Mycobacterial isocitrate lyase gene and uses thereof

Abstract

The present invention provides a purified and isolated nucleic acid encoding mycobacterial isocitrate lyase, as well as mutated forms of the nucleic acid. Further provided are purified and isolated isocitrate lyase proteins and mutated isocitrate lyase proteins. Additionally, the present invention provides vectors which comprises nucleic acid sequences encoding mycobacterial isocitrate lyase and mutated forms of this nucleic acid, as well as host cells containing these vectors. Also provided is a mycobacterium containing one or more mutations in its isocitrate lyase gene. Further provided by the present invention are agents that inhibit the activity or expression of a mycobacterial lyase protein, a method of identifying these, and a method of producing them. Finally, the present invention also provides a method of identifying genes required for persistence of mycobacteria.

Description

BACKGROUND OF THE INVENTION

Pulmonary tuberculosis initiates with the inhalation and retention in the lung alveoli of a “droplet nucleus” containing from 1-10 tubercle bacilli. Most cases of human tuberculosis originate from a single primary lesion in the lung parenchyma; the number of bacilli initiating an infection is therefore extremely small (Medlar). Patent tuberculous disease develops only after expansion of this initially small bacillary population by replication within host macrophages. In order to grow, persist, and cause disease, tubercle bacilli must obtain nutrients from the parasitized host. Little is known, however, of the mechanisms involved in nutrient acquisition by tubercle bacilli in vivo. Writing in 1976, Ratledge opined that “[T]he entire subject of in vivo nutrition of bacteria when within the phagocytic cells of the host is probably the largest single area of ignorance in the whole of our knowledge concerning the physiology of the mycobacteria. Clearly this is a crucial area where knowledge should be sought as it is only by understanding the true behavior and requirements of the bacteria when growing in vivo that we shall learn how to prevent their multiplication and, hopefully, how to cause their death” (Ratledge, 1976) Unfortunately, the intervening decades have marked little progress in this area. With the advent of molecular genetic tools for the manipulation of the pathogenic mycobacteria, a genetic approach to this problem is now feasible.

In the infected host, M. tuberculosis bacilli replicate within host macrophages. Following phagocytosis, tubercle bacilli reside within modified phagosomes that apparently fuse with vacuoles derived from the endosomal compartment (Sturgill-Koszycki et al., 1996) but that fail to acidify fully or to fuse with lysosomes (reviewed in Clemens, 1996). As an intracellular parasite, M. tuberculosis would potentially have access to a variety of nutrients that are abundant within the host cell cytoplasm (Wheeler and Ratledge, 1994). The enclosure of tubercle bacilli within tightly apposed membranous vacuoles (Moreira et al., 1997) might, however, limit access to cytoplasmic constituents. This idea was supported by the recent demonstration that a leuD auxotroph of the attenuated bacille Calmette-Guerin (BCG) strain of tubercle bacillus was incapable of replicating in mice (McAdam et al., 1995) or in cultured macrophages (Bange et al., 1996). Although M. tuberculosis is not a nutritionally fastidious organism, bacillary growth does require a carbon substrate(s) to provide building blocks for biosynthetic reactions and energy for metabolism. In vitro, M. tuberculosis is capable of utilizing a wide range of carbon substrates, including carbohydrates, amino acids, and C2 carbon sources such as acetate and fatty acids (Wayne, 1994). It is not known which of these substrates are available to M. tuberculosis replicating within the confines of the phagosomal compartment.

Extensive biochemical studies have been made of tubercle bacilli isolated directly from the lungs of chronically infected mice (reviewed in Segal 1984). Using manometry, Segal and Bloch (1956) showed that these “in vivo grown” bacilli displayed a vigorous respiratory response to fatty acids but failed to respond to a variety of other substrates. In contrast, respiration of tubercle bacilli grown in vitro was readily stimulated by both glucose and glycerol, which are the preferred substrates for in vitro cultivation of tubercle bacilli. These observations suggested that tubercle bacilli in vivo may be adapted to utilization of fatty acids and may repress pathways for utilization of other carbon sources. Later studies revealed that in vivo grown bacilli retained the ability to oxidize 14 C-glucose to 14 C—CO 2 , but that addition of exogenous glucose suppressed the respiration of endogenous substrates presumably including fatty acids (Artman and Bekierkunst, 1960).

Two specialized pathways are required for utilization of fatty acids as sole carbon source. The b-oxidation pathway catalyzes the breakdown of fatty acids to assimilable acetyl CoA units, which are further oxidized via the Krebs cycle (Clark and Cronan, 1996). The glyoxylate shunt is an anaplerotic pathway for replenishment of essential Krebs cycle intermediates consumed by biosynthetic pathways during growth on C 2 carbon sources such as fatty acids and acetate (Cronan and LaPorte, 1996). This anaplerotic function is subsumed by pyruvate carboxylase when cells are grown on carbohydrates. Wheeler and Ratledge (1988) found that in vivo grown mycobacteria readily oxidized [ 14 C]-palmitate to [ 14 C]—CO2, implying that the enzymes required for b-oxidation of fatty acids were expressed in vivo. (In fact, evolution of [ 14 C]—CO2 from [ 14 C]-palmitate is the basis of the widely used “BACTEC” system for detection of M. tuberculosis in clinical specimens [Heifets and Good, 1994].) In addition, these authors demonstrated expression of both enzymes of the glyoxylate shunt (malate synthase and isocitrate lyase) by in vivo grown mycobacteria. In Escherichia coli , expression of the enzymes of the b-oxidation pathway and of the glyoxylate shunt is under transcriptional control: transcription is repressed during growth on carbohydrates and is induced during growth on fatty acids. Although these enzymes and their regulation have been characterized only partially in mycobacteria, their expression by in vivo grown bacilli suggests that fatty acids may be utilized in vivo. If so, then the b-oxidation pathway and the glyoxylate shunt may be essential for in vivo growth or persistence of tubercle bacilli.

SUMMARY OF THE INVENTION

The present invention provides a purified and isolated nucleic acid encoding mycobacterial isocitrate lyase. The present invention specifically provides for nucleic acid sequences encoding mycobacterial isocitrate lyase that are obtained from M. tuberculosis and M. smegmatis . Also provided by the present invention are mutated nucleic acid sequences encoding mycobacterial isocitrate lyase.

Additionally, the present invention provides vectors which comprises the nucleic acid sequences encoding mycobacterial isocitrate lyase of the present invention, and vectors which comprises the mutated nucleic acid sequences encoding mycobacterial isocitrate lyase of the present invention, as well as host cells containing these vectors.

Further provided by the present invention is an agent that inhibits the activity or expression of a mycobacterial lyase protein, a method of identifying agents that inhibit the activity or expression of a mycobacterial lyase protein, and a method of producing the agents.

Finally, the present invention provides a method of identifying genes required for persistence of mycobacteria.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1A sets forth the nucleotide sequence (SEQ ID NO:1) of the M. tuberculosis isocitrate lyase gene.

FIG. 1B sets forth the amino acid sequence (SEQ ID NO:2) of the M. tuberculosis isocitrate lyase gene.

FIG. 2A sets forth the nucleotide sequence (SEQ ID NO:3) of the M. smegmatis isocitrate lyase gene.

FIG. 2B sets forth the amino acid sequence (SEQ ID NO:4) of the M. smegmatis isocitrate lyase gene.

FIGS. 3A-3H set forth the screening results of Ace mutants of M. smegmatis.

FIG. 4A sets forth a diagram indicating the position of the gene encoding 3 -hydroxybutyryl-CoA dehydrogenase in relation to the isocitrate lyase gene in M. tuberculosis .

FIG. 4B sets forth a diagram indicating the position of the gene encoding 3-hydroxybutyryl-CoA dehydrogenase in relation to the isocitrate lyase gene in M. smegmatis.

FIG. 5 sets forth an amino acid sequence comparison between the M. tuberculosis isocitrate lyase gene (SEQ ID NO:2), the M. smegmatis isocitrate gene (SEQ ID NO:4), and the isocitrate lyase gene from Rhodococcus fasciens (SEQ ID NO:5).

FIG. 6A sets forth a diagram showing the targeted disruption of the isocitrate lyase gene in M. tuberculosis .

FIG. 6B sets forth the results of a Southern blot analysis of mutants generated by the targeted disruption.

FIG. 7A sets forth a graph depicting the growth of an M. tuberculosis isocitrate lyase mutant.

FIG. 7B sets forth a graph depicting the percent survival of an M. tuberculosis isocitrate lyase mutant.

FIG. 8A sets forth a graph depicting the ability of an M. tuberculosis isocitrate lyase mutant to grow and persist in a mouse model.

FIG. 8B indicates that persistence of the M. tuberculosis isocitrate lyase mutant in infected mice was impaired.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides a purified and isolated nucleic acid encoding mycobacterial isocitrate lyase. As used herein, the nucleic acid may be genomic DNA, cDNA, or RNA. Due to the degeneracy of the genetic code, the nucleic acid of the present invention also includes a multitude of nucleic acid substitutions which will encode isocitrate lyase.

The present invention specifically provides for a nucleic acid encoding mycobacterial isocitrate lyase that is isolated from Mycobacteria tuberculosis . Preferably, the nucleic acid sequence encoding M. tuberculosis isocitrate lyase encodes the amino acid sequence contained in FIG. 1 (SEQ ID NO:2). More preferably, the M. tuberculosis isocitrate lyase nucleic acid has the nucleotide sequence contained in FIG. 1 (SEQ ID NO:1). The present invention also provides for nucleic acid encoding mycobacterial isocitrate lyase that is isolated from Mycobacteria smegmatis . Preferably, the nucleic acid sequence encoding M. smegmatis isocitrate lyase encodes the amino acid sequence contained in FIG. 2 (SEQ ID NO:4). More preferably, the M. smegmatis isocitrate lyase nucleic acid has the nucleotide sequence contained in FIG. 2 (SEQ ID NO:3).

Further provided by the present invention is a mutated nucleic acid sequence encoding mycobacterial isocitrate lyase. The mutated nucleic acid sequence encoding mycobacterial isocitrate lyase may be isolated from M. tuberculosis, M. smegmatis, M. avium, M. kansasii, M. zenopi, M. simiae, M. gastri, M. szulgai, M. gordonae, M. chelonea, M. leprae, M. bovis -BCG, M. intracellulare, M. habana, M. lufu, M. phlei, M. fortuitum, M. paratuberculosis and M. scrofulaceum . The mutation may be generated in said nucleic acid using methods known to one of skill in the art. Such methods of mutation include, but are not limited to, signature-tagged mutagenesis, transposon mutagenesis, targeted gene disruption, illegitimate recombination and chemical mutagenesis. In a preferred embodiment of the invention, the mutated nucleic acid encoding isocitrate lyase is M. tuberculosis nucleic acid. In a more preferred embodiment on the invention, the mutation in the M. tuberculosis nucleic acid encoding isocitrate lyase is generated by disruption. Disruption of a nucleic acid encoding isocitrate lyase may be performed, for example, by allelic exchange. It is to be understood that the present invention also provides for nucleic acid sequences wherein any or all of the above described mutations coexist in the nucleic acid encoding mycobacterial isocitrate lyase in any combinations thereof.

The mutated nucleic acid sequence encoding mycobacterial isocitrate lyase provided by the present invention may also be obtained from a library of mutants wherein the mutated mycobacteria are generated using methods of mutation which include, but are not limited to, signature-tagged mutagenesis, transposon mutagenesis, targeted gene disruption, illegitimate recombination and chemical mutagenesis. The disruption of a nucleic acid encoding isocitrate lyase may be performed, for example, by allelic exchange.

The mutant nucleic acid sequences encoding mycobacterial isocitrate lyase of the present invention may be prepared in several ways. For example, they can be prepared by isolating the nucleic acid sequences from a natural source, or by synthesis using recombinant DNA techniques. In addition, mutated nucleic acid sequences encoding mycobacterial isocitrate lyase can be prepared using site mutagenesis techniques.

The present invention also provides a vector which comprises the nucleic acid encoding mycobacterial isocitrate lyase of the present invention, and a vector which comprises the mutated nucleic acid encoding mycobacterial isocitrate lyase of the present invention. Such vectors may be constructed by inserting the nucleic acid encoding mycobacterial isocitrate lyase, or the mutated nucleic acid encoding mycobacterial isocitrate lyase into a suitable vector. The term “inserted” as used herein means the ligation of a foreign DNA fragment and vector DNA by techniques such as the annealing of compatible cohesive ends generated by restriction endonuclease digestion or by use of blunt end ligation techniques. Other methods of ligating DNA molecules will be apparent to one skilled in the art.

Vectors may be derived from a number of different sources. They can be plasmids, viral-derived nucleic acids, lytic bacteriophage derived from phage lambda (λ), cosmids or filamentous single-stranded bacteriophages such as M13. Depending upon the type of host cell into which the vector is introduced, vectors may be bacterial or eukaryotic. Bacterial vectors are derived from many sources including the genomes of plasmids and phage. Eukaryotic vectors are also constructed from a number of different sources, e.g. yeast plasmids and viruses. Some vectors, called shuttle vectors, are capable of replicating in both bacteria and eukaryotes. The nucleic acid from which the vector is derived is usually greatly reduced in size so that only those genes essential for its autonomous replication remain. The reduction in size enables the vectors to accommodate large segments of foreign DNA. Examples of suitable vectors into which the nucleic acid encoding mycobacterial isocitrate lyase or the mutated nucleic acid encoding mycobacterial isocitrate lyase can be inserted include but are not limited to the shuttle vector pYUB412, shuttle vector pMP7, pJM056, pBR322, pUC18, pUC19, pHSV-106, pJS97, pJS98, M13mp18, M13mp19, pSPORT 1, pGem, pSPORT 2, pSV•SPORT 1, pBluescript II, λZapII, λgt10, λgt11, λgt22A, and λZIPLOX. Other suitable vectors are obvious to one skilled in the art.

The vector of the present invention may be introduced into a host cell and may exist in integrated or unintegrated form within the host cell. When in unintegrated form, the vector is capable of autonomous replication. The term “host cell” as used herein means the bacterial or eukaryotic cell into which the vector is introduced. As used herein, “introduced” is a general term indicating that one of a variety of means has been used to allow the vector to enter the intracellular environment of the host cell in such a way that it exists in stable and expressible form therein.

Some bacterial and eukaryotic vectors have been engineered so that they are capable of expressing inserted nucleic acids to high levels within the host cell. Such vectors utilize one of a number of powerful promoters to direct the high level of expression. For example, in vectors for the expression of a gene in a bacterial host cell such as E. coli , the lac operator-promoter or the tac promoter are often used. Eukaryotic vectors use promoter-enhancer sequences of viral genes, especially those of tumor viruses. Expression can be controlled in both bacterial and eukaryotic cells using inducible promoters such as the lac operator-promoter in E. coli or metallothionine or mouse mammary tumor virus promoters in eukaryotic cells. As used herein, “expression” refers to the ability of the vector to transcribe the inserted nucleic acid into mRNA so that synthesis of the protein encoded by the inserted nucleic acid can occur.

Vectors may be introduced into host cells by a number of techniques known to those skilled in the art, e.g. electroporation, DEAE dextran, cationic liposome fusion, protoplast fusion, DNA coated-microprojectile bombardment, and infection with recombinant replication-defective retroviruses. The term “transformation” denotes the introduction of a vector into a bacterial or eukaryotic host cell. As such, it encompasses transformation of bacterial cells and transfection, transduction and related methods in eukaryotic cells.

Any one of a number of suitable bacterial or eukaryotic host cells may be transformed with the vector of the present invention. Examples of suitable host cells are known to one skilled in the art and include but are not limited to mycobacterial cells such as M. tuberculosis, M. smegmatis, M. avium, M. kansasii, M. zenopi, M. simiae, M. gastri, M. szulgai, M. gordonae, M. chelonea, M. leprae, M. bovis -BCG, M. intracellulare, M. habana, M. lufu, M. phlei, M. fortuitum, M. paratuberculosis and M. scrofulaceum , and bacterial cells such as E.coli strains c600, c600hfl, HB101, LE392, Y1090, JM103, JM109, dM101, dM107, Y1088, Y1089, Y1090, Y1090(ZZ), DM1, PH10B, DH11S, DH125, RR1, TB1 and SURE, Bacillus subtilis, Agrobacterium tumefaciens, Bacillus megaterium ; and eukaryotic cells such as Pichia pastoris, Chlamydomonas reinhardtii, Cryptococcus neoformans, Neurospora crassa, Podospora anserina, Saccharomyces cerevisiae, Saccharomyces pombe, Uncinula necator , cultured insect cells, cultured chicken fibroblasts, cultured hamster cells, cultured human cells such as HT1080, MCF7, 143B and cultured mouse cells such as EL4 and NIH3T3 cells.

The present invention also provides a purified and isolated mycobacterial isocitrate lyase protein and analogues thereof, and includes mycobacterial isocitrate lyase protein isolated from nature and mycobacterial isocitrate lyase protein which is recombinantly produced. As used herein “analogues” may be any protein having the same action as isocitrate lyase.

The isocitrate lyase protein provided by the present invention may be isolated from any species of mycobacteria, including, but not limited to, M. tuberculosis, M. smegmatis, M. avium, M. kansasii, M. zenopi, M. simiae, M. gastri, M. szulgai, M. gordonae, M. chelonea, M. leprae, M. bovis -BCG, M. intracellulare, M. habana, M. lufu, M. phlei, M. fortuitum, M. paratuberculosis and M. scrofulaceum . In a preferred embodiment of the invention, the mycobacterial isocitrate lyase is isolated from M. tuberculosis . In another embodiment of the invention, mycobacterial isocitrate lyase is isolated from M. smegmatis.

In a preferred embodiment of the invention, the isocitrate lyase protein is M. tuberculosis isocitrate lyase and has the amino acid sequence containing in FIG. 1 (SEQ ID NO:2). In another embodiment of the invention, the isocitrate lyase protein is M. smegmatis isocitrate lyase and has the amino acid sequence containing in FIG. 2 (SEQ ID NO:4).

The present invention further provides for proteins encoded by mutated nucleic acids encoding mycobacterial isocitrate lyase. The mutation in the nucleic acid encoding the protein of the present invention may be generated in said nucleic acid using methods known to one of skill in the art. Such methods of mutation include, but are not limited to, signature-tagged mutagenesis, transposon mutagenesis, targeted gene disruption, illegitimate recombination and chemical mutagenesis. In a preferred embodiment of the invention, the isocitrate lyase protein is encoded by a mutated M. tuberculosis nucleic acid. In a more preferred embodiment on the invention, the mutation in the M. tuberculosis nucleic acid encoding isocitrate lyase is generated by disruption. Disruption of a nucleic acid encoding isocitrate lyase may be performed, for example, by allelic exchange. It is to be understood that the present invention also provides for nucleic acid sequences wherein any or all of the above described mutations coexist in the nucleic acid encoding mycobacterial isocitrate lyase in any combinations thereof.

The isocitrate protein of the present may also be encoded by a mutated nucleic acid sequence obtained from a library of mutants wherein the mutated mycobacteria are generated using methods of mutation which include, but are not limited to, signature-tagged mutagenesis, transposon mutagenesis, targeted gene disruption, illegitimate recombination and chemical mutagenesis. The disruption of a nucleic acid encoding isocitrate lyase may be performed, for example, by allelic exchange.

The isocitrate proteins and the amino acid sequences of these proteins may be isolated from mycobacteria such as M. tuberculosis, M. smegmatis, M. avium, M. kansasii, M. zenopi, M. simiae, M. gastri, M. szulgai, M. gordonae, M. chelonea, M. leprae, M. bovis -BCG, M. intracellulare, M. habana, M. lufu, M. phlei, M. fortuitum, M. paratuberculosis and M. scrofulaceum . The isocitrate proteins of the present invention and the amino acid sequences of these proteins also be synthesized by methods commonly known to one skilled in the art ( Modern Techniques of Peptide and Amino Acid Analysis , John Wiley & Sons (1981); M. Bodansky, Principles of Peptide Synthesis , Springer Verlag (1984)). Examples of methods that may be employed in the synthesis of the amino acids sequences, and mutants of these sequences include, but are not limited to, solid phase peptide synthesis, solution method peptide synthesis, and synthesis using any of the commercially available peptide synthesizers. The amino acid sequences, and mutants thereof, may contain coupling agents and protecting groups used in the synthesis of the protein sequences, and are well known to one of skill in the art.

The present invention also provides a host cell transformed with a vector encoding mycobacterial isocitrate lyase. The introduction of the recombinant vector containing the DNA sequence into the cell may be effected by methods known to one skilled in the art, such as electroporation, DEAE Dextran, cationic liposome fusion, protoplast fusion, DNA coated microprojectile bombardment, injection with recombinant replication-defective viruses, homologous recombination, and naked DNA transfer. It will be appreciated by those skilled in the art that any of the above methods of DNA transfer may be combined.

The present invention also provides for antibodies immunoreactive with mycobacterial isocitrate lyase and analogues thereof. The antibodies of the present invention include antibodies immunoreactive with non-functional mycobacterial isocitrate lyase, i.e., isocitrate lyase which is inactive or exhibits only reduced activity in vivo. The non-functional isocitrate lyase recognized by the antibodies of the present invention may result from one or more mutations in the nucleic acid encoding mycobacterial isocitrate lyase or from one or more deficiencies in the cell s protein synthesis and maturation pathways which result in a mycobacterial isocitrate lyase with altered secondary or tertiary structure.

The antibodies of the present invention may be monoclonal or polyclonal and are produced by techniques well known to those skilled in the art, e.g., polyclonal antibody can be produced by immunizing a rabbit, mouse, or rat with purified mycobacterial isocitrate lyase and monoclonal antibody may be produced by removing the spleen from the immunized rabbit, mouse or rat and fusing the spleen cells with myeloma cells to form a hybridoma which, when grown in culture, will produce a monoclonal antibody. Labeling of the antibodies of the present invention may be accomplished by standard techniques using one of the variety of different chemiluminescent and radioactive labels known in the art. The antibodies of the present invention may also be incorporated into kits which include an appropriate labeling system, buffers and other necessary reagents for use in a variety of detection and diagnostic applications.

Further provided by the present invention is a mycobacterium that contains a mutation in its isocitrate lyase gene. The mycobacterium may be, for example, M. tuberculosis, M. smegmatis, M. avium, M. kansasii, M. zenopi, M. simiae, M. gastri, M. szulgai, M. gordonae, M. chelonea, M. leprae, M. bovis -BCG, M. intracellulare, M. habana, M. lufu, M. phlei, M. fortuitum, M. paratuberculosis or M. scrofulaceum.

The mutation may be generated in the isocitrate gene of the mycobacterium using methods known to one of skill in the art. Such methods of mutation include, but are not limited to, transposon mutagenesis, targeted gene disruption, illegitimate recombination and chemical mutagenesis. In a preferred embodiment of the invention, the mycobacterium is M. tuberculosis . In a more preferred embodiment of the invention, the mutation in the M. tuberculosis nucleic acid encoding isocitrate lyase is generated by disruption. Disruption of a nucleic acid encoding isocitrate lyase may be performed, for example, by allelic exchange. It is to be understood that the present invention also provides for nucleic acid sequences wherein any or all of the above described mutations coexist in the nucleic acid encoding mycobacterial isocitrate lyase in any combinations thereof.

The mycobacterium having a mutated isocitrate lyase gene provided by the present invention may also be obtained from a library of mutants wherein the mutated mycobacteria are generated using methods of mutation which include, but are not limited to, transposon mutagenesis, targeted gene disruption, illegitimate recombination and chemical mutagenesis. The disruption of a nucleic acid encoding isocitrate lyase may be performed, for example, by allelic exchange.

The present invention also provides an agent that inhibits the activity or expression of a mycobacterial lyase protein. The inventors have shown that the isocitrate lyase gene of M. tuberculosis is required for stationary-phase persistence of M. tuberculosis . Agents that inhibit the activity or expression of the mycobacterial lyase protein would specifically kill stationary phase M. tuberculosis in vivo. By attacking stationary phase ‘persisters’, an isocitrate lyase inhibitor could significantly accelerate the eradication of infection with chemotherapy.

Further provided by the present invention is a method of producing a compound that inhibits isocitrate lyase activity comprising: (a) providing purified isocitrate lyase; (b) determining the molecular structure of said isocitrate lyase; (c) locating the binding sites of said isocitrate lyase; (d) creating a compound with a similar structure to a binding site; (e) determining that said compound inhibits the biochemical activity of isocitrate lyase. The design and synthesis of an isocitrate lyase inhibitor should be relatively simple for two reasons: 1) the enzyme is a small protein of just 428 amino acids; 2) the ICL substrate (isocitrate) is a small molecule of known molecular structure. Isocitrate lyase is a particularly attractive target for rational drug design because this enzyme is not found in human cells; therefore, an isocitrate lyase inhibitor would not be expected to display toxicity for human cells. Because the isocitrate lyase substrate is a small molecule, a specific inhibitor might be obtained by high-throughput screening of a small-molecule library using purified isocitrate lyase enzyme. This approach would be facilitated by the fact that a simple in vitro assay for isocitrate lyase activity already exists. Alternatively, structure-based rational design of an isocitrate lyase inhibitor would ideally proceed by the following steps: 1) The M. tuberculosis enzyme isocitrate lyase would be overproduced in Escherichia coli and purified; 2) The 3-dimensional structure of the purified isocitrate lyase protein bound to its substrate (isocitrate) would be obtained by X-ray crystallography; 3) knowledge of the 3-dimensional co-crystal structure would permit chemical modifications of the substrate to be made in such a way that the modified substrate would act as a ‘pseudo-substrate’. Binding of the ‘pseudo-substrate’ to the isocitrate lyase enzyme would sterically hinder binding of the bona fide substrate (isocitrate) and would therefore inhibit isocitrate lyase function. It might also be possible to design isocitrate lyase inhibitors that would become covalently linked to the isocitrate lyase enzyme, resulting in irreversible inhibition.

Also provided by the present invention is a method of determining whether a drug is effective against Mycobacterium tuberculosis comprising (a) providing isolated isocitrate lyase; (b) providing a candidate drug; (c) mixing isocitrate lyase with substrates the glyoxylate shunt in the presence or absence of the candidate drug; and (d) measuring any inhibition of biosynthesis of malate caused by the presence of the drug.

Further provided by the present invention is a method for treating or preventing tuberculosis in a subject comprising administering an effective amount of an agent that inhibits the activity or expression of mycobacterial isocitrate lyase protein to treat the tuberculosis.

Finally, the present invention provides a method of identifying a gene required for persistence of Mycobacteria tuberculosis in a subject comprising: (a) obtaining a library of M. tuberculosis mutants; (b) screening said library for an inactivated gene; (c) infecting a mammal with M. tuberculosis containing the inactivated gene; (d) determining whether there is persistence of the M. tuberculosis containing the inactivated gene in said mammal, said absence of persistence indicating that the inactive gene is necessary for persistence of M. tuberculosis.

Examples of mycobacterial genes which may be analyzed using this method of identifying genes required for persistence include, but are not limited to, the malate synthase gene, and genes involved in fatty acid catabolism.

The mutation in the mycobacterial gene may be generated using methods known to one of skill in the art. Such methods of mutation include, but are not limited to, signature-tagged mutations, transposon mutagenesis, targeted gene disruption, illegitimate recombination and chemical mutagenesis. In a preferred embodiment of the invention, the mycobacterium is M. Tuberculosis . In a more preferred embodiment of the invention, the mutation in M. Tuberculosis is in the isocitrate lyase gene, and is mutated by disruption. Disruption of an M. Tuberculosis gene may be performed, for example, by allelic exchange.

The mycobacterial library containing the mutations is then screened using a phenotypic analysis.

The present invention is described in the following Experimental Details Section which is set forth to aid in the understanding of the invention, and should not be construed to limit in any way the invention as defined in the claims which follow thereafter.

Experimental Details Section

I. Materials and Methods

Mycobacterial strains and growth conditions. mc 2 155 is an “efficient plasmid transformation” (ept) mutant of Mycobacterium smegmatis (Snapper et al., 1990). Virulent Mycobacterium tuberculosis strain Erdman (Trudeau Institute, saranac Lake, N.Y.) was passaged through mice, grown once in culture, washed twice with phosphate buffered saline containing 0.1% Tween-80 and 10% glycerol, and stored in aliquots at 80° C.

Liquid growth medium was Middlebrook 7H9 broth (4.7 g/L 7H9 broth (DifCo), 0.2% dextrose, 0.5% glycerol, 0.5% bovine serum albumin (BSA) Fraction V (Boehringer Mannheim Biochemicals), 15 mM NaCl, 0.1% Tween-80). Solid growth medium for M. smegmatis was Middlebrook 7H10 agar (19 g/L 7H10 agar (DifCo), 0.2% dextrose, 0.5% glycerol, 0.5% BSA, 15 mM NaCl). Solid growth medium for M. tuberculosis was Middlebrook 7H10 oleic acid agar (19 g/L 7H10 agar (DifCo), 0.5% glycerol, 10% Middlebrook OADC Enrichment (BBL)). For analysis of M. smegmatis growth on alternative carbon sources, solid growth medium was Mycobacterial Basal (MB) medium (1.5% Bacto agar (DifCo), 0.5 mM CaCl 2 , 0.5 mM MgCl 2 , 0.1% KH 2 PO 4 , 0.25% Na 2 HPO 4 , 0.5% NH 4 Cl, 0.2% K 2 SO 4 , 0.08 mg/L ZnCl 2 , 0.4 mg/L FeCl 3 .6H 2 O, 0.02 mg/L CuCl 2 .2H 2 O, 0.02 mg/L MnCl 2 .4H 2 O, 0.02 mg/L Na 2 B 4 O 7 .10H 2 O, 0.02 mg/L (NH 4 )6Mo 7 O24.4H 2 O) supplemented with either 0.5% glucose or 0.5% sodium acetate. For growth of M. tuberculosis , MB medium was supplemented with 0.5% BSA. Inclusion of BSA alone did not support growth of M. tuberculosis in the absence of an added carbon source (data not shown). All mycobacterial media contained 100 μg/mL cycloheximide to prevent fungal contamination. Where noted, 50 μg/mL hygromycin (Boehringer Mannheim Biochemicals) or 30 μg/mL kanamycin (Sigma) was included.

For assessment of survival during anaerobiosis, 3.5 liter DifCo anaerobic jars and anaerobic system envelopes were used as per the manufacturer's instructions. Mycobacteria were pre-adapted to anaerobiosis essentially as described previously (Wayne, 1982). Briefly, mycobacterial cells were inoculated into Middlebrook 7H9 broth at approximately 1×10 8 CFU per mL, aliquoted in 15 mL plastic screwcap tubes (Corning), and incubated at 37° C. upright without agitation for 6 weeks before use.

Ethyl Methane Sulfonate (EMS) mutagenesis. M. smegmatis strain mc 2 155 bacilli were grown to mid-log phase (A600 0.5-1.0) in Middlebrook 7H9 broth and harvested by centrifugation. Cells were washed twice and resuspended in an equal volume of 0.1 M phosphate buffer (pH 7.0) containing 0.1% Tween-80. Ethyl methane sulfonate (EMS) (Sigma) was added to 2.5% and cells were incubated at 37° C. for 75-90 minutes, resulting in ˜25% cell survival. Mutagenesis was terminated by the addition of thiosulfate (Sigma) to 4%. Cells were washed once with 4% thiosulfate containing 0.1% Tween-80, washed twice with Middlebrook 7H9 broth, and resuspended in Middlebrook 7H9 broth. After 3 hours' recovery at 37° C., the mutagenized cell suspension was sonicated and passed through a 5.0 micron pore syringe-filter (Micron Separations, Inc.) to remove clumps. Filtered cells were diluted and plated on Middlebrook 7H10 agar supplemented with 5 g/L Casamino acids (Sigma), 0.1 g/L DL-a,e-diaminopimelic acid (DAP) (Sigma), and 0.02 g/L tryptophan (Sigma) to permit recovery of amino acid auxotrophs. Colonies were patched to fresh plates to form an ordered collection of mutants and screened for the presence of auxotrophs to assess the complexity of the mutant bank. Out of 6000 individual colonies analyzed, 136 amino acid auxotrophs were recovered (frequency 2.3%), representing most of the classes of mutants expected.

Isolation and complementation of Ace − mutants of M. smegmatis . The EMS mutant bank was screened for isolates unable to grow on MB medium containing acetate as sole carbon source (Ace − phenotype). Eleven Ace − mutants were recovered from 3000 picks screened (frequency 0.37%). To identify potential isocitrate lyase (icl) mutants among these, each of the eleven Ace − mutants was transformed with a plasmid expressing the Escherichia coli icl gene from the mycobacterial hsp60 heat shock promoter (pJM007, see “Plasmids”) and screened for growth on MB+acetate medium. Two of the eleven Ace − mutants (ACE1023 and ACE2832) were complemented by E. coli icl (frequency 0.067%).

The mycobacterial icl genes were isolated from cosmid libraries consisting of large (20-40 kbp) fragments of genomic DNA from M. smegmatis or M. tuberculosis inserted into the cosmid vector pYUB412. pYUB412 is an E.coli -Mycobacterium shuttle vector containing the oriE replication origin for maintenance in E. coli , the mycobacteriophage L5 attachment/integration system for site-specific insertion into the mycobacterial genome (Lee et al. 1991), the hygromycin phosphotransferase gene conferring hygromycin resistance in mycobacteria, the b-lactamase gene conferring ampicillin resistance in E. coli , and dual cos sites for packaging in phage l heads. The pYUB412 polylinker is flanked by recognition sites for restriction endonuclease PacI (New England Biolabs), which has few or no recognition sites in mycobacterial genomic DNA; digestion with PacI therefore releases the intact genomic insert. Construction of the mycobacterial genomic libraries (generously provided to us by F.-C. Bange) will be described elsewhere. The libraries were electroporated into the Ace − strain ACE1023 and Ace+ transformants were selected on MB+acetate medium.

Integrated cosmid inserts were recovered from the mycobacterial genomic DNA as follows. pYUB412 cosmid arms were prepared by digestion with XbaI (New England Biolabs) to separate cos sites, dephosphorylation with calf intestinal phosphatase (Boehringer Mannheim Biochemicals) to prevent self-ligation, and digestion with PacI. Genomic DNA was prepared from individual Ace+ transformants as described (Mizuguchi and Tokunaga 1970) and digested with PacI. pYUB412 cosmid arms and PacI-digested genomic DNA were ligated (DNA ligase from Boehringer Mannheim Biochemicals), packaged into phage l heads using GigaPack Gold (Stratagene) packaging mix, and transduced into E. coli strain STBL2 (Stratagene), all according to the manufacturers' instructions. Transductants were selected on LB medium containing 50 μg/mL ampicillin. Plasmid DNA was isolated from individual transductants using standard methods and electroporated into ACE1023. Transformants were selected on Middlebrook 7H10 agar containing 50 μg/mL hygromycin and screened for the ability to grow on MB+dextrose and MB+acetate.

Southern blot analysis. Genomic and plasmid DNAs were digested with restriction endonucleases (New England Biolabs) as indicated in the text and separated on 1.0% agarose-TBE gels. Gels were processed and transferred to Hybond-N+ nylon membranes (Amersham) as per the manufacturer's instructions. The M. tuberculosis icl probe fragment was prepared by polymerase chain reaction (PCR) amplification of a 981 bp SacII fragment subcloned into the vector pKS+ (Stratagene), using T3 and T7 oligonucleotides flanking the polylinker site and Vent polymerase (New England Biolabs). The amplified fragment was labeled using the Enhanced Chemiluminescence kit (Amersham) and the blot was probed and developed according to the manufacturer's instructions.

Analysis of mycobacterial growth and persistence in mice. Male C57BL/6J mice were obtained from Jackson Laboratories (Bar Harbor, Me.). Female 129SvEv mice were obtained from Taconic (Germantown, N.Y.). The B6X129 F1 progeny of the C57BL/6J×129SvEv cross were used for experiments. Frozen stocks of wild-type (icl+) and icl − M. tuberculosis strain Erdman were prepared by growing cells to mid-log phase (A600 0.5-1.0) in Middlebrook 7H9 broth, washing cells twice with phosphate-buffered saline containing 0.1% Tween-80 and 10% glycerol, and storing in aliquots at/−80° C. Aliquots were thawed, diluted as appropriate in phosphate-buffered saline containing 0.1% Tween-80, and sonicated in two 10 sec bursts using a cup-horn sonicator. Mice were infected intravenously by injection into a lateral tail vein of approximately 1×10 6 CFU of tubercle bacilli in a volume of 0.1 mL.

At timepoints indicated in the text, mice (four per group) were sacrificed by cervical dislocation and organs were removed aseptically. Organs were transferred to plastic Stomacher bags (Tekmar, Cincinnati, Ohio) with phosphate buffered saline containing 0.1% Tween-80 and homogenized using a Stomacher homogenizer (Tekmar). Organ homogenates were diluted in phosphate buffered saline containing 0.1% Tween-80 and plated on Middlebrook 7H10 oleic acid agar. Colonies were scored after 3-4 weeks' incubation at 37° C.

II. Results

The Krebs cycle serves dual functions in metabolism: generation of metabolic energy by oxidation of acetyl CoA, and provision of intermediates for several essential biosynthetic pathways. Sustained operation of the Krebs cycle therefore requires an anaplerotic function to replenish intermediates that are siphoned off for biosyntheses. Pyruvate carboxylase satisfies this requirement for cells growing on carbohydrates. This pathway is not operative when cells are grown on C2 carbon sources such as acetate or fatty acids, since carbon from these substrates enters metabolism at the level of acetyl CoA. Instead, a novel anaplerotic pathway, the glyoxylate shunt, is induced during growth on C2 substrates. The glyoxylate shunt consists of two enzymes, isocitrate lyase and malate synthase, which catalyze the formation of one molecule of malate (a Krebs cycle intermediate) from two molecules of acetyl CoA. Synthesis of these enzymes is repressed during growth on carbohydrates. The glyoxylate shunt is present in many eubacterial species and in some simple eukaryotes (including fungi) but is absent in vertebrates.

Metabolic studies of tubercle bacilli purified directly from the lungs of chronically infected mice suggested that fatty acids may serve as an important source of carbon and energy for mycobacteria within the infected host. If so, then the fatty acid b-oxidation pathway and the glyoxylate shunt may be essential for in vivo growth or persistence. The inventors have begun to address this hypothesis using newly-developed molecular genetic techniques for the generation of targeted mutations in mycobacteria, focusing first on the enzymes of the glyoxylate shunt. Here, we describe the isolation of the genes encoding isocitrate lyase in fast- and slow-growing mycobacteria, targeted disruption of the icl locus in virulent M. tuberculosis , and phenotypic analysis of the M. tuberculosis icl mutant.

Isolation of Ace mutants of Mycobacterium smegmatis . In order to identify functions required for utilization of C 2 carbon sources in mycobacteria, a genetic screen was conducted in the fast-growing species Mycobacterium smegmatis . A library of mutant clones was generated by mutagenesis with ethane methyl sulfonate (EMS), as described in Materials and Methods. From a collection of 3000 mutant clones, 11 mutants (frequency 0.37%) were identified that were incapable of growth on acetate as sole carbon source (Ace − phenotype). To identify potential isocitrate lyase (icl) mutants, the 11 Ace mutants were transformed with an E. coli -Mycobacterium shuttle plasmid expressing the E. coli icl gene from the mycobacterial hsp60 promoter. Growth of two of the 11 Ace mutants on acetate (frequency 0.067%) was restored by expression of E. coli icl. One of these mutants (ACE 1023) displayed a tight Ace-phenotype ( FIGS. 3A , 3 E) and a low reversion rate (<10 −7 ; data not shown) and was selected for further analysis.

Complementation of a putative icl mutant of M. smegmatis with genomic libraries of M. smegmatis and M. tuberculosis . The ACE 1023 mutant of M. smegmatis was transformed with genomic cosmid libraries containing inserts of M. smegmatis or M. tuberculosis genomic DNA. These libraries were constructed in the shuttle vector pYUB412, which utilizes the mycobacteriophage L5 attachment/integration system for single-copy insertion into the attB site of the mycobacterial chromosome. Transformants were selected on 7H10+AD medium containing 50 μg/mL hygromycin and screened for complementation of the Ace phenotype. Growth on acetate was restored in approximately 1 of 250 transformants obtained with the M. smegmatis library and in approximately 1 of 200 transformants obtained with the M. tuberculosis library. In order to ensure that growth on acetate resulted from expression of the complementing clone and not from reversion of the mutation, the integrated plasmid inserts were retrieved (see Materials and Methods) and retransformed into the ACE 1023 strain. Twelve independent clones from the M. smegmatis library and 11 independent clones from the M. tuberculosis library were analyzed; all restored growth on acetate when retransformed into ACE 1023. One clone from each library was arbitrarily selected for further anaiysis. These cosmid clones contained inserts of 20-40 kbp. By a combination of subcloning and complementation analysis, smaller complementing fragments were obtained: a 2558 base-pair HpaI-EcoRI genomic fragment from M. smegmatis and a 2674 base-pair BamHI-ClaI genomic fragment from M. tuberculosis ( FIGS. 4B and 4A respectively.

Nucleotide sequence and Southern blot analysis of the M. smegmatis and M. tuberculosis genes encoding isocitrate lyase (ICL). The nucleotide sequences of the putative icl loci from M. smegmatis and M. tuberculosis (see previous section) were determined and potential open reading frames (ORFs) were identified. Each fragment contained an ORF encoding a conceptual protein homologous to the isocitrate lyase proteins of other gram-positive and gram-negative organisms. The conceptual ICL proteins from M. smegmatis and M. tuberculosis are 92% identical to each other and both are ˜84% identical to the ICL protein from Rhodococcus fasciens (FIG. 5 ).

Situated just downstream of the icl genes in both M. smegmatis and M. tuberculosis are ORFs with significant homology to genes encoding 3-hydroxybutyryl-CoA dehydrogenase (BHBD) in other eubacterial species ( FIGS. 4B and 4A respectively). The putative BHBD proteins encoded by M. smegmatis and M. tuberculosis are 83% identical to each other and both are ˜45% identical to the BHBD protein from Clostridium acetobutylicum . In the latter species, BHBD catalyzes the conversion of acetoacetyl-CoA to 3-hydroxybutyryl-CoA in the butyrate/butanol fermentation pathway for generation of ATP and regeneration of oxidized NAD+ during anaerobic growth. Mycobacteria, however, are obligate aerobes and are not capable of growing anaerobically by fermentation. The possible significance of a BHBD homolog in mycobacteria will be discussed later.

The identity of the cloned icl genes was confirmed by Southern blot analysis of M. smegmatis and M. tuberculosis genomic DNAs using fragments derived from the cloned icl genes as probes.

Targeted disruption of the isocitrate lyase gene in virulent M. tuberculosis . The icl gene was disrupted in the virulent Erdman strain of M. tuberculosis using an efficient method for allelic exchange. This method employs the counter-selectable marker sacB, which is lethal in the presence of sucrose. Successful application of sacB for efficient allelic exchange in M. tuberculosis was described recently by Pelicic et al. (1997). A 685 base-pair XhoI fragment internal to the M. tuberculosis icl gene was replaced with the hygromycin phosphotransferase (hpt) gene from Streptomyces hygroscopicus (FIG. 6 A). The recombinant icl::hpt allele was incapable of rescuing growth of the ACE 1023 mutant on acetate, confirming that the disrupted gene was not functional (data not shown). The icl::hpt cassette was inserted into the shuttle vector pMP7, which contains the oriE and oriM replication origins for plasmid maintenance in E. coli and mycobacteria (respectively), the aph gene conferring kanamycin resistance, and the counter-selectable sacB marker from Bacillus subtilis . The resulting plasmid (pJM056) was electroporated into M. tuberculosis strain Erdman MC 2 3030 and transformants were selected on solid medium containing 50 μg/mL hygromycin. MC 2 3030, containing the icl::hpt recombinant allelle has been deposited under the terms of the Budapest Treaty on Apr. 3, 1998 with the American Type Culture Collection (ATCC), located at 10801 University Boulevard, Manassas, Va. 20110-2209, and assigned ATCC Accession No. 202104. In the absence of antibiotic selection, the plasmid was rapidiy lost in broth cultures (data not shown). Therefore, transformants grown in the presence of hygromycin were expected to lose the plasmid following allelic exchange between the chromsomal icl gene and the icl::hpt allele on the plasmid.

Five individual colonies obtained from independent transformations with pJM056 were picked, inoculated separately into liquid medium containing 50 μg/mL hygromycin, and grown to saturation to allow time for recombination to occur between the plasmid and the bacterial chromosome. The saturated broth cultures were diluted and plated on solid medium containing 50 μg/mL hygromycin +/−5% sucrose. Expression of sacB in M. tuberculosis was lethal on solid medium containing 5% sucrose, permitting selection against cells that retained the pMP7 vector. The relative plating efficiencies of the individual broth cultures on medium plus/minus sucrose were variable (10 0 to 10 −3 ), suggesting that loss of sacB function occurred at different times in the growth of the cultures. Twenty-five hgmr sucr colonies derived from each liquid culture were screened for the ability to grow on kanamycin. Two of five cultures yielded colonies that were uniformly (25/25) resistant to kanamycin; these presumably carried mutations in sacB and were discarded. The three remaining cultures yielded hgmr sucr colonies that were sensitive (25/25) to kanamycin. From each of these cultures, individual hgmr sucr kans colonies were expanded and analyzed by Southern blot (FIG. 6 B). Of the 10 colonies analyzed, three colonies obtained from two independent cultures contained only the disrupted icl::hpt allele, establishing that allelic exchange had occurred (FIG. 6 B).

Phenotypic analysis of the M. tuberculosis isocitrate lyase mutant. As expected, disruption of icl abrogated growth on solid medium containing acetate as sole carbon source (data not shown). In contrast, growth of the M. tuberculosis icl mutant was normal when glucose and glycerol were provided as carbon sources ( FIG. 7A ). Suryanarayana et al. (1973) demonstrated that ICL levels increased during entry of M. tuberculosis into stationary phase, suggesting that the glyoxylate shunt might play a role in stasis survival. They postulated that endogenous fatty acids might serve as an alternative carbon source for maintenance metabolism following depletion of exogenous carbon sources. However, we found that the ability of the icl mutant to survive long-term stasis was unimpaired (FIG. 7 A).

Wayne and Lin (1982) found that ICL levels increased during adaptation of tubercle bacilli to anaerobiosis. They proposed the existence of a novel pathway invoMng ICL and another enzyme, glycine dehydrogenase, for the regeneration of NAD+ from NADH at oxygen tensions too low to support respiration. However, the demonstration that survival of oxygen starvation was not impaired by disruption of icl ( FIG. 7B ) suggests that this pathway, if it exists, is not essential for adaptation to anaerobiosis.

The aim of the studies described herein was to determine whether the glyoxylate shunt is important for in vivo nutrition of tubercle bacilli. The ability of the M. tuberculosis icl mutant to grow and persist in the mouse model of tuberculosis was therefore assessed. Mice were infected by the intravenous route with approximately 2×10 6 colony-forming units (CFU) of either wild-type (icl+) M. tuberculosis or the icl-mutant. Bacterial loads in the lungs were determined at 1 day and at 1, 2, 4, 8, 12, and 16 weeks post-infection (FIG. 8 A). In the early phase of infection (up to 2 weeks), prior to the emergence of adaptive immunity (Orme, 1994), in vivo growth of the icl- and wild-type (icl+) bacilli was similar. Following the emergence of bacteriostatic immunity after 2 weeks, growth of wild-type M. tuberculosis ceased and a constant bacterial load was maintained thereafter. In contrast, from 2 weeks onwards, the titer of the icl mutant in the lungs fell steadily, resulting in a 40-fold reduction in the bacterial burden by 16 weeks post-infection. These results demonstrate that isocitrate lyase is not required for early growth of M. tuberculosis prior to the emergence of bacteriostatic immunity, but is important for chronic persistence once growth ceases. The “persistence defect” of the icl mutant resulted in a striking attenuation of disease progression (FIG. 8 B).

III. Discussion

It is a truism that M. tuberculosis must acquire nutrients from the infected host in order to replicate and cause disease. Little is known, however, of the mechanisms that are involved in nutrient acquisition in vivo. A number of potential sources of carbon and energy are abundant in mammalian cells, but it is not known which of these substrates are available to mycobacteria growing within the confines of tightly-apposed vacuolar membranes. Tuberele bacilli may modify the vacuolar membrane in order to gain access to the rich variety of substrates that are abundant in the cytoplasm of the host cell. However, the inability of a leucine auixotroph of M. bovis BCG to replicate within macrophages suggests that access to cytoplasmic constituents may be limited. One substrate that would be readily accessible to mycobacteria growing within the parasitophorous vacuole is the fatty acids of the vacuolar membrane itself. In mammalian cells, fatty acids are potentially one of the most abundant carbon substrates available (Wheeler and Ratledge, 1994). M. tuberculosis produces a number of lipases and phospholipases capable of liberating free fatty acids from membrane-associated and storage forms such as phospholipids and triglycerides. Continuous fusion of the mycobacterium-containing vacuole with host-derived vesicles could serve to replenish membrane consumed by the parasite. M. tuberculosis also encodes the molecular machinery required for utilization of fatty acids as sole carbon source: the b-oxidation pathway for breakdown of fatty acids to assimilable acetyl-CoA units, and the glyoxylate shunt required for replenishment of Krebs cycle intermediates depleted by biosynthetic pathways. The enzymes of both pathways are expressed by pathogenic mycobacteria growing in vivo. Metabolic studies of in vivo grown mycobacteria also suggested that fatty acids may serve as a major source of carbon and energy during growth within the infected host.

5 1 1287 DNA Mycobacterium smegmatis gene (1)..(1285) 1atgtctgtcg tcggcacccc gaagagcgcg gagcagatcc agcaggaatg ggacacgaac 60ccgcgctgga aggacgtcac ccgcacctac tccgccgagg acgtcgtcgc cctccagggc 120agcgtggtcg aggagcacac gctggcccgc cgcggtgcgg aggtgctgtg ggagcagctg 180cacgacctcg agtgggtcaa cgcgctgggc gcgctgaccg gcaacatggc cgtccagcag 240gtgcgcgccg gcctgaaggc catctacctg tcgggctggc aggtcgccgg cgatgccaac 300ctgtccgggc acacctaccc cgaccagagc ctgtatcccg ccaactcggt gccgcaggtg 360gtccgccgga tcaacaacgc actgcagcgc gccgaccaga tcgccaagat cgagggcgat 420acttcggtgg agaactggct ggcgccgatt gtcgccgacg gcgaggccgg ctttggcggc 480gcgctcaacg tctacgagct gcagaaagcc ctgatcgccg cgggcgttgc gggttcgcac 540tgggaggacc agttggcctc tgagaagaag tgcggccacc tgggcggcaa ggtgttgatc 600ccgacccagc agcacatccg cactttgacg tctgctcggc tcgcggccga tgtggctgat 660gttcccacgg tggtgatcgc ccgtaccgac gccgaggcgg ccacgctgat cacctccgac 720gtcgacgagc gcgaccagcc gttcatcacc ggcgagcgca cccgggaagg cttctaccgc 780accaagaacg gcatcgagcc ttgcatcgct cgggcgaagg cctacgcccc gttcgccgac 840ttgatctgga tggagaccgg taccccggac ctcgaggccg cccggcagtt ctccgaggcg 900gtcaaggcgg agtacccgga ccagatgctg gcctacaact gctcgccatc gttcaactgg 960aaaaagcacc tcgacgacgc caccatcgcc aagttccaga aggagctggc agccatgggc 1020ttcaagttcc agttcatcac gctggccggc ttccatgcgc tgaactactc gatgttcgat 1080ctggcctacg gctacgccca gaaccagatg agcgcgtatg tcgaactgca ggaacgcgag 1140ttcgccgccg aagaacgggg ctacaccgcg accaagcacc agcgcgaggt cggcgccggc 1200tacttcgacc ggattgccac caccgtggac ccgaattcgt cgaccaccgc gttgaccggt 1260tccaccgaag agggccagtt ccactag 1287 2 428 PRT Mycobacterium tuberculosis 2Met Ser Val Val Gly Thr Pro Lys Ser Ala Glu Gln Ile Gln Gln Glu 1 5 10 15Trp Asp Thr Asn Pro Arg Trp Lys Asp Val Thr Arg Thr Tyr Ser Ala 20 25 30Glu Asp Val Val Ala Leu Gln Gly Ser Val Val Glu Glu His Thr Leu 35 40 45Ala Arg Arg Gly Ala Glu Val Leu Trp Glu Gln Leu His Asp Leu Glu 50 55 60Trp Val Asn Ala Leu Gly Ala Leu Thr Gly Asn Met Ala Val Gln Gln 65 70 75 80Val Arg Ala Gly Leu Lys Ala Ile Tyr Leu Ser Gly Trp Gln Val Ala 85 90 95Gly Asp Ala Asn Leu Ser Gly His Thr Tyr Pro Asp Gln Ser Leu Tyr 100 105 110Pro Ala Asn Ser Val Pro Gln Val Val Arg Arg Ile Asn Asn Ala Leu 115 120 125Gln Arg Ala Asp Gln Ile Ala Lys Ile Glu Gly Asp Thr Ser Val Glu 130 135 140Asn Trp Leu Ala Pro Ile Val Ala Asp Gly Glu Ala Gly Phe Gly Gly145 150 155 160Ala Leu Asn Val Tyr Glu Leu Gln Lys Ala Leu Ile Ala Ala Gly Val 165 170 175Ala Gly Ser His Trp Glu Asp Gln Leu Ala Ser Glu Lys Lys Cys Gly 180 185 190His Leu Gly Gly Lys Val Leu Ile Pro Thr Gln Gln His Ile Arg Thr 195 200 205Leu Thr Ser Ala Arg Leu Ala Ala Asp Val Ala Asp Val Pro Thr Val 210 215 220Val Ile Ala Arg Thr Asp Ala Glu Ala Ala Thr Leu Ile Thr Ser Asp225 230 235 240Val Asp Glu Arg Asp Gln Pro Phe Ile Thr Gly Glu Arg Thr Arg Glu 245 250 255Gly Phe Tyr Arg Thr Lys Asn Gly Ile Glu Pro Cys Ile Ala Arg Ala 260 265 270Lys Ala Tyr Ala Pro Phe Ala Asp Leu Ile Trp Met Glu Thr Gly Thr 275 280 285Pro Asp Leu Glu Ala Ala Arg Gln Phe Ser Glu Ala Val Lys Ala Glu 290 295 300Tyr Pro Asp Gln Met Leu Ala Tyr Asn Cys Ser Pro Ser Phe Asn Trp305 310 315 320Lys Lys His Leu Asp Asp Ala Thr Ile Ala Lys Phe Gln Lys Glu Leu 325 330 335Ala Ala Met Gly Phe Lys Phe Gln Phe Ile Thr Leu Ala Gly Phe His 340 345 350Ala Leu Asn Tyr Ser Met Phe Asp Leu Ala Tyr Gly Tyr Ala Gln Asn 355 360 365Gln Met Ser Ala Tyr Val Glu Leu Gln Glu Arg Glu Phe Ala Ala Glu 370 375 380Glu Arg Gly Tyr Thr Ala Thr Lys His Gln Arg Glu Val Gly Ala Gly385 390 395 400Tyr Phe Asp Arg Ile Ala Thr Thr Val Asp Pro Asn Ser Ser Thr Thr 405 410 415Ala Leu Thr Gly Ser Thr Glu Glu Gly Gln Phe His 420 425 3 1287 DNA Mycobacterium smegmatis gene (1)..(1287) 3atgtcgaccg ttggcacccc gaagtccccc gagcagatcc agcacgactg ggatcacaac 60ccccgctgga agggcatcaa gcgcgactac acccccgagg acgtcgtggc cctgcagggc 120accgtcgtcg aggagcacac cctggcccgc cgcggcgccg aggtgctgtg ggagcagctg 180cacgacatgg acttcgtcaa cgcgctcggc gcgctgaccg gcaacatggc cgtccagcag 240gttcgcgcgg gcctcaaggc catctacctg tccggctggc aggtcgccgg tgacgccaac 300ctgtccggtc acacctaccc cgaccagagc ctgtacccgg ccaactcggt gccgcaggtg 360gtccgccgca tcaacaacgc gctgctgcgc gccgacgaga tcgccaaggt cgagggcgac 420acctcggtgg agaactggct ggctccgatc gtcgccgacg gcgaggccgg cttcggtggt 480gccctcaacg tctacgagct gcagaaggcg atgatcgccg cgggtgtcgc gggctcgcac 540tgggaagatc agctggcctc ggagaagaag tgcggccacc tcggtggcaa ggtgctgatc 600ccgacccagc agcacatccg caccctgacc tcggcgcgcc tggcggccga cgtggccgac 660gtgcccaccg tcgtcatcgc ccgcaccgac gccgaggccg ccacgctgat cacgtccgac 720gtcgacgagc gcgaccagcc gttcatcacc ggtgagcgca ccaaggaagg cttcttccgc 780gtgaagaacg gcctggagcc ctgcatcgcg cgcgccaagg cctacgcgcc gtactccgac 840ctgatctgga tggagaccgg cacgccggat ctcgagctcg ccaagaagtt cgccgagggc 900gtcaaggcgg agttccccga ccagatgctg gcctacaact gctcgccgtc gttcaactgg 960aagaagcacc tcgacgacgc caccatcgcg aagttccaga aggaactggg cgccatgggc 1020ttcaagttcc agttcatcac gctggccggc ttccacgcgc tcaactactc gatgttcgat 1080ctggcctacg gctacgcccg caaccagatg agcgcgtacg tcgaactgca ggagcgcgag 1140ttcgctgccg aggagcgcgg ctacaccgcc accaagcacc agcgcgaggt gggtgccggc 1200tacttcgacc gcatcgccac cacggtcgac cccaacagct cgaccaccgc gctcgcgggc 1260tcgaccgaag agggtcagtt ccactga 1287 4 428 PRT Mycobacterium smegmatis 4Met Ser Thr Val Gly Thr Pro Lys Ser Pro Glu Gln Ile Gln His Asp 1 5 10 15Trp Asp His Asn Pro Arg Trp Lys Gly Ile Lys Arg Asp Tyr Thr Pro 20 25 30Glu Asp Val Val Ala Leu Gln Gly Thr Val Val Glu Glu His Thr Leu 35 40 45Ala Arg Arg Gly Ala Glu Val Leu Trp Glu Gln Leu His Asp Met Asp 50 55 60Phe Val Asn Ala Leu Gly Ala Leu Thr Gly Asn Met Ala Val Gln Gln 65 70 75 80Val Arg Ala Gly Leu Lys Ala Ile Tyr Leu Ser Gly Trp Gln Val Ala 85 90 95Gly Asp Ala Asn Leu Ser Gly His Thr Tyr Pro Asp Gln Ser Leu Tyr 100 105 110Pro Ala Asn Ser Val Pro Gln Val Val Arg Arg Ile Asn Asn Ala Leu 115 120 125Leu Arg Ala Asp Glu Ile Ala Lys Val Glu Gly Asp Thr Ser Val Glu 130 135 140Asn Trp Leu Ala Pro Ile Val Ala Asp Gly Glu Ala Gly Phe Gly Gly145 150 155 160Ala Leu Asn Val Tyr Glu Leu Gln Lys Ala Met Ile Ala Ala Gly Val 165 170 175Ala Gly Ser His Trp Glu Asp Gln Leu Ala Ser Glu Lys Lys Cys Gly 180 185 190His Leu Gly Gly Lys Val Leu Ile Pro Thr Gln Gln His Ile Arg Thr 195 200 205Leu Thr Ser Ala Arg Leu Ala Ala Asp Val Ala Asp Val Pro Thr Val 210 215 220Val Ile Ala Arg Thr Asp Ala Glu Ala Ala Thr Leu Ile Thr Ser Asp225 230 235 240Val Asp Glu Arg Asp Gln Pro Phe Ile Thr Gly Glu Arg Thr Lys Glu 245 250 255Gly Phe Phe Arg Val Lys Asn Gly Leu Glu Pro Cys Ile Ala Arg Ala 260 265 270Lys Ala Tyr Ala Pro Tyr Ser Asp Leu Ile Trp Met Glu Thr Gly Thr 275 280 285Pro Asp Leu Glu Leu Ala Lys Lys Phe Ala Glu Gly Val Lys Ala Glu 290 295 300Phe Pro Asp Gln Met Leu Ala Tyr Asn Cys Ser Pro Ser Phe Asn Trp305 310 315 320Lys Lys His Leu Asp Asp Ala Thr Ile Ala Lys Phe Gln Lys Glu Leu 325 330 335Gly Ala Met Gly Phe Lys Phe Gln Phe Ile Thr Leu Ala Gly Phe His 340 345 350Ala Leu Asn Tyr Ser Met Phe Asp Leu Ala Tyr Gly Tyr Ala Arg Asn 355 360 365Gln Met Ser Ala Tyr Val Glu Leu Gln Glu Arg Glu Phe Ala Ala Glu 370 375 380Glu Arg Gly Tyr Thr Ala Thr Lys His Gln Arg Glu Val Gly Ala Gly385 390 395 400Tyr Phe Asp Arg Ile Ala Thr Thr Val Asp Pro Asn Ser Ser Thr Thr 405 410 415Ala Leu Ala Gly Ser Thr Glu Glu Gly Gln Phe His 420 425 5 428 PRT Rhodococcus fascians 5Met Ser Thr Thr Gly Thr Pro Lys Thr Thr Ala Glu Ile Gln Gln Asp 1 5 10 15Trp Asp Thr Asn Pro Arg Trp Lys Gly Val Thr Arg Asn Phe Thr Ala 20 25 30Gln Gln Val Ser Asp Leu Gln Gly Thr Val Val Glu Glu Ala Thr Leu 35 40 45Ala Arg Arg Gly Ser Glu Ile Leu Trp Asp Leu Val Asn Asn Glu Asp 50 55 60Tyr Ile Asn Ser Leu Gly Ala Leu Thr Gly Asn Gln Ala Val Gln Gln 65 70 75 80Ile Arg Ala Gly Leu Gln Ala Ile Tyr Leu Ser Gly Trp Gln Val Ala 85 90 95Gly Asp Ala Asn Leu Ser Gly His Thr Tyr Pro Asp Gln Ser Leu Tyr 100 105 110Pro Ala Asn Ser Val Pro Ser Val Val Arg Arg Ile Asn Asn Ala Leu 115 120 125Leu Arg Ala Asp Glu Ile Ala Lys Ile Glu Gly Asp Thr Ser Val Lys 130 135 140Asn Trp Val Ala Pro Ile Val Ala Asp Ala Glu Ala Gly Phe Gly Gly145 150 155 160Ala Leu Asn Ala Tyr Glu Leu Gln Lys Ala Met Ile Val Ala Gly Ala 165 170 175Ala Gly Val His Trp Glu Asp Gln Leu Ala Ser Glu Lys Lys Cys Gly 180 185 190His Leu Gly Gly Lys Val Leu Ile Pro Thr Gln Gln His Ile Arg Thr 195 200 205Leu Thr Ser Ala Arg Leu Ala Ser Asp Val Ala Asp Val Pro Ser Val 210 215 220Ile Ile Ala Arg Thr Asp Ala Glu Ala Ala Thr Leu Ile Thr Ser Asp225 230 235 240Val Asp Glu Arg Asp Arg Glu Phe Leu Asp Gly Thr Arg Thr Ala Glu 245 250 255Gly Phe Phe Gly Val Lys Asn Gly Ile Glu Pro Cys Ile Ala Arg Ala 260 265 270Lys Ala Tyr Ala Pro Tyr Ala Asp Leu Ile Trp Met Glu Thr Gly Val 275 280 285Pro Asp Leu Glu Val Ala Lys Lys Phe Ser Glu Ser Val Arg Ser Glu 290 295 300Phe Pro Asp Gln Leu Leu Ala Tyr Asn Trp Ser Pro Ser Phe Asn Trp305 310 315 320Lys Ala His Leu Asp Asp Ala Thr Ile Ala Lys Phe Gln Lys Glu Leu 325 330 335Gly Ala Met Gly Phe Lys Phe Gln Phe Ile Thr Leu Ala Gly Phe His 340 345 350Ser Leu Asn Tyr Gly Met Phe Asp Leu Ala Tyr Gly Tyr Ala Gln Asn 355 360 365Gln Met Ser Ala Tyr Val Glu Leu Gln Glu Arg Glu Phe Ala Ala Glu 370 375 380Glu Arg Gly Tyr Thr Ala Thr Lys His Gln Arg Glu Val Gly Ala Gly385 390 395 400Tyr Phe Asp Arg Ile Ala Thr Thr Val Asp Pro Asn Ser Ser Thr Thr 405 410 415Ala Leu Thr Gly Ser Thr Glu Glu Gly Gln Phe His 420 425

References

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Claims

1. A Mycobacterium tuberculosis that contains a mutation in its isocitrate lyase gene, wherein the unmutated gene encodes an isocitrate lyase having the amino acid sequence set forth in SEQ ID NO:2 and wherein the mutation is generated using a chemical or recombinant method.

2. The Mycobacterium tuberculosis of claim 1, wherein the unmutated gene comprises the nucleotide sequence set forth in SEQ ID NO:1.

3. The Mycobacterium tuberculosis of claim 1, wherein the Mycobacterium tuberculosis is a recombinant Mycobacterium tuberculosis.

4. The Mycobacterium tuberculosis of claim 1, wherein the mutation is generated using a chemical method.

5. The Mycobacterium tuberculosis of claim 1, wherein the mutation is an allelic exchange, ethyl methane sulfonate, disruption, deletion, insertion, point, substitution, nonsense, missense, polymorphism or rearrangement mutation.

6. The Mycobacterium tuberculosis of claim 5, wherein the mutation is a disruption mutation.

7. The Mycobacterium tuberculosis of claim 6, wherein the mutation is an allelic exchange mutation.

8. A Mycobacterium smegmatis that contains a mutation in its isocitrate lyase gene, wherein the unmutated gene encodes an isocitrate lyase having the amino acid sequence set forth in SEQ ID NO:4 and wherein the mutation is generated using a chemical or recombinant method.

9. The Mycobacterium smegmatis of claim 8, wherein the unmutated gene comprises the nucleotide sequence set forth in SEQ ID NO:3.

10. The Mycobacterium smegmatis of claim 8, wherein the Mycobacterium smegmatis is a recombinant Mycobacterium smegmatis.

11. The Mycobacterium smegmatis of claim 8, wherein the mutation is generated using a chemical method.

12. The Mycobacterium smegmatis of claim 8, wherein the mutation is an allelic exchange, ethyl methane sulfonate, disruption, deletion, insertion, point, substitution, nonsense missense, polymorphism or rearrangement mutation.

13. The Mycobacterium smegmatis of claim 12, wherein the mutation is an ethyl methane sulfonate mutation.