CA2162868A1 - Methods and compositions for detecting and treating mycobacterial infections using an inha gene - Google Patents

Abstract

The embodiments of the invention are based upon the identification and characterization of genes that determine mycobacterial resistance to the antibiotic isoniazid (INH) and its analogs. These genes, termed inhA, encode a polypeptide, InhA, that is the target of action of mycobacteria for isoniazid. The sequences of wild-type INH-sensitive as well as allelic or mutant INH-resistant inhA genes and their operons are provided. Also provided are isolated InhA polypeptides of both INH-resistant and the INH-sensitive types.

Description

~094/2~ 2 ~ ~ ~ g ~ g PCT~S94/0~3~

METHODS AND COMPOSITIONS FOR DETECTING AND TREATING
MYCOBACTERIAL INFECTIONS USING AN inhA GENE

Statement of Government Interest This invention was made with government support under NIH Grant No. A126170 and National Cooperative Drug Discovery Group Grant No. UOlA130189. As such, the United States government has certain rights in the invention.

CROSS-REFERENCE TO RELATED APP~ICATIONS
This i9 a Continuation-in-Part of Application Serial No. 08/062,409 filed May 14, 1993, entitled USE OF
GENES OF M. TUBERCULOSIS AND M. SMEGMATIS WHICH ~ON~ ~k ISONIAZID RESISTANCE TO TREAT TUBERCULOSIS AND TO ASSESS
DRUG RESISTANCE.

FIELD OF THE lNv~NllON
The invention relates to materials and methods used in the diagnosis and treatment of mycobacterial diseases, and more specifically to DNA sequence(s) associated with resistance to isoniazid and its analogs in mycobacteria, methods for isolating such sequences), and the use of such sequence(s) in human and ~nim~l medical practice.

~ACKGROUND OF THE lN V~N'l'lON
Tuberculosis caused by members of the M.
tuberculosis complex including M. tuberculosis, M. bovis, and M. africanum r~m~i n~ the largest cause of hllm~n death W094/2~ 21 6 2 8 6 8 - PCT~S94/053~

in the world from a single infectious disease, and is responsible for one in four avoidable adult deaths in developing countries. In addition, in 1990, there was a 10~ increase in the incidence of tuberculosis in the United States. Further, M. bovis causes tuberculosis in a wide range of ~n~mAl9, and is a major cause of ~nim~l suffering and economic loss in ~n m~ 1 industries.
Infection with drug-sensitive strains of the M.
tuberculosis complex can be effectively cured with a combination of antibiotics, including isoniazid (isonicotinic acid hydrazide, INH), rifampicin, and pyrazinamide. INH was first reported to be active against M. tuberculosis in 1952, and particularly active against M.
tuberculosis and M. bovis. However, mutants resistant to INH have emerged since then, and today such mutants account for as many as 26~ of the clinical M. tuberculosis isolates in certain U.S. cities.
Some INH-resistant strains are associated with a 1099 of catalase activity, and deletions of the catalase-peroxidase gene (katG) correlate with INH resistance incertain M. tuberculosis isolates. Furthermore, transfer of the wild-type (wt) M. tuberculosis katG gene to INH-resistant M. smegmatis and M. tuberculosis confers INH
sensitivity, suggesting that catalase-peroxidase activity is required for INH-sensitivity. However, in some studies only 10 to 25~ of the INH-resistant isolates appear to be catalase negative, indicating that INH resistance can be due to other factors.
Drug resistance can be caused by many mechanisms, including mutations in the drug target that reduce the binding of the drug or mutations that lead to increa9ed production of the target. The mechanism by which INH
inhibits mycobacteria and its preci9e target of action are unknown. Biochemical evidence has suggested that both INH
and ethionamide (ETH, a structural analog of INH) block '094/26312 2 1 6 2 8 6 8 PCT~S94/05344 mycolic acid biosynthesis in mycobacteria. INH has been found to inhibit mycolic acid biosynthesi9 in cell-free extracts of mycobacteria, but the target protein has not been identified. In addition, in certain cases, low-level INH resistance correlates not with the 1099 of catalase activity but with the coacquisition of ETH resistance, suggesting that the two drugs may share a common target.
~ ecause such a high percentage of the M.
tuberculosis complex strains are resistant to INH, a great need exists to identify its targets of action, and thereby to devise rapid methods for identification of INH-resistant strains and methods of treating individuals for prevention and/or treatment of the disease associated with them.

SUMM~RY OF THE lNv~NllON
This invention is based upon the discovery of a gene, inhA (also called E~), that encodes an enzyme (InhA). InhA is the target of action of isoniazid in mycobacteria. Mutations within the inhA gene result in isoniazid resistance. Thus, the present invention provides isolated and recombinant polynucleotide sequences and polypeptides encoded therein that are associated with resistance to INH and its structural analogs in members of the genus mycobacteria, particularly those of the M.
tuberculosis complex, including M. tuberculosis, M.
africanum and M. bovis; the M. avium complex, including M.
avium, M. intracellulare, M. scrofulaceum, and M
paratuberculosis; M. ~ e~ll~tis. It also provides the allelic counterparts that are associated with INH
sensitivity. The polynucleotides of the invention have many uses. For example, they are useful in assessing the susceptibility of various strains of the M. tuberculosis complex to isoniazid type antibiotics, as decoys and antisense oligonucleotides to prevent the expression of W094/2~ ~1 6 2 8 6 8 PCT~S94/053~

polypeptides associated with isoniazid resistance, and for the expression of the polypeptides encoded therein. The polypeptides encoded in the polynucleotides and/or antibodies directed to them may also have use in immunoassays for the detection of INH-resistant strains, in the determination of whether an INH-type antibiotic may be effective against tuberculosis, and in the treatment of individuals for infection with these strains.
Accordingly, embodiments of the invention include the following.
An isolated wild-type gene which encodes an enzyme which is~the target of action for isonia2id.
An isolated wild-type gene which encodes a polypeptide (InhA) which is the target of action for isoniazid (INH). These wild type genes also include those from M. tuberculosis, M. avium, M. smegmatis, and M. bovis.
An isolated mutant gene that encodes InhA wherein the mutant gene is associated with INH-resistance.
An isolated polynucleotide encoding an InhA
polypeptide or fragment or variant thereof. These polynucleotides include recombinant expression vectors comprised of control sequences operably linked to a segment encoding the InhA polypeptide of fragment or variant thereof.
A host cell comprised of any of the aforementioned polynucleotides.
A method of treating an individual for infection caused by a member of the mycobacterial complex comprising:
(a) providing a composition comprised of a polynucleotide capable of inhibiting mRNA activity from an 1 A operon of the infecting speCies and a suitable excipient; and (b) administering a p~Arm~cologically effective amount of said composition to the individual.
The above-mentioned method wherein the mode of V094/263~ 2 1 6 2 8 6 8 PCT~S94/05344 ~m; n; stration of the polynucleotides i9 oral, enteral, subcutaneous, intraperitoneal or intravenous.
A method of assessing suqceptibility of a strain of mycobacteria in a biological sample to INH comprising:
(a) providing the mycobacterial DNA from the biological sample;
(b) amplifying a region of the inhA operon;
(c) determ; n; ng whether a mutation exists within the inhA operon from the biological sample, the presence of the mutation indicating that said mycobacterial strain is resistant to INH.
The aforementioned method of wherein the amplification is by a polymerase chain reaction (PCR).
In addition, the aforementioned method further comprised of providing a comparable portion of wild-type INH-sensitive inhA operon from the mycobacteria, and the determ;n~tion of whether a mutation exists in the biological sample is by comparison with the wild-type inhA
operon.
The aforementioned method wherein determ;n;ng whether a mutation exists is performed by single strand conformation polymorphism analysis.
A method of determ; n; ng whether a drug is effective against mycobacterial infection comprising:
(a) providing isolated InhA;
(b) providing a candidate drug;
(c) mixing InhA with substrateq for mycolic acid biosynthesis in the preqence or absence of the candidate drug; and (d) measuring the inhibition of biosynthesis of mycolic acid caused by the presence of the drug, if any.
A method of producing a tuberculosis-~pecific mycolic acid comprising adding purified InhA to substrates required for the biosynthesis of mycolic acid.
A method for producing a compound that inhibits W094/2~ 2 1 6 2 8 6 8 PCT~S94/053~

InhA activity comprising:
a. providing purified InhA;
b. determining the molecular structure of said InhA;
c. creating a compound with a similar molecular structure to INH; and d. determining that said compound inhibits the biochemical activity of InhA.
An isolated InhA polypeptide or fragment or variant thereof.
A recombinant mycobacterial vaccine comprised of attenuated mutants selected from the group consisting of BCG, M. tuberculosis, and M.
bovis, wherein the mutants are host cells contA;n;ng a mutated inhA gene.

BRIEF DESCRIPTION OF THE DRAWINGS
Figure 1 is a table listing inhA genes from different mycobacteria that confer resistance to INH
and ETH in M. smegmatis mc2 155.
Figure 2, comprised of sheets 2A through 2F, presents a comparison of the coding strands of DNA
sequences from M. bovis that confer resistance to INH
and from M. tuberculosis and M. smeqmatis that confer sensitivity to INH. The mutation in mc2651 that causes INH-resistance is indicated by the arrow.
Figure 3 is a diagram of the subcloning strategy used to demonstrate that the isoniazid resistance phenotype is conferred by the inhA open reading frame.
Figure 4, comprised of sheets 4A and 4B, shows the alignment of the amino acid sequences of InhA proteins from M. tuberculosis H37R, M. bovis, M.
bovis NZ, M. smeqmatis mc2155 and M. smeqmatis mc265 with EnvM proteins from S. ty~himurium and E. coli.
Figure 5 is a bar graph showing the results of cell-free assays of mycolic acid biosynthesis, and the effect of insertion of inhA genes on the effect of INH. SUBSTITUTE SHEET (RULE 26~

'094/263~ 21 6 28 68 PCT~S94/05344 Figure 6 is a diagram of the allelic PYchAnge experiment demonstrating that the point mutation in the mc2651 inhA polynucleotide results in INH-resistance, and the results obtAi~e~ from the experiment.
Figure 7, comprised of sheets 7A-1 through 7A-2, 7B-1 through 7B-3, and 7C-1 through 7C-2, shows the nucleic acid sequence that includes the M.
smeqmatis inhA gene.
Figure 8, comprised of sheets 8A, 8B, and 8C, shows the nucleic acid sequence that includes the M. tuberculosis inhA gene.
Figure 9, comprised of sheets 9A, 9B, 9C and 9D, shows the nucleic acid sequence for PS5 and the amino acid sequence from two large open reading frames encompassed within it.
Figure 10 presents the amino acid sequence of a fragment Pn~o~P~ by nucleic acid residues 1256-2062 (ORF2) of the pS5 operon.
Figure 11 presents the amino acid sequence encoded by nucleic acid residues 494-1234 (ORF1) of the ~S5 operon.
Figure 12, comprised of sheets 12A throufh 12C, presents the amino acid sequence of the M. bovis PS5 operon.
Figure 13 presents a restriction enzyme map of pYUB18 showing some significant features of the genome.

DETAILED DESCRIPTION OF THE lNV~NllON
The invention stems from the discovery of inhA, a gene that PnCo~pc a polypeptide that is a target for INH and ETH in members of the M.
tuberculosis complex. Mutations of the gene render mycobacteria INH- and ETH-resistant. The gene and mutations within it were identified using a genetic strategy. Genomic libraries were constructed in shuttle cosmid vectors from INH-SUBSTl~U~ SHEET (RULE 26) W094/263~ ~ 6 ~ 8 6 8 PCT~S94/05344 resistant mutants of M. smeqmatis and M. bovis.Transferral of the libraries into wild type (i.e., INH-sensitive) M. smeqmatis strains allowed the identification of clones that consistently conferred INH-resistance (shown in the table in Figure 1). The transformation of cosmids cont~n~ng a cross-hybridizing DNA fragment from wt (INH-ETH-sensitive strains of M. smegmatis, M. tuberculosis, M.
bovis, M. bovis BCG, and M. avium yielded clones that conferred INH-ETH resistance. These results were suggestive that overexpression of a putative target gene, inhA, on a multi-copy plasmid conferred an INH-resistance phenotype. This led to the conclusion that InhA, the gene product of inhA, is the target of action for INH in members of the M. tuberculosis complex. Moreover, the results showing that a 3 kb BamHI DNA fragment from the M.
smegmatis cosmid that conferred INH-resistance strongly hybridized to all of eleven mycobacterial species tested demonstrated that the inhA gene i8 highly conserved among mycobacteria.
The DNA fragments that conferred INH-sensitivity to M. smeqmatis and M. tuberculosis, as well as those that were isolated from mutant INH-resistant M. smeqmatis and M.
bovis strains were subjected to DNA sequencing. These DNA
sequences are shown in Figure 2. Figure 2 presents the DNA
sequences of the INH-resistant polynucleotide from M. bovis and the INH-sensitive polynucleotides of M. tuberculosis and M. smegmatis. Sequence analysis revealed two ORFs, encoding proteins of 29 and 32 kD. Subcloning analyses of the M . smegmatis fragment ~Pmo~trated that the ORF
encoding the 29 kD protein was responsible for the INH-resistance phenotype, and was termed the inhA gene. In the M. bovis and M. tuberculosis g~nomP~ it appears that the inhA genes are positioned such that they are subject to the same transcriptional control elements (including the promoter) as is ORF1, whereas the inhA gene has its own ~o 94/26312 2 1 6 2 8 6 8 PCT~S94/05344 g promoter in the M. smegmatis genome.
The M. tuberculosis and M. smegmatis inhA gene products show 38 and 40~ homologies to the envM gene product of S. typh;m~rium. In addition, in the M.
smegmatis, M tuberculosis, and M. bovis genomP~ the inhA
ORFs are preceded by another ORF that shares 40~ identity with acetyl CoA reductases. The similaritie3 of the inhA
ORF and ORF1 to lipid biosynthetic genes are consistent with the hypothesis that INH inhibits an enzyme involved in mycolic acid biosynthesis.
Sequence analysis and comparison of inhA from the mutant INH-resistant and wt INH-qensitive strains of M.
smegmatis (See Figure 4) and M. bovis revealed the presence of a single base pair difference that resulted in the amino acid substitution of an alanine for a serine at position 94 of the InhA protein. (See Figure 4.) As shown in the Examples, this difference caused the Inh-resistance phenotype.
Polynucleotides from M. smegmatis, M.
tuberculosis, and M. bovis that encode InhA have been identified, isolated, cloned, sequenced and characterized.
The nucleic acid sequences for these polynucleotides are shown in Figures 7, 8, and 9 respectively. Figure 9 also shows the amino acids encoded in the polynucleotide.
A comparison of the sequences for M. tuberculosis inhA and M. bovis inhA shows that the inhA gene from INH-sensitive M. tuberculosis and INH-sensitive M. bovis are identical. Given that the mutation of Ser to Ala conferring INH-resistance is conserved in M. ~megmatis and M. bovis phenotypes, it can be anticipated that other INH-resistant isolates will be found that are due to mutations in the inhA operon. For example, INH-resistance may also be due to missense mutations in the coding region of inh, or to mutations that cause the overexpression of InhA
(e.g., mutations in the regulatory regions of the operon, W094/2~ ~ 6 ~ 8 6 8 PCT~S94/053~

and/or duplications that allow overexpression).
The discovery of inhA genes and operons of the mycobacterial complex that confer INH-resistance allows for the preparation and use of compositions and methods useful in the diagnosis and treatment of pathogenic states resulting from infection with these microorganisms, and particularly with INH-resistant strains.
The practice of the present invention will employ, unless otherwise indicated, conventional techniques of molecular biology, microbiology, recombinant DNA, and ~mml~nology~ 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, Second Edition (1989), OLIGONUCLEOTIDE
SYNTHESIS (M.J. Gait Ed., 1984), the series METHODS IN
ENZYMOLOGY (Academic Press, Inc.); GENE TRANSFER VECTORS
FOR M~MMALIAN CELLS (J.M. Miller and M.P. Calos eds. 1987), HANDBOOK OF EXPERIMENTAL IMMUNOLOGY, (D.M. Weir and C.C.
Blackwell, Eds.), CURRENT PROTOCOLS IN MOLECULAR BIOLOGY
(F.M. Ausubel, R. Brent, R.E. Ringston, D.D. Moore, J.G.
Siedman, J.A. Smith, and K. Struhl, eds., 1987), and CURRENT PROTOCOLS IN IMMUNOLOGY (J.E. Coligan, A.M.
Kruisbeek, D.H. Margulies, E.M. Shevach and W. Strober, eds., 1991).
As used herein the term "target of action for isoniazid" refers to a polypeptide, InhA, encoded in an inhA operon of mycobacteria, and preferably in members of the mycobacterial complex.
As used herein, the term "inhA gene" refers to a polynucleotide that encodes a polypeptide that is present in mycobacteria, wherein the polypeptide has substantial amino acid homology and equivalent function to the InhA
proteins of M. tuberculo9is, M. bovis, or M. smegmatis;
amino acid sequences of variants of the9e InhA proteins are shown in Figure 4. In this context substantial amino acid V094/26312 2 1 6 2 8 6 8 PCT~S94/05344 homology means at least about 60~ homology, generally at least about 70~ homology, even more generally at least about 80~ homology, and at times at least about 90 homology to any of the indicated polypeptides.
As used herein the term "polynucleotide" refers to a polymeric form of nucleotides of any length, either ribonucleotides or deoxyribonucleotides. This term refers only to the primary structure of the molecule. Thus, this term includes double- and single-stranded DNA and RNA. It also includes known types of modifications, for example, labels which are known in the art (e.g., Sambrook, et al.), methylation, "caps", substitution of one or more of the naturally occurring nucleotides with an analog, internucleotide modifications such as, for example, those with uncharged linkages (e.g., methyl phosphonates, phosphotriesters, phosphoamidates, carbamates, etc.), those cont~;n;ng pendant moieties, such as, for example, proteins (including for e.g., nucleases, toxins, antibodies, signal peptides, poly-L-lysine, etc.), those with intercalators (e.g., acridine, psoralen, etc.), those cont~;n;ng chelators (e.g., metals, radioactive metals, boron, oxidative metals, etc.), those cont~;n;ng alkylators, those with modified linkages (e.g., alpha ~nnmeriC nucleic acids, etc.), as well as unmodified forms of the polynucleotide.
The invention includes as an emboA;m~nt an isolated polynucleotide comprised of a sequence encoding a polypeptide associated with isoniazid (INH) resistance in mycobacteria or active fragment thereof. These isolated polynucleotides contain less than about 50~, preferably less than about 70~, and more preferably less than about 90~ of the chromosomal genetic material with which the sequence encoding the polypeptide is usually associated in nature. An isolated polynucleotide "consisting essentially of" a sequence encoding an isoniazid resistance associated polypeptide lacks other sequences encoding other W094/26312 ~1 6~& 68 PCT~S94/05344 polypeptides derived from the mycobacterial chromosome.
As used herein "isoniazid" ("INH") refers to isoniazid and analogs thereof that inhibit mycobacterial replication by inhibiting the activity of the same polypeptide(s) INH inhibits, for example, etho~Amide (ETH).
The invention also includes as embodiments recombinant polynucleotides contA;n;ng a region encoding inhA gene products for mycobacteria. The term "recombinant polynucleotide" as used herein intends a polynucleotide of genomic, cDNA, semisynthetic, or synthetic origin which, by virtue of its origin or manipulation: (1) is not associated with all or a portion of a polynucleotide with which it is associated in nature; or (2) is linked to a polynucleotide other than that to which it is linked in nature; or (3) does not occur in nature.
A purified or recombinant polynucleotide comprised of a sequence encoding InhA of mycobacteria or variant or active fragment thereof, may be prepared by any technique known to those of skill in the art using the polynucleotide sequences provided herein. For example, they can be prepared by isolating the polynucleotides from a natural source, or by chemical synthesis, or by synthesis using recombinant DNA techniques.
It is contemplated that the sequence encoding an InhA encodes a polypeptide that is associated with isoniazid resistance or sensitivity in mycobacteria, and that allelic variations of the sequences, some of which are shown in the Figures are contemplated herein. The term "polypeptide" refers to a polymer of amino acids and does not refer to a specific length of the product; thus, peptides, oligopeptide~, and proteins are included within the definition of polypeptide. This term also does not refer to or exclude post-expression modifications of the polypeptide, for example, glycosylations, acetylations, phosphorylations and the like. Included within the TO 94/26312 2 1 6 2 8 6 8 PCT~S94/05344 definition are, for example, polypeptides cont~;n;ng one or more analogs of an amino acid (including, for example, unnatural amino acids, etc.), polypeptides with substituted linkages, as well as the modifications known in the art, both naturally occurring and non-naturally occurring.
Also contemplated within the invention are cloning vectors and expres9ion vectors comprised of a sequence encoding InhA or variant or fragment thereof.
Suitable cloning vectors may be constructed according to standard techniques, or may be selected from the large number of cloning vectors available in the art. While the cloning vector selected may vary according to the host cell intended to be used, useful cloning vectors will generally have the ability to self replicate, may possess a single target for a restriction en~o~-lclease, and may carry genes for a readily selectable marker (e.g., antibiotic resistance or sensitivity markers). Suitable examples include plasmids and bacterial viruses, e.g., PUC18, mpl8, mpl9, PBR322, pMB9, ColE1, pCR1, RP4, phage DNAs, and shuttle vectors (e.g., pSA3 and pAT28. Preferred vectors include p31uescript IIks (Stratagene), and pYUB18.
Expression vectors generally are replicable polynucleotide constructs that encode a polypeptide operably linked to suitable transcriptional and translational regulatory elements. Examples of regulatory elements usually included in expression vectors are promoters, enhancers, ribosomal binding sites, and transcription and translation initiation and term;n~tion sequences. The regulatory elements employed in the expression vectors cont~;n;ng a polynucleotide encoding InhA or an active fragment would be functional in the host cell used for expression. It is also contemplated that the regulatory sequences may be derived from the inhA operon;
thus, a promoter or term;n~tor sequenCe may be homologous (i.e., from mycobacteria) to the coding sequence.

2 ~ 6 ~ 8 6 8 PCT~S94/05344 The invention also includes recombinant host cells comprised of any of the above described polynucleotides that contain a sequence encoding an InhA
polypeptide of mycobacteria. The polynucleotides may be inserted into the host cell by any means known in the art.
As used herein, "recombinant host cells", "host cells", llcells", "cell lines", "cell cultures", and other such terms denoting microorganisms or higher eukaryotic cell lines cultured as unicellular entities refer to cells which can be, or have been, used as recipients for recombinant vector or other transfer DNA, and include the progeny of the original cell which has been transformed. It is understood that the progeny of a single parental cell may not necessarily be completely identical in morphology or in genomic or total DNA complement as the original parent, due to natural, accidental, or deliberate mutation. Hosts which may be used include prokaryotic cells (e.g., bacterial cells such as E. coli, mycobacteria, and the like) and eukaryotic cells (e.g., fungal cells, insect cells, An;mAl cells, and plant cells, and the like).
Prokaryotic cells are generally preferred, and E. coli and M. smeqmatis are particularly suitable. Of the latter, mc2l55 is particularly preferred.
"Transformation", as used herein, refers to the insertion of an exogenous polynucleotide into a host cell, irrespective of the method used for the insertion, for example, direct uptake, transduction, f-mating or electroporation. The exogenous polynucleotide may be maintained as a non-integrated vector, for example, a plasmid, or alternatively, may be integrated into the host cell genome.
The polynucleotides comprised of sequences encoding InhA are of use in the detection of INH-resistant forms of mycobacteria in biological samples. As used herein, a nbiological sample" refers to a sample of tissue ~094/26312 2 1 6 2 8 6 8 PCT~S94/05344 or fluid isolated from an individual, including but not limited to, for example, plasma, serum, spinal fluid, lymph fluid, the external sections of the skin, respiratory, - intestinal, and genitourinary tracts, tears, saliva, milk, blood cells, tumors, organs, and also samples of ln vitro cell culture constituents (including but not limited to conditioned medium resulting from the growth of cells in cell culture medium, putatively infected cells, recombinant cells, and cell components). As used herein, the term "clinical sample" is synonymous with "biological sample".
The term "individual" as used herein refers to vertebrates, particularly member~ of the mAmmAl ian or avian species, and includes but i9 not limited to domestic An;m~ls, sports An;mAls, and primates, including hllmAn~.
Using the disclosed portions of the isolated polynucleotides encoding InhA as a basis, oligomers of approximately 8 nucleotides or more can be prepared, either by excision from recombinant polynucleotides or synthetically, which hybridize with the mycobacterial sequences in the plasmids and are useful in identification of the INH-resistant and INH-sensitive mycobacteria. The probes are a length which allows the detection of the InhA
encoding sequences by hybridization. While 6-8 nucleotides may be a workable length, se~enC~ of 10-12 nucleotides are preferred, and about 20 nucleotides appears optimal.
These probes can be prepared using routine methods, including automated oligonucleotide synthetic methods.
For use as probes, complete complementarity is desirable, though it may be unnecessary as the length of the fragment is increased.
Thus, a polynucleotide comprising all or part of the nucleic acid sequences of an inhA operon, and particularly an inhA gene may be used as probes for identifying nucleic acids which code for polynucleotides associated with INH-resistance. The probes may be W094/26312 ~l 6~8 68 PCT~S94/05344 labelled, for example with radioactive isotopes. Usual isotopes include, for example 32p and 33P. The probes are capable of hybridizing to the genetic elements associated with INH-resistance. Preferably, the probes are specific for sequences that encode the INH-resistance gene. ~y way of example, the probe may be the entire nucleotide sequence depicted in Figure 12. However, shorter probes are preferred.
For use of such probes as diagnostics, the bio-logical sample to be analyzed, such as blood or serum, maybe treated, if desired, to extract the nucleic acids contained therein. The resulting nucleic acid from the sample may be subjected to gel electrophoresis or other size separation techniques; alternatively, the nucleic acid sample may be dot blotted without size separation. The probes are usually labeled. Suitable labels, and methods for labeling probes are known in the art, and include, for example, radioactive labels incorporated by nick transla-tion or kinasing, biotin, fluorescent probes, and ch~m;luminescent probes. The nucleic acids extracted from the sample are then treated with the labeled probe under hybridization conditions of suitable stringencies. The probes can be made completely complementary to the allelic form of polynucleotide that has been targeted. With this goal, high stringency conditions usually are desirable in order to prevent false positives. The stringency of hybridization is determined by a number of factors during hybridization and during the washing procedure, including temperature, ionic strength, length of time, and concentration of formamide. These factors are outlined in, for example, Maniatis, T. (19a2).
It may be desirable to use amplification techniques in hybridization assays. Such techniques are known in the art and include, for example, the polymerase chain reaction (PCR) technique described which is by Saiki V094/263~ 2 1 6 2 ~ 6 8 PCT~S94/053~

et al. (1986), by Mullis, U.S. Patent No. 4,683,195, and by Mullis et al. U.S. Patent No. 4,683,202. This technique may be used in conjunction with other techniques, for example, in single-strand conformation polymorphism analysis (see infra., in the Examples).
The probes can be packaged into diagnostic kits.
Diagnostic kits include the probe DNA, which may be labeled; alternatively, the probe DNA may be unlabeled and the ingredients for labeling may be included in the kit in separate containers. The kit may also contain other suit-ably packaged reagents and materials needed for the particular hybridization protocol, for example, st~n~rds, as well as instructions for conducting the test. If the kit is to be used for an assay system which include~ PCR
technology it may also include primers for the PCR
reaction.
The inhA gene sequence and polypeptides encoded therein may also be used for screening for drugs against mycobacteria, particularly members of the mycobacterial complex, and more particularly M. tuberculosis and M.
bovis. For example, it can be used to express the INH-resistant and INH-sensitive polypeptides encoded in the allelic forms of inhA. Utilizing these polypeptides in vitro assays, one could monitor the effect of candidate drugs on mycolic acid biosynthesis. Drugs that inhibit mycolic acid biosynthesis are candidates for therapy of mycobacterial diseases. Drugs that may be tested for effectiveness in this type of system include INH, ETH, rifampicin, streptomycin, ethambutol, ciprofloxacin, novobiocin and cyanide.
The inhA operon sequences may also be used to design polynucleotides that can be used for treatment of mycobacterial infections, including those caused by M
tuberculosis, M. avium, M. smeom~t;s, and M. bovis. One method of treating a mycobacterial infection utilizing the W094/263~ 2 1 6 2 8 6 8 PCTtUS94tO53~

InhA gene is by providing antisense polynucleotides or triplex forming polynucleotides which can be used to inhibit the transcription or translation of MRNA from the inhA operon, for example antisense polynucleotides, triplex forming polynucleotides, decoys, and ribozymes. Thus, these types of polynucleotides are also included within the invention. These polynucleotides may be prepared by a variety of techniques known in the art, including chemical synthesis and recombinant technology. After preparation they can then be Aflmi n; stered, either alone or in combination with other compositions to treat mycobacterial infections, including tuberculosis. The compositions contA;n;ng these polynucleotides may also include suitable excipients.
The sequence of inhA can also be used to assess the susceptibility of various qtrains of mycobacteria, and particularly of M. tuberculosis or M. bovis, in a clinical sample to INH. This susceptibility comparison is based upon the detection of a mutant allele as compared to the wild-type i A allele that is INH-sensitive. Procedures to perform this type of assessment will be readily evident to those of skill in the art. For example, one procedure to perform this assessment is described in the Examples, and is based upon i~olation of the chromosomal DNA of the bacterium, amplification of the inhA region by PCR using primers specific for the region (based upon the inhA
sequences provided herein, and detPrm~nAtion whether a mutation exists in the isolated DNA by the method of single strand conformation polymorphism analysis.
In addition, compounds which block the activity of InhA polypeptides (which may be enzymes) can be prepared utilizing the sequence information of inhA. This is performed by overexpressing InhA, purifying the polypeptide, and then performing X-ray crystallography on the purified InhA polypeptide to obtain its molecular V094/2~ 2 1 6 2 8 6 8 PCT~S94/053~

structure. Next, compounds are created which have similar molecular structures to all or portions of the polypeptide.
The compounds are then combined with the polypeptide and attached thereto so as to block the biochemical activity of the InhA polypeptide.
The inhA polynucleotides may also be used produce or improve live attenuated or killed tuberculosis vaccines.
For example, a tuberculosis strain which contains a mutated inhA can be ~m;nlstered in vaccine form to eliminate INH-resistance which i9 typically conferred by mutant inhA. Inaddition, mutated inhA genes may be added to BCG or M.
tuberculosis vaccines to provide attenuated mutant tuberculosis vaccines. These vaccines may be used to treat and prevent a wide variety of diseases, including tuberculosis, AIDS, leprosy, polio, malaria and tetanus.
The polypeptides of the invention include those encoded in allelic variants of inhA, some of which are shown in the Figures herein, and are in purified or recombinant form. These polypeptides include fragments of the entire polypeptides encoded in the ORFs, particularly fragments that exhibit activity in mycolic acid biosynthesis. In addition, polypeptides of the invention include variants of InhA which differ from the native amino acid sequences by the insertion, substitution, or deletion of one or more amino acids. These variants may be prepared chemically, or by alteration of the polynucleotide sequence encoding InhA, using techniques known in the art, for example, by site-specific primer directed mutagenesis.
These polypeptides can be purified by any means known in the art, including, for example freeze-thaw extraction, salt fractionation, column chromatography, affinity chromatography and the like.
The polypeptides of the invention may find use as therapeutic agents for treatment of mycobacterial infection. "Treatment" as used herein refers to W094/263~ 2 1 6 2 8~6 8 PCT~S94/053~

prophylaxis and/or therapy.
The InhA polypeptides can be prepared as discrete entities or incorporated into a larger polypeptide, and may find use as described herein. The ;mm~lnogenicity of the epitopes of InhA may also be enhanced by preparing them in mAmmAlian or yeast systems fused with or assembled with particle-fonming proteins such as, for example, that associated with hepatitis B surface antigen. See, e.g., U.S. Pat. No. 4,722,840. Vaccines may be prepared from one or more immunogenic polypeptides derived from InhA.
The preparation of vaccines which contain an ;mmllnogenic polypeptide(s) as active ingredients, 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 ;mmllnogenic ingredients are often m;~ with excipients which are phArm~ceutically 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-isoglutAm;ne (CGP 11637, r e f e r r e d t o a 9 n o r - M D P ) N-acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-(1'-2'-dipalmitoyl-sn-glycero-3-hydroxyphosphoryloxy)-ethylam ine (CGP 19~35A, referred to as MTP-PE), and RIBI, which contains three components extracted from bacteria, -21- PCT~594/05344 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 antibodie9 directed against an immunogenic polypeptide cont~;n;ng an InhA antigenic sequence resulting from ~m;n;stration of this polypeptide in vaccines which are also comprised of the various adjuvants.
The vaccines are conventionally ~mt n;stered parenterally, by injection, for example, either subcutane-ously or intramuscularly. Additional formulations which are suitable for other modes of ~m; n;stration include suppositories and, in some cases, oral formulations or formulations suitable for distribution as aerosols. For suppositories, traditional binders and carriers may include, for example, polyalkylene glycols or triglycerides; such suppositories may be formed from mixtures cont~;n;ng the active ingredient in the range of 0.5~ to 10~, preferably 1%-2%. Oral formulations include such normally employed excipients as, for example, ph~rmAceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate, and the like. These compositions take the form of solutions, suspensions, tablets, pills, capsules, sust~;ne~ release formulations or powders and contain 10~-95% of active ingredient, preferably 25%-70%.
The proteins may be formulated into the vaccine as neutral or salt forms. Pharmaceutically acceptable salts include the acid addition salts (formed with free amino groups of the peptide) and which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids such as acetic, oxalic, tartaric, maleic, and the like. Salts formed with the free carboxyl groups may also be derived from inorganic bases such as, for example, sodium, potassium, ~mmo~;um, W094/2~ ~l 6 2 8 6 8 PCT~S94/053 calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, 2-ethylamino ethanol, histidine, procaine, and the like.
The vaccines are ~m; n; stered in a manner compatible with the dosage formulation, and in such amount as will be prophylactically and/or therapeutically effec-tive. The quantity to be ~m;n;stered, which is generally in the range of 5 micrograms to 250 micLoyLams of antigen per dose, depends on the subject to be treated, capacity of the subject~s ;mmllne system to synthesize antibodies, and the degree of protection desired. Precise amounts of active ingredient required to be ~m;n;stered may depend on the judgment of the practitioner and may be peculiar to each subject.
The vaccine may be given in a single dose schedule, or preferably in a multiple dose schedule. A
multiple dose srh~ e is one in which a primary course of vaccination may be with 1-10 separate doses, followed by other doses given at subsequent time intervals required to maintain and or reenforce the ;mml~ne response, for example, at 1-4 months for a second dose, and if needed, a subsequent dose(s) after several months. The dosage regimen will also, at least in part, be determ;ne~ by the need of the individual and be dependent upon the judgment of the practitioner.
In addition, the vaccine cont~;n;ng the im-munogenic InhA antigen(s) may be ~m; n; stered in conjunc-tion with other ;mmllnoregulatory agents, for example, im-mune globulins, as well as antibiotics.
The InhA antigens may be used for the preparation of antibodies. The immunogenic polypeptides prepared as described above are used to produce antibodies, including polyclonal and monoclonal. If polyclonal antibodies are desired, a selected m~mm~l (e.g., mouse, rabbit, goat, horse, etc.) is ;mmlln;zed with an immllnogenic polypeptide 1094/2~ 2 1 6 2 8 6 8 PCT~S94/053~

bearing an InhA epitope(s). Serum from the ;mm~lnized ~n;m~l is collected and treated according to known procedures. If serum cont~;n;ng polyclonal antibodies to an InhA epitope contains antibodies to other antigens, the polyclonal antibodies can be purified by ;mml~no~ffinity chromatography. Techniques for producing and processing polyclonal antisera are known in the art, see for example, Mayer and Walker (1987).
Monoclonal antibodies directed against InhA
epitopes can also be readily produced by one skilled in the art. The general methodology for making monoclonal antibodies by hybridomas is well known. Immortal antibody-producing cell lines can be created by cell fu-sion, and also by other techniques such as direct trans-formation of B lymphocytes with oncogenic DNA, or transfection with Epstein-Barr virus. See, e.g., M.
Schreier et al. (1980); ~mm~rling et al. (1981); ~ennett et al. (1980); see also, U.S. Patent Nos. 4,341,761;
4,399,121; 4,427,783; 4,444,887; 4,466,917; 4,472,500;
4,491,632; and 4,493,890. Panels of monoclonal antibodies produced against InhA epitopes can be screened for various properties; i.e., for isotype, epitope affinity, etc.
Antibodies, both monoclonal and polyclonal, which are directed against InhA epitopes are particularly useful in diagnosis, and those which are neutralizing may be useful in passive ;mmllnotherapy. Monoclonal antibodies, in particular, may be used to raise anti-idiotype antibodies.
Anti-idiotype antibodies are ;m~nQglobulins which carry an "internal image" of the antigen of the infectious agent against which protection is desired. See, for example, Nisonoff, A., et al. (1981) and Dreesman et al. (1985). Techniques for raising anti-idiotype anti-bodies are known in the art. See, for example, Grzych (1985), MacNamara et al. (1984), and Uytdehaag et al.
(1985). These anti-idiotype antibodie~ may also be useful wo 94/263~ 2 1 6 2 8 6 8 PCT~S94/05344 for treatment, vaccination and/or diagnosis of mycobacterial infections, as well as for an elucidation of the immunogenic regions of InhA antigens.
Both the InhA polypeptides and anti-InhA
antibodies are useful in immllns~qsays to detect presence of antibodies to mycobacteria, or the presence of the InhA
antigens, and particularly the presence of INH-resistant InhA in biological samples. Design of the immllnoAqsays is subject to a great deal of variation, and many formats are known in the art. The imml~no~qsay will utilize at least one epitope derived from InhA. In one embodiment, the immllno~qgay uges a combination of epitopes derived from InhA. These epitopes may be derived from the same or from different bacterial polypeptides, and may be in separate recombinant or natural polypeptides, or together in the same recombinant polypeptides. An immllnoAqsay may use, for example, a monoclonal antibody directed towards an InhA
epitope(s), a combination of monoclonal antibodies directed towards epitopes of one mycobacterial antigen, monoclonal antibodies directed towards epitopes of different mycobacterial antigens, polyclonal antibodies directed towards the same antigen, or polyclonal antibodies directed towards different antigen~. Protocols may be based, for example, upon competition, or direct reaction, or sandwich type assays. Protocols may also, for example, use solid supports, or may be by ;~l~noprecipitation. Most assays involve the use of labeled antibody or polypeptide;
the labels may be, for example, enzymatic, fluorescent, chemiluminescent, radioactive, or dye molecules. Assays which amplify the signals from the probe are al90 known;
examples of which are as5ay9 which utilize biotin and avidin, and enzyme-labeled and me~;~ted imm~lno~says~ such as ELISA aqsays.
Typically, an im~lno~qsay for an anti-InhA
antibody(s) will involve selecting and preparing the test V094/2~ 2 1 6 2 8 6 8 PCT~S94/053~

sample suspected of containing the antibodies, such as a biological sample, then incubating it with an antigenic (i.e., epitope-containing) InhA polypeptide(s) under condi-tions that allow antigen-antibody complexes to form, and then detecting the formation of such complexes. Suitable incubation conditions are well known in the art. The ;mmllno~say may be, without limitations, in a heterogenous or in a homogeneous format, and of a st~n~rd or competitive type.
In a heterogeneous format, the polypeptide is typically bound to a solid support to facilitate separation of the sample~from the polypeptide after incubation.
Examples of solid supports that can be used are nitro-cellulose (e.g., in membrane or microtiter well form), polyvinyl chloride (e.g., in sheets or microtiter wells), polystyrene latex (e.g., in beads or microtiter plates, polyvinylidine fluoride (known as Immulon), diazotized paper, nylon membranes, activated beads, and Protein A
beads. For example, Dynatech Immulon 1 or Immulon 2 microtiter plates or 0.25 inch polysterene beads (Precision Plastic Ball) can be used in the heterogeneous format. The solid support cont~; n; ng the antigenic polypeptide is typically washed after separating it from the test sample, and prior to detection of bound antibodies. Both st~n~rd and competitive formats are known in the art.
Complexes formed comprising anti-InhA antibody (or, in the case of competetive a8says, the amount of competing antibody) are detected by any of a number of known techniques, depending on the format. For example, unlabeled anti-InhA antibodies in the complex may be detected using a conjugate of antixenogeneic Ig complexed with a label, (e.g., an enzyme label).
In ;mmllno~says where InhA polypeptides are the analyte, the test sample, typically a biological sample, is incubated with anti-InhA antibodie~ under conditions that W094/263~ 2 1 6 2 ~ 6 8 PCT~S94/05344 allow the formation of antigen-antibody complexes. It may be desirable to treat the biological sample to release putative bacterial components prior to testing. Various formats can be employed. For example, a "sandwich assay"
may be employed, where antibody bound to a solid support is incubated with the test sample; washed; incubated with a second, labeled antibody to the analyte, and the support is washed again. Analyte is detected by determ;n;ng if the second antibody i8 bound to the support. In a competitive format, which can be either heterogeneous or homogeneous, a test sample i8 usually incubated with antibody and a labeled, competing antigen is also incubated, either sequentially or simultaneously. These and other formats are well known in the art.
The following examples are pro~ided only for illustrative purposes, and not to limit the scope of the present invention. In light of the present disclosure numerous emboA;ments within the scope of the claims will be apparent to those of ordinary skill in the art.

EXAMPLES

Example 1 Selection of INH-Resistant M. bovis Strains In order to select M. bovis INH-resistant strains, a virulent wild-type New Zealand strain of M.
bovis was cloned by four serial passages using a combination of liquid Tween albumin broth (TAB) and 7H10 pyruvate agar culture media. A single colony of M. bovis was inoculated into TAB and incubated until visible growth was apparent. An appropriate dilution of the bacterial suspension in TAB was plated onto the agar mP~;~ to obtain discrete colonies. After incubation, a single colony was picked and inoculated into TAB and the cloning procedure was repeated. After four cloning cycles a G4 strain was obtained. INH-resistant strains were obt~;nerl by growing the GI strain in liquid TAB media cont~;n;ng differing concentrations of INH. After incubation, the strain that had luxuriant growth in the highest concentration of INH
was inoculated onto INH-cont~;n;ng solid media and incubated for growth. A colony was picked, used as inoculum for INH-cont~;n;ng TAB, and incubated under growth conditions. When visible growth was apparent, the medium was used to inoculate liquid TAB media cont~;n;ng INH, and the inoculated medium was allowed to incubate under growth conditions. Aliquots of the culture were then grown again in liquid TAB media contA;n;ng increased differing concentrations of INH, and cloning of a colony from a strain that had luxuriant growth in the highest concentration of Ir~H was repeated. This selection procedure was repeated and a series of clones of M. bovis with increasing resistance to isoniazid were obtained. The last strain selected, G4/100, was resistant to 100 ~Lg/ml of INH.

Exam~le 2 Isolation of INH-resistant Clones from a Cosmid Library pre~ared from an TN~-Res~s~nt Strain A cosmid library from strain G4/100 was prepared in the shuttle vector pYUB18. Plasmid pYUB18 is a multicopy E. coli-mycobacteria ~huttle cosmid that contains a selectable kanamycin gene and a C09 site (J.T. Beslile et al., J. Bacteriol. 173, 6991 (1991); S.B. Snapper et al., Mol. Microbiol. 4:1911 (1990); W.R. Jacobs et al., Methods Enzymol. 204:537 (1991)). A restriction enzyme Bp of pYUB18 showing some significant features of the genome is shown in Figure 13.
The cosmid library was prepared as follows using st~nrl~rd techniques. Chromosornal DNA was purified from W094/263~ 2 1 6 2 8 6 8 28- PCT~S94/053~

G4/100, and subjected to partial digestion with Sau3A1;
fragments between about 30-50 kb were purified by sucrose gradient purification and ligated to linearized pYUB18.
Resulting cosmids were packaged into ~-phage using a commercial kit (Gigapack Gold Stratagene) according to the manufacturer's directions, and transfected into E. coli;
approximately 5000 colonies were obtained. The colonies were pooled and the plasmids amplified, using standard plasmid preparation techniques.
The cosmid library was then transformed into M.
smegmatis strain mc2 155 by electroporation. Transformants were ~elected by growth on medium cont~;n;ng kanamycin.
Approximately 1200 kanamycin resistant clones were patched onto media containing INH. Four INH resistant clones were identified.

Example 3 Isolation and Sequencing of pS5 In order to obtain a plasmid cont~;n;ng mycobacterial genetic material that conferred INH-resistance, the plasmids were extracted from the transformants. Cultures of M. smegmatis (5ml) were incubated with cycloserine and ampicillin for 3 hours before harvest. The cells were pelleted and resu~pended in 0.25 ml of 40 mM Tris acetate, 2 mM EDTA, pH 7.9. To this, 0.5 ml of lysing solution was added (50 mM Tris, 3~ Rodium dodecylsulfate (SDS)) and the solution was mixed for 30 minutes. The sample was heated to 60C for 20 minutes, cooled for 10 minutes and the DNA was extracted by adding 0.8 ml of phenol (cont~;n;ng 50 mM NaCl). This was centrifuged and the upper layer contA~n;ng the DNA was remo~ed. To precipitate the DNA, a half ~olume of 7.5 M
~mmon;um acetate was added, incubated on ice for 30 minutes and then centrifuged for 30 minutes. The DNA wasresuspended in 10 mM Tris, 1 mM EDTA.

PCT~S94/053 10 g4t26312 The smallest plasmid obtained which conferred an Inh-resistance phenotype on M. smegmatis was 2.3 kb in size and was designated pS5.
The sequence of pS5 was obt~ineA as follows. pS5 was cloned into the vector pBluescript II KS+ (Stratagene, California). This vector contains the T3 and T7 promoters which were used for the sequencing. Sequencing was carried out using the dsDNA cycle sequencing system from GIBC0 BRL, Life Technologies, according to the manufacturer' 8 directions. The radioactive labelled nucleotide was either [y 32p] ATP or [~-33P] ATP, available from Amersham. The sequencing prog~am used was GCG, Sequence analysis software package. The nucleic acid sequence for pS5 and the amino acid sequence from two large open reading frames encompassed within it are shown in Figure 9. Figure 10 presents the amino acid sequence of a fragment encoded by nucleic acid residues 1256^2062 (the InhA gene) of the pS5 operon. Figure 11 presents the amino sequence of a fragment encoded by nucleic acid residues 494-1234 of the pS5 operon. Figure 12 presents the nucleic acid sequence of the pS5 M. bovis NZ operon.

Exam~le 4 Determin~tion of Catalase Activity in an INH-Resistant Strain Catalase activity of an INH-sensitive strain of M. bovis was detPrmi n~ . The enzyme was ~irst isolated from the strain by pelleting a culture of M. bovis, resuspending it in 50 mM potassium phosphate buffer, pH 7, and adding it to a tube cont~in;ng 0.5 g zirconium beads (Biospecs products), and vortexing for 5 min. The sample was centrifuged briefly, the supernatant collected and diluted to 4 ml with 50 mM potassium phosphate buffer, and filter sterilized through 0.22 ~m filters.

Catalase catalyzes the conversion of H2O2 to H2O
and 2 Catalase activity was assayed by incubating an aliquot of supernatant, prepared as above, with 3 ~rn H202 in a total volume of 3 ml for 5 minutes. The reaction was stopped by adding 1.5 ml of titanium tetrachloride reagent (1.5 mg/ml TiC14 in 4.5 M H2SO4). The absorbance was read at 410 nm and the catalase activity was calculated using a stAn-lArd curve of the amount of hydrogen peroxide versus wavelength at 410 nm; the activity was expressed as ~mol/min/mg protein.
Catalase activity of G4/100, G4 and another virulent M. bovis strain were also determ;nerl using the above-described procedure. The G4 strain and other virulent M. bovis strains contA;ne~l similar levels of catalase activity. Catalase activity was not detected in the G4/100 strain.
To ~ m~n~trate that the development of INH-resistance in G4/100 was not due entirely to 108s of catalase activity, the plasmid pS5 was electroporated into G5 to produce G4(S5). G4(S5) grew on m~tl;A contA;n;ng a level of INH that prevented growth of G4. Using the method described above, catalase activity was tested in both G4 and G4(S5). G4~S5) which i8 INH-resistant, and G4 which is INH-sensitive, both showed similar levels of catalase activity.

Example 5 Identification of the InhA Gene of M. smegmatis A spontaneous INH-ETH-resistant mutant of M.
sme~matis, mc2651, was isolated from wt M. sme~matis in a single step with a mutational frequency of 10-7. A genomic library from mc2651 was constructed in a multicopy (5 to 10 copies) shuttle cosmid vector; the vector was described by Y. Zhang et al., Mol. Microbiol. 8, 521 (1993). Upon transfer of the library into wt M. smegmatitis strains, PCT~S94/053 ~094l2~

cosmid clones were identified that consistently conferred INH-ETH resistance. These results are shown in the table in Figure 1.
Cells of M. smeqmatis mc2155 bearing the indicated plasmids (derived from insertion into pYUB18) were grown in 7H9 broth cont~;n;ng kanamycin (15~g/ml), and dilutions were plated on 7H10 agar plates containing kanamycin alone or kanamycin with various concentrations of INH or ETH. The strains without any plasmid were grown in 7H9 broth, and dilutions were plated on 7H10 agar plates and on 7H10 agar plates with various concentrations of INH
or ETH.
The transformation of cosmids cont~;n;ng a cross-hybridizing DNA fragment from wt (INH-ETH-sensitive strains) of M. smegmatis, M. tuberculosis, M. bovis, M.
bQvis BCG, and M. avium yielded clones that conferred INH-ETH resistance. The INH-ETH resistance conferred by the transfer of the wt DNA fragment could be due to overexpression of the target, as iq the case for the resistance phenotype seen with several antibiotics.
A 3-kb Bam HI DNA fragment from the M. smegmatis cosmid pYUB286 that conferred INH resistance was used as a probe for Southern (DNA) analysiq. This probe strongly hybridized to all of the 11 different mycobacterial species tested, including the pathogenic strains M. tuberculosis, M. bovis, M. avium, and M. leprae, ~emonqtrating that this sequence is highly conqerved among the mycobacteria.
The DNA fragments hybridizable with those that conferred resistance to INH were isolated from the wt (INH-9ensitive) strains of M. ~ ey-,~tis, M. bovis, and M
tuberculosis, as well as from the INH-resiqtant mutants of M. smegmatis and M. bovis. Sequence analysis revealed that each strain contains two open reading frames (ORFs), one encoding a 29-kD protein followed by another encoding a 32-kD protein. Figure 2 presents the DNA sequences of INH-W094l2~ 2 1 6 2 8 6 8 PCT~S94/053~

resistant polynucleotides from M. tuberculosis, M. bovis, and M. smegmatis. The point mutation that differs between the INH-resistant and INH-sensitive M. smegmatis strains, and that determines resistance, i9 shown in the Figure.
Subcloning studies to det~rm;ne the smallest fragments to confer INH-resistance were performed; the strategy is shown in Figure 3. In the Figure, panel A is subcloning of M. smegmatis mc2155, and panel B is of M.
tuberculosis H37Rv. The M. smegmatis mc2155 were transformed with a pool of E. coli-mycobacteria shuttle cosmids, and individual clones were scored for resistance (r,+) or sensitivity (-) to INH and ETH. The ORF preceding inhA is labeled orfl and the sequence of the intervening DNA is shown. The ribosome binding sites are indicated in boldface letters. The following enzymes were used for subcloning: B, Bam HI; P, Pst I;, S, Spe I, V, Pvu II, N, Nla III; G, Bgl II, H, Nhe I. All the subclones were tested in both orientations. Subcloning analysis of M.
bovis DNA yielded results s;m;l~r to those obt~;neA with M
tuberculosis. Plasmid pYUB291 was also shown to confer INH
and ETH resistance in M. bovis BCG host.
The subcloning studies demonstrated that the second ORF from M. smegmatis was sufficient to confer the INH-resistance phenotype. This second ORF was thus named the lnhA gene. In contrast to the M. smegmatis gene, the M. tuberculosis and M. bovis lnhA genes appear to be in an operon with the gene encoding the 29-kD ORF, an obser~ation confirmed by subcloning. In M. tuberculo9is and M. bovis DNA, the noncoding region between the two ORFs was substantially shorter than that in M. smegmatis and may lack a promoter that appears to be present in the latter strain. The inhA DNA sequences have been submitted to G~nR~nk. The accession numbers are U02530 ~for M.
smegmatis) and U02492 (for M. tuberculosis). The M. bovis gequence i9 identical to that of M. tuberculosis.

~094/263~ 2 1 6 2 8 6 8 PCT~S94/05344 The InhA protein may use nicotinamide or flavin nucleotides as substrates or cofactors, as translation of the putative protein encoded therein indicates that it has a putative binding site for these molecules.

Example 6 Effect of InhA on Mycolic Acid Biosynthesis As shown in Figure 4, the predicted InhA proteins of M. tuberculosis, M. bovis, and M. smegmatis show strong sequence similarity (about 40~ identity over 203 amino acids) to the EnvM proteins of S. typh;mllrium and E. coli.
The figure aligns the amino acid sequences of InhA proteins from the indicated strains with the EnvM proteins from E.
coli and S. ty~h;murium. The amino acid sequences were obtained by conceptual translation of the inhA and envM
ORFs. Over a stretch of 203 amino acids, InhA and EnvM
show about 75~ sequence similarity (40~ identity). InhA is highly conserved among mycobacterial strains. The InhA
proteins of M. tuberculosis H37Rv and M. bovis are identical and hence are represented by a single sequence.
The M. tuberculosis-M. bovis InhA has greater than 95~
identity with the M. sme~matis InhA. The various envM gene products are also highly conserved (98~ identity)(F.
Turnowsky et al., J. Bacteriol. 171, 6555 (1989); H.
Bergler et al., J. Gen. Microbiol. 138, 2093 (1992). The protein EnvM is thought to be involved in fatty acid biosynthesis. The relatively close homologies suggest that inhA may be involved in lipid biosynthesis.
The effect of inhA on mycolic acid biosynthesis was determined in cell-free assays. The M. smegmatis mc2155 gene was transformed with pYUB18 vector (strain - mc2144) or pYUB18 carrying the inhA genes of M. smegmatis (pYUB291, product of subcloning of pYUB286, strain mc2801), M. avium (pYUB317, strain mc2832), or M. bovis BCG
(pYUB316, strain mc2799). Cell-free extracts were prepared W094/263~ 2 1 6 2 8 6 8 PCT~S94/0~3~

from each of these strains and from the spontaneous INH-resistant mutant (mc2651 of M. smeqmatis. Incorporation of [1-14C]acetate into mycolic acids was measured using an assay described in L.M. Lopez-Marin et al., Biochim.
Biophys. Acta 1086, 22 (1991), after preincubation with or without Inh. Protein concentrations in cell-free extracts were adjusted to 0.37 to 0.50 mg/ml, which resulted in the linear incorporation of radioactivity into the mycolic acids after a 1-hour incubation of the cell-free extract with the radioactive acetate. Each assay was done in duplicate, and the experimental error between different experiments was~no more than 15~. The results of the cell-free assays of mycolic acid biosynthesis are shown in Figure 5. The INH concentration necessary for strong inhibition of mycolic acid biosynthesis in cell-free extracts of the sensitive strain was about 20 times greater than the MIC (here, 20 x MIC = 100 ~g/ml, solid bars.) Open bars, 0~g/ml; crosshatched bars, 250 ~g/ml. A 20- to 50- fold accumulation of INH has been reported to occur inside the mycobacteria.
As seen from the results in Figure 5, compared to wt extracts, cell-free extracts from the resistant mutant mc2651 or from resistant merodiploids cont~; ni ng multiple copies of inhA 3howed marked resistance to the INH-mediated inhibition of mycolic acid biosynthesis. Thi~ result is supportive of the suggestion that InhA is required for mycolic acid biosynthesis.

Example 7 Allele Exchange of inhA Genes Conferrinq Inh-Resistance and Sensitivity Phenotypes The InhA protein from the INH-resi9tant mutant (mc2651) differs from the wt (mc2155) by a single substitution of Ser to Ala at position 94. To test whether this difference caused the INH resistance phenotype in '094/26312 2 t 6 2 8 6 8 PCT~S94/05344 mc2651, an allele exchange was performed on the M.
smegmatis chromosome. The mc2651 cellc were transformed with a 45 kb M. smeqmatis DNA fragment that contained the wt inhA gene linked to a kanr marker gene.
A 45 kb long DNA fragment containing the inhA
allele from mc2155 was cloned into a vector with Pac I
sites flanking the insert, and a Tn5sequl transposon (cont~;n;ng the kanr gene) was introduced near inhA. The linear Pac I fragment cont~;n;ng lnhA linked to kanr was transformed into mc2651 by electroporation. The transformants were plated on 7H10 plates containing kanamycin (15 mg/ml). The kanamycin-resistant transformants were then scored for INH sensitivity on 7H10 plates cont~;n;ng both kanamycin ~15~g/ml) and INH
(lO~g/ml). INH sensitivity contransformed with kanamycin resistance in 93 of 130 (72%) transformants tested. The rPm~;n;ng transformants were as resistant to INH as was mc2651 (MIC = 50 ~g/ml). Figure 6 presents a diagram of the allelic P~ch~nge experiment.
Allelic ~ch~nge was confirmed by restriction fragment length polymorphism analysis of the inhA
polymerase chain reaction (PCR) products obt~;nPA from the recombinants and by Southern blots.
This result provides evidence that the mutation of Ser to Ala94 mP~;~tes the INH-resistance phenotype in M.
smegmatis.
An allelic P~rh~nge could not be performed in M.
bovis because a homologous recombination system i9 lacking.
However, the mutant M. bQvis gene conferred a higher level of resistance to INH (100% survival in 20 ~g/ml of INH, MIC
= 30 ~g/ml) than did the wt M. bovis gene (0~ ~urvival in 20 ~g/ml of INH, MIC = 15 ~g/ml) when transformed into M.
sme~matis mc2155 on a pYUB18 cosmid vector. These results shown in the table in Figure 1, ~Pmonctrate that the identical mutation of Ser to Ala caused INH resistance in WO94126312 21 6 ~8 68 PCT~S94/05344 M. bovis NZ.

Example 8 Susceptibility of M. tuberculosis in a Clinical Sample to INH:
Single Strand Polymorphism Conformation Analysis A polynucleotide encoding InhA can be used to assess the susceptibility of various strains of M.
tuberculosis in a clinical sample to INH.
The chromosomal DNA of M. tuberculosis is isolated from a clinical sample. Oligonucleotides are prepared using- the wild-type inhA sequence of M.
tuberculosis. This sequence is depicted in Figure 8.
Regions of the inhA gene of M. tuberculosis from the clinical sample which are identified by use of the oligonucleotides are amplified using polymerase chain reaction (PCR) to obtain double stranded DNA. Next, in order to determine whether a mutant inhA gene exists, single strand conformation polymorphism analysis is performed. An example of single strand conformation polymorphism analysis is described by Telenti et al. in "Detection of Rifampicin-Resistance Mutations in Mycobacterium Tuberculosis", Vol. 341 pages 647-650 (March 1993).
In order to perform single strand conformation polymorphism, PCR is performed after substitution of half of the dCTP by 32P-~-dCTP or ch~m;lllm;n~cent substrates per reaction to generate a labelled 157 bp product. After amplification, the PCR product is diluted to an appropriate concentration with dilution buffer. An aliquot of diluted product is m;xe~ with an appropriate aliquot of sequence loading buffer (Sequenase kit), heated for ten minutes at about 94C, cooled on ice and loaded onto a non-denaturing sequencing format 0.5~ MDE gel (Hydrolink, AT Biochem, Malvern, Penn.) Electrophoresis is then performed at room '094/26312 2 1 6 2 8 6 8 PCT~S94/05344 termperature and constant power overnight. The gels are then dried and exposed for autoradiography overnight.

Claims (18)

Claims

1. An isolated wild-type gene which encodes an enzyme which is the target of action for isoniazid.

2. An isolated wild-type gene which encodes a polypeptide (InhA) which is the target of action for isoniazid (INH).

3. A wild-type gene according to claim 2, wherein the gene is selected from the group consisting of that in M. tuberculosis, M. avium, M. smegmatis, and M.
bovis.

4. An isolated mutant gene that encodes InhA
wherein the mutant gene is associated with INH-resistance.

5. An isolated polynucleotide encoding an InhA
polypeptide or fragment or variant thereof.

6. A polynucleotide according to claim 5, wherein the polynucleotide is a recombinant expression vector comprised of control sequences operably linked to a segment encoding the InhA polypeptide of fragment or variant thereof.

7. A host cell comprised of a polynucleotide selected from the group of polynucleotides according to claim 2, or claim 3, or claim 4, or claim 5, or claim 6.

8. A method of treating an individual for infection caused by a member of the mycobacterial complex comprising:
(a) providing a composition comprised of a polynucleotide capable of inhibiting mRNA activity from an inhA operon of the infecting species and a suitable excipient; and (b) administering a pharmacologically effective amount of said composition to the individual.

9. The method of claim 6 wherein the mode of administration of the polynucleotides is selected from oral, enteral, subcutaneous, intraperitoneal and intravenous.

10. A method of assessing susceptibility of a strain of mycobacteria in a biological sample to INH
comprising:
(a) providing the mycobacterial DNA from the biological sample;
(b) amplifying a region of the inhA operon;
(c) determining whether a mutation exists within the inhA operon from the biological sample, the presence of the mutation indicating that said mycobacterial strain is resistant to INH.

11. The method of claim 10 wherein the amplification is by a polymerase chain reaction (PCR).

12. The method of claim 11 further comprised of providing a comparable portion of wild-type INH-sensitive inhA operon from the mycobacteria, and the determination of whether a mutation exists in the biological sample is by comparison with the wild-type inhA operon.

13. The method of claim 12, wherein determining whether a mutation exists is performed by single strand conformation polymorphism analysis.

14. A method of determining whether a drug is effective against mycobacterial infection comprising:
(a) providing isolated InhA;
(b) providing a candidate drug;
(c) mixing InhA with substrates for mycolic acid biosynthesis in the presence or absence of the candidate drug; and (d) measuring the inhibition of biosynthesis of mycolic acid caused by the presence of the drug, if any.

15. A method of producing a tuberculosis-specific mycolic acid comprising adding purified InhA to substrates required for the biosynthesis of mycolic acid.

16. A method for producing a compound that inhibits InhA activity comprising:
a. providing purified InhA;
b. determining the molecular structure of said InhA;
c. creating a compound with a similar molecular structure to INH; and d. determining that said compound inhibits the biochemical activity of InhA.

17. An isolated InhA polypeptide or fragment or variant thereof.

18. A recombinant mycobacterial vaccine comprised of attenuated mutants selected from the group consisting of BCG, M. tuberculosis, and M. bovis, wherein the mutants are host cells containing a mutated inhA gene.