting transformed plants may be reproduced sexually or asexually, using methods well known in the art, to give successive generations of transgenic plants and practically unlimited amounts of tagged plant-derived products.

[0118] The polynucleotides of the present invention may be further employed as non-disruptive tags for marking organisms, particularly microbes. Other organisms may, however, be tagged with the polynucleotides of the present invention, including commercially valuable plants, animals, fish, fungi and yeasts. Genetic constructs comprising polynucleotides of the present invention may be stably introduced into an organism as heterologous, non-functional, non-disruptive tags. It is then possible to identify the origin or source of the organism at a later date by determining the presence or absence of the tag(s) in a sample of material. Detection of the tag(s) may be accomplished using a variety of conventional techniques, and will generally involve the use of nucleic acid probes. Sensitivity in assaying the presence of probe can be usefully increased by using branched oligonucleotides, as described by Horn et al., Nucleic Acids Res. 25(23):4842-4849, 1997, enabling detection of as few as 50 DNA molecules in the sample.

[0119] Polynucleotides of the present invention may also be used to spacifically suppress gene expression by methods that operate post-transcriptionally to block the synthesis of products of targeted genes, such as RNA interference (RNAi), and quelling. Briefly, traditional methods of gene suppression, employing anti-sense RNA or DNA, operate by binding to the reverse sequence of a gene of interest such that binding interferes with subsequent cellular processes and therefore blocks synthesis of the corresponding protein. RNAi also operates on a post-translational level and is sequence specific, but suppresses gene expression far more efficiently. Exemplary methods for controlling or modifying gene expression using RNAi are provided in WO 99/49029 and WO 99/53050. In these methods, post-transcriptional gene silencing is brought about by a sequence-specific RNA degradation process which results in the rapid degradation of transcripts of sequence-related genes. Studies have shown that double-stranded RNA may act as a mediator of sequence-specific gene silencing (see, for example, Montgomery and Fire, Trends in Genetics, 14:255-258, 1998). Gene constructs that produce transcripts with self-complementary regions are particularly efficient at gene silencing. A unique feature of this post-transcriptional gene silencing 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.

[0120] The polynucleotides of the present invention may thus be employed to generate gene silencing constructs and/or gene-specific self-complementary RNA sequences that can be delivered by conventional art-known methods to cells, such as microbial cells. Within genetic constructs, sense and antisense sequences can be placed in regions flanking an intron sequence in proper splicing orientation with donor and acceptor splicing sites, such that intron sequences are removed during processing of the transcript and sense and antisense sequences, as well as splice junction sequences, bind together to form double-stranded RNA. Alternatively, spacer sequences of various lengths may be employed to separate self-complementary regions of sequence in the construct. During processing of the gene construct transcript, intron sequences are spliced-out, allowing sense and anti-sense sequences, as well as splice junction sequences, to bind forming double-stranded RNA. Select ribonucleases then 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. The double-stranded RNA must have sufficient homology to the targeted gene to mediate RNAi and is preferably at least 25 nucleotides in length. Preferably, the double-stranded RNA corresponds specifically to a polynucleotide of the present invention. Gene silencing RNA sequences comprising the polynucleotides of the present invention are useful for creating genetically modified organisms with desired phenotypes as well as for characterizing genes (for example, in high-throughput screening of sequences), and studying their functions in intact organisms.

[0121] 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.

[0122] 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.

[0123] 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.

[0124] 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.

[0125] 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.

[0126] 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 μg 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.

[0127] 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

[0128] Lactobacillus rhamnosus strain HN001 DNA libraries were constructed and screened as follows.

[0129] DNA was prepared in large scale by cultivating the bacteria in 2×100 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° C. for approx. 16 hours with shaking (220 rpm).

[0130] 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° 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).

[0131] 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 μg/ml mutanolysin) and incubated at 37° 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° C. for 90 min. 50 μl Proteinase K (Gibco BRL, Gaithersburg, Md.) from a stock solution of 20 mg/ml was added and tubes incubated at 65° C. for 15 min.

[0132] 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° C. overnight.

[0133] After resuspension in 500 μl TE buffer, DNase-free RNase was added to a final concentraion of 100 μg/ml and incubated at 37° C. for 30 min. The incubation was extended for a further 30 min after adding 100 μl 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 μl TE buffer.

[0134] DNA was digested with Sau3AI at a concentration of 0.004 U/μg in a total volume of 1480 μl, with 996 μl DNA, 138.75 μl 10×REACT 4 buffer and 252.75 μl H2O. Following incubation for 1 hour at 37° C., DNA was divided into two tubes. 31 μl 0.5 M EDTA was added to stop the digestion and 17 μl 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.

[0135] 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° 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° 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 analyze 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° C.

[0136] DNA pellets were resuspended in 300 μl TE buffer and re-precipitated for approx. 6 hours at −20° C. after adding {fraction (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 μl TE buffer.

[0137] DNA was ligated into dephosphorylated BamHI-digested pBluescript SK II+ 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° C.

[0138] 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-β-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.

[0139] 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.

[0140] 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 NOS: 1-121 disclosed herein.

[0141] 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.

[0142] The determined DNA sequences were compared to and aligned with known sequences in the public databases. Specifically, the polynucleotides identified in SEQ ID NO: 1-121 were compared to polynucleotides in the EMBL database as of Aug. 12, 2002, 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. The polypeptides identified in SEQ ID NO: 122-253 were compared to polypeptides in the SwissPROT-TrEMBL database as of Aug. 12, 2002, using BLASTP algorithm Version 2.0.11 [Jan. 20, 2000], set to the following running parameters: Unix running command: blastall -p blastp -d swissprottrembledb -e 10 -G 0 -E 0 -v 30 -b 30 -i queryseq-o results.

[0143] BLASTN Polynucleotide Analysis

[0144] The sequences of SEQ ID NOS: 1-18, 20-50, 52-62, 64-69, 71-83, 85-93 and 95-122 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 sequence of SEQ ID NO: 94 was determined to have less than 75% identity, determined as described above, to sequences in the EMBL database using the computer algorithm BLASTN, as described above. Finally, the sequence of SEQ ID NO: 19 was determined to have less than 98% identity, determined as described above, to sequences in the EMBL database using the computer algorithm BLASTN, as described above.

[0145] BLASTP Amino Acid Analysis

[0146] The predicted amino acid sequences of SEQ ID NOS: 124, 133, 134, 137-139, 141, 148, 150-156, 159, 162, 164-168, 170-172, 174, 175, 178, 184, 187, 188, 190, 194, 195, 198-200, 202, 203, 205-208, 212-214, 216, 221-224, 227, 229, 234, 235, 237, 240, 242-245, 249 and 252 were determined to have less than 50% identity, determined as described above, to sequences in the SWISSPROT-TrEMBL database using the BLASTP computer algorithm as described above. The predicted amino acid sequences of SEQ ID NOS: 123, 125-129, 131, 144, 149, 158, 160, 161, 163, 169, 173, 176, 179-181, 183, 185, 186, 191-193, 197, 201, 209, 211, 215, 217, 218, 225, 226, 228, 230-233, 238, 239, 247, 248, 250, 251, 253, 254 and 256 were determined to have less than 75% identity, determined as described above, to sequences in the SWISSPROT-TrEMBL database using the computer algorithm BLASTP, as described above. The predicted amino acid sequences of SEQ ID NOS: 132, 135, 142, 145-147, 157, 182, 204, 219, 241, 246 and 255 were determined to have less than 90% identity, determined as described above, to sequences in the SWISSPROT-TrEMBL database using the computer algorithm BLASTP, as described above. The predicted amino acid sequences of SEQ ID NOS: 140 and 236 were determined to have less than 98% identity, determined as described above, to sequences in the SWISSPROT-TrEMBL database using the computer algorithm BLASTP, as described above.

[0147] BLASTX Polynucleotide Analysis

[0148] The cDNA sequences of SEQ ID NOS: 1-10, 12-18, 20-30, 32-42, 44-50, 52, 53, 55, 58, 59, 61, 62, 64, 66-69, 71-77, 79-83, 85-88, 90, 92, 95-105, 107-109, 111-114, 116-119, 121 and 122 were determined to have less than 50% identity, determined as described above, to sequences in the SWISSPROT-TrEMBL database using the computer algorithm BLASTX, as described above. The cDNA sequences of SEQ ID NOS: 11, 19, 43, 54, 57, 60, 65, 70, 78, 89, 91, 93, 106, 110, 115 and 120 were determined to have less than 75% identity, determined as described above, to sequences in the SWISSPROT-TrEMBL database using BLASTX, as described above. The cDNA sequences of SEQ ID NOS: 31, 51, 56 and 63 were determined to have less than 90% identity, determined as described above, to sequences in the SWISSPROT-TrEMBL database using BLASTN, as described above. The cDNA sequence of SEQ ID NO: 94 was determined to have less than 98% identity, determined as described above, to sequences in the SWISSPROT-TrEMBL database using BLASTX, as described above.

[0149] Based on similarity to known sequences, the isolated polynucleotides of the present invention identified as SEQ ID NOS: 1-121 were putatively identified as encoding polypeptides having similarity to the polypeptides shown above in Table 1. The amino acid sequences encoded by the DNA sequences of SEQ ID NO: 1-121 are provided in SEQ ID NO: 122-253, respectively.

[0150] Several of the sequences provided in SEQ ID NO: 1-121 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 2 below.

TABLE 2
Polynucleotide		Polypeptide
SEQ ID NO:	ORF	SEQ ID NO:
1	4828-5511	122
2	370-1485	123
3	617-2071	124
4	344-1162	125
4	1172-1936	126
6	513-1217	128
7	543-1352	130
8	599-1265	131
9	449-1189	132
10	1530-2306	133
11	164-1432	134
13	340-2367	136
14	92-2407	137
17	505-1884	140
19	5-271	142
20	6159-6464	143
20	5293-6171	144
20	3761-5293	145
22	282-1235	147
23	1938-3620	148
24	1965-2924	149
25	2978-3901	150
26	1212-1991	151
27	10894-11889	152
28	3687-5126	153
29	250-1275	154
30	464-2593	155
34	92-397	159
36	460-1098	161
37	651-1481	162
40	92-2407	165
45	713-2266	170
47	237-1049	172
50	30-1469	175
52	40-1221	177
55	196-1347	180
59	505-1827	184
69	1192-2109	194
70	118-822	195
73	25-1419	198
77	63-638	202
97	424-1743	221
98	1008-1571	222
100	4987-6948	224
101	90-1090	225
102	1702-2514	226
106	5-915	230
107	925-2592	231
108	167-2155	232
109	131-1024	233
110	57-923	234
111	611-1962	235
112	53-748	236
113	348-1301	237
114	235-1659	238
115	634-1458	239
116	2339-3190	240
117	649-1527	241
118	94-924	242
119	1-1221	243
120	4011-5249	244
120	8691-9464	245
120	5246-5701	246
120	6229-7578	247
120	7594-8409	248
120	2357-3280	249
120	3461-4006	250
120	1347-2327	251
121	146-1168	252

[0151] SEQ ID NO: 106, 107, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118 and 119 are full-length sequences of SEQ ID NO: 5, 12, 16, 44, 65, 71, 72, 78, 79, 81, 83, 103 and 21, respectively, with SEQ ID NO: 108 being a full-length sequence of SEQ ID NO: 15 and 42. SEQ ID NO: 253 is the full-length sequence of SEQ ID NO: 99.

[0152] SEQ ID NOS: 1-253 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.

[0153] All references cited herein, including patent references and non-patent publications, are hereby incorporated by reference in their entireties.

[0154] 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.

Claims

1. An isolated polynucleotide comprising a sequence selected from the group consisting of: SEQ ID NO: 1-121.

2. An isolated polynucleotide comprising a sequence selected from the group consisting of: (a) complements of SEQ ID NO: 1-121; (b) reverse complements of SEQ ID NO: 1-121; and (c) reverse sequences of SEQ ID NO: 1-121.

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: 1-121; (b) sequences having at least 90% identity to a sequence of SEQ ID NO: 1-121; and (c) sequences having at least 95% identity to a sequence of SEQ ID NO: 1-121, wherein the polynucleotide encodes a polypeptide having substantially the same functional properties as a polypeptide encoded by SEQ ID NO: 1-121.

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: 1-121; (b) nucleotide sequences that are 100-mers of a sequence recited in SEQ ID NO: 1-121; (c) nucleotide sequences that are 40-mers of a sequence recited in SEQ ID NO: 1-121; and (d) nucleotide sequences that are 20-mers of a sequence recited in SEQ ID NO: 1-121;

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. An isolated polynucleotide comprising a nucleotide sequence that differs from a nucleotide sequence recited in SEQ ID NOS: 1-121 as a result of deletions and/or insertions totaling less than 10% of the total sequence length.

10. An isolated polynucleotide comprising a nucleotide sequence that differs from a nucleotide sequence recited in SEQ ID NOS: 1-121 as a result of substitutions, insertions, and/or deletions totaling less than 15% of the total sequence length.

11. 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: 122-253; and (2) a polynucleotide comprising a non-coding region of a polynucleotide of any one of claims 1-3.

12. The genetic construct of claim 11, wherein the polynucleotide is in a sense orientation.

13. The genetic construct of claim 11, wherein the polynucleotide is in an anti-sense orientation.

14. The genetic construct of claim 11, wherein the gene promoter sequence is functional in a prokaryote or eukaryote.

15. A transgenic host cell comprising a construct of claim 11.

16. A transgenic organism comprising a transgenic host cell according to claim 15, or progeny thereof.

17. The transgenic organism of claim 16, wherein the organism is selected from the group consisting of Lactobacillus species.

19. 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.

20. The method of claim 19, wherein the organism is a microbe.

21. An isolated polypeptide comprising an amino acid sequence selected from the group consisting of: sequences recited in SEQ ID NO: 122-253.

22. 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: 122-253; (b) sequences having at least 90% identity to a sequence of SEQ ID NO: 122-253; and (c) sequences having at least 95% identity to a sequence of SEQ ID NO: 122-253, wherein the polypeptide has substantially the same functional properties as a polypeptide of SEQ ID NO: 122-253.

23. An isolated polynucleotide that encodes a polypeptide of any one of claims 21 and 22.

24. A fusion protein comprising at least one polypeptide according to any one of claims 21 and 22.

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

26. A composition comprising a polypeptide according to any one of claims 21 and 22 and at least one component selected from the group consisting of: physiologically acceptable carriers and immunostimulants.

27. 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.

28. A method for treating a disorder in a mammal, comprising administering a composition according to claim 26.

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

30. A method of identifying an organism, or reproductive material or an extract therefrom, as having a specific origin, comprising detecting in the genetic complement of the organism, material or extract the presence or absence of a polynucleotide identifier representative of said origin, wherein the polynucleotide identifier comprises a sequence recited in SEQ ID NOS: 1-121.

31. A method for improving the properties of microbes used in the manufacture of milk-derived products, food products, food additives, nutritional supplements, bioactive substances or probiotic supplements, comprising modulating the polynucleotide content or composition of the microbes by transforming the microbes with a polynucleotide of any one of claims 1-3.

32. A method for modifying the flavor, aroma, texture and/or nutritional, immune system modulating, and health benefits of a milk-derived, food, food additive, nutritional supplement, bioactive or probiotic supplement product comprising adding one or more polypeptides of claim 21 to the milk or other material from which the product is derived.

33. A composition comprising one or more species of probiotic microbes, or extracts thereof, that are non-pathogenic to mammalian organisms, said microbes comprising at least one isolated polynucleotide according to claim 1.

34. The composition of claim 33, wherein said microbes are selected from the group consisting of: Bacillus, Lactobacillus, Sporolactobacillus and Bifidiobacterium species.

35. A transgenic microbial population for use in cheese ripening, flavor development and bioactive peptide production, wherein the transgenic microbial population comprises a polynucleotide of SEQ ID NO: 3, 11, 20-24, 36, 53-57, 60-62, 67, 75-78, 80, 82-92, 95, 97, 100, 101, 105, 114, 117, 119, and 120.

36. A transgenic microbial population with modified survivability in manufacturing processes, storage in product formats or in intestinal or other environments, wherein the transgenic microbial population comprises a polypeptide selected from the group consisting of SEQ ID NO: 3, 11, 20-24, 36, 53-57, 60-62, 67, 75-78, 80, 82-92, 95, 97, 100, 101, 105, 114, 117, 119 and 120.

37. A transgenic Lactobacillus rhamnosus HN001 strain comprising a genetic construct that leads to the insertional mutagenesis and/or targeted disruption of polynucleotides selected from the group consisting of SEQ ID NO: 1-121, wherein the transgenic Lactobacillus rhamnosus HN001 strain possesses modified properties of flavor, aroma, texture, nutrition, immune system modulation, bioactive compound production, probiotic or health-related benefits, adhesion, or survival of industrial processes, in storage or in the environment.

38. A method for identifying microorganisms having a trait associated with a polynucleotide of SEQ ID NO: 1-121, the method comprising detecting in the genetic complement of the microorganism, the presence or absence of a polynucleotide of SEQ ID NO: 1-121.