Nucleic acid and amino acid sequences relating to mycobacterium tuberculosis and leprae for diagnostics and therapeutics

Abstract

Embodiments of the present invention feature nucleic acid and proteins derived from Mycobacterium tuberculosis and leprae. The proteins and nucleic acid of the present invention have applications in diagnostics and therapeutics.

Description

FIELD OF THE INVENTION

The present invention relates to non-naturally occurring nucleic acid and peptides corresponding to nucleic acid and peptides of Mycobacterium tuberculosis and Mycobacterium leprae . The nucleic acid and peptides of the present invention have utility for diagnostics and therapeutics.

BACKGROUND OF THE INVENTION

Mycobacterium tuberculosis is the causative agent of tuberculosis. Tuberculosis is a chronic bacterial infection characterized by the formation of granulomas in infected tissues and by cell mediated hypersensitivity. The usual site of the disease is the lungs but other organs may be involved. In countries where human immuno-deficiency virus (HIV) infection is endemic, tuberculosis is a frequent cause of morbidity in AIDS patients. Tuberculosis has shown a resurgence in recent years worldwide. Mycobacteria contain an array of protein and polysaccharide antigens giving rise to a cell mediated hypersensitivity. The hypersensitivity is often used to diagnose tuberculosis and to monitor the disease pathogenesis. See: Harrison's Principles of Internal Medicine , Twelfth Edition, McGraw-Hill, Inc., (1991), pp. 637-645.

Mycobacterium leprae is the causative agent of Hanson's disease or leprosy. Leprosy is a chronic infection of superficial tissues, especially the skin and peripheral nerves. Mycobacterium leprae multiplies slowly, and has not been grown in tissue culture or artificial media. Mycobacterium leprae does not elicit strong immunological responses in infected individuals. However, a serodiagnostic test for the detection of antibody to Mycobacterium leprae antigen is used to aid in the diagnosis. See Harrison, supra, pp. 645-648.

Patient care, as well as the prevention and transmission of Mycobacterium tuberculosis and leprae , requires reliable diagnostic and prognostic tools to detect nucleic acid, antigens and antibodies relating to tuberculosis and leprosy.

A number of therapeutic agents are currently available for combatting Mycobacterium tuberculosis and Mycobacterium leprae infections in man. However, limitations to these therapies, particularly for Mycobacterium tuberculosis infection, demonstrate that new, more effective agents are needed. For example, agents such as isoniazid and rifampicin are currently in use for Mycobacterium tuberculosis infections, but strains which are resistant to one or the other or both of these agents are being reported with increasing frequency (eg., Chawla et al., 1992, Am. Rev. Respir. Dis. 146, 278-279). In addition, Mycobacterium tuberculosis bacilli treated by drug therapy frequently remain viable, but dormant as latent infections in macrophage phagolysosomes which may re-emerge as full-blown tuberculosis at a later date (eg., Dannenberg, in “The Mycobacteria: A Sourcebook”, Kubica and Wayne, eds., Dekker, N.Y., pp. 721-760).

BRIEF DESCRIPTION OF THE INVENTION

This invention relates to diagnostics and therapeutics for Mycobacterium tuberculosis, M. leprae and other mycobacterial species including, but not limited to: M. avium, M. bovis, M. chitae, M. fortuitum, M. gorodonae, M. intracellulare, M. kansaii, M. paratuberculosis, M. smegmatis, M. terrae , and M. ulcerans . One embodiment of the present invention features, as an article of manufacture or as a composition, a non-naturally occurring nucleic acid having twenty or more nucleotides in a sequence corresponding to a sequence of Mycobacterium tuberculosis or Mycobacterium leprae nucleic acid. The non-naturally occurring nucleic acid of the present invention is exemplified by Seq. ID No. 1 with respect to Mycobacterium tuberculosis and by Seq. ID Nos. 23-26 and 120-140 with respect to Mycobacterium leprae . Preferably, the sequence has at least twenty, and more preferably at least thirty nucleotides in a sequence corresponding to Mycobacterium tuberculosis or Mycobacterium leprae nucleic acid. The sequence may correspond to the entire coding sequence for the gene or a part of the coding sequence. However, sequences larger than 1000 nucleotides in length are difficult to synthesize.

One embodiment of the present invention features a non-naturally occurring nucleic acid wherein the nucleic acid encodes a peptide of Mycobacterium tuberculosis or M. leprae or other mycobacterial species. The peptide has utility for diagnostics and therapeutics.

A further embodiment of the present invention comprises a non-naturally occurring nucleic acid wherein the nucleic acid is capable of binding messenger RNA of Mycobacterium tuberculosis or M. leprae or other mycobacterial species. Such non-naturally occurring nucleic acid is capable of acting as anti-sense nucleic acid to control the translation of messenger RNA of Mycobacterium tuberculosis, M. leprae or other mycobacterial species. The non-naturally occurring nucleic acid inhibits the translation of Mycobacterium tuberculosis, M. leprae or other mycobacterial gene products, which by way of example, relate to the synthesis of antibiotics and the constituents of the cell wall, intermediary metabolism, transport processes, nucleic acid biosynthesis and modification, and antibiotic resistance. One of ordinary skill in the art would readily be able to discern which proteins were involved in the above metabolic processes. The above listed processes, as well as the proteins involved in such processes, are well described in any cellular biology textbook such as Molecular Cell Biology, Darnell, J., Lodish, H., and Baltimore, D. Scientific American Books, N.Y. Such non-naturally occurring nucleic acids have utility in therapeutics and diagnostics. A further embodiment of the present invention features a non-naturally occurring nucleic acid which nucleic acid is capable of binding specifically to Mycobacterium tuberculosis or leprae nucleic acid. Such non-naturally occurring nucleic acid has utility as probes and as capture reagents.

One embodiment of the present invention features an expression system comprising an open reading frame of DNA corresponding to Mycobacterium tuberculosis or leprae DNA. The nucleic acid further comprises a control sequence compatible with an intended host. The expression system is useful for making peptides corresponding to Mycobacterium tuberculosis or leprae nucleic acid.

A further embodiment of the present invention features a cell transformed with the expression system to make Mycobacterium tuberculosis or leprae proteins and peptides.

Several non-naturally occurring nucleic acids of the present invention feature nucleic acid relating to products involved in cell wall biosynthesis of Mycobacterium tuberculosis . Such nucleic acids have sequences of twenty or more nucleotides which correspond to sequences of Seq. ID No. 1. One such nucleic acid has a sequence of twenty or more nucleotides which correspond to a sequence within nucleotides 28,325 to 31,285 of Seq. ID No. 1. Nucleotides 28,325 to 31,285 encode a gene for polyketide or fatty acid synthesis. The gene codes for an enzyme with acyl transferase, enoyl reductase and dehydratase domains. The putative amino acid sequence of the gene product is set forth in Seq. ID No. 2.

An enzyme, ketoacyl ACP synthase of Mycobacterium tuberculosis , is encoded by nucleotides 26750 to 28237 of Seq. ID No. 1. The putative amino acid sequence of the enzyme is set forth in Seq. ID No. 3.

Nucleic acid encoding a gene for the enzyme beta-keto reductase of Mycobacterium tuberculosis corresponds to nucleotides 24636 to 26753 of Seq. ID No. 1. The putative amino acid sequence is set forth in Seq. ID No. 4.

Nucleic acid encoding COA ligases correspond to nucleotides 22136 to 23371 or 23251 to 23994 of Seq. ID No. 1. The putative amino acid sequence is set forth in Seq. ID No. 5 and Seq. ID No. 118.

Nucleic acids encoding two UDP-sugar transferases of Mycobacterium tuberculosis corresponds to nucleotides 9489 to 10846 of Seq. ID No. 1 and 12604 to 13995 of Seq. ID No. 1. The putative amino acid sequence are set forth in Seq. ID Nos. 6 and 7.

Nucleic acid encoding a methyltransferase of Mycobacterium tuberculosis corresponds to nucleotides 20006 to 19347 of Seq. ID No. 1. The putative amino acid sequence is set forth in Seq. ID No. 8.

Nucleic acid encoding a KdtB protein of Mycobacterium tuberculosis corresponds to nucleotides 5790 to 6275 of Seq. ID No. 1. KdtB protein is an essential 12 kD protein associated with the synthesis of lipopolysaccharide. The putative amino acid sequence is set forth in Seq. ID No. 9.

A further non-naturally occurring nucleic acid of the present invention has a sequence of twenty nucleotides which correspond to proteins involved in intermediary metabolism. One non-naturally occurring nucleic acid corresponds to a pyruvate carboxylase of Mycobacterium tuberculosis . Pyruvate carboxylase is involved in gluconeogenesis. The enzyme catalyzes ATP-dependent carboxylation of pyruvate to oxaloacetate in the presence of cofactors biotin and zinc. The nucleotides 1565 to 4939 of Seq. ID No. 1 encode the enzyme pyruvate carboxylase. The putative amino acid sequence of the enzyme is set forth in Seq. ID No. 10.

One non-naturally occurring nucleic acid has a sequence of twenty or more nucleotides corresponding to a phosphoribosylglycinamide formyltransferase. Phosphoribosylglycinamide formyltransferase catalyzes the third step in de novo purine biosynthesis. The nucleotides encoding phosphoribosylglycinamide formyltransferase are 8061 to 7144 of Seq. ID No. 1. The putative amino acid sequence of the enzyme is set forth in Seq. ID No. 11.

A further non-naturally occurring nucleic acid of the present invention corresponds to gene products involved in transport processes. One non-naturally occurring nucleic acid encodes a structural gene for an anion pump protein of Mycobacterium tuberculosis . The nucleic acid has a sequence which corresponds to a sequence within nucleotides 9369 to 8149 of Seq. ID No. 1 which encode the pump. The putative amino acid sequence is set forth in Seq. ID No. 12.

A further non-naturally occurring nucleic acid has a sequence of twenty or more nucleotides which correspond to gene products involved in DNA biosynthesis and cell division. One non-naturally occurring nucleic acid of the present invention corresponds to a Mycobacterium tuberculosis cell division protein. A Mycobacterium tuberculosis cell division protein is encoded at nucleotide positions 5042 to 5704 of Seq. ID No. 1. The putative amino acid sequence is set forth in Seq. ID No. 13.

One embodiment of the present invention features a non-naturally occurring nucleic acid having a sequence of twenty or more nucleotides which correspond to gene products that are involved in antibiotic resistance. One non-naturally occurring nucleic acid of the present invention corresponds to a ribosomal RNA methylase. The nucleic acid has a sequence of twenty or more nucleotides which corresponds to a sequence within nucleotides 17223 to 17933 of Seq. ID No. 1 encoding for the enzyme. The putative amino acid sequence is set forth in Seq. ID No. 14.

A further non-naturally occurring nucleic acid has a sequence of twenty or more nucleotides which correspond to a sequence of Mycobacterium tuberculosis useful as a probe to identify Mycobacterium tuberculosis genes or homologous genes in other mycobacteria or other related bacterial species. Nucleic acid sequences that are specific to Mycobacterium tuberculosis genes correspond to nucleotides 15841 to 15203, nucleotides 15131 to 14306, nucleotides 20491 to 21489, nucleotides 911 to 1540, nucleotides 16223 to 17161, nucleotides 24020 to 24619, nucleotides 3 to 902, nucleotides 11313 to 11651, and nucleotides 11766 to 12503. The putative amino acid sequences are set forth in Seq. ID Nos. 15, 16, 17, 18, 19, 20, 21, 22, 118 and 119. These amino acid sequences may define proteins which are specific to Mycobacterium tuberculosis . Such proteins may give rise to antibodies which are specific to Mycobacterium tuberculosis.

The Mycobacterium tuberculosis peptides, the functions of such peptides, and the nucleotide positions associated with such peptides within Seq. ID No. 1 are summarized in Table I below.

TABLE I
		Enzyme name or activity
Gene	Position	(SeqID No.)	Function
ermK	17223-17933	ribosomal RNA methylase	:resistance
		(# 14)
gltA	9489-10846	putative UDP-sugar	:synth:carbo
		transferase (# 6)
gltB	12604-13995	putative UDP-sugar	:synth:carbo
		transferase (# 7)
kdtB	5790-6275	12 kDa; lipopolysaccharide	:synth:lipid
		biosynth (# 9)
ligA	22136-23371	CoA ligase subunit (# 5)	:synth:lipid
ligB	23251-23994	CoA ligase subunit (# 118)	:synth:lipid
mtrA	20006-19347	putative methyl transferase	:synth
		(# 8)
pksA	28325-31285	polyketide synthase; AT, ER,	:synth:lipid
		DH (# 2)
pksB	26750-28237	polyketide synthase; AS (# 3)	:synth:lipid
pksC	24636-26753	polyketide synthase; KR (# 4)	:synth:lipid
pur3	8061-7144	phosphoribosylglycinamide	:synth:nt
		formyltr..(# 11)
pycA	1565-4939	pyruvate carboxylase (# 10)	:metab
ttbc2a	9369-8149	anion pump protein (# 12)	:transport
yhhF	5042-5704	cell division protein (# 13)	:cell division
utbc2a	15841-15203	M. tuberculosis gene	:M.tb-specific
		sequence (# 15)
utbc2b	15131-14306	M. tuberculosis gene	:M.tb-specific
		sequence (# 16)
utbc2c	20491-21489	M. tuberculosis gene	:M.tb-specific
		sequence (# 17)
utbc2d	911-1540	M. tuberculosis gene	:M.tb-specific
		sequence (# 18)
utbc2e	16223-17161	M. tuberculosis gene	:M.tb-specific
		sequence (# 19)
utbc2f	24020-24619	M. tuberculosis gene	:M.tb-specific
		sequence (# 20)
utbc2g	3-902	M. tuberculosis gene	:M.tb-specific
		sequence (# 21)
utbc2h	11313-11651	M. tuberculosis gene	:M.tb-specific
		sequence (# 22)
utbc2i	11766-12503	M. tuberculosis gene	:M.tb-specific
		sequence (# 119)

Tables I-XXVI contain information on the genes encoded by the cosmid sequences with the corresponding Seq. ID Nos. (see table headings). Tables I-XIX consist of four columns with the heading gene, position, enzyme name or activity with Seq. ID No., and function. Tables XX-XXVI consist of five columns with the heading gene, SegID, position, enzyme or protein name, and function. Under the heading “gene”, a specific name is provided where the gene is positively identified by homology to other organisms, or a letter followed by the cosmid number. The letter “d” represents dehydrogenase, “t” represents transport associated, “a” represents ATPase. Under the heading “SeqID”, a specific sequence ID number is provided. Under the heading “position”, a range of nucleotides with the first and last numbers corresponding to the start and stop positions are identified which correspond to the respective Seq. ID No. In tables I-V, the start positions correspond to probable translation initiation codons; in tables VI-XXVI, the start positions correspond to the beginning of the reading frame which includes the predictable in vivo start site but usually is some distance away. Under the heading “Enzyme name or activity”, an exact name may be given, an activity (e.g., dehydrogenase), an indication of homology to other sequences in public databases, or the designation— M. leprae gene sequence, indicating a previously un-described gene. Under the heading “function”, a number of functional categories, as described in the text are identified; for example, “metab” denotes intermediary metabolism. In some cases metabolism is more specifically broken down in the following manner; “synth” denotes biosynthesis, “catab” denotes breakdown. Further information is sometimes given on the compounds involved; “lipid” denotes lipid, “aa” denotes amino acid, “nt” denotes nucleotide, “carbo” denotes carbohydrate, “glyco” denotes glycolysis, “antibiotic” denotes antibiotics, “protein” denotes “protein”, “tca” denotes tricarboxylic acid cycle, “wall” denotes cell wall, “cofact” denotes cofactor (an indication of the specific cofactor sometimes follows), “ M. tb -specific” denotes an M. tuberculosis gene useful as a probe, “ M. leprae -specific” denotes an M. leprae gene useful as a probe, “transport” denotes a gene involved in transport, cell division denotes a gene involved in “cell division”, “resistance” denotes a gene implicated in antibiotic resistance, “repair” denotes a DNA repair gene, “cell div.” denotes a gene involved in cell division, “antigen” denotes a gene that is known to be a mycobacterial antigen, or an antigen in another organism that may be useful for vaccine development, “redox” denotes involved in electron transport, “stress” denotes a gene that is involved in cellular stress responses, “regulatory” denotes regulatory gene, “translation” denotes a gene whose product is involved in ribosome function, and “recombination” denotes a gene involved in recombination.

Several non-naturally occurring nucleic acids of the present invention feature nucleic acid relating to products of Mycobacterium Leprae . One non-naturally occurring nucleic acid of the present invention has a sequence of twenty or more nucleotides which correspond to a sequence within Seq.

ID Nos. 23-26 and 120-140. The Mycobacterium Leprae peptides, the functions of such peptides, and nucleotide positions associated with such peptides within Seq. ID No. 23 are summarized in Table II below.

Table II
		Enzyme name or activity
Gene	Position	(SeqID No.)	Function
ybaB	32443-32093	12 kD protein (# 27)	: M.
			leprae -specific
dhaS	23517-22465	aspartate-semialdehyde	:metab.
		dehydrog. (# 28)
glpK	14121-12658	glycerol kinase (# 29)	:metab.
akaB	24783-23520	aspartokinase (# 30)	:metab.
recM	32078-31470	recM/recR (# 31)	:repair:cell div.
leu1	25583-27298	2-isopropylmalate	:metab.
		synthase (# 32)
pbpA	3032-5494	penicillin binding	:resistance
		protein (# 33)
arsA	1060-1914	anion-transporting	:transport
		ATPase (# 34)
u0577a	38-1063	M. leprae gene	: M.leprae -specific
		sequence (# 35)
u0577b	1911-2204	M. leprae gene	: M.leprae -specific
		sequence (# 37)
u0577c	5513-6622	M. leprae gene	: M.leprae -specific
		sequence (# 38)
u0577d	7161-7474	M. leprae gene	: M.leprae -specific
		sequence (# 39)
u0577e	10765-11355	M. leprae gene	: M.leprae -specific
		sequence (# 40)
u0577f	11789-12388	M. leprae gene	: M.leprae -specific
		sequence (# 41)
u0577g	14034-14276	M. leprae gene	: M.leprae -specific
		sequence (# 42)
u0577h	14269-14880	M. leprae gene	: M.leprae -specific
		sequence (# 43)
u0577i	15548-15922	M. leprae gene	: M.leprae -specific
		sequence (# 44)
u0577j	28664-29812	M. leprae gene	: M.leprae -specific
		sequence (# 45)
u0577k	29805-30512	M. leprae gene	: M.leprae -specific
		sequence (# 46)
u0577l	33851-35230	M. leprae gene	: M.leprae -specific
		sequence (# 47)
u0577m	35227-36546	M. leprae gene	: M.leprae -specific
		sequence (# 48)
u0577n	18608-17988	M. leprae gene	: M.leprae -specific
		sequence (# 49)
u0577o	22453-21305	M. leprae gene	: M.leprae -specific
		sequence (# 50)
u0577p	33762-33325	M. leprae gene	: M.leprae -specific
		sequence (# 51)

Nucleotides 32443 to 32093 of Seq. ID No. 23 encode a hypothetical 12 kD protein in the DNAX-RECR intergenic region. The putative amino acid sequence is set forth in Seq. ID No. 27.

One non-naturally occurring nucleic acid of the present invention corresponds to a sequence encoding the enzyme aspartate-semialdehyde dehydrogenase. The enzyme, aspartate-semialdehyde dehydrogenase, is involved in intermediary metabolism and is encoded by nucleotides 23517 to 22465 of Seq. ID No. 23. The putative amino acid sequence is set forth in Seq. ID No. 28.

One non-naturally occurring nucleic acid of the present invention has a sequence which corresponds to a sequence encoding the enzyme glycerol kinase. The enzyme, glycerol kinase, is involved in intermediary metabolism. The nucleotides encoding glycerol kinase are 14121 to 12658 of Seq. ID No. 23. The putative amino acid sequence is set forth in Seq. ID No. 29.

One non-naturally occurring nucleic acid of the present invention has a sequence which corresponds to a sequence encoding the enzyme aspartate kinase. The enzyme, aspartate kinase, is involved in intermediary metabolism. The nucleotide sequence encoding aspartate kinase are 24783 to 23520 of Seq. ID No. 23. The putative amino acid sequence is set forth in Seq. ID No. 30.

One non-naturally occurring nucleic acid of the present invention has a sequence which corresponds to a sequence encoding the RecM protein. This protein is involved in DNA repair DNA replication and cell division. The nucleotides encoding RecM protein are 32078 to 31470 of Seq. ID No. 23. The putative amino acid sequence is set forth in Seq. ID No. 31.

One non-naturally occurring nucleic acid of the present invention has a sequence which corresponds a sequence encoding to 2-isopropyl malate synthase. The enzyme, 2-isopropyl malate synthase, is involved in intermediary metabolism. The nucleotides encoding 2-isopropyl malate synthase are 25583 to 27298 of Seq. ID No. 23. The putative amino acid sequence is set forth in Seq. ID No. 32.

One non-naturally occurring nucleic acid of the present invention has a sequence which corresponds to a sequence encoding a penicillin binding protein, involved in antibiotic resistance. The nucleotides encoding the penicillin binding protein are 3032 to 5494 of Seq. ID No. 23. The putative amino acid sequence is set forth in Seq. ID No. 33.

One non-naturally occurring nucleic acid of the present invention has a sequence which corresponds to a sequence encoding an anion-transporting ATPase involved in transport processes. The nucleotides encoding this transport protein are 1060 to 1914 of Seq. ID No. 23. The putative amino acid sequence is set forth in Seq. ID No. 34.

Non-naturally occurring nucleic acids having a sequence of twenty or more nucleotides which correspond to a sequence of Mycobacterium leprae are useful as probes to identify Mycobacterium leprae genes or homologous genes in other mycobacteria or other related bacterial species. Nucleic acid sequences that are specific to Mycobacterium leprae genes correspond to nucleotides 38 to 1063, nucleotides 1060 to 1917, nucleotides 1911 to 2204, nucleotides 5513 to 6622, nucleotides 7161 to 7474, nucleotides 10765 to 11355, nucleotides 11789 to 12388, nucleotides 14034 to 14276, nucleotides 14269 to 14880, nucleotides 15548 to 15922, nucleotides 28664 to 29812, nucleotides 29805 to 30512, nucleotides 33851 to 35230, nucleotides 35227 to 36546, nucleotides 18608 to 17988, nucleotides 22453 to 21305, nucleotides 33762 to 33325 of Seq. ID No. 23. The respective putative amino acid sequences are set forth in Seq. ID Nos. 35-51.

Mycobacterium leprae peptides, the function of such peptides, and the nucleotide positions associated with such peptide within Seq. ID No. 24 are summarized in Table III set forth below.

TABLE III
		Enzyme name or activity
Gene	Position	(SeqID No.)	Function
f1912a	16941-18311	CoA ligase modifying	:metab.
		enzyme (# 52)
dhpS	28531-29322	dihydropteroate synthase	:metab.
		(fol. acid) (# 53)
3mg1	30740-31315	dna-3-methyladenine	:metab, :repair
		glycosidase (# 54)
glgC	33059-34315	glucose-1-P-	:synth:carbo
		adenylyltransferase (# 55)
u1912a	693-2900	68 kD tpp-requiring	:metab.
		protein (# 56)
ag45	20486-21097	45 kD serine-rich	:antigen
		antigen (# 57)
dcuP	7954-9044	uroporphyrinogen	:metab.
		decarboxylase (# 58)
u1912b	4637-5104	M. leprae gene	: M.leprae -specific
		sequence (# 59)
u1912c	25695-26399	M. leprae gene	: M.leprae -specific
		sequence (# 60)
u1912d	26195-26758	M. leprae gene	: M.leprae -specific
		sequence (# 61)
u1912e	27975-28217	M. leprae gene	: M.leprae -specific
		sequence (# 62)
u1912f	29399-30484	M. leprae gene	: M.leprae -specific
		sequence (# 63)
u1912g	30396-30740	M. leprae gene	: M.leprae -specific
		sequence (# 64)
u1912h	30737-31315	M. leprae gene	: M.leprae -specific
		sequence (# 65)
u1912i	31589-31756	M. leprae gene	: M.leprae -specific
		sequence (# 66)
u1912j	34389-35042	M. leprae gene	: M.leprae -specific
		sequence (# 67)
u1912k	6290-5001	M. leprae gene	: M.leprae -specific
		sequence (# 68)
u1912l	6882-6292	M. leprae gene	: M.leprae -specific
		sequence (# 69)
u1912m	9041-10396	M. leprae gene	: M.leprae -specific
		sequence (# 70)
u1912n	19930-18315	M. leprae gene	: M.leprae -specific
		sequence (# 71)
u1912o	23399-22446	M. leprae gene	: M.leprae -specific
		sequence (# 72)
u1912p	32508-32260	M. leprae gene	: M.leprae -specific
		sequence (# 73)
u1912q	10402-11097	M. leprae gene	: M.leprae -specific
		sequence (# 74)
u1912r	35946-35617	M. leprae gene	: M.leprae -specific
		sequence (# 75)
u1912s	12935-13234	M. leprae gene	: M.leprae -specific
		sequence (# 76)
u1912t	13486-13779	M. leprae gene	: M.leprae -specific
		sequence (# 77)
u1912u	21186-21488	M. leprae gene	: M.leprae -specific
		sequence (# 78)
u1912v	21540-21827	M. leprae gene	: M.leprae -specific
		sequence (# 79)
u1912w	22002-22355	M. leprae gene	: M.leprae -specific
		sequence (# 80)
u1912x	23315-24517	M. leprae gene	: M.leprae -specific
		sequence (# 81)

One non-naturally occurring nucleic acid of the present invention has a sequence which corresponds to a sequence encoding a CoA ligase modifying enzyme. The enzyme, CoA ligase, is involved in intermediary metabolism. The nucleotides encoding this CoA ligase are 16941 to 18311 of Seq. ID No. 24. The putative amino acid sequence is set forth in Seq. ID No. 52.

One non-naturally occurring nucleic acid of the present invention has a sequence which corresponds to a sequence encoding dihydropteroate synthase (DHPS). The enzyme, dihydropteroate synthase is involved in intermediary metabolism. The nucleotides encoding DHPS are 28531 to 29322 of Seq. ID No. 24. The putative amino acid sequence is set forth in Seq. ID No. 53.

One non-naturally occurring nucleic acid of the present invention has a sequence which corresponds to a sequence encoding DNA-3-methyladenine glycosidase I. The enzyme, DNA-3-methyladenine glycosidase I, is involved in intermediary metabolism. The nucleotides encoding this glycosidase are 30740 to 31315 of Seq. ID No. 24. The putative amino acid sequence is set forth in Seq. ID No. 54.

One non-naturally occurring nucleic acid of the present invention has a sequence which corresponds to a sequence encoding glucose-1-phosphate adenyltransferase. The enzyme, glucose-1-phosphate adenyltransferase, is involved in intermediary metabolism. The nucleotides encoding this enzyme are 33059 to 34315 of Seq. ID No. 24. The putative amino acid sequence is set forth in Seq. ID No. 55.

One non-naturally occurring nucleic acid of the present invention has a sequence which corresponds to a sequence encoding a 68 kD thiamine pyrophosphate-requiring protein. The 68 kD enzyme is involved in intermediary metabolism. The nucleotides encoding this protein are 693 to 2900 of Seq. ID No. 24. The putative amino acid sequence is set forth in Seq. ID No. 56.

One non-naturally occurring nucleic acid of the present invention has a sequence which corresponds to a sequence encoding a probable antigen identified in Mycobacterium tuberculosis . The nucleotides encoding this probable antigen are 20486 to 21097 of Seq. ID No. 24. The putative amino acid sequence is set forth in Seq. ID No. 57.

One non-naturally occurring nucleic acid of the present invention has a sequence which corresponds to a sequence encoding uroporphyrinogen decarboxylase. The enzyme, uroporphyrinogen decarboxylase, is involved in intermediary metabolism. The nucleotides encoding this enzyme are 7954 to 9044 of Seq. ID No. 24. The putative amino acid sequence is set forth in Seq. ID No. 58.

Non-naturally occurring nucleic acids having a sequence of twenty or more nucleotides which correspond to a sequence of Mycobacterium leprae are useful as a probe to identify Mycobacterium leprae genes or homologous genes in other mycobacteria or other related bacterial species. Nucleic acid sequences that are specific to Mycobacterium leprae genes include nucleotides at positions 4637 to 5104, nucleotides 25695 to 26399, nucleotides 26195 to 26758, nucleotides 27995 to 28217, nucleotides 29399 to 30484, nucleotides 30396 to 30740, nucleotides 30737 to 31315, nucleotides 31589 to 31756, nucleotides 34389 to 35042, nucleotides 6290 to 5001, nucleotides 6882 to 6292, nucleotides 9041 to 10396, nucleotides 19930 to 18315, nucleotides 23399 to 22446, nucleotides 32508 to 32260, nucleotides 10402 to 11097, nucleotides 35946 to 35617, nucleotides 12935 to 13234, nucleotides 13486 to 13779, nucleotides 21186 to 21488, nucleotides 21540 to 21827, nucleotides 22002 to 22355, and nucleotides 23315 to 24517 of Seq. ID No. 24. The putative amino acid sequences are set forth in Seq. ID Nos. 59-81.

Mycobacterium leprae peptides, the function of such peptides, the nucleotide positions associated with, such peptides within Seq. ID No. 25 are summarized in Table IV set forth below.

TABLE IV
		Enzyme name or activity
Gene	Position	(SeqID No.)	Function
adhA	3301-4332	alcohol dehydrogenase (# 82)	:metab.
fbp	26808-25829	fibronectin binding	:antigen:stress
		prot./85-B Ag (# 83)
ahpC	12402-11818	alkyl hydroperoxide	:antigen:redox
		reductase C (# 84)
bfr	15629-16105	bacterioferritin (# 85)	:redox
adhT	28957-28664	alcohol dehydrogenase (# 86)	:metab.
cysT	139-396	sulfate permease (# 87)	:transport
cpx	22311-22078	cytochrome P450	:synth:
		hydroxylase (# 88)	antibiotic:
oxyR	12485-13447	inducible regulatory	:metab.
		protein (# 89)
gox	9872-8631	2-hydroxy-acid	:metab
		oxidase (# 90)
u0038a	24755-24309	M. leprae gene sequence	: M.leprae -
		(# 92)	specific
u0038b	34108-33197	M. leprae gene sequence	: M.leprae -
		(# 93)	specific
u0038c	717-859	M. leprae gene sequence	: M.leprae -
		(# 94)	specific
u0038d	1047-1268	M. leprae gene sequence	: M.leprae -
		(# 95)	specific
u0038e	1928-2791	M. leprae gene sequence	: M.leprae -
		(# 96)	specific
u0038f	2951-3250	M. leprae gene sequence	: M.leprae -
		(# 97)	specific
u0038g	10854-11063	M. leprae gene sequence	: M.leprae -
		(# 98)	specific
u0038h	5683-4985	M. leprae gene sequence	: M.leprae -
		(# 99)	specific
u0038i	10433-10176	M. leprae gene sequence	: M.leprae -
		(# 100)	specific
u0038j	24266-23821	M. leprae gene sequence	: M.leprae -
		(# 101)	specific

One non-naturally occurring nucleic acid of the present invention has a sequence which corresponds to a sequence encoding alcohol dehydrogenase (ADH). The enzyme, alcohol dehydrogenase, is involved in intermediary metabolism and detoxification. The nucleotides encoding ADH are 3301 to 4332 of Seq. ID No. 25. The putative amino acid sequence is set forth in Seq. ID No. 82.

One non-naturally occurring nucleic acid of the present invention has a sequence which corresponds to a sequence encoding the Mycobacterium leprae 85-B antigen (alpha antigen). The nucleotides associated with 85-B antigen are 26808 to 25829 of Seq. ID No. 25. The putative amino acid sequence is set forth in Seq. ID No. 83.

One non-naturally occurring nucleic acid of the present invention has a sequence which corresponds to a sequence encoding a major mycobacterial antigen and the enzyme alkyl hydroperoxide reductase (AHPC). The enzyme, mycobacterial antigen, is a detoxifying enzyme. The nucleotides encoding AHPC are 12402 to 11818 of Seq. ID No. 25. The putative amino acid sequence is set forth in Seq. ID No. 84.

One non-naturally occurring nucleic acid of the present invention has a sequence which corresponds to a sequence encoding bacterioferritin (BFR). Bacterioferritin is involved in iron detoxification and storage. The nucleotides encoding BFR are 15629 to 16105 of Seq. ID No. 25. The putative amino acid sequence is set forth in Seq. ID No. 85.

One non-naturally occurring nucleic acid of the present invention has a sequence which corresponds to a sequence encoding alcohol dehydrogenase-T (ADH-T). The enzyme, alcohol dehydrogenase-T, is involved in intermediary metabolism. The nucleotides encoding ADH-T are 28957 to 28664 of Seq. ID No. 25. The putative amino acid sequence is set forth in Seq. ID No. 86.

One non-naturally occurring nucleic acid of the present invention has a sequence which corresponds to a sequence encoding a molybdenum or sulfate transport protein. The nucleotides encoding this transport protein are located at positions 139 to 396 of Seq. ID No. 25. The putative amino acid sequence is set forth in Seq. ID No. 87.

One non-naturally occurring nucleic acid of the present invention has a sequence which corresponds to a sequence encoding a cytochrome P450-like hydroxylase. This enzyme is involved in detoxification processes or antibiotic synthesis. The nucleotides encoding this protein are 22311 to 22078 of Seq. ID No. 25. The putative amino acid sequence is set forth in Seq. ID No. 88.

One non-naturally occurring nucleic acid of the present invention has a sequence which corresponds to a sequence encoding a hydrogen peroxide inducible regulatory protein (OXYR). The nucleotides OXYR are 12485 to 13447 of Seq. ID No. 25. The putative amino acid sequence is set forth in Seq. ID No. 89.

One non-naturally occurring nucleic acid of the present invention has a sequence which corresponds to a sequence encoding an enzyme (S)-2-hydroxy-acid oxidase (GOX). The enzyme, GOX is involved in intermediary metabolism. The nucleotides encoding GOX are 9872 to 8631 of Seq. ID No. 25. The putative amino acid sequence is set forth in Seq. ID No. 290.

Non-naturally occurring nucleic acids having a sequence of twenty or more nucleotides which correspond to a sequence of Mycobacterium leprae are useful as probes to identify Mycobacterium leprae genes or homologous genes in other mycobacteria or other related bacterial species. Nucleic acid sequences that are specific to Mycobacterium leprae genes include nucleotides at positions 139 to 396, nucleotides 24755 to 24309, nucleotides 34108 to 33197, nucleotides 717 to 859, nucleotides 1047 to 1268, nucleotides 1928 to 2791, nucleotides 2951 to 3250, nucleotides 10854 to 11063, nucleotides 5683 to 4985, nucleotides 10433 to 10176, and nucleotides 24266 to 23821 of Seq. ID No. 25. The putative amino acid sequences are set forth in Seq. ID Nos. 91-101.

Mycobacterium leprae peptides, the function of such peptides and the sequences associated with such peptides within Seq. ID No. 26 are summarized in Table V set forth below.

TABLE V
		Enzyme name or activity
Gene	Position	(SeqID No.)	Function
cspA	27760-28176	cold-shock protein (# 102)	:stress
erc	20362-19211	DNA helicase excision	:DNA repair
		repair (# 103)
fadA	7672-8880	fatty acid oxidase beta	:metab.
		subunit (# 104)
fadB	8855-11029	fatty acid oxidase alpha	:metab.
		subunit (# 105)
dciP	4228-2522	indolepyruvate	:metab.
		decarboxylase
		(# 106)
u1935a	37098-36712	putative Ca-binding	:metab.
		protein (# 107)
u1935b	4745-5074	M. leprae gene sequence	: M.leprae -specific
		(# 108)
u1935c	35805-34525	M. leprae gene sequence	: M.leprae -specific
		(# 109)
u1935d	16602-17078	M. leprae gene sequence	: M.leprae -specific
		(# 110)
u1935e	36372-37181	M. leprae gene sequence	: M.leprae -specific
		(# 111)
u1935f	6871-6071	M. leprae gene sequence	: M.leprae -specific
		(# 112)
u1935g	20856-20293	M. leprae gene sequence	: M.leprae -specific
		(# 113)
u1935h	21696-20893	M. leprae gene sequence	: M.leprae -specific
		(# 114)
u1935i	22673-21702	M. leprae gene sequence	: M.leprae -specific
		(# 115)
u1935j	25445-24921	M. leprae gene sequence	: M.leprae -specific
		(# 116)
u1935k	34517-34029	M. leprae gene sequence	: M.leprae -specific
		(# 117)

One non-naturally occurring nucleic acid of the present invention has a sequence which corresponds to a sequence encoding a cold-shock protein (CSPA). The protein, CSPA, is involved in cellular regulation processes. The nucleotides encoding CSPA are 27760 to 28176 of Seq. ID No. 26. The putative amino acid sequence is set forth in Seq. ID No. 102.

One non-naturally occurring nucleic acid of the present invention has a sequence which corresponds to a sequence encoding a DNA helicase similar to a human DNA excision repair protein. The enzyme is involved in DNA synthesis and replication. The nucleotides encoding this helicase are 20362 to 19211 of Seq. ID No. 26. The putative amino acid sequence is set forth in Seq. ID No. 103.

One non-naturally occurring nucleic acid of the present invention has a sequence which corresponds to a sequence encoding the M. leprae fatty acid oxidation complex beta subunit beta-ketothiolase (FadA). The enzyme, FadA is involved in intermediary metabolism. The nucleotides FadA are 7672 to 8880 of Seq. ID No. 26. The putative amino acid sequence is set forth in Seq. ID No. 104.

One non-naturally occurring nucleic acid of the present invention has a sequence which corresponds to a sequence encoding the multifunctional fatty acid oxidation complex alpha subunit (FadB). The enzyme, FadB, is involved in intermediary metabolism. The nucleotides encoding FadB are 8855 to 11029 of Seq. ID No. 26. The putative amino acid sequence is set forth in Seq. ID No. 105.

One non-naturally occurring nucleic acid of the present invention has a sequence which corresponds to a sequence encoding the M. leprae enzyme indolepyruvate decarboxylase (DCIP). The enzyme, DCIP, is involved in intermediary metabolism. The nucleotides encoding DCIP are located at positions 4228 to 2522 of Seq. ID No. 26. The putative amino acid sequence is set forth in Seq. ID No. 106.

One non-naturally occurring nucleic acid of the present invention has a sequence which corresponds to a sequence encoding a putative calcium binding protein. The protein is involved in intermediary metabolism. The nucleotides encoding this protein are 37098 to 36712 of Seq. ID No. 26. The putative amino acid sequence is set forth in Seq. ID No. 107.

Non-naturally occurring nucleic acids having a sequence of twenty or more nucleotides which correspond to a sequence of Mycobacterium leprae are useful as probes to identify Mycobacterium leprae genes or homologous genes in other mycobacteria or other related bacterial species. Nucleic acid sequences that are specific to Mycobacterium leprae genes include nucleotides at positions 4745 to 5074, nucleotides 35805 to 34525, nucleotides 16602 to 17078, nucleotides 36372 to 37181, nucleotides 6871 to 6071, nucleotides 20856 to 20293, nucleotides 21696 to 20893, nucleotides 22673 to 21702, nucleotides 25445 to 24921, and nucleotides 34517 to 34029 of Seq. ID No. 26. The putative amino acid sequences are set forth in Seq. ID Nos. 108-117.

One embodiment of the present invention features a non-naturally occurring protein or peptide of Mycobacterium tuberculosis . The protein or peptide preferably corresponds to a sequence encoded by Seq. ID No. 1. Preferably the protein or peptide is an antigen, or is involved in antibiotic or cell wall synthesis, intermediary metabolism, transport processes, nucleic acid biosynthesis or modification, cell division or antibiotic/drug resistance. Proteins and peptides of Mycobacterium tuberculosis are exemplified by Seq. ID Nos. 2-22, 118 and 119.

A further embodiment features a non-naturally occurring protein or peptide of Mycobacterium leprae . The protein or peptide preferably corresponds to a sequence within Seq. ID Nos. 23-26 or 120-140. Preferably, the protein or peptide is an antigen, or a protein involved in antibiotic or cell wall synthesis, intermediary metabolism, transport processes, nucleic acid biosynthesis or modification, cell division or antibiotic/drug resistance. Proteins and peptides of Mycobacterium leprae are exemplified by Seq. ID Nos. 27-117 and 141-411.

Mycobacterium leprae peptides, the function of such peptides, and the nucleotide positions associated with such peptides within Seq. ID No. 120 are summarized in Table VI set forth below.

TABLE VI
Gene	Position	Enzyme name	Function
drrA	25472-26569	daunorubicin	:transport
		resistance protein
drrB	26533-27432	transmembrane	:transport
		ATPase
drrC	27423-28163	probable membrane	:transport
		component
pksA	35-1963	polyketide synthase	:synth:lipid:antibiotic
pksB	1501-4395	polyketide synthase	:synth:lipid:antibiotic
pksC	4396-8736	polyketide synthase	:synth:lipid:antibiotic
pksD	8971-15621	polyketide synthase	:synth:lipid:antibiotic
pksE	15573-21065	polyketide synthase	:synth:lipid:antibiotic
pksF	21088-25563	polyketide synthase	:synth:lipid:antibiotic
u1518a	28289-29578	match to M. bovis	: M. leprae -specific
		MAS orf4
u1518b	32481-33395	M. leprae gene	: M. leprae -specific
		sequence
u1518c	30755-30982	M. leprae gene	: M. leprae -specific
		sequence

Mycobacterium leprae peptides, the function of such peptides, and the nucleotide positions associated with such peptide within Seq. ID No. 121 are summarized in Table VII set forth below.

TABLE VII
Gene	Position	Enzyme name	Function
acd	24367-25548	acyl-coA dehydrogenase	:metab
bccA	16077-14224	biotin carboxyl carrier	:metab
		protein
d1308a	7737-7183	probable dehydrogenase	:metab
d1308b	8117-7905	aldehyde dehydrogenase	:metab
latB	10602-10970	lysine 6-amino	:synth:aa
		transferase
latB	11263-11829	lysine 6-amino	:synth:aa
		transferase
pabB	28229-27210	probable antigen B	:antigen
		precursor
pccB	20220-18535	propionyl-coA	:metab
		carboxylase
pur6	23643-24284	phosphoribosylamino-	:catab:tca
		imidazole carbox..
purK	22402-23769	phosphoribosylamino-	: M. leprae -specific
		imidazole carbox . . .
rpsB	13687-14100	sigma factor B	:regulation
thtR	17448-16555	thiosulfate	:metab
		sulfotransferase
t1308a	28904-28638	transport protein	:transport
u1308a	4339-4593	M. leprae gene sequence	: M. leprae -specific
u1308b	4822-5190	M. leprae gene sequence	: M. leprae -specific
u1308c	4385-4654	M. leprae gene sequence	: M. leprae -specific
u1308d	32525-33139	M. leprae gene sequence	: M. leprae -specific
u1308e	13080-13358	M. leprae gene sequence	: M. leprae -specific
u1308f	20175-20507	M. leprae gene sequence	: M. leprae -specific
u1308g	25497-25760	M. leprae gene sequence	: M. leprae -specific
u1308h	29565-30092	M. leprae gene sequence	: M. leprae -specific
u1308i	3819-3325	M. leprae gene sequence	: M. leprae -specific
u1308j	9309-9025	M. leprae gene sequence	: M. leprae -specific
u1308k	22368-21676	M. leprae gene sequence	: M. leprae -specific
u1308l	22368-21676	M. leprae gene sequence	: M. leprae -specific
u1308m	30058-29828	M. leprae gene sequence	: M. leprae -specific
u1308n	33166-32813	M. leprae gene sequence	: M. leprae -specific
u1308o	32734-32330	M. leprae gene sequence	: M. leprae -specific
u1308p	1121-2224	M. leprae gene sequence	: M. leprae -specific
u1308q	21071-21721	M. leprae gene sequence	: M. leprae -specific
u1308r	18512-17646	match to 21.2 kDa	: M. leprae -specific
		protein (yhde_ecoli)
u1308s	7193-6450	M. leprae gene sequence	: M. leprae -specific

Mycobacterium leprae peptides, the function of such peptides, and the nucleotide positions associated with such peptides within Seq. ID No. 122 are summarized in Table VIII set forth below.

TABLE VIII
Gene	Position	Enzyme name or activity	Function
bioA	39641-38292	adenosylmethionine-	:synth:cofac:biotin
		8-amino-7-oxon . . .
bioB	35815-34661	biotin synthetase	:synth:cofac:biotin
bioD	37191-36451	dethiobiotin synthase	:synth:cofac:biotin
bioF	38291-37128	8-amino-7-	:synth:cofac:biotin
		oxononanoate synthase
echa	1673-771	enoyl-CoA hydratase	:catab:lipid:betaox
ligA	9978-10628	coenzyme A ligase	: M. leprae -specific
m1170a	23927-17547	mycocerosic acid	:synth:lipid
		synthase
m1170b	7464-7087	polyketide synthase	:synth:lipid
m1170c	5853-5548	polyketide synthase	:synth:lipid
nadA	31541-30432	quinolinate synthase	:synth:cofac:nad
nadB	30657-29158	L-aspartate oxidase	:synth:cofac:nad
nadC	28896-27994	nicotinate-nucleotide	:synth:cofac:nad
		pyrophosphorylase
r1170a	2601-2861	resistance protein	:resistance
t1170a	16050-13018	transport protein	:transport
u1170a	9168-8884	Mycobacterium MCAS-	: M. leprae -specific
		associated gene
u1170b	17493-16051	weak match to surfactin	: M. leprae -specific
		synthase
u1170c	4045-3581	weak match to chalcone	: M. leprae -specific
		synthases
u1170d	8875-10011	MCAS-associated protein	: M. leprae -specific
U1170e	40416-41171	p60 homolog of listeria	: M. leprae -specific
		invasion protein
u1170f	4507-4767	M. leprae gene sequence	: M. leprae -specific
U1170g	31411-32289	M. leprae gene sequence	: M. leprae -specific
U1170h	33070-33471	M. leprae gene sequence	: M. leprae -specific
u1170i	39532-39804	M. leprae gene sequence	: M. leprae -specific
u1170j	2093-2725	M. leprae gene sequence	: M. leprae -specific
u1170k	10598-11350	M. leprae gene sequence	: M. leprae -specific
u1170l	2916-3173	M. leprae gene sequence	: M. leprae -specific
u1170m	11403-12590	M. leprae gene sequence	: M. leprae -specific
u1170n	29546-28851	M. leprae gene sequence	: M. leprae -specific
u1170o	34561-33800	M. leprae gene sequence	: M. leprae -specific
u1170p	36171-35953	M. leprae gene sequence	: M. leprae -specific

Mycobacterium leprae peptides, the function of such peptides, and the nucleotide positions associated with such peptides within Seq. ID No. 123 are summarized in Table IX set forth below.

TABLE IX
Gene	Position	Enzyme name or activity	Function
adaB	30510-31031	adenosine deaminase	:repair:metab
ars	7367-6513	arylsulfatase	:catab
c1549a	13733-13236	k + channel protein	:transport
cysM	9487-9263	cysteine synthase B	:synth:aa
glbA	20087-20614	1,4-alpha-glucan	:synth:carbo
		branching enzyme
glbB	21425-21721	1,4-alpha-glucan	:synth:carbo
		branching enzyme
glbC	21722-22156	1,4-alpha-glucan	:synth:carbo
		branching enzyme
glbD	20676-20894	1,4-alpha-glucan	:synth:carbo
		branching enzyme
glbE	21039-21509	1,4-alpha-glucan	:synth:carbo
		branching enzyme
glr	8234-7368	glutamate racemase	:synth:aa
rnpH	6432-5644	ribonuclease PH	:translation:tRNA
rrnF	5S rRNA	ribosomal RNA	:translation:rRNA
rrnL	35S rRNA	ribosomal RNA	:translation:rRNA
rrnS	16S rRNA	ribosomal RNA	:translation:rRNA
rx1549a	2253-2029	acetoacetyl-CoA	:redox
		reductase
t1549a	19490-19170	acetyltransferase	:synth
thi1	23184-22417	thioredoxin	:redox
thiL	24489-23299	acetyl-coa	:synth:PHB
		acetyltransferase
u1549a	11993-10752	nylonase-like	: M. leprae -specific
u1549b	5852-4947	M. leprae gene sequence	: M. leprae -specific
u1549c	17362-16871	M. leprae gene sequence	: M. leprae -specific
u1549d	15871-15551	M. leprae gene sequence	: M. leprae -specific
u1549e	9262-8945	M. leprae gene sequence	: M. leprae -specific
u1549f	8944-8183	M. leprae gene sequence	: M. leprae -specific
u1549g	12574-11840	M. leprae gene sequence	: M. leprae -specific
u1549h	1756-1974	M. leprae gene sequence	: M. leprae -specific
u1549i	32119-32415	M. leprae gene sequence	: M. leprae -specific
u1549j	4535-4906	M. leprae gene sequence	: M. leprae -specific
u1549k	24494-25039	M. leprae gene sequence	: M. leprae -specific
u1549l	35735-36052	M. leprae gene sequence	: M. leprae -specific
u1549m	36071-36361	M. leprae gene sequence	: M. leprae -specific
u1549n	4155-4550	M. leprae gene sequence	: M. leprae -specific
u1549o	19122-19421	M. leprae gene sequence	: M. leprae -specific
u1549p	27441-27722	M. leprae gene sequence	: M. leprae -specific
u1549q	30279-30494	M. leprae gene sequence	: M. leprae -specific
u1549r	32346-32780	M. leprae gene sequence	: M. leprae -specific
u1549s	28692-28183	M. leprae gene sequence	: M. leprae -specific
u1549t	15489-15094	M. leprae gene sequence	: M. leprae -specific
u1549u	1515-1138	M. leprae gene sequence	: M. leprae -specific
u1549v	18653-18051	M. leprae gene sequence	: M. leprae -specific
u1549w	16790-16266	M. leprae gene sequence	: M. leprae -specific
u1549x	12866-12453	M. leprae gene sequence	: M. leprae -specific
u1549y	29230-28556	M. leprae gene sequence	: M. leprae -specific
u1549z	26107-25427	M. leprae gene sequence	: M. leprae -specific

Mycobacterium leprae peptides, the function of such peptides, and the nucleotide positions associated with such peptides within Seq. ID No. 124 are summarized in Table X set forth below.

TABLE X
Gene	Position	Enzyme name	Function
d2235a	977-1282	dehydrogenase	:metab
d2335b	1500-1901	dehydrogenase	:metab
dapF	19144-18239	diaminopimelate	:synth:aa
		epimerase
hflX	18329-16710	hflx protein E. coli	: M. leprae -specific
lexA	7697-8425	lexA	:regulatory:repair
miaA	20197-19196	tRNA:isopentenyltransferase	:translation
pgsA	35747-35088	cdp-diacylglycerol-	:synth:lipid
		glycerol-3-phosp
recA	30502-28253	recA	:recombination
thyA	5415-5711	thymidylate synthase	:synth:nt
tra9	14824-15039	transposase	:transposon
u2235a	6806-6318	match to ybaD_Ecoli	: M. leprae -specific
u2235b	28290-27772	recA-related ORF	: M. leprae -specific
u2235c	31946-30756	crtX UDP-	: M. leprae -specific
		glucuronosyl-
		transferase
u2235d	7489-6944	M. leprae gene	: M. leprae -specific
		sequence
u2235e	20835-20128	M. leprae gene	: M. leprae -specific
		sequence
u2235f	26340-25534	M. leprae gene	: M. leprae -specific
		sequence
u2235g	27755-26160	M. leprae gene	: M. leprae -specific
		sequence
u2235h	33858-33313	M. leprae gene	: M. leprae -specific
		sequence
u2235i	10587-8464	Corynebacterium M.	: M. leprae -specific
		leprae -specific
u2235j	2896-3927	M. leprae gene	: M. leprae -specific
		sequence
u2235k	34556-34050	M. leprae gene	: M. leprae -specific
		sequence
u2235l	34222-33722	M. leprae gene	: M. leprae -specific
		sequence
u2235m	35718-36032	M. leprae gene	: M. leprae -specific
		sequence
u2235n	3937-4191	weak match to	: M. leprae -specific
		haloacetate
		dehalogenase
u2235o	5125-5343	M. leprae gene	: M. leprae -specific
		sequence
u2235p	11383-11604	M. leprae gene	: M. leprae -specific
		sequence
u2235q	24715-25299	M. leprae gene	: M. leprae -specific
		sequence
u2235r	32479-32832	M. leprae gene	: M. leprae -specific
		sequence
u2335s	1283-1714	M. leprae gene	: M. leprae -specific
		sequence
u2235t	4970-5296	M. leprae gene	: M. leprae -specific
		sequence
u2235u	12323-12664	M. leprae gene	: M. leprae -specific
		sequence
u2235v	22556-22801	M. leprae gene	: M. leprae -specific
		sequence
u2235w	21376-21143	M. leprae gene	: M. leprae -specific
		sequence
u2235x	30885-32420	M. leprae gene	: M. leprae -specific
		sequence
u2235y	33312-33082	M. leprae gene	: M. leprae -specific
		sequence
u2235z	16431-16171	M. leprae gene	: M. leprae -specific
		sequence
u2235aa	15771-15535	M. leprae gene	: M. leprae -specific
		sequence
u2235bb	2583-2272	M. leprae gene	: M. leprae -specific
		sequence
u2235cc	16091-15858	M. leprae gene	: M. leprae -specific
		sequence
u2335dd	15177-15389	M. leprae gene	: M. leprae -specific
		sequence
u2235ee	30751-30539	M. leprae gene	: M. leprae -specific
		sequence

Mycobacterium leprae peptides, the function of such peptides, and the nucleotide positions associated with such peptides within Seq. ID No. 125 are summarized in Table XI set forth below.

TABLE XI
		Enzyme name
Gene	Position	or activity	Function
apt	9663-9400	adenine	:DNA
		phosphoribosyl-
		transferase
apt2	9538-9005	adenine	:nt
		phosphoribosyl-
		transferase
cypH	5736-6650	proline cis-trans	: M. leprae -specific
		isomerase-like
ligA	16651-19251	long-chain fatty	:lipid:metab
		acid-CoA
		ligase
gabT	15206-16630	aminotransferase	: M. leprae -specific
pol1	19055-20293	polyketide synthase	:synth:lipid
		[Anabaena sp.]
ruvA	22895-22275	DNA repair protein	:repair
ruvB	22408-21230	DNA repair protein	:repair
ruvC	23488-22883	DNA repair protein	:repair
secD	14403-12196	protein secretion	:transport
secF	12706-11429	protein secretion	:transport
spoT	9168-6709	guanosine 3′ 5′	:synth:nt
		bis
		(diphosphate)
		3′ . . .
syH	4942-3656	histidinyl-tRNA	:synth:protein
		synthetase
yebC	28331-27555	yebC Ecoli	: M. leprae -specific
		homolog
u1177a	23715-23464	M. leprae gene	: M. leprae -specific
		sequence
u1177b	10824-9718	dciAE gene	: M. leprae -specific
		product
		Bsubtilus
u1177c	37821-38612	ycb9_	: M. leprae -specific
		Psede/ycfA —
		Ecoli homolog
u1177f	25360-25803	M. leprae gene	: M. leprae -specific
		sequence
u1177g	7681-8391	Ecoli 77.2 Kd	: M. leprae -specific
		protein
		homolog
u1177h	36689-36009	weak match to	: M. leprae -specific
		gramicidin synth
u1177i	26410-26790	M. leprae gene	: M. leprae -specific
		sequence
u1177j	26923-27207	M. leprae gene	: M. leprae -specific
		sequence
u1177k	33331-33618	M. leprae gene	: M. leprae -specific
		sequence
u1177l	35257-35559	M. leprae gene	: M. leprae -specific
		sequence
u1177m	20321-20662	M. leprae gene	: M. leprae -specific
		sequence
u1177n	28658-28897	M. leprae gene	: M. leprae -specific
		sequence
u1177o	24507-25343	M. leprae gene	: M. leprae -specific
		sequence
u1177p	32772-33068	M. leprae gene	: M. leprae -specific
		sequence
u1177q	39762-39442	M. leprae gene	: M. leprae -specific
		sequence
u1177r	31446-31000	M. leprae gene	: M. leprae -specific
		sequence
u1177s	30642-30397	M. leprae gene	: M. leprae -specific
		sequence
u1177t	30989-30717	M. leprae gene	: M. leprae -specific
		sequence
u1177u	21368-21078	M. leprae gene	: M. leprae -specific
		sequence
u1177v	37342-37052	M. leprae gene	: M. leprae -specific
		sequence
u1177w	15028-14678	M. leprae gene	: M. leprae -specific
		sequence
u1177x	6268-5732	M. leprae gene	: M. leprae -specific
		sequence
u1177y	29259-28531	S. coelicolor	:synth:aa
		histidine
		biosynthesis
u1177aa	3393-3073	ipiB1 gene product	: M. leprae -specific
		[Phytophthora sp]
u1177ab	40088-39681	dedA protein Ecoli	: M. leprae -specific
u1177ac	11570-10143	M. leprae gene	: M. leprae -specific
		sequence
u1177ad	10447-10235	M. leprae gene	: M. leprae -specific
		sequence
u1177ae	5698-4943	M. leprae gene	: M. leprae -specific
		sequence

Mycobacterium leprae peptides, the function of such peptides, and the nucleotide positions associated with such peptides within Seq. ID No. 126 are summarized in Table XII set forth below.

TABLE XII
Gene	Position	Enzyme name	Function
a2126a	16422-14530	ATPase	: M.
			leprae -specific
bacA	38533-38192	bacitracin resistance prot	:resistance
		homology Ecoli
cysQ	35494-34562	match to E. coli cycQ	: M. leprae -
			specific
his1	22371-21487	ATP-phosphoribosyl	:synth:aa
		transferase
his2	22661-22353	phosphoribosyl-amp	:synth:aa
		cyclohydrolase
lysP	28847-29650	lysine-specific permease	:transport
		Ecoli
metH	25145-24129	methionine synthase	:synth:aa
metH	27780-25078	methionine synthase	:synth:aa
aroP	29574-30434	aromatic aa transport	:transport
		Ecoli
aroP	30482-32080	aromatic aa transport	:transport
		Ecoli
pimT	18549-17647	protein-beta-aspartate	:catab:prot
		methylt-ase
prcB	8970-8047	proteasome, beta subunit	:catab:prot
pyrD	40218-41330	dihydroorotate	:synth:nt
		dehydrogenase
syC	34469-33606	cys tRNA synthetase	:translation
u2126a	1095-133	match to yigU and yigV	: M. leprae -
		E. coli	specific
u2126b	1470-1132	match to yigT	: M. leprae -
		E. coli	specific
u2126c	13279-13665	M. leprae gene sequence	: M. leprae -
			specific
u2126d	14335-14763	M. leprae gene sequence	: M. leprae -
			specific
u2126e	22993-23226	M. leprae gene sequence	: M. leprae -
			specific
u2126f	27793-28779	M. leprae gene sequence	: M. leprae -
			specific
u2126g	40207-40503	M. leprae gene sequence	: M. leprae -
			specific
u2126h	21422-21694	M. leprae gene sequence	: M. leprae -
			specific
u2126i	39908-40240	M. leprae gene sequence	: M. leprae -
			specific
u2126j	17189-17533	Match to Bsu ORF	: M. leprae -
			specific
u2126k	41405-41887	M. leprae gene sequence	: M. leprae -
			specific
u2126l	16641-17231	M. leprae gene sequence	: M. leprae -
			specific
u2126m	20814-21263	M. leprae gene sequence	: M. leprae -
			specific
u2126n	23049-23768	M. leprae gene sequence	: M. leprae -
			specific
u2126o	38937-39989	M. leprae gene sequence	: M. leprae -
			specific
u2126p	37821-36883	M. leprae gene sequence	: M. leprae -
			specific
u2126q	36390-35416	M. leprae gene sequence	: M. leprae -
			specific
u2126r	20103-19813	M. leprae gene sequence	: M. leprae -
			specific
u2126s	12489-11986	M. leprae gene sequence	: M. leprae -
			specific
u2126t	10764-9142	M. leprae gene sequence	: M. leprae -
			specific
u2126u	1776-1471	M. leprae gene sequence	: M. leprae -
			specific
u2126v	18554-19447	mycobacteriophage L5	: M. leprae -
		homology	specific
u2126w	38246-37632	M. leprae gene sequence	: M. leprae -
			specific
u2126x	7187-6822	M. leprae gene sequence	: M. leprae -
			specific
u2126y	5618-5373	M. leprae gene sequence	: M. leprae -
			specific
u2126z	4916-3861	M. leprae gene sequence	: M. leprae -
			specific
u2126aa	2522-1701	M. leprae gene sequence	: M. leprae -
			specific
u2126ab	36910-36215	M. leprae gene sequence	: M. leprae -
			specific
u2126ac	33577-33215	M. leprae gene sequence	: M. leprae -
			specific
u2126ad	19744-19427	M. leprae gene sequence	: M. leprae -
			specific
u2126ae	17800-17372	M. leprae gene sequence	: M. leprae -
			specific
u2212af	13921-13640	M. leprae gene sequence	: M. leprae -
			specific
u2126ag	13345-12950	M. leprae gene sequence	: M. leprae -
			specific
u2126ah	8053-7253	M. leprae gene sequence	: M. leprae -
			specific
u2126ai	6868-6569	M. leprae gene sequence	: M. leprae -
			specific
u2126aj	4114-3443	M. leprae gene sequence	: M. leprae -
			specific
u2126ak	3442-2441	M. leprae gene sequence	: M. leprae -
			specific
u2126al	23716-23928	ham34 gene product	: M. leprae -
		[Bremia lactucae]	specific

Mycobacterium leprae peptides, the function of such peptides, and the nucleotide positions associated with such peptides within Seq. ID No. 127 are summarized in Table XIII set forth below.

TABLE XIII
Gene	Position	Enzyme name or activity	Function
capP	26821-24005	phosphoenolpyruvate	:catab:tca
		carboxylase
coxX	17264-16155	cytochrome assembly	:redox
		factor
g3p	32185-31115	glyceraldehyde-3-	:catab:carbo:glyco
		phosphate deHase
g6pdA	21301-21672	glucose-6-phosphate	: M. leprae -specific
		dehydrogenase
g6pdB	20997-21308	glucose-6-phosphate	: M. leprae -specific
		dehydrogenase
g6pdC	21633-21884	glucose-6-phosphate	: M. leprae -specific
		dehydrogenase
nifS	3821-2514	homologue of nitrogen	: M. leprae -specific
		fixation gene
nifU	2571-2020	homologue of nitrogen	: M. leprae -specific
		fixation gene
pgk	31145-29862	phosphoglycerate kinase	:catab:carbo:glyco
t1496a	4693-3773	traffic ATPase	:transport
t1496b	11040-11993	drrA traffic ATPase	:transport
tkt	17317-19419	transketolase	:synth:carbo
tpiS	29886-29080	TPI (TIM)	:catab:carbo:glyco
u1496a	15109-14645	M. leprae gene sequence	: M. leprae -specific
u1496b	718-275	M. leprae gene sequence	: M. leprae -specific
u1496c	9253-11049	M. leprae gene sequence	: M. leprae -specific
u1496d	15082-15306	M. leprae gene sequence	: M. leprae -specific
u1496e	15499-15978	M. leprae gene sequence	: M. leprae -specific
u1496f	19885-20562	M. leprae gene sequence	: M. leprae -specific
u1496g	22186-23022	M. leprae gene sequence	: M. leprae -specific
u1496h	23023-23781	match to yeast ORF	: M. leprae -specific
u1496i	962-1405	M. leprae gene sequence	: M. leprae -specific
u1496j	11762-12790	M. leprae gene sequence	: M. leprae -specific
u1496k	13397-14356	M. leprae gene sequence	: M. leprae -specific
u1496l	19085-19915	transaldolase	: M. leprae -specific
u1496m	32324-33412	M. leprae gene sequence	: M. leprae -specific
u1496n	28857-28507	M. leprae gene sequence	: M. leprae -specific
u1496o	27336-27085	M. leprae gene sequence	: M. leprae -specific
u1496p	24039-23698	M. leprae gene sequence	: M. leprae -specific
u1496q	5844-4552	yca_yeast homolog	: M. leprae -specific
u1496r	1728-1459	fungus ORF homolog	: M. leprae -specific
u1496s	29207-28821	M. leprae gene sequence	: M. leprae -specific
u1496t	28358-28131	M. leprae gene sequence	: M. leprae -specific
u1496u	22439-22086	M. leprae gene sequence	: M. leprae -specific
u1496v	21134-20700	M. leprae gene sequence	: M. leprae -specific
u1496w	9248-8388	M. leprae gene sequence	: M. leprae -specific
u1496x	8387-5727	yca3_yeast homolog	: M. leprae -specific
u1496y	2087-1698	M. leprae gene sequence	: M. leprae -specific
u1496z	27079-26840	M. leprae gene sequence	: M. leprae -specific

Mycobacterium leprae peptides, the function of such peptides, and the nucleotide positions associated with such peptides within Seq. ID No. 128 are summarized in Table XIV set forth below.

TABLE XIV
Gene	Position	Enzyme name	Function
cfa	22851-23921	cyclopropane-fatty-	:synth:lipid
		acyl-phospholip Ecoli
cysG	18016-16592	uroporphyrin-iii	:synth:cofac:heme
		c-methylt-ase
gsa	7593-6190	glutamate-1-	: M. leprae -specific
		semialdehyde
		2,1-aminot-ase
hem1	20446-18974	glutamyl-trna	:synth:cofac:heme
		reductase
hem2	16297-15284	delta-aminolevulinic	:synth:cofac:heme
		acid deh2oase
hem3	18490-18017	porphobilinogen	:synth:cofac:heme
		deaminase
hem3	18969-18427	porphobilinogen	:synth:cofac:heme
		deaminase
phoP	36607-35969	phosphate sensor	:regulatory
phoR	37960-36608	phosphate sensor	:regulatory
pmgY	38851-38096	phosphoglycerate	:catab:carbo:glyco
		mutase
ppx	31790-30552	exopolyphosphatase	:catab
proC	27878-26970	pyrroline-5-	:synth:aa
		carboxylate
		reductase
serB	21424-22380	phosphoserine	:synth:aa
		phosphatase
t2168a	10404-10156	permease	:transport
t2168b	11030-10557	permease	:transport
u2168a	31534-32508	M. leprae gene	: M. leprae -specific
		sequence
u2168b	26163-25567	match to rfbE	: M. leprae -specific
u2168c	5624-4917	weak match to	: M. leprae -specific
		thioredoxin
u2168d	26844-26569	weak match to	: M. leprae -specific
		excisionase
u2168e	39445-38852	M. leprae gene	: M. leprae -specific
		sequence
u2168f	40823-39480	match to rfaG	:synth
		or susY
u2168g	42424-42741	M. leprae gene	: M. leprae -specific
		sequence
u2168h	4965-4132	M. leprae gene	: M. leprae -specific
		sequence
u2168i	8633-8926	M. leprae gene	: M. leprae -specific
		sequence
u2168j	22442-22984	M. leprae gene	: M. leprae -specific
		sequence
u2168k	33293-33805	M. leprae gene	: M. leprae -specific
		sequence
u2168l	34346-34630	M. leprae gene	: M. leprae -specific
		sequence
u2168m	34827-35060	M. leprae gene	: M. leprae -specific
		sequence
u2168n	35061-35300	M. leprae gene	: M. leprae -specific
		sequence
u2168o	35397-35762	M. leprae gene	: M. leprae -specific
		sequence
u2168p	25068-23950	M. leprae gene	: M. leprae -specific
		sequence
u2168q	15246-14935	M. leprae gene	: M. leprae -specific
		sequence
u2168r	13170-12910	M. leprae gene	: M. leprae -specific
		sequence
u2168s	12411-12139	M. leprae gene	: M. leprae -specific
		sequence
u2168t	12009-11608	M. leprae gene	: M. leprae -specific
		sequence
u2168u	3177-2509	M. leprae gene	: M. leprae -specific
		sequence
u2168v	591-247	M. leprae gene	: M. leprae -specific
		sequence
u2168w	33014-32673	M. leprae gene	: M. leprae -specific
		sequence
u2168x	30281-29487	M. leprae gene	: M. leprae -specific
		sequence
u2168y	29486-28614	M. leprae gene	: M. leprae -specific
		sequence
u2168z	25703-25059	M. leprae gene	: M. leprae -specific
		sequence
u2168aa	4145-2997	M. leprae gene	: M. leprae -specific
		sequence
u2168ab	6244-5582	M. leprae gene	: M. leprae -specific
		sequence
u2168ac	30576-30199	M. leprae gene	: M. leprae -specific
		sequence
u2168ad	26443-26225	M. leprae gene	: M. leprae -specific
		sequence
u2168ae	16682-16320	M. leprae gene	: M. leprae -specific
		sequence
u2168af	2557-1529	M. leprae gene	: M. leprae -specific
		sequence
u2168ag	11776-11420	match to	:catab
		phospholipase
u2168ah	41938-42423	M. leprae gene	: M. leprae -specific
		sequence

Mycobacterium leprae peptides, the function of such peptides, and the nucleotide positions associated with such peptides within Seq. ID No. 129 are summarized in Table XV set forth below.

TABLE XV
		Enzyme name
Gene	Position	or activity	Function
abc1	40693-39500	Yeast mt protein	:transport
cysA	17806-18105	sulfate permease	:transport
cysW	17098-17553	sulfate permease	:transport
dnaJ	24656-25825	heat shock	:stress
erA	30210 31199	GTPase?	: M. leprae -specific
lepA	9501-11474	lethal when	: M. leprae -specific
		overexpressed
phoH	26887-27978	phosphate metabolism	:metab
recQ	37286-38086	DNA helicase RECQ	:repair
subI	15124-16245	Sulfate-binding protein	:transport
uvrD	35866-37278	DNA helicase	:repair
ygrp	23572-24180	match to 38.8 kD	: M. leprae -specific
		protein (SP:P30727)
u1937a	1195-1440	M. leprae gene	: M. leprae -specific
		sequence
u1937b	3361-5052	match to 35.9 kDa	: M. leprae -specific
		protein (PIR:JQ1236)
u1937c	27994-28545	M. leprae gene	: M. leprae -specific
		sequence
u1937d	28972-29418	M. leprae gene	: M. leprae -specific
		sequence
u1937e	32542-33534	M. leprae gene	: M. leprae -specific
		sequence
u1937f	1481-1723	M. leprae gene	: M. leprae -specific
		sequence
u1937g	1730-2935	M. leprae gene	: M. leprae -spedfic
		sequence
u1937h	5903-6868	M. leprae gene	: M. leprae -specific
		sequence
u1937i	6881-7465	M. leprae gene	: M. leprae -specific
		sequence
u1937j	8642-8857	M. leprae gene	: M. leprae -specific
		sequence
u1937k	33431-34417	match to (gp:z26494)	: M. leprae -spedfic
u1937m	14585-14881	M. leprae gene	: M. leprae -specific
		sequence
u1937n	16523-16933	sulfate permease	: M. leprae -specific
		T protein
u1937o	26192-26629	M. leprae gene	: M. leprae -specific
		sequence
u1937p	38468-38806	M. leprae gene	: M. leprae -specific
		sequence
u1937q	750-1076	M. leprae gene	: M. leprae -specific
		sequence
u1937r	4923-6029	M. leprae gene	: M. leprae -speciflc
		sequence
u1937s	19449-19667	M. leprae gene	: M. leprae -specific
		sequence
u1937t	20292-20852	M. leprae gene	: M. leprae -specific
		sequence
u1937u	24126-24617	M. leprae gene	: M. leprae -specific
		sequence
u1937v	25728-26255	match to S.coelicolor	: M. leprae -specific
		gene
u1937w	28677-29045	M. leprae gene	: M. leprae -specific
		sequence
u1937x	29835-30173	M. leprae gene	: M. leprae -specific
		sequence
u1937y	38112-38543	M. leprae gene	: M. leprae -specific
		sequence
u1937z	18537-18292	M. leprae gene	: M. leprae -specific
		sequence
u1937aa	8397-7645	M. leprae gene	: M. leprae -specific
		sequence
u1937ab	39581-38883	M. leprae gene	: M. leprae -specific
		sequence
u1937ac	21140-20898	M. leprae gene	: M. leprae -specific
		sequence
u1937ad	19160-18858	M. leprae gene	: M. leprae -specific
		sequence
u1937ae	18317-17802	M. leprae gene	: M. leprae -specific
		sequence
u1937af	11795-11532	M. leprae gene	: M. leprae -specific
		sequence
u1937ag	42766-41321	M. leprae gene	: M. leprae -specific
		sequence
u1937ah	38932-38603	M. leprae gene	: M. leprae -specific
		sequence
u1937aj	35383-35072	M. leprae gene	: M. leprae -specific
		sequence
u1937ak	13666-13298	M. leprae gene	: M. leprae -specific
		sequence
u1937al	3235-2972	M. leprae gene	: M. leprae -specific
		sequence

Mycobacterium leprae peptides, the function of such peptides, and the nucleotide positions associated with such peptides within Seq. ID No. 130 are summarized in Table XVI set forth below.

TABLE XVI
		Enzyme name
Gene	Position	or activity	Function
acvS	32477-32112	cysteinyl synthetase	:synth:aa
alr	9181-7928	alanine racemase	:synth:wall
chA	4066-3749	10 kd chaperonin	:antigen:stress
dceA	10449-10117	glutamate	:metab
		decarboxylase(DCEA)
dceB	10104-9784	glutamate	:metab
		decarboxylase(DCEA)
dceC	9977-9624	glutamate	:metab
		decarboxylase(DCEA)
glmS	14311-12359	glucosamine-fructose-	: M. leprae -specific
		5-phosphate
groE1	3679-2057	groE1 protein- m.	:antigen:stress
		leprae
ilvi1	29556-28255	acetolactate synthase	:synth:aa:iv:1
ilvi2	29864-29337	acetolactate synthase	:synth:aa:iv:1
rim	6561-5383	ribosomal	:translation
		acetyltransferase
rl13	20260-19787	large ribosomal	:translation
		subunit p13
rs9	19886-19329	small ribosomal	:translation
		subunit p9
u0229a	1054-1458	Regulatory protein	:regulation
u0229b	14239-15270	M. leprae gene	: M. leprae -specific
		sequence
u0229c	24448-24750	M. leprae gene	: M. leprae -specific
		sequence
u0229d	26443-26712	M. leprae gene	: M. leprae -specific
		sequence
u0229e	35122-35457	M. leprae gene	: M. leprae -specific
		sequence
u0229f	13748-14269	M. leprae gene	: M. leprae -specific
		sequence
u0229g	15620-16030	M. leprae gene	: M. leprae -specific
		sequence
u0229h	9024-9443	M. leprae gene	: M. leprae -specific
		sequence
u0229i	25887-26549	M. leprae gene	: M. leprae -specific
		sequence
u0229j	27486-27274	pyrophosphokinase	: M. leprae -specific
u0229k	21717-21499	M. leprae gene	: M. leprae -specific
		sequence
u0229l	20796-20482	M. leprae gene	: M. leprae -specific
		sequence
u0229m	17346-17002	M. leprae gene	: M. leprae -specific
		sequence
u0229n	15735-15499	M. leprae gene	: M. leprae -specific
		sequence
u0229o	8088-6937	M. leprae gene	: M. leprae -specific
		sequence
u0229p	825-1	M. leprae gene	: M. leprae -specific
		sequence
u0229q	31751-31473	M. leprae gene	: M. leprae -specific
		sequence
u0229r	31118-30891	M. leprae gene	: M. leprae -specific
		sequence
u0229s	30179-29865	M. leprae gene	: M. leprae -specific
		sequence
u0229t	23951-23682	M. leprae gene	: M. leprae -specific
		sequence
u0229u	1076-810	M. leprae gene	: M. leprae -specific
		sequence
u0229v	24568-24311	M. leprae gene	: M. leprae -specific
		sequence
u0229w	23686-23450	M. leprae gene	: M. leprae -specific
		sequence
u0229x	22795-22484	M. leprae gene	: M. leprae -specific
		sequence
u0229y	12019-11570	M. leprae gene	: M. leprae -specific
		sequence
u0229z	18863-17832	match to 47.5 kd	: M. leprae -specific
		E. coli protein
u0229aa	19279-18701	match to 47.5 kd	: M. leprae -specific
		E. coli protein
u0229ab	5530-4514	match to 36.0 kd	: M. leprae -specific
		E. coli ribosomal
u0229ac	7058-6459	match to 16.9 kd	: M. leprae -specific
		E. coli protein
u0229ad	11891-10677	match to E. coli amiB	: M. leprae -specific
		5′ regulatory

Mycobacterium leprae peptides, the function of such peptides, and the nucleotide positions associated with such peptides within Seq. ID No. 131 are summarized in Table XVII set forth below.

TABLE XVII
		Enzyme name
Gene	Position	or activity	Function
ag42	5160-3910	45 KDa antigen	:antigen
		(gp:z21952
chA	40918-40409	10 KDa chaperonin	:antigen:stress
choD	30517-28730	cholesterol oxidase	:catab:lipid
groE1	40339-38717	groE1	:antigen:stress
guaA	23093-21258	gmp synthase	:synth:nt
impA	31856-30504	inosine-5′-	:synth:nt
		monophosphate
		dehydrog
impB	33271-31640	inosine-5′-	:synth:nt
		monophosphate
		dehydrog
otsB	616-1908	trehalose-	: M. leprae -specific
		phosphatase
rbsB	16757-17830	ribose binding	:transport
		protein
rbsC	18050-19951	ribose transport	:transport
		protein
s1620a	37713-38117	sigma factor	:regulatory
s1620b	36241-35942	sigma factor	:regulatory
u1620a	6328-6816	transposase	: M. leprae -specific
u1620b	7618-7286	transposase	: M. leprae -specific
u1620c	42190-40991	match to	: M. leprae -specific
		glycoproteinase
u1620f	25213-27627	M. leprae gene	: M. leprae -specific
		sequence
u1620g	20058-21176	M. leprae gene	: M. leprae -specific
		sequence
u1620h	10682-9489	M. leprae gene	: M. leprae -specific
		sequence
u1620i	7738-8049	M. leprae gene	: M. leprae -specific
		sequence
u1620j	2166-1690	M. leprae gene	: M. leprae -specific
		sequence
u1620k	5660-5262	weak match 32 KD	: M. leprae -specific
		protein (sp:p16645)
u1620l	9446-9111	M. leprae gene	: M. leprae -specific
		sequence
u1620m	2191-1979	weak match 42.1 KD	: M. leprae -specific
		protein(sp:p29156)
u1620n	2542-2282	weak match to	: M. leprae -specific
		(gp:x66077)
u1620o	9256-8447	M. leprae gene	: M. leprae -specific
		sequence
u1620p	13237-13515	M. leprae gene	: M. leprae -specific
		sequence
u1620q	13642-13956	M. leprae gene	: M. leprae -specific
		sequence
u1620r	12686-12976	M. leprae gene	: M. leprae -specific
		sequence
u1620s	12480-12836	weak match to	: M. leprae -specific
		(gp:104527)
u1620t	23445-23975	weak match 44.7 KD	: M. leprae -specific
		protein(sp:p31049)
u1620u	24399-25235	M. leprae gene	: M. leprae -specific
		sequence
u1620v	27945-27673	M. leprae gene	: M. leprae -specific
		sequence
u1620w	33375-33797	M. leprae gene	: M. leprae -specific
		sequence
u1620x	34396-34049	M. leprae gene	: M. leprae -specific
		sequence
u1620y	35014-34772	M. leprae gene	: M. leprae -specific
		sequence
u1620z	35428-35153	M. leprae gene	: M. leprae -specific
		sequence
u1620aa	35791-35549	M. leprae gene	: M. leprae -specific
		sequence
u1620ab	37444-36605	M. leprae gene	: M. leprae -specific
		sequence
u1620ac	37735-37469	M. leprae gene	: M. leprae -specific
		sequence

Mycobacterium leprae peptides, the function of such peptides, and the nucleotide positions associated with such peptides within Seq. ID No. 132 are summarized in Table XVIII set forth below.

TABLE XVIII
Gene	Position	Enzyme name	Function
add	16658-15639	adenosine deaminase	:catab:nt
d0308a	2859-2626	dehydrogenase	: M. leprae -specific
d0308b	2017-1757	dehydrogenase	: M. leprae -specific
dhsA1	18908-19738	succinate	:catab:tca
		dehydrogenase
dhsA2	17886-19190	succinate	:catab:tca
		dehydrogenase
dhsB	19618-20532	succinate	:catab:tca
		dehydrogenase
glpD	2478-703	aerobic glycerol-3-	:catab
		phosphate deh-ase
idhpA	34023-33808	isocitrate	:catab:tca
		dehydrogenase
idhpB	33644-33378	isocitrate	:catab:tca
		dehydrogenase
idhpC	34369-34142	isocitrate	:catab:tca
		dehydrogenase
idhpB	33976-33593	isocitrate	:catab:tca
		dehydrogenase
idhpB	33535-33218	isocitrate	:catab:tca
		dehydrogenase
met2	36069-36410	homoserine	:synth:aa
		acetyltransferase
met5a	34828-35145	homoserine	synth:aa
		sulfhydralase
met5b	35410-36102	homoserine	:synth:aa
		sulfhydralase
met5c	35087-35434	homoserine	:synth:aa
		sulfhydralase
pbpB	25732-26523	penicillin binding	:wall
		protein
pbpC	25085-25837	penicillin binding	:wall
		protein
pnpH	7955-8950	purine nucleoside	:catab:nt
		phosphorylase
syW	32289-31243	Trp tRNA synthetase	:translation
tpeA	32298-33221	match to	: M. leprae -specific
		tropinesterase
merA	3987-3766	match to merA	: M. leprae -specific
		protein
u0308a	23625-23867	probable	: M. leprae -specific
		acetyltransferase
u0308b	8878-10563	match to	: M. leprae -specific
		phosphomannomutase
u0308c	7438-8073		: M. leprae -specific
u0308d	12202-12771		: M. leprae -specific
u0308e	12202-12771		: M. leprae -specific
u0308f	29947-30240		: M. leprae -specific
u0308g	12926-13525		: M. leprae -specific
u0308h	16709-17476		: M. leprae -specific
u0308i	22067-22306		: M. leprae -specific
u0308j	23432-23689		: M. leprae -specific
u0308k	27758-28018		: M. leprae -specific
u0308l	28748-28978		: M. leprae -specific
u0308m	4092-4625		: M. leprae -specific
u0308n	12708-13025	match to nusG protein	: M. leprae -specific
u0308o	26865-27119	possible glucose	: M. leprae -specific
		transporter
u0308p	28953-28495		: M. leprae -specific
u0308q	25818-25273		: M. leprae -specific
u0308r	14874-14437		: M. leprae -specific
u0308s	11262-10900	match to uracil	: M. leprae -specific
		phosphoribosyl-
		transferase
u0308t	5475-5038		: M. leprae -specific
u0308u	35264-34986		: M. leprae -specific
u0308v	23081-22758		: M. leprae -specific
u0308w	22592-22317		: M. leprae -specific
u0308x	18272-17928		: M. leprae -specific
u0308y	11018-10704	match to uracil	: M. leprae -specific
		phosphoribosyl-
		transferase
u0308z	7823-7425		: M. leprae -specific
u0308aa	31480-30290	match to	: M. leprae -specific
		metallothioneins
u0308ab	21010-20654		: M. leprae -specific
u0308ac	6043-5720		: M. leprae -specific

Mycobacterium leprae peptides, the function of such peptides, and the nucleotide positions associated with such peptides within Seq. ID No. 133 are summarized in Table XIX set forth below.

TABLE XIX
Gene	Position	Enzyme name	Function
poIIA	2289-643	DNA Polymerase I-	:replication
		M.tuberculosis
poIIB	3382-2273	DNA Polymerase I	:replication
pyrG	27752-25824	CTP synthase	:synth:nt
recN	31868-30105	recombinase	:recombination
syy	39193-38282	Tyr tRNA-synthetase	:translation
u0247a	33657-32824	hemolysin	: M. leprae -specific
u0247b	23927-22857	M. leprae -specific	: M. leprae -specific
		family
u0247c	8082-7870	probable oxidase	: M. leprae -specific
u0247d	25243-24260	match to integrase	: M. leprae -specific
u0247e	19935-18493	M. leprae gene	: M. leprae -specific
		sequence
u0247f	33076-31892	utrl Sce M. leprae -	: M. leprae -specific
		specific
u0247g	21289-20543	E. coli rpsA region	: M. leprae -specific
		protein
u0247h	3617-3390	M. leprae gene	: M. leprae -specific
		sequence
u0247i	8062-8460	M. leprae gene	: M. leprae -specific
		sequence
u0247j	36797-37066	M. leprae gene	: M. leprae -specific
		sequence
u0247k	5304-5561	M. leprae gene	: M. leprae -specific
		sequence
u0247l	2870-2490	M. leprae gene	: M. leprae -specific
		sequence
u0247m	30111-28738	M. leprae gene	: M. leprae -specific
		sequence
u0247n	28737-28309	M. leprae gene	: M. leprae -specific
		sequence
u0247o	25878-25207	M. leprae gene	: M. leprae -specific
		sequence
u0247p	22881-22054	M. leprae gene	: M. leprae -specific
		sequence
u0247q	15463-15092	M. leprae gene	: M. leprae -specific
		sequence
u0247r	36647-36378	M. leprae gene	: M. leprae -specific
		sequence
u0247s	34199-33831	M. leprae gene	: M. leprae -specific
		sequence
u0247t	28106-27753	M. leprae gene	: M. leprae -specific
		sequence
u0247u	11296-10754	M. leprae gene	: M. leprae -specific
		sequence
u0247v	15883-15497	M. leprae gene	: M. leprae -specific
		sequence
u0247w	22091-21312	M. leprae gene	: M. leprae -specific
		sequence
u0247x	20558-19875	M. leprae gene	: M. leprae -specific
		sequence
u0247y	14366-14088	M. leprae gene	: M. leprae -specific
		sequence
u0247z	10739-10425	M. leprae gene	: M. leprae -specific
		sequence
u0247aa	9839-9510	M. leprae gene	: M. leprae -specific
		sequence
u0247ab	6764-6123	M. leprae gene	: M. leprae -specific
		sequence
u0247ac	4532-4245	M. leprae gene	: M. leprae -specific
		sequence

Mycobacterium Leprae peptides, the functions of such peptides, and nucleotide positions associated with such peptides within Seq. ID No. 134 are summarized in Table XX below.

TABLE XX
Name	SeqID	Position	Enzyme or Protein Name	Function
atp6	141	14735-13968	ATP synthase A chain	:metab
atpA	142	11700-10009	ATP synthase alpha chain	:metab
atpB	143	9167-7611	ATP synthase beta chain	:metab
atpC	144	13884-13627	ATP synthase C chain	:metab
atpD	145	13120-11747	ATP synthase delta chain	:metab
atpE	146	7596-7213	ATP synthase epsilon chain	:metab
atpF	147	13626-13093	ATP synthase B chain	:metab
atpG	148	10021-9095	ATP synthase gamma chain	:metab
dcda	149	27058-25505	diaminopimelate decarboxylase	:synth:aa
dhom	150	25504-24176	homoserine dehydrogenase	:synth:aa
khse	151	23107-22082	homoserine kinase	:synth:aa
largs	152	29031-26920	arginyl-tRNA synthetase	:translation
murZ	153	5599-4302	UDP-N-acetyglucosamine 1-carboxyvinyl transferase	:synth:carbo
orfWT	154	5657-6256	C. freundii orfW homologue	: M. leprae specifi
prfA	155	18264-17668	protein synthesis release factor	:translation
rfl	156	19325-18240	peptide chain release factor 1	:regulatory
rfe	157	16655-15444	rfe protein	:antigen
rho	158	21836-19980	transcription termination factor R	:regulatory:transc
r131	159	19879-19415	ribosomal protein L31	:synth:prot
sua5	160	17342-16674	yeast SUA5 protein	:mitochondrial
thrc	161	24233-23097	threonine synthase	:synth:aa
u471a	162	7212-6763	M. leprae gene sequence	: M. leprae specific
u471b	163	6400-6624	M. leprae gene sequence	: M. leprae specific
u471c	164	15190-14720	M. leprae gene sequence	: M. leprae specific
u471c	165	22118-21837	M. leprae gene sequene	: M. leprae specific
u471d	166	17762-17376	M. leprae gene sequence	: M. leprae specific

Mycobacterium Leprae peptides, the functions of such peptides, and nucleotide positions associated with such peptides within Seq. ID No. 135 are summarized in Table XXI below.

TABLE XXI
Name	SeqID	Position	Enzyme or Protein Name	Function
cciptfd	167	6705-7274	P450 cytochrome,isopentenyltransf, ferridox.	:synth:antibiotic
corA	168	35018-33603	magnesium and cobalt transport protein	:transport
dhps	169	9042-9920	dihydropteroate synthase	:synth
GLGC	170	13535-14827	glucose-1-phosphate adenylyltransferase	:synth:carbo
htra1	171	21012-22637	heat shock protein htrA	:antigen:stress
malf	172	29904-30938	maltose transport inner membrane protein	:transport
malg	173	30883-31791	maltose transport inner membrane protein	:transport
maox	174	37206-37997	malate oxireductase(NAD)	:metab
mdhc	175	34923-35924	malate dehydrogenase	:metab
mdmc	176	19306-18650	O-methyltransferase	:synth:nt
mg1	177	11117-11827	DNA-3-methyladenine glycosidase I	:chemotaxis
mrp	178	25338-24019	MRP protein	:synth
rpoE	179	19796-20395	RNA polymerase sigma-E factor	:regulatory
sus1	180	12702-12388	sucrose synthase 1	:synth:carbo
thrb2a	181	17482-17144	TnrB2 protein	:resistance
thrb2b	182	17938-17615	TnrB2 protein	:resistance
ugpC	209	31784-32974	ugpC gene product	:transport
u1756a	183	624-941	M. leprae gene sequence	: M. leprae specifi
u1756b	208	986-161	serine rich antigen - M. leprae	:antigen
u1756c	184	1698-2003	M. leprae gene sequence	: M. leprae specific
u1756d	185	2004-2342	M. leprae gene sequence	: M. leprae specific
u1756e	186	2511-2870	M. leprae gene sequence	: M. leprae specific
u1756f	187	3947-2961	M. leprae gene sequence	: M. leprae specific
u1756g	188	3803-5032	M. leprae gene sequence	: M. leprae specific
u1756h	189	5234-4989	M. leprae gene sequence	: M. leprae specific
u1756i	190	5865-5461	M. leprae gene sequence	: M. leprae specific
u1756j	191	8473-8733	M. leprae gene sequence	: M. leprae specific
u1756k	192	8619-9041	M. leprae gene sequence	: M. leprae specific
u1756l	193	9722-10873	M. leprae gene sequence	: M. leprae specific
u1756m	194	10893-11252	M. leprae gene sequence	: M. leprae specific
u1756n	195	12026-12268	M. leprae gene sequence	: M. leprae specific
u1756o	196	13176-12772	M. leprae gene sequence	: M. leprae specific
u1756p	197	14898-15554	M. leprae gene sequence	: M. leprae specific
u1756q	198	15921-15505	M. leprae gene sequence	: M. leprae specific
u1756r	199	16551-16129	M. leprae gene sequence	: M. leprae specific
u1756s	200	17051-16577	M. leprae gene sequence	: M. leprae specific
u1756t	201	18229-17957	M. leprae gene sequence	: M. leprae specific
u1756u	202	19570-19944	M. leprae gene sequence	: M. leprae specific
u1756v	203	27394-26282	M. leprae gene sequence	: M. leprae specific
u1756w	204	28547-30938	M. leprae gene sequence	: M. leprae specific
u1756x	205	36803-37099	M. leprae gene sequence	: M. leprae specific
u1756y	206	37769-38674	M. leprae gene sequence	: M. leprae specific
u1756z	207	22634-22999	M. leprae gene sequence	: M. leprae specific

Mycobacterium Leprae peptides, the functions of such peptides, and nucleotide positions associated with such peptides within Seq. ID No. 136 are summarized in Table XXII below.

TABLE XXII
Name	SeqID	Position	Enzyme or Protein Name	Function
4CL1	210	33126-31948	4-Coumarate-CoA ligase	:metab
ag84	211	27120-26890	antigen Ag84	:antigen
anp4	212	31293-31631	antifreeze peptide 4 precursor	:regulatory
cpsA	213	20816-22444	cpsA gene product	:synth:carbo
DHG	214	22804-22529	glucose 1-dehydrogenase	:synth:carbo
DHMA	215	23283-23074	N-acylmannosamine 1-dehydrogenase	:synth:carbo
glvr1	216	35001-33718	glvr-1 protein	:antibiotic
mtrA	217	9475-8901	phosphate regulatory protein( M. tuberculosis )	:regulatory
otsa	218	27834-29330	alpha,alpha-trehalose-phosphate synthase	:redox
pkc1	219	6931-7422	protein kinase C inhibitor 1	:regulatory
pur2	220	5183-3909	phosphoribosylamine-glysine ligase	:synth
srcO	221	18805-18602	sarcosine oxidase	:catab
u296a	222	315-1	M. leprae gene sequence	: M. leprae specific
u296b	223	1966-1733	M. leprae gene sequence	: M. leprae specific
u296c	224	3256-3534	M. leprae gene sequence	: M. leprae specific
u296d	225	5498-5184	M. leprae gene sequence	: M. leprae specific
u296e	226	6019-5636	M. leprae gene sequence	: M. leprae specific
u296f	227	6259-6576	M. leprae gene sequence	: M. leprae specific
u296g	228	8070-7768	M. leprae gene sequence	: M. leprae specific
u296g	229	8488-8727	M. leprae gene sequence	: M. leprae speciflc
u296h	230	10580-10371	M. leprae gene sequence	: M. leprae specific
u296i	231	11570-11280	M. leprae gene sequence	: M. leprae specific
u296j	232	12480-11617	hypothetical 26.6K protein ( M. fortuitum )	: M. leprae specifi
u296k	233	15238-15053	M. leprae gene sequence	: M. leprae specific
u296l	234	16952-17338	M. leprae gene sequence	: M. leprae specific
u296m	235	17578-17276	M. leprae gene sequence	: M. leprae specinc
u296n	236	18592-18293	M. leprae gene sequence	: M. leprae specific
u296o	237	20439-20239	M. leprae gene sequence	: M. leprae specific
u296p	238	20685-20894	M. leprae gene sequence	: M. leprae specific
u296q	239	23759-23992	M. leprae gene sequence	: M. leprae specific
u296r	240	23878-24234	M. leprae gene sequence	: M. leprae specific
u296s	241	26577-26338	M. leprae gene sequence	: M. leprae specliic
u296t	242	30960-30700	M. leprae gene sequence	: M. leprae specific
u296u	243	33751-33431	M. leprae gene sequence	: M. leprae specific
u296v	244	33437-33099	M. leprae gene sequence (ATP site)	: M. leprae specific
u296w	245	35512-35060	M. leprae gene sequence	: M. leprae specific

Mycobacterium Leprae peptides, the functions of such peptides, and nucleotide positions associated with such peptides within Seq. ID No. 137 are summarized in Table XXIII below.

TABLE XXIII
Name	SeqID	Position	Enzyme or Protein Name	Function
ampL	246	675-2018	vacular aminopeptidase I precusor	:metab:protein
glnR	247	22621-22818	GlnR protein (response regulator; similar to phoP)	:regulatory
gocp	248	7775-6135	capsule gene complex(galE)(rfbB)(rfbC/D)	:synth:carbo
icc	249	5243-6220	ICC protein	:regulatory
ntrB	250	31848-30655	ntrB gene	:regulatory
pdp	251	23955-25253	phosp-repressible,periplasmicphosph.-binding prot	:transport
phoB	252	28555-27839	phosphate regulatory protein	:transport
pstA	253	26324-26926	phosphate transport protein PSTA	:transport
pstB	254	26991-27812	phosphate transport protein PSTB	:transport
pstC	255	25357-25863	phosphate transport protein	:transport
pur1	256	9799-11472	aminophosphoribosyl transferase precursor	:synth:nt
pur5	257	11547-12140	phosphoribosylformulglycinamidine cyclo-ligase	:synth:nt
purL	258	2834-5134	Phosphoribosylformylglycinamidine	:synth:nt
purM	259	12023-12664	phosphoribosylamine-glycine ligase	:synth:nt
stad	260	32890-31853	[acyl-carrier protein] desaturase precusorR	:synth:lipid
thi1	261	21277-20753	thioredoxin	:redox
thtr	262	20164-19190	thiosulfate sulfurtransferase	:synth:aa
u2266a	263	286-81	M. leprae gene sequence	: M. leprae specific
u2266b	264	512-309	M. leprae gene sequence	: M. leprae specific
u2266c	265	793-332	M. leprae gene sequence	: M. leprae Specific
u2266d	266	8748-8509	M. leprae gene sequence	: M. leprae specific
u2266e	267	8960-8721	M. leprae gene sequence	: M. leprae specific
u2266f	268	14252-13113	M. leprae gene sequence	: M. leprae specific
u2266g	269	15539-15751	M. leprae gene sequence	: M. leprae specific
u2266h	270	15996-15757	M. leprae gene sequence	: M. leprae specific
u2266i	271	18690-17941	M. leprae gene sequence	: M. leprae specific
u2266j	272	19344-18886	M. leprae gene sequence	: M. leprae speciflc
u2266k	273	20639-20055	M. leprae gene sequence	: M. leprae specific
u2266l	274	20752-20537	M. leprae gene sequence	: M. leprae speciflc
u2266m	275	22137-21268	M. leprae gene sequence	: M. leprae specific
u2266n	276	23030-23971	M. leprae gene sequence	: M. leprae specific
u2266o	277	29564-28860	M. leprae gene sequence	: M. leprae specific
u2266p	278	33161-32964	M. leprae gene sequence	: M. leprae specific
u2266q	279	37362-36865	M. leprae gene sequence	: M. leprae specific
u2266r	280	37443-37745	M. leprae gene sequence	: M. leprae specific
u2266s	281	38205-38435	M. leprae gene sequence	: M. leprae specific
u2266t	282	39609-39872	M. leprae gene sequence	: M. leprae specific

Mycobacterium Leprae peptides, the functions of such peptides, and nucleotide positions associated with such peptides within Seq. ID No. 138 are summarized in Table XXIV below.

TABLE XXIV
Name	SeqID	Position	Enzyme or Protein Name	Function
4c11	283	32892-34358	4-coumarate-coA ligase	:repair
cut	284	9824-10657	deoxyuridine 5′-triphosphate nucleotidohydrolase	:metab:nt
dcup	285	23904-25109	uroporphyrinogen decarboxylase	:synth
hemy	286	24716-26461	hemy protein	:synth
msg45mp	287	16345-15056	M. leprae gene sequence	:transport
myoP	288	7650-8537	myo-inositol-1(OR 4)-monophosphatase	:antigen
rps	289	6746-5004	DNA-directed RNA polymerase sigma	:regulatory:transc
tkt	290	16569-18965	transketolase	:transport
traA	291	35961-34381	possible transcriptional activator (srmR)	:regulatory
u1764a	292	1187-150	DNA-directed RNA polymerase	:regulatory:transc
u1764aa	293	28189-27923	M. leprae gene sequence	: M. leprae specific
u1764ab	294	28583-28398	M. leprae gene sequence	: M. leprae specific
u1764ac	295	28952-29299	M. leprae gene sequence	: M. leprae specific
u1764ad	296	30616-30837	M. leprae gene sequence	: M. leprae specific
u1764ae	297	31124-31477	M. leprae gene sequence	: M. leprae specific
u1764af	298	31478-31675	M. leprae gene sequence	: M. leprae specific
u1764b	299	1776-1276	M. leprae gene sequence	: M. leprae specific
u1764c	300	1687-2046	M. leprae gene sequence	: M. leprae specific
u1764d	301	3055-2033	M. leprae gene sequence	: M. leprae specific
u1764e	302	3610-3260	M. leprae gene sequence	: M. leprae specific
u1764f	303	4856-4431	M. leprae gene sequence	: M. leprae specific
u1764fg	304	8124-6739	M. leprae gene sequence	: M. leprae specific
u1764h	305	9200-8541	M. leprae gene sequence	: M. leprae specific
u1764i	306	10278-9694	M. leprae gene sequence	: M. leprae specific
u1764j	307	9375-9689	M. leprae gene sequence	: M. leprae specific
u1764k	308	10570-11475	M. leprae gene sequence	: M. leprae specific
u1764l	309	12239-11520	M. leprae gene sequence	: M. leprae specific
u1764m	310	12539-12772	M. leprae gene sequence	: M. leprae specific
u1764n	311	13087-13278	M. leprae gene sequence	: M. leprae specific
u1764o	312	14085-14282	M. leprae gene sequence	: M. leprae specific
u1764p	313	14568-14756	M. leprae gene sequence	: M. leprae specific
u1764q	314	16964-16398	M. leprae gene sequence	: M. leprae specific
u1764r	315	18966-19160	M. leprae gene sequence	: M. leprae specific
u1764s	316	19585-20049	M. leprae gene sequence	: M. leprae specific
u1764t	317	20669-21169	M. leprae gene sequence	: M. leprae specific
u1764u	318	22490-21066	M. leprae gene sequence	: M. leprae specific
u1764v	319	22953-22357	M. leprae gene sequcnce	: M. leprae specific
u1764w	320	23419-23063	M. leprae gene sequence	: M. leprae specific
u1764x	321	23773-23468	M. leprae gene sequence	: M. leprae specific
u1764y	322	26203-27162	M. leprae gene sequence	: M. leprae specific
u1764z	323	27612-27869	M. leprae gene sequence	: M. leprae specific

Mycobacterium Leprae peptides, the functions of such peptides, and nucleotide positions associated with such peptides within Seq. ID No. 139 are summarized in Table XXV below.

TABLE XXV
Name	SeqID	Position	Enzyme or Protein Name	Function
achA	324	2747-3214	acetyl-hydrolase	:regulatory:transp
cys	325	3622-5029	cysteine synthase	:synth:aa
dhay	326	16015-15797	aldehyde dehydrogenase (NAD+)	:metab
eutP1	327	15605-15339	ethanolamine permease (eutP) gene	:transport
eutP2	328	15289-15101	ethanolamine permease (eutP) gene	:transport
grea	329	7902-7237	transcription elongation factor GREA	:regulatory:transc
kre1	330	18977-19327	weak homolog of Saccharomyces cerevisiae KRE1	:synth:cell wall
lmbE	331	8458-9366	lmbE gene product	:synth
metB	332	6002-7174	cystathionine gamma-synthase	:synth:aa
prAG	333	5140-5928	proline-rich antigen	:antigen
u1740	334	1795-1463	weak match to tyrocidine synthetase I	: M. leprae specific
u1740a	335	3-296	M. leprae gene sequence	: M. leprae specific
u1740aa	336	29246-29563	M. leprae gene sequence	: M. leprae specific
u1740ab	337	29952-30137	M. leprae gene sequence	: M. leprae specific
u1740ac	338	30331-30693	M. leprae gene sequence	: M. leprae speclfic
u1740ad	339	30879-30550	M. leprae gene sequence	: M. leprae specific
u1740ae	340	30861-31070	M. leprae gene sequence	: M. leprae specific
u1740af	341	32594-33013	M. leprae gene sequence	: M. leprae specific
u1740ag	342	36000-36353	M. leprae gene sequence	: M. leprae specific
u1740ah	343	36801-36322	M. leprae gene sequence	: M. leprae specific
u1740ai	344	32476-32718	M. leprae gene sequence	: M. leprae specific
u1740aj	345	15049-14792	M. leprae gene sequence	: M. leprae specific
u1740b	346	9141-9668	M. leprae gene sequence	: M. leprae specific
u1740c	347	9502-9927	M. leprae gene sequence	: M. leprae specific
u1740d	348	9824-10078	M. leprae gene sequence	: M. leprae specific
u1740e	349	10059-10307	M. leprae gene sequence	: M. leprae seecific
u1740f	350	10271-10705	M. leprae gene sequence	: M. leprae specific
u1740g	351	11468-11716	M. leprae gene sequence	: M. leprae specific
u1740h	352	12672-12361	M. leprae gene sequence	: M. leprae specific
u1740i	353	14108-12684	lipoamide dehydrogenase	:catab
u1740j	354	14584-14219	M. leprae gene sequence	: M. leprae specific
u1740k	355	16311-15868	M. leprae gene sequence	: M. leprae specific
u1740l	356	16448-16176	aldehyde dehydrogenase	:catab:aa
u1740m	357	17439-17735	M. leprae gene sequence	: M. leprae specific
u1740n	358	17701-17949	M. leprae gene sequence	: M. leprae specific
u1740o	359	18415-18858	prolyl endopeptidase	:catab
u1740p	360	19727-19461	M. leprae gene sequence	: M. leprae specific
u1740q	361	19621-20019	M. leprae gene sequence	: M. leprae specific
u1740r	362	21077-20697	M. leprae gene sequence	: M. leprae specific
u1740s	363	24193-21263	transport protein	;transport:antibiot
u1740t	364	24672-24139	M. leprae gene sequence	: M. leprae specific
u1740u	365	24695-24880	M. leprae gene sequence	: M. leprae specific
u1740v	366	24881-25093	M. leprae gene sequence	: M. leprae specific
u1740w	367	25762-25944	M. leprae gene sequence	: M. leprae specific
u1740x	368	26293-26742	M. leprae gene sequence	: M. leprae specific
u1740y	369	27179-28414	transport protein	;transport:antibiot
u1740z	370	28620-28907	M. leprae gene sequence	: M. leprae specific

Mycobacterium Leprae peptides, the functions of such peptides, and nucleotide positions associated with such peptides within Seq. ID No. 140 are summarized in Table XXVI below.

TABLE XXVI
Name	SeqID	Position	Enzyme or Protein Name	Function
accY	371	32168-32404	weak match to acetyl-Co-Acarboxylase carboxyltrans.	:metab
atcB	372	27392-27045	calcium-transportin ATPase	:transport
atnA	373	27907-27596	Na+, K+-ATPase alpha subunit	:transport
b650	374	19208-18924	M. leprae gene sequence	: M. leprae specific
b650	375	19585-19325	M. leprae gene sequence	: M. leprae specific
phoP	376	35833-36063	alk phosph syn transcriptional regulatory protein	:regulalory:transc
pstA	377	1914-871	phosphate transport protein PSTA	:transport
pstC	378	2804-1803	phosphate transport protein PSTC	:transport
pstS	379	3923-2805	phosphate-repressible, periplasmic	:transport
smf2	380	6236-7522	SMF2 protein	:resistance
znfy1	410	31567-32214	zinc finger protein	:regulatory
znfy2	411	31347-31709	zinc finger protein	:regulatory
u650	381	24796-24281	M. leprae gene sequence	: M. leprae specific
u650	382	27595-27386	M. leprae gene sequence	: M. leprae specific
u650a	383	4393-4013	M. leprae gene sequence	: M. leprae specific
u650a	384	285-37	M. leprae gene sequence	: M. leprae specific
u650ab	385	32699-32932	M. leprae gene sequence	: M. leprae specific
u650ac	386	33365-33613	M. leprae gene sequence	: M. leprae specific
u650b	387	4523-4840	M. leprae gene sequence	: M. leprae specific
u650e	388	5417-5632	M. leprae gene sequence	: M. leprae specific
u650f	389	8177-7995	M. leprae gene sequence	: M. leprae specific
u650g	390	8860-8624	M. leprae gene sequence	: M. leprae specific
u650h	391	10471-10154	M. leprae gene sequence	: M. leprae specific
u650i	392	10711-10472	M. leprae gene sequence	: M. leprae specific
u650j	393	10880-11248	M. leprae gene sequence	: M. leprae specific
u650k	394	12043-12450	M. leprae gene sequence	: M. leprae specific
u650l	395	13094-12894	M. leprae gene sequence	: M. leprae specific
u650m	396	14944-15813	M. leprae gene sequence	: M. leprae specific
u650n	397	15878-16153	M. leprae gene sequence	: M. leprae specific
u650o	398	16958-16734	M. leprae gene sequence	: M. leprae specific
u650p	399	18652-18467	M. leprae gene sequence	: M. leprae specific
u650q	400	20450-20656	M. leprae gene sequence	: M. leprae specific
u650r	401	22198-22539	M. leprae gene sequence	: M. leprae specific
u650s	402	22591-22776	M. leprae gene sequence	: M. leprae specific
u650t	403	22777-22959	lignostilbene alphabeta-dioxygenase	:catab
u650u	404	25611-25315	M. leprae gene sequence	: M. leprae specific
u650v	405	26166-25612	M. leprae gene sequence	: M. leprae specific
u650w	406	28135-27908	M. leprae gene sequence	: M. leprae specific
u650x	407	28993-28640	M. leprae gene sequence	: M. leprae specific
u650y	408	29213-28989	M. leprae gene sequence	: M. leprae specific
u650z	409	31263-30511	4-chlorobenzoate-CoA dehalogenase	:snyth:lipid
dnfa	410	31567-32214	zinc finger protein	:regulatory
dnfb	411	31347-31709	zinc finger protein	:regulatory

Proteins and peptides of the present invention have further utility for use as vaccines or as screens for new tuberculosis drugs. The purified proteins derived from Mycobacterium tuberculosis or leprae may elicit a specific immune response. The production of purified proteins by recombinant means is not limited to the use of pathogenic bacteria. The proteins of this invention, derived from M. tuberculosis or M. leprae , may also be expressed in M. bovis -BCG by recombinant means, and the resulting recombinant BCG cells may be used as a vaccine. See published PCT application WO90/00594, for example.

The availability of large quantities of Mycobacterium tuberculosis and/or leprae proteins and peptides allows the use of such proteins and peptides as specific binding agents for drugs. The proteins and peptides may also be used to elicit immune responses for the development of antibodies. Such antibodies may have therapeutic value. Proteins and peptides may also be used diagnostically to detect hypersensitivity reactions of individuals exposed to Mycobacterium tuberculosis or leprae . The proteins and peptides may be affixed to solid supports to detect antibodies from patient's sera typical of hypersensitivity reactions.

For example, one method comprises the step of forming an admixture of a sera of an individual with a peptide corresponding to a peptide of Mycobacterium tuberculosis or leprae . Upon imposition of reaction conditions in the presence of an antibody to the peptide, an affinity complex forms. The method further includes the step of detecting the affinity complex which affinity complex is indicative of the presence of a hypersensitivity reaction.

One embodiment of the present invention features, as an article of manufacture, a kit comprising a non-naturally occurring nucleic acid corresponding to Mycobacterium tuberculosis or leprae nucleic acid. A further embodiment of the present invention features a kit comprising a non-naturally occurring peptide corresponding to a peptide of Mycobacterium tuberculosis or leprae or an antibody capable of binding such peptides.

These and other features will be apparent to individuals skilled in the art upon reading the detailed description of the present invention.

DETAILED DECSRIPTION

The present invention relates to nucleic acid and amino acid sequences relating to Mycobacterium tuberculosis and leprae . As used herein, the term “ Mycobacterium tuberculosis ” is used in the sense of the causative agent of tuberculosis in humans. The term “ Mycobacterium leprae ” refers to the causative agent of leprosy in humans.

As used herein the term “corresponding to”, referring to a nucleic acid, means nucleotides in a sequence which is homologous or complementary to other nucleic acid or with reference to a peptide, homologous or complementary to the nucleic acid which encodes such peptides. The derived nucleic acid may be generated in any manner, including, for example, chemical synthesis, or DNA polymerase or reverse transcription which are based on the sequence information.

Similarly, the term “corresponding to”, referring to a peptide or a protein, means having an amino acid sequence encoded by a designated nucleic acid sequence, or which is immunologically identical with a peptide encoded in the sequence, or having the amino acid sequence of a designated peptide. The peptide encoded by the sequence is the gene product. A corresponding peptide is not necessarily translated from a corresponding nucleic acid sequence but may be generated in any manner, including, for example, chemical synthesis, or expression of a recombinant expression system or isolation from mutated Mycobacterium tuberculosis or leprae.

The term “non-naturally occurring nucleic acid” comprises genomic, synthetic DNA, semi-synthetic, or a synthetic nucleic acid which by virtue of its origin or manipulation is not associated with all or a portion of the nucleic acid with which it is associated in nature, and/or in a form of a library, and/or is linked to a nucleic acid other than that to which it is linked in nature. The term “associated with” is used to denote linkage such as that between adjacent segments of nucleic acid.

“Host cells” and other such terms denoting micro-organisms or higher eukaryotic cell lines cultured as unicellular entities refers to cells which can become or have been used as recipients for a recombinant vector or other transfer DNA, and include the progeny of the original cell which has been transfected. It is understood by individuals skilled in the art that the progeny of a single parental cell may not necessarily be completely identical in genomic or total DNA compliment to the original parent, due to accident or deliberate mutation.

The term “control sequence” refers to a nucleic acid having a base sequence which is recognized by the host organism to effect the expression of encoded sequences to which they are ligated. The nature of such control sequences differs depending upon the host organism; in prokaryotes, such control sequences generally include a promoter, ribosomal binding site and terminators; in eukaryotes, generally such control sequences include promoters, terminators and in some instances, enhancers. The term control sequence is intended to include at a minimum, all components whose presence is necessary for expression, and may also include additional components whose presence is advantageous, for example, leader sequences.

The term “operably linked” refers to sequences joined or ligated to function in their intended manner. For example, a control sequence is operably linked to coding sequence by ligation in such a way that expression of the coding sequence is achieved under conditions compatible with the control sequence and lost cell.

An “open reading frame” is a region of nucleic acid which encodes a peptide. This region may represent a portion of a coding sequence or a total sequence.

A “coding sequence” is a nucleic acid sequence which is transcribed into messenger RNA and/or translated into a peptide when placed under the control of appropriate regulatory sequences. The boundaries of the coding sequence are determined by a translation start code at the five prime terminus and a translation stop code at the three prime terminus. A coding sequence can include but is not limited to messenger RNA, synthetic DNA, and recombinant nucleic acid sequences.

A “gene product” is a protein or structural RNA which is specifically encoded for by a gene.

The term “probe” refers to a nucleic acid, peptide or other chemical entity which specifically binds to a molecule of interest. Probes are often associated with or capable of associating with a label. A label is a chemical moiety capable of detection. Typical labels comprise dyes, radioisotopes, luminescent and chemiluminescent moieties, fluorophores, enzymes, precipitating agents, amplification sequences, and the like. Similarly, a nucleic acid, peptide or other chemical entity which specifically binds to a molecule of interest and immobilizes such molecule is referred herein as a “capture ligand”. Capture ligands are typically associated with or capable of associating with a support such as nitro-cellulose, glass, nylon membranes, beads, particles and the like. The specificity of hybridization is dependent on conditions such as the base pair composition of the nucleotides, and the temperature and salt concentration of the reaction. These conditions are readily discernable to one of ordinary skill in the art using routine experimentation. The experimental manipulation of such conditions has been well described in the literature including such books as Molecular Cloning; A Laboratory Manual , Sambrook, J., Fritsch, E. F., Maniatis, T., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 2nd ed. (1989).

The term “primer” is used to denote nucleic acid capable of binding to a specific sequence and initiating a polymerase reaction.

The practice of the present invention will employ, unless otherwise indicated, conventional techniques of chemistry, molecular biology, microbiology, recombinant DNA, and immunology, which are within the skill of the art. Such techniques are explained fully in the literature. See e.g., Sambrook, Fritsch, and Maniatis, Molecular Cloning; A Laboratory Manual 2nd ed. (1989); DNA Cloning , Volumes I and II (D. N Glover ed. 1985); Oligonucleotide Synthesis (M. J. Gait ed, 1984); Nucleic Acid Hybridization (B. D. Hames & S. J. Higgins eds. 1984); the series, Methods in Enzymology (Academic Press, Inc.), particularly Vol. 154 and Vol. 155 (Wu and Grossman, eds.) and PCR - A Practical Approach (McPherson, Quirke, and Taylor, eds., 1991).

The DNA sequences relating to Mycobacterium tuberculosis are derived from nucleic acid sequences present in Mycobacterium tuberculosis. Mycobacterium tuberculosis from which the sequences are derived was acquired from the American Type Culture Collection and has an ATCC designation 25618. This particular Mycobacterium tuberculosis has features which are consistent with those described of Mycobacterium tuberculosis in general and is believed to be representative of all Mycobacterium tuberculosis . The Mycobacterium tuberculosis of the deposit is available through the catalogue of the American Type Culture Collection without restriction. It is believed the Mycobacterium tuberculosis of the deposit has been and is widely available.

The nucleic acid sequences of this invention may be obtained directly from the DNA of the above referenced Mycobacteria tuberculosis strain by using the polymerase chain reaction (PCR). See “ PCR, A Practical Approach ” (McPherson, Quirke, and Taylor, eds., IRL Press, Oxford, UK, 1991) for details about the PCR. Alternatively, the sequences of this invention may be obtained from libraries of Mycobacteria DNA fragments carried in clones of suitable host organisms such as E. coli . Suitable libraries include those of Eiglmeier et al. (1993, Mol. Microbiol. 7, 197-206) and Clark-Curtiss et al. (1985, J. Bacteriol. 161, 1093-1102) for M. leprae and those of Kalpana et al. (1991, Proc. Natl. Acad. Sci. USA 88, 5433-5437) and Bhargava et al. (1990, J. Bacteriol. 172, 2930-2934) for M. tuberculosis . Clones carrying the desired sequences described in this invention may be obtained by screening the libraries by means of the PCR or by hybridization of synthetic oligonucleotide probes to filter lifts of the library colonies or plaques as known in the art (see, eg, Sambrook et al., “ Molecular Cloning, A Laboratory Manual ” 2nd edition, 1989, Cold Spring Harbor Press, NY).

Nucleic acids isolated or synthesized in accordance with features of the present invention are useful, by way of example, without limitation, as probes, primers, capture ligands, anti-sense genes and for developing expression systems for the synthesis of proteins and peptides corresponding to such sequences.

As probes, primers, capture ligands and anti-sense agents, the nucleic acid will normally comprise approximately twenty or more nucleotides for specificity as well as the ability to form stable hybridization products.

Probes

A nucleic acid isolated or synthesized in accordance with Seq. ID No. 1 or Seq. ID Nos. 23-26 and 120-140 can be used as a probe to specifically detect Mycobacterium tuberculosis or M. leprae , respectively. With the sequence information set forth in the present application, sequences of twenty or more nucleotides are identified which provide the desired inclusivity and exclusivity with respect to Mycobacterium tuberculosis and/or M. leprae , and extraneous nucleic acid sequences likely to be encountered during hybridization conditions. More preferably, the sequence will comprise at least twenty to thirty nucleotides to convey stability to the hybridization product formed between the probe and the intended target molecules.

Sequences larger than 1000 nucleotides in length are difficult to synthesize but can be generated by recombinant DNA techniques. Individuals skilled in the art will readily recognize that the nucleic acid sequences, for use as probes, can be provided with a label to facilitate detection of a hybridization product.

Nucleic acid isolated and synthesized in accordance with Seq. ID No. 1 or Seq. ID Nos. 23-26 and 120-140 may also be useful as probes to detect homologous regions (especially homologous genes) of M. tuberculosis, M. leprae, M. avium, M. bovis , or other mycobacterial species using relaxed stringency hybridization conditions, as will be obvious to anybody skilled in the art.

Capture Ligand

For use as a capture ligand, the nucleic acid selected in the manner described above with respect to probes, can be readily associated with a support. The manner in which nucleic acid is associated with supports is well known. Nucleic acid having twenty or more nucleotides in a sequence corresponding to Seq. ID No. 1 with respect to Mycobacterium tuberculosis , or Seq. ID Nos. 23-26 and 120-140 with respect to Mycobacterium M. leprae have utility to separate Mycobacterium tuberculosis or leprae nucleic acid from the nucleic acid of each other and other organisms. Nucleic acid having twenty or more nucleotides in a sequence corresponding to Seq. ID Nos. 1 and 23-26 and 120-140 may also have utility to separate M. avium or M. bovis or other mycobacterial species from each other and from other organisms. Preferably, the sequence will comprise at least twenty nucleotides to convey stability to the hybridization product formed between the probe and the intended target molecules. Sequences larger than 1000 nucleotides in length are difficult to synthesize but can be generated by recombinant DNA techniques.

Primers

Nucleic acid isolated or synthesized in accordance with the sequences described herein have utility as primers for the amplification of Mycobacterium tuberculosis and M. leprae nucleic acid. These nucleic acids may also have utility as primers for the amplification of nucleic acid sequences in M. avium, M. bovis , or other mycobacterial species. With respect to polymerase chain reaction (PCR) techniques, nucleic acid sequences of twenty or more nucleotides corresponding to Seq. ID No. 1 or Seq. ID Nos. 23-26 and 120-140 have utility in conjunction with suitable enzymes and reagents to create copies of Mycobacterium tuberculosis and/or leprae nucleic acid. More preferably, the sequence will comprise twenty to thirty nucleotides to convey stability to the hybridization product formed between the probe and the intended target molecules. Sequences larger than 1000 nucleotides in length are difficult to synthesize but can be generated by recombinant DNA techniques. Binding conditions of probes greater than 100 nucleotides are more difficult to control to obtain specificity.

The copies can be used in diagnostic assays to detect specific sequences, including genes Mycobacterium tuberculosis and/or M. leprae and/or M. avium, M. bovis , or other mycobacteria species. The copies can also be incorporated into cloning and expression vectors to generate polypeptides corresponding to the nucleic acid synthesized by PCR, as will be described in greater detail below.

Anti-sense

Nucleic acid or nucleic acid-hybridizing derivatives isolated or synthesized in accordance with the sequences described herein have utility as anti-sense agents to prevent the expression of Mycobacterium tuberculosis or M. leprae genes. These sequences may also have utility as anti-sense agents to prevent expression of genes of M. avium, M. bovis , or other mycobacteria species.

Nucleic acid or derivatives corresponding to Mycobacterium tuberculosis or M. leprae nucleic acid sequences is loaded into a suitable carrier such as a liposome or mycobacteriaphage for introduction into a mycobacterial cells. For example, a nucleic acid having twenty or more nucleotides is capable of binding to bacteria nucleic acid or bacteria messenger RNA. Preferably, the anti-sense nucleic acid is comprised of 20 or more nucleotides to provide necessary stability of a hybridization product of non-naturally occurring nucleic acid and bacterial nucleic acid and/or bacterial messenger RNA. Nucleic acid having a sequence greater than 1000 nucleotides in length is difficult to synthesize but can be generated by recombinant DNA techniques. Methods for loading anti-sense nucleic acid in liposomes is known in the art as exemplified by U.S. Pat. No. 4,241,046 issued Dec. 23, 1980 to Papahadjopoulos et al.

Expressing Mycobacterial Genes

The function of a specific gene or operon can be ascertained by expression in a bacterial strain under conditions where the activity of the gene product(s) specified by the gene or operon in question can be specifically measured. Alternatively, a gene product may be produced in large quantities in an expressing strain for use as an antigen, an industrial reagent, for structural studies, etc. This expression could be accomplished in a mutant strain which lacks the activity of the gene to be tested, or in a strain that does not produce the same gene product(s). This includes, but is not limited to, mycobacterial strains such as BCG and M. Smegmatis , and other bacterial strains such as E. coli , Norcardia, Corynebacterium, and Streptomyces species. In some cases the expression host will utilize the natural mycobacterial promoter whereas in others, it will be necessary to drive the gene with a promoter sequence derived from the expressing organism (e.g., an E. coli beta-galactosidase promoter for expression in E. coli ).

To express a gene product using the natural mycobacterial promoter, a procedure such as the following is used. A restriction fragment containing the gene of interest, together with its associated natural promoter elements and regulatory sequences (identified using the DNA sequence data) is cloned into an appropriate recombinant plasmid containing the following components: an origin of replication that functions in the host organism, and an appropriate selectable marker. This can be accomplished by a number of procedures known to those skilled in the art. It is most preferably done by cutting the plasmid and the fragment to be cloned with the same restriction enzyme to produce compatible ends that can be ligated to join the two pieces together. The recombinant plasmid is introduced into the host organism by electroporation and cells containing the recombinant plasmid are identified by selection for the marker on the plasmid. Expression of the desired gene product is detected using an assay specific for that gene product.

In the case of a gene that requires a different promoter, the body of the gene (coding sequence) is specifically excised and cloned into an appropriate expression plasmid. This subcloning can be done by several methods, but is most easily accomplished by PCR amplification of a specific fragment and ligation into to expression plasmid after treating the PCR product with a restriction enzyme or exonuclease to create suitable ends for cloning.

Expressed Genes in Therapeutics

Nucleic acid isolated or synthesized in accordance with the sequences described herein have utility to generate proteins and peptides. The nucleic acid exemplified by Seq. ID No. 1 or Seq. ID No. 23-26 and 120-140 can be cloned into suitable vectors or used to isolate nucleic acid. The isolated nucleic acid is combined with suitable DNA linkers and cloned into a suitable vector. The vector can be used to transform a suitable host organism such as E. coli and the peptide or protein encoded by the sequences isolated.

Molecular cloning techniques are described in the text Molecular Cloning: A Laboratory Manual , 2nd edition, Sambrook et al., Coldspring Harbor Laboratory (1989). The isolated peptide has utility as an antigenic substance for the development of vaccines and antibodies directed to Mycobacterium tuberculosis or M. leprae.

The isolated protein or peptide also has utility in screening assays to identify inhibitors or potentiators of the activity of said protein or peptide. Such inhibitors or potentiators may be useful as new therapeutic agents to combat Mycobacterial infections in man. Screening assays may be constructed in vitro with purified Mycobacterial enzyme such that the action of the enzyme produces an easily detectable reaction product. Suitable products include those with distinctive absorption, fluorescence, or chemi-luminescence properties, for example, because detection may be easily automated. A variety of synthetic or naturally occurring compounds may be tested in the assay to identify those which inhibit or potentiate the activity of the mycobacterial enzyme. Some of these active compounds may directly, or with chemical alterations to promote membrane permeability or solubility, also inhibit or potentiate the same enzymatic activity in whole, live mycobacterial cells. Such compounds may be used as anti-mycobacterials in therapy. Since cells of M. tuberculosis and M. leprae grow poorly or not at all in culture, in vitro assays with isolated M. tuberculosis or M. leprae enzymes provide a practical approach for detecting potential new therapeutic agents.

Alternatively, new therapeutic agents may be discovered by use of screening assays which incorporate the M. tuberculosis or leprae genes of this invention or fragments thereof into other micro-organisms such as other Mycobacteria species. For example, M. tuberculosis or M. leprae genes expressed in heterologous micro-organisms may create new products whose activity or presence can be assayed. Agents which alter the activity or presence of these products may be useful therapeutic agents to combat M. tuberculosis or M. leprae infections in man. This approach is useful even when the function or activity of the protein or enzyme encoded by the gene is poorly understood or difficult to assay. Preferably, the genes are essential for growth or viability of the organism. Mycobacteria smegmatis and M. bovis are non-pathogenic but are closely related to M. tuberculosis and M. leprae and are much easier to grow and manipulate in culture. Molecular genetic methods permit the transformation of M. bovis and M. smegmatis with autonomously replicating vectors and with integrating vectors capable of carrying new genes. See, for example, details provided in published PCT applications WO 88/06626, WO 90/00594, WO 92/01783, WO 92/01796, and WO 92/22326.

This methodology may be used to replace M. bovis or M. smegmatis genes with their M. tuberculosis or M. leprae homologs provided in this invention. For example, the M. bovis or M. smegmatis gene which is homologous to the M. tuberculosis or M. leprae gene of interest is identified from appropriate clone libraries (see, for example, Kalpana et al., 1991, Proc. Natl. Acad. Sci. USA 88, 5433-5437) by colony or plaque hybridization using the M. tuberculosis or M. leprae genes of this invention or fragments thereof as probes. The resulting M. bovis or M. smegmatis gene is rendered non-functional by disruption or deletion of the coding region and re-introduced into M. bovis or M. smegmatis by homologous recombination as a linear fragment (see Kalpana et al., 1991, above). Homologous replacements may be distinguished from the background of illegitimate integrations-by using the PCR with appropriate primers. Nested PCR primers may be used in a two-stage PCR to increase specificity if necessary as is known in the art. Clones carrying the replacement will be inviable if the gene is essential. However, the replacement may also be performed simultaneously with clones carrying the homologous M. tuberculosis or leprae gene either on an autonomously replicating plasmid or integrated elsewhere in the genome. If the M. tuberculosis or leprae gene complements the function of the homologous M. bovis or M. smegmatis gene, then the resulting replacement clones will be viable.

Resulting clones carrying specific M. tuberculosis or leprae genes as functional replacements for the homologous M. bovis or smegmatis genes are useful in in vivo screens for new therapeutic agents. Specifically, synthetic or naturally occurring compounds may be applied to cultures of these functional replacement clones and simultaneously to cultures of unmodified M. bovis or smegmatis . Compounds which inhibit measurable properties such as the growth or viability of the functional replacement clones significantly more effectively than they inhibit the unmodified control clones may be useful therapeutic agents for specific treatment of M. tuberculosis or leprae infections in man.

Expressed Genes in Vaccines

The peptide materials of the present invention have utility for the development of antibodies and vaccines.

The availability of nucleotide sequences derived from Mycobacterium tuberculosis and/or leprae (including segments and modifications of the sequence), permits the construction of expression vectors encoding antigenically active regions of a peptide.

Such expression vectors may be introduced into mycobacteria such as M. bovis -BCG to provide stable production of the desired peptide by the recombinant mycobacteria cells. See, for example, details of the expression method provided in published PCT applications WO 88/06626, WO 90/00594, and WO 92/01796. In this manner, the excellent adjuvant properties of the mycobacteria are used to full advantage for the production of M. tuberculosis or M. leprae vaccines. Alternatively, the peptides may be produced by recombinant means in a variety of host cells including, but not limited to, E. coli and subsequently purified for use in vaccines and diagnostic tests.

Fragments encoding the desired peptides are derived from the clones using conventional restriction digestion or by synthetic methods, and are ligated into vectors which may, for example, contain portions of fusion sequences such as beta galactosidase or superoxide dismutase (SOD), preferably SOD. Methods and vectors which are useful for the production of polypeptides which contain fusion sequences of SOD are described in European Patent Office Publication number 0196056, published Oct. 1, 1986.

Any desired portion of the Seq. ID No. 1 or Seq. ID Nos. 23-26 and 120-140 containing an open reading frame, can be obtained as a recombinant peptide, such as a mature or fusion protein; alternatively, a peptide encoded in an open reading frame can be provided by chemical synthesis.

The DNA encoding the desired peptide, whether in fused or mature form, and whether or not containing a signal sequence to permit secretion, may be ligated into expression vectors suitable for any convenient host. Both eukaryotic and prokaryotic host systems are presently used in forming recombinant peptides. The peptide is then isolated from lysed cells or from the culture medium and purified to the extent needed for its intended use. Purification may be by techniques known in the art, for example, differential extraction, salt fractionation, chromatography on ion exchange resins, affinity chromatography, centrifugation, and the like. See, for example, Methods in Enzymology , supra, for a variety of methods for purifying proteins. Such peptides can be used as diagnostics, or those which give rise to neutralizing antibodies may be formulated into vaccines. Antibodies raised against these peptides can also be used as diagnostics, or for passive immunotherapy or for isolating and identifying Mycobacterium tuberculosis or leprae.

An antigenic region of a peptide is generally relatively small—typically 8 to 10 amino acids or less in length. Fragments of as few as 5 amino acids may characterize an antigenic region. Accordingly, DNAs encoding short segments of Mycobacterium tuberculosis or leprae peptides can be expressed recombinantly either as fusion proteins, or as isolated peptides. In addition, short amino acid sequences can be conveniently obtained by chemical synthesis. In instances wherein the synthesized peptide is correctly configured so as to provide the correct epitope, but is too small to be immunogenic, the peptide may be linked to a suitable carrier.

A number of techniques for obtaining such linkage are known in the art, including the formation of disulfide linkages using N-succinimidyl-3-(2-pyridylthio)propionate (SPDP) and succinimidyl 4-(N-maleimido-methyl)cyclohexane-1-carboxylate (SMCC) obtained from Pierce Company, Rockford, Ill., (if the peptide lacks a sulfhydryl group, this can be provided by addition of a cysteine residue). These reagents create a disulfide linkage between themselves and peptide cysteine residues on one protein and an amide linkage through the epsilon-amino on a lysine, or other free amino group in the other. A variety of such disulfide/amide-forming agents are known. See, for example, Immun Rev (1982) 62:185. Other bifunctional coupling agents form a thioether rather than a disulfide linkage. Many of these thio-ether-forming agents are commercially available and include reactive esters of 6-maleimidocaprioc acid, 2-bromoacetic acid, 2-iodoacetic acid, 4-N-maleimido-methyl)cyclohexane-1-carboxylic acid, and the like. The carboxyl groups can be activated by combining them with succinimide or 1-hydroxyl-2 nitro-4-sulfonic acid, sodium salt. Additional methods of coupling antigens employ the rotavirus “binding peptide” system described in EPO Pub. No. 259,149, the disclosure of which is incorporated herein by reference. The foregoing list is not meant to be exhaustive, and modifications of the named compounds can clearly be used.

Any carrier may be used which does not itself induce the production of antibodies harmful to the host. Suitable carriers are typically large, slowly metabolized macromolecules such as proteins; polysaccharides, such as latex functionalized sepharose, agarose, cellulose, cellulose beads and the like; polymeric amino acids, such as polyglutamic acid, polylysine, and the like; amino acid copolymers; and inactive virus particles. Especially useful protein substrates are serum albumins, keyhole limpet hemocyanin, immunoglobulin molecules, thyroglobulin, ovalbumin, tetanus toxoid, and other proteins well known to those skilled in the art.

Peptides comprising Mycobacterium tuberculosis or leprae amino acid sequences encoding at least one epitope are useful immunological reagents. For example, peptides comprising such truncated sequences can be used as reagents in an immunoassay. These peptides also are candidate subunit antigens in compositions for antiserum production or vaccines. While the truncated sequences can be produced by various known treatments of native Mycobacterium tuberculosis or leprae protein, it is generally preferred to make synthetic or recombinant peptides. Peptides comprising these truncated sequences can be made up entirely of Mycobacterium tuberculosis or leprae sequences (one or more epitopes, either contiguous or noncontiguous), or Mycobacterium tuberculosis or leprae sequences and heterologous sequences in a fusion protein. Useful heterologous sequences include sequences that provide for secretion from a recombinant host, enhance the immunological reactivity of the epitope(s), or facilitate the coupling of the polypeptide to an immunoassay support or a vaccine carrier. See, E.G., EPO Pub. No. 116,201; U.S. Pat. No. 4,722,840; EPO Pub. No. 259,149; U.S. Pat. No. 4,629,783.

The size of peptides comprising the truncated sequences can vary widely, the minimum size being a sequence of sufficient size to provide an epitope, while the maximum size is not critical. For convenience, the maximum size usually is not substantially greater than that required to provide the desired epitope and function(s) of the heterologous sequence, if any. Typically, the truncated amino acid sequence will range from about 5 to about 100 amino acids in length. More typically, however, the sequence will be a maximum of about 50 amino acids in length, preferably a maximum of about 30 amino acids. It is usually desirable to select sequences of at least about 10, 12 or 15 amino acids, up to a maximum of about 20 or 25 amino acids.

Mycobacterium tuberculosis or leprae amino acid sequences comprising epitopes can be identified in a number of ways. For example, the entire protein sequence corresponding to each open reading frame is screened by preparing a series of short peptides that together span the entire protein sequence of such open reading frame. By starting with, for example, peptides of approximately 100 amino acids, it would be routine to test each peptide for the presence of epitope(s) showing a desired reactivity, and then testing progressively smaller and overlapping fragments from an identified peptides of 100 amino acids to map the epitope of interest. Screening such peptides in an immunoassay is within the skill of the art. It is also known to carry out a computer analysis of a protein sequence to identify potential epitopes, and then prepare peptides comprising the identified regions for screening.

The immunogenicity of the epitopes of Mycobacterium tuberculosis and/or leprae may also be enhanced by preparing them in mammalian or yeast systems fused with or assembled with particle-forming proteins. Constructs wherein the Mycobacterium tuberculosis and/or leprae epitope is linked directly to the particle-forming protein coding sequences produce hybrids which are immunogenic with respect to the Mycobacterium tuberculosis and/or leprae epitope.

Vaccines

Vaccines may be prepared from one or more immunogenic peptides derived from Mycobacterium tuberculosis or leprae . The observed homology between Mycobacterium tuberculosis and/or leprae with other bacteria provides information concerning the peptides which are likely to be most effective as vaccines, as well as the regions of the genome in which they are encoded. Multivalent vaccines against Mycobacterium tuberculosis or leprae may be comprised of one or more epitopes from one or more proteins.

The preparation of vaccines which contain an immunogenic peptide as an active ingredient, is known to one skilled in the art. Typically, such vaccines are prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid prior to injection may also be prepared. The preparation may also be emulsified, or the protein encapsulated in liposomes. The active immunogenic ingredients are often mixed with excipients which are pharmaceutically acceptable and compatible with the active ingredient. Suitable excipients are, for example, water, saline, dextrose, glycerol, ethanol, or the like and combinations thereof. In addition, if desired, the vaccine may contain minor amounts of auxiliary substances such as wetting or emulsifying agents, pH buffering agents, and/or adjuvants which enhance the effectiveness of the vaccine. Examples of adjuvants which may be effective include but are not limited to: aluminum hydroxide, N-acetyl-muramyl-L-threonyl-D-isoglutamine (thr-MDP), N-acetyl-nor-muramyl-L-alanyl-D-isoglutamine (CGP 11637, referred to as nor-MDP), N-acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-(1-2-dipalmitoyl-sn-glycero-3-hydroxyphosphoryloxy)-ethylamine (CGP 19835A, referred to as MTP-PE), and RIBI, which contains three components extracted from bacteria, monophosphoryl lipid A, trehalose dimycolate and cell wall skeleton (MPL+TDM+CWS) in a 2% squalene/Tween 80 emulsion. The effectiveness of an adjuvant may be determined by measuring the amount of antibodies directed against an immunogenic peptide containing an HCV antigenic sequence resulting from administration of this peptide in vaccines which are also comprised of the various adjuvants.

The vaccines are conventionally administered parenterally, by injection, for example, either subcutaneously or intramuscularly. Additional formulations which are suitable for other modes of administration include suppositories and, in some cases, oral formulations. For suppositories, traditional binders and carriers may include, for example, polyalkylene glycols or triglycerides; such suppositories may be formed from mixtures containing the active ingredient in the range of 0/5% to 10%, preferably 1%-2%. Oral formulations include such normally employed excipients as, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate, and the like.

Kits

The nucleic acid, peptides and antibodies of the present invention can be combined with other reagents and articles to form kits. Kits for diagnostic purposes typically comprise the nucleic acid, peptides or antibodies in vials or other suitable vessels. Kits typically comprise other reagents for performing hybridization reactions, polymerase chain reactions (PCR), or for reconstitution of lyophilized components, such as aqueous media, salts, buffers, and the like. Kits may also comprise reagents for sample processing such as detergents, chaotropic salts and the like. Kits may also comprise immobilization means such as particles, supports, wells, dipsticks and the like. Kits may also comprise labeling means such as dyes, developing reagents, radioisotopes, fluorescent agents, luminescent or chemiluminescent agents, enzymes, intercalating agents and the like. With the nucleic acid and amino acid sequence information provided herein, individuals skilled in art can readily assemble kits to serve their particular purpose.

Embodiments of the present invention are further described with respect to the sequence listings which follow.

SEQUENCE LISTING
The patent contains a lengthy “Sequence Listing” section. A copy of the “Sequence Listing” is available in electronic form from the USPTO
web site (http://seqdata.uspto.gov/sequence.html?DocID=06583266B1). An electronic copy of the “Sequence Listing” will also be available from the
USPTO upon request and payment of the fee set forth in 37 CFR 1.19(b)(3).

Claims

1. A non-naturally occurring peptide of Mycobacterium tuberculosis comprising an amino acid sequence corresponding to the amino acid sequence of SEQ ID NO:12.