Methods of identifying compounds that inhibit DNA synthesis in mycobacterium tuberculosis and compositions, reagents and kits for performing the same

FIELD OF THE INVENTION
The invention relates to methods of identifying specific inhibitors of Mycobacterium tuberculosis DNA synthesis enzymes including complementation assays and in vitro activity assays. The invention relates to the identification and cloning of genes encoding the small subunit (R2) of the M. tuberculosis ribonucleotide reductase (RR) gene and the gene encoding topoisomerase I gene, to the isolated proteins encoded by the genes and to methods of using the genes and the proteins.
BACKGROUND OF THE INVENTION
Tuberculosis (TB) in all of its manifestations is the leading cause of death from a single infectious agent. Studies from two urban centers indicate that 30-40% of new cases are the result of recent infection rather than reactivation of old disease, and cases acquired by recent transmission accounted from almost 2/3 of drug resistant TB.
Highly resistant strains of M. tuberculosis have been isolated from patients in the Philadelphia area at a rate that requires physicians to treat every new case of presumed TB with at least four drugs, i.e., to consider every new case as if it were caused by one of these resistant strains. Clearly, new approaches to the development of antituberculous therapy are necessary. However, the difficulties of working with Mycobacterium tuberculosis has kept the field from developing apace with the advances in molecular biology and biotechnology. In particular, the analysis of the regulation of DNA replication, traditionally a rich area for the discovery of new antimicrobial agents and one that would provide major new insights into the growth of Mycobacteria, has been slow to develop.
The biochemistry of DNA replication of Mycobacteria is not fully understood. The mean generation time for M. tuberculosis is 24 hours compared to 3 hours of M. smegmatis and 1.3 hours for E. coli. Genomic DNA is replicated in approximately 10 hours in M. tuberculosis whereas the comparable times for M. smegmatis and E. coli are 1.8 and 1 hours respectively. The de novo and scavenging pathways for purines and pyrimidines in Mycobacteria avium, microti and leprae have been described. However the molecular characterization of the enzymes in these pathways has not yet been accomplished.
There is a need for compounds which selectively inhibit M. tuberculosis enzymes involved in DNA synthesis. There is a need for reagents, compositions, kits and methods of identifying such compounds.
SUMMARY OF THE INVENTION
The present invention provides complementation assays which are useful to identify agents that inhibit the activity of M. tuberculosis DNA synthesis enzymes. According to the invention, host cells are provided which do not have a functioning endogenous DNA synthesis enzyme but which are provided with a functioning homologous M. tuberculosis DNA synthesis enzyme. Test compounds are evaluated for their ability to inhibit the M. tuberculosis DNA synthesis enzyme in the complemented host cell.
The effect of test compounds on the host cells that contain a non-functioning endogenous DNA synthesis enzyme and the homologous M. tuberculosis DNA synthesis enzyme is compared to the effect of test compounds on host cells that contain a functioning endogenous DNA synthesis enzyme or a homologous non-M. tuberculosis DNA synthesis enzyme.
As used herein, the term "first host cells" is meant to refer to the host cells that contain a non-functioning endogenous DNA synthesis enzyme and the homologous M. tuberculosis DNA synthesis enzyme.
As used herein, the term "second host cells" is meant to refer to host cells that contain a functioning endogenous DNA synthesis enzyme or a homologous non-M. tuberculosis DNA synthesis enzyme.
The first host cells and the second host cells are the same species. In some preferred embodiments, the first host cells and the second host cells are E. coli, Bacillus sp., Salmonella sp. and S. cerevisiae. In some preferred embodiments, the first host cells and the second host cells are E. coli.
The first host cells contain a non-functioning endogenous DNA synthesis enzyme. The first host cells may be temperature sensitive mutants in which the endogenous DNA synthesis enzyme functions within a temperature range but is non-functioning outside of the range, usually non-functioning at an elevated temperature. The first host cells may be designed so that the express the functional endogenous DNA synthesis enzyme under specific conditions which can be changed to prevent expression of the functioning endogenous enzyme. For example, the gene that encodes the endogenous enzyme may be placed under the control of a regulatable promoter. In preferred embodiments, the host cell is a mutant E. coli in which the endogenous DNA synthesis enzyme functions within a temperature range but is non-functioning at an elevated temperature.
M. tuberculosis DNA synthesis enzymes are those which participate in the reactions which occur in the synthesis of DNA. Examples of such M. tuberculosis DNA synthesis enzyme include: ribonucleotide reductase (RR), topoisomerase enzymes including topoisomerase I, dihydrofolate reductase, thymidylate synthase, DNA polymerase and RNA polymerase as well as any of the other several enzymes involved in the pathways which lead to DNA synthesis. In some preferred embodiments, the present invention provides complementation assays which are useful to identify agents that inhibit the activity of M. tuberculosis DNA synthesis enzyme ribonucleotide reductase or topoisomerase I.
The second host cells contain either a functioning endogenous DNA synthesis enzyme or a homologous non-M. tuberculosis DNA synthesis enzyme.
Separate cultures of the first host cells and the second host cells are contacted with test compounds to determine whether they effect the M. tuberculosis DNA synthesis enzyme. In some embodiments of the invention, the preferred concentration of test compound is between 1 nM and 1 mM. A preferred concentration is 10 nM to 0.5 mM. A preferred concentration is 0.1 .mu.M to 250 .mu.M. A preferred concentration is 1 .mu.M to 100 .mu.M. A preferred concentration is 10 .mu.M to 100 .mu.M. In some preferred embodiments, it is desirable to use a series of dilutions of test compounds.
After contacting the cultures of host cells with the test compound, the level of DNA synthesis in the culture of first host cells and the level of DNA synthesis in culture of second host cells is measured. The level of DNA synthesis in a culture of host cells can be measured by a number of well known and routine methods. For example, the cells may be cultured with radiolabelled nucleotides. If DNA synthesis is occurring, the radiolabelled nucleotides will be used incorporated into the synthesized DNA. The unincorporated radiolabelled nucleotides can be removed with the culture medium and the level of incorporated radiolabelled nucleotides in DNA can be measured routinely such as by using a scintillation counter. Another example of measuring DNA synthesis is to measure the amount of host cells in the culture. DNA synthesis is essential to cell replication. The number of cells present in a culture is indicative of the level of cell replication. If DNA synthesis is inhibited, cell replication is inhibited and therefore the number of cells present will be reduced as compared to the number of cells present if DNA synthesis is not inhibited. Preferred methods include those which assess DNA synthesis as a function of cell growth. Complemented and control cultures of E. coli are cultured in 96 well plates. After incubation time in the presence of test compound, cell growth is determined using a spectrophotometer. The cell density of complemented and control cultures of E. coli are compared. As an additional control, complemented and control cultures of E. coli are grown in the absence of test compound and cell growth is measured. In some embodiments, "diffusion disk" assays are performed using disks that contain test compounds. The disks are placed on lawns of complemented and control cultures of E. coli and any differences in cell growth of cells surrounding the disks is observed.
The methods of the invention are useful to identify selective inhibitors of M. tuberculosis DNA synthesis enzymes. Inhibitors are useful as anti-M. tuberculosis agents. Kits are provided for screening compounds for identifying selective inhibitors of M. tuberculosis DNA synthesis enzymes.
The present invention relates to substantially pure M. tuberculosis R2 proteins R2-1 and R2-2.
The present invention relates to substantially pure M. tuberculosis R2 protein R2-2 having the amino acid sequence of SEQ ID NO:2 and to substantially pure M. tuberculosis R2 protein R2-1 having the amino acid sequence of SEQ ID NO:6.
The present invention relates to nucleic acid molecules that encode M. tuberculosis R2 proteins R2-1 and R2-2.
The present invention relates to nucleic acid molecules encoding M. tuberculosis R2 protein R2-2 that consists of SEQ ID NO:1 and to nucleic acid molecules encoding M. tuberculosis R2 protein R2-1 that consists of SEQ ID NO:5.
The present invention relates to recombinant expression vectors that comprise a nucleic acid sequence that encodes an M. tuberculosis R2 protein.
The present invention relates to host cells that comprise recombinant expression vectors that encode an M. tuberculosis R2 protein.
The present invention relates to methods of making recombinant M. tuberculosis R2 protein comprising the steps of culturing host cells in medium that comprise recombinant expression vectors that encode an M. tuberculosis R2 protein and purifying the R2 protein from the cultured cells and medium.
The present invention relates to fragments of nucleic acid molecules with sequences encoding an M. tuberculosis R2 protein that have at least 10 nucleotides.
The present invention relates to oligonucleotide molecules that comprise a nucleotide sequence complimentary to a nucleotide sequence of at least 10 nucleotides of SEQ ID NO:1 or SEQ ID NO:5.
The present invention relates to isolated antibodies which bind to an epitope on SEQ ID NO:2 or SEQ ID NO:6.
The present invention provides in vitro assays to identify inhibitors of M. tuberculosis ribonucleotide reductase. The method comprises the steps of combining isolated R1 protein, an isolated R2 protein, a substrate and a test compound. The R1 and R2 proteins complex to form a functional ribonucleotide reductase enzyme. According to the invention, the R1 and R2 proteins are produced by recombinant means and are free from all other M. tuberculosis proteins. As used herein, the term "recombinantly produced R1 protein and recombinantly produced R2 protein" is meant to refer to R1 and R2 proteins that are produced by recombinant means and that are free from all other M. tuberculosis proteins. The substrate is a ribonucleotide, specifically a ribonucleotide diphosphate. It is processed by ribonucleotide reductase into deoxyribonucleotide, specifically a ribonucleotide diphosphate. In preferred embodiments, ribonucleotides are selected from the group consisting of ADP, CDP, GDP, TDP and UDP, which are processed into dADP, dCDP, dGDP, dTDP and dUDP. The level of processing of the ribonucleotide by the ribonucleotide reductase complex into a deoxyribonucleotide is measured either by measuring the amount of ribonucleotide remaining or by measuring the amount of deoxyribonucleotide produced. The amount of ribonucleotide remaining or the amount of deoxyribonucleotide produced is compared to the amount of ribonucleotide remaining or the amount of deoxyribonucleotide produced when the ribonucleotide is processed into a deoxyribonucleotide by the R1 and R2 proteins in the absence of the test compound. If the level of processing of the ribonucleotide is reduced in the presence of said test compound, the test compound can be an inhibitor of ribonucleotide reductase activity. Inhibitors are useful as anti-M. tuberculosis agents. In preferred embodiments, the ribonucleotide is labelled, preferably radiolabelled and the processing of the ribonucleotide is determined by measuring the amount of deoxyribonucleotide produced. The unprocessed ribonucleotide can be separated from the deoxyribonucleotide using a phenylboronate agarose gel column.
Kits are provided for screening compounds for identifying inhibitors of M. tuberculosis ribonucleotide reductase. The kits comprise a container with R1 and R2 and directions for performing the assay. Optionally, R1 and R2 may be provided in separate containers. Optionally, a container with the ribonucleotide may be provided. Optionally, means to measure the presence and/or amount ribonucleotide may be provided. Optionally, means to measure the presence and/or amount deoxyribonucleotide may be provided. Optionally, positive and/or negative controls may be provided. Examples of positive controls include known inhibitors such as neutralizing anti-R1 antibodies or neutralizing anti-R2 antibodies. Known quantities of ribonucleotide or deoxyribonucleotide may be provided as controls for measuring such reagents and comparing to results from test assays.
The present invention relates to substantially pure M. tuberculosis topoisomerase I protein.
The present invention relates to substantially pure M. tuberculosis topoisomerase I protein having the amino acid sequence of SEQ ID NO:4.
The present invention relates to nucleic acid molecules that encode M. tuberculosis topoisomerase I protein.
The present invention relates to nucleic acid molecules encoding M. tuberculosis topoisomerase I protein that consists of SEQ ID NO:3.
The present invention relates to recombinant expression vectors that comprise a nucleic acid sequence that encodes M. tuberculosis topoisomerase I protein.
The present invention relates to host cells that comprise recombinant expression vectors that encode M. tuberculosis topoisomerase I protein.
The present invention relates to methods of making recombinant M. tuberculosis topoisomerase I protein comprising the steps of culturing host cells in medium that comprise recombinant expression vectors that encode M. tuberculosis topoisomerase I protein and purifying the topoisomerase I protein from the cultured cells and medium.
The present invention relates to fragments of nucleic acid molecules with sequences encoding M. tuberculosis topoisomerase I protein that have at least 10 nucleotides.
The present invention relates to oligonucleotide molecules that comprise a nucleotide sequence complimentary to a nucleotide sequence of at least 10 nucleotides of SEQ ID NO:3.
The present invention relates to isolated antibodies which bind to an epitope on SEQ ID NO:4.
DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS OF THE INVENTION
As used herein, the terms "M. tuberculosis R2 protein" and "R2 protein" are used interchangably and meant to refer to the M. tuberculosis R2 protein R2-1 and the M. tuberculosis R2 protein R2-2. The cDNA encoding the R2-1 protein is disclosed in SEQ ID NO:5 and SEQ ID NO:6 contains the corresponding amino acid sequence. The cDNA encoding the R2-2 protein is disclosed in SEQ ID NO:1 and SEQ ID NO:2 contains the corresponding amino acid sequence.
A rate limiting step in DNA replication is the conversion of ribonucleotides to deoxyribonucleotides which is catalyzed by the allosterically regulated, two subunit enzyme, ribonucleotide reductase (RR). In accordance with some aspects of the present invention, this enzyme system has been cloned from M. tuberculosis (M. tuberculosis) and expressed and purified the M. tuberculosis recombinant enzyme in E. coli. In some aspects of the invention, a complementation system is provided in which the genes encoding M. tuberculosis ribonucleotide reductase are transferred into an E. coli host that is temperature sensitive (ts) for its own ribonucleotide reductase (nrd A and nrd B mutants) (Yale Depository, New Haven Conn.). In some aspects of the invention purification of large quantities of recombinant M. tuberculosis ribonucleotide reductase which can are active in vitro and can be used to identify inhibitors of M. tuberculosis activity.
Another enzyme involved in M. tuberculosis DNA synthesis is topoisomerase I. DNA topoisomerases are ubiquitous enzymes that control the topology of DNA and play an essential role in biological processes, such as replication, transcription and recombination. The topoisomerases have been classified into subfamilies based on shared catalytic mechanisms. Type 1 topoisomerases, that make single stranded break, include the prokaryotic and eukaryotic Topo I, prokaryotic and yeast Topo III. Type 2 topoisomerases, making double stranded breaks, include DNA gyrase (Topo II) and Topo IV. Type 1-5' DNA topoisomerases, mainly distributed in prokaryotic species, relax negatively supercoiled DNA by making transient single-stranded DNA breaks, passing another single-strand DNA through the nick site and thereby resealing the breaks, changing the linking number in steps of one. The catalytic mechanism of this type of topoisomerase is ATP independent and involves a covalent linkage between a tyrosine residue in the active site of the N-terminal domain of the enzyme and the 5' phosphoryl group of the cleaved DNA strand. The reaction requires magnesium, is inhibited by polyamines and is insensitive to camptothecin. Type 1-3' DNA topoisomerases, found predominantly in eukaryotic cells, is also ATP-independent and relaxes both positively and negatively supercoiled DNA. Members of this subfamily bind preferentially to double stranded DNA and cleave one of the DNA strands forming a protein-DNA covalent intermediate between a tyrosyl residue and 3'-phosphate at the break site. The active site tyrosine is located in the highly conserved carboxyl-terminal domain. The enzymatic activity can be inhibited by camptothecin and stimulated by polyamine. Prokaryotic Topo III, while similar to prokaryotic Topo I in amino acid sequence has a k.sub.cat almost an order of magnitude higher for decatenation than for relaxation of negative supercoils at 30.degree. C.
In accordance with some aspects of the present invention, the M. tuberculosis topoisomerase I is inserted into expression vectors which are incorporated into E. coli. The M. tuberculosis topoisomerase I protein is expressed and purified as a recombinant enzyme from E. coli. Similarly, the M. tuberculosis topoisomerase I coding sequence can be used to complement E. coli mutants that are temperature sensitive for topoisomerase I activity. E. coli host cells that are temperature sensitive (ts) for endogenous ribonucleotide reductase (nrd A and nrd B mutants) can be readily obtained such as from the Yale Depository.
To screen compounds according to some of the methods of the present invention, the first host cells are E. coli that contain a temperature sensitive mutation for topoisomerase I or ribonucleotide reductase and are complemented with functional M. tuberculosis topoisomerase I or M. tuberculosis ribonucleotide reductase (both R1 and an R2 protein), respectively. The second host cells either contain a functional endogenous topoisomerase I or ribonucleotide reductase, respectively, or they are complemented with a non-M. tuberculosis topoisomerase I or non-M. tuberculosis ribonucleotide reductase, respectively. The groups are contacted with test compounds and either uptake by the host cells of radiolabelled nucleotides added to the culture medium, or the survivability of each of the two groups of host cells is observed. If a test compound leads to the reduction in nucleotide uptake host cells complemented with M. tuberculosis topoisomerase I or ribonucleotide reductase, or the death of the host cells complemented with M. tuberculosis topoisomerase I or ribonucleotide reductase, but not to the reduction of nucleotide uptake or cell death of those with endogenous or non-M. tuberculosis topoisomerase I or ribonucleotide reductase, the compound is a selective inhibitor of M. tuberculosis topoisomerase I or ribonucleotide reductase, respectively.
Kits are provided which comprise containers with host cells or reagents necessary to produce host cells and/or screen test compounds. In additions, kits comprise instructions for performing such methods. Host cells include complemented host cells or those mutants which can be complemented. Reagents include expression vectors including M. tuberculosis topoisomerase I or ribonucleotide reductase genes.
The present invention provides cloned genes that encodes M. tuberculosis DNA synthesis enzymes topoisomerase I protein and the small subunit (R2) of ribonucleotide reductase (RR). The discovery of these M. tuberculosis genes and the proteins that they encode provides the means to design and discover specific inhibitors of M. tuberculosis topoisomerase I protein or ribonucleotide reductase.
As used herein the terms "specific inhibitor of M. tuberculosis topoisomerase I" and "selective inhibitor of M. tuberculosis topoisomerase I" are used interchangeably and are meant to refer to compounds that inhibit DNA synthesis in M. tuberculosis by inhibiting of activity of M. tuberculosis topoisomerase I. The compounds do not inhibit non-M. tuberculosis species topoisomerase I activity. Inhibition of M. tuberculosis topoisomerase I activity essentially leads to cell death due to the cells inability to replicate in the absence of the ability to synthesize DNA. Compounds that selectively inhibit M. tuberculosis topoisomerase I activity are those which inhibit M. tuberculosis topoisomerase I activity but not the activity of non-M. tuberculosis topoisomerase I enzyme.
As used herein the terms "specific inhibitor of M. tuberculosis ribonucleotide reductase" and "selective inhibitor of M. tuberculosis ribonucleotide reductase" are used interchangeably and are meant to refer to compounds that inhibit DNA synthesis in M. tuberculosis through the inhibition of activity of M. tuberculosis ribonucleotide reductase enzyme. The compounds do not inhibit non-M. tuberculosis species ribonucleotide reductase activity. Inhibition of ribonucleotide reductase activity essentially leads to cell death due to the cells inability to replicate in the absence of the ability to synthesize DNA. Compounds that selectively inhibit M. tuberculosis ribonucleotide reductase activity are those which inhibit M. tuberculosis ribonucleotide reductase activity but not the activity of non-M. tuberculosis ribonucleotide reductase enzyme.
According to the present invention, the gene that encodes M. tuberculosis topoisomerase I protein or the genes that encode the subunits of ribonucleotide reductase enzyme, i.e. the large subunit (R1) and the small subunit (R2), may be used to produce recombinant microorganisms that are useful to screen compounds for specific inhibitors. Two R2 proteins, R2-1 and R2-2, have been identified.
A host organism deficient in endogenous topoisomerase I protein may be "complemented" with M. tuberculosis topoisomerase I, i.e. furnished with a functional copy of the M. tuberculosis topoisomerase I gene or cDNA. Expression of the nucleotide sequence that encodes M. tuberculosis topoisomerase I protein results in production of functional protein which functions in place of the missing or non-functional endogenous topoisomerase I.
Similarly, a host organism deficient in endogenous ribonucleotide reductase enzymes may be "complemented" with M. tuberculosis ribonucleotide reductase, i.e. furnished with a functional copies of the M. tuberculosis R1 and R2 genes or cDNAs. Expression of the nucleotide sequences that encode M. tuberculosis ribonucleotide reductase subunits results in production of functional ribonucleotide reductase enzyme which functions in place of the missing or non-functional endogenous ribonucleotide reductase.
Comparative studies can be performed to evaluate the effect that test compounds have on the hosts that are complemented with M. tuberculosis topoisomerase I or ribonucleotide reductase enzyme compared to the effect the same test compounds have on the hosts with functional endogenous topoisomerase I or ribonucleotide reductase, respectively. Comparisons between M. tuberculosis topoisomerase I- or ribonucleotide reductase-complemented hosts and hosts that are complemented with non-M. tuberculosis topoisomerase I or ribonucleotide reductase, respectively, can also be performed.
The methods of the invention are useful to identify selective inhibitors of M. tuberculosis topoisomerase I or ribonucleotide reductase. Inhibitors are useful as anti-M. tuberculosis agents. Kits are provided for screening compounds for identifying selective inhibitors of M. tuberculosis DNA synthesis enzymes including topoisomerase I and ribonucleotide reductase.
In addition to complementation assays, the present invention provides in vitro assays to identify inhibitors of M. tuberculosis ribonucleotide reductase. According to one aspect of the invention, a method of screening compounds is provided to identify inhibitors of M. tuberculosis ribonucleotide reductase. The method comprises the steps of combining isolated R1 protein, an isolated R2 protein, a substrate and a test compound under conditions in which the substrate would be processed by the R1 and R2 into a product in absence of said test compound. The R1 and R2 proteins complex to form a functional ribonucleotide reductase enzyme. The substrate is a ribonucleotide diphosphate that is processed by ribonucleotide reductase into a deoxyribonucleotide diphosphate. In preferred embodiments, ribonucleotides are selected from the group consisting of ADP, CDP, GDP, TDP and UDP, which are processed into dADP, dCDP, dGDP, dTDP and dUDP. The level of processing of the ribonucleotide by the ribonucleotide reductase complex into a deoxyribonucleotide is measured either by measuring the amount of ribonucleotide remaining or by measuring the amount of deoxyribonucleotide produced. The amount of ribonucleotide remaining or the amount of deoxyribonucleotide produced is compared to the amount of ribonucleotide remaining or the amount of deoxyribonucleotide produced when the ribonucleotide is processed into a deoxyribonucleotide by the R1 and R2 proteins in the absence of the test compound. If the level of processing of the ribonucleotide is reduced in the presence of said test compound, the test compound can be an inhibitor of ribonucleotide reductase activity. Inhibitors are useful as anti-M. tuberculosis agents. In preferred embodiments, the ribonucleotide is labelled, preferably radiolabelled and the processing of the ribonucleotide is determined by measuring the amount of deoxyribonucleotide produced. The unprocessed ribonucleotide can be separated from the deoxyribonucleotide using a phenylboronate agarose gel column. If the level of processing of the ribonucleotide is reduced in the presence of the test compound, the test compound can be an inhibitor of ribonucleotide reductase activity. Inhibitors are useful as anti-M. tuberculosis agents.
Kits are provided for screening compounds for identifying inhibitors of M. tuberculosis ribonucleotide reductase. The kits comprise a container with R1 and R2 and directions for performing the assay. Optionally, R1 and R2 may be provided in separate containers. Optionally, a container with the ribonucleotide may be provided. Optionally, means to measure the presence and/or amount ribonucleotide may be provided. Optionally, means to measure the presence of ribonucleotide may be provided. Optionally, means to measure the presence and/or amount of deoxyribonucleotide may be provided. Optionally, positive and/or negative controls may be provided. Examples of positive controls include known inhibitors such as neutralizing anti-R1 antibodies or neutralizing anti-R2 antibodies. Known quantities of ribonucleotide or deoxyribonucleotide may be provided as controls for measuring such reagents and comparing to results from test assays.
The nucleotide sequence that encodes an M. tuberculosis R2 protein allows for the production of complemented host cells which are deficient in functioning endogenous ribonucleotide reductase but which can synthesize DNA due to the presence of functional M. tuberculosis ribonucleotide reductase protein. In the host cell, the deficiency of functioning ribonucleotide reductase can be due to a deficiency in the functioning of R1 protein, R2 protein or both. In order for the ribonucleotide reductase deficient host cell to be complemented, both R1 protein and an R2 protein from M. tuberculosis must be provided. Accordingly, coding sequence for the M. tuberculosis R1 protein and R2 protein must be introduced into the host cells.
SEQ ID NO:24 encodes the R1 protein. In preparing gene constructs for complementation of deficient hosts, SEQ ID NO:24 and either SEQ ID NO:1 or SEQ ID NO:5 are introduced into a host cell and expressed. The coding sequences for R1 and R2 may be inserted into a single expression vector or separate expression vectors. The coding sequences must be operably linked to regulatory elements required for gene expression in the host. As controls, deficient host cells may be complemented with nucleotide sequences that encode a functional endogenous ribonucleotide reductase subunits or functional non-M. tuberculosis ribonucleotide reductase subunits, or the host cells may be maintained in conditions in which the endogenous ribonucleotide reductase is functional.
The nucleotide sequence that encodes M. tuberculosis R2-2 protein and that is disclosed herein as SEQ ID NO:1 allows for the production of pure M. tuberculosis R2-2 protein and the design of probes which specifically hybridize to nucleic acid molecules that encode M. tuberculosis R2-2 protein and antisense compounds to inhibit transcription of the gene that encodes M. tuberculosis R2-2 protein. The R2 protein may be combined with M. tuberculosis R1 protein to form an active ribonucleotide reductase enzyme complex.
The nucleotide sequence that encodes M. tuberculosis R2-1 protein and that is disclosed herein as SEQ ID NO:5 allows for the production of pure M. tuberculosis R2-1 protein and the design of probes which specifically hybridize to nucleic acid molecules that encode M. tuberculosis R2-1 protein and antisense compounds to inhibit transcription of the gene that encodes M. tuberculosis R2-1 protein. The R2 protein may be combined with M. tuberculosis R1 protein to form an active ribonucleotide reductase enzyme complex.
The nucleotide sequence that encodes M. tuberculosis topoisomerase I protein and that is disclosed herein as SEQ ID NO:3 allows for the production of complemented host cells which are deficient in functioning endogenous topoisomerase I but which can synthesize DNA due to the presence of functional M. tuberculosis topoisomerase I protein. In preparing gene constructs for complementation of deficient hosts, SEQ ID NO:3 is introduced into a host cell and expressed. SEQ ID NO:3 may be inserted into an expression vector in which the coding sequence is operably linked to regulatory elements required for gene expression in the host. As controls, deficient host cells may be complemented with a functional endogenous topoisomerase I, a functional non-M. tuberculosis topoisomerase I, or maintained in conditions in which the endogenous topoisomerase I is functional. The nucleotide sequence that encodes M. tuberculosis topoisomerase I protein and that is disclosed herein as SEQ ID NO:3 allows for the production of pure M. tuberculosis topoisomerase I protein and the design of probes which specifically hybridize to nucleic acid molecules that encode M. tuberculosis topoisomerase I protein and antisense compounds to inhibit transcription of the gene that encodes M. tuberculosis topoisomerase I protein.
The present invention provides a substantially purified M. tuberculosis R2 protein. The present invention provides substantially purified M. tuberculosis R2-2 protein which has the amino acid sequence consisting of SEQ ID NO:2. The present invention provides substantially purified M. tuberculosis R2-1 protein which has the amino acid sequence consisting of SEQ ID NO:6. An M. tuberculosis R2 protein can be isolated from natural sources or produced by recombinant DNA methods.
The present invention provides substantially purified M. tuberculosis topoisomerase I protein. The present invention provides substantially purified M. tuberculosis topoisomerase I protein which has the amino acid sequence consisting of SEQ ID NO:4. M. tuberculosis topoisomerase I protein can be isolated from natural sources or produced by recombinant DNA methods.
Antibodies that specifically bind to an M. tuberculosis R2 protein or topoisomerase I protein are provided. Such antibodies are specific inhibitors of M. tuberculosis ribonucleotide reductase and topoisomerase I protein, respectively. Such antibodies may be used in methods of isolating a pure M. tuberculosis R2 protein and topoisomerase I protein, respectively. Likewise, such antibodies may be used in methods of inhibiting M. tuberculosis ribonucleotide reductase enzyme activity and topoisomerase I protein activity, respectively.
The antibodies may be used to purify the protein from natural sources using well known techniques and readily available starting materials. Anti-M. tuberculosis R2 antibodies may be used to purify the M. tuberculosis R2 protein that they are specific for from natural sources or from material present when producing the protein by recombinant DNA methodology. The present invention relates to antibodies that bind to an epitope which is specific for M. tuberculosis R2 protein. Anti-M. tuberculosis topoisomerase I antibodies may be used to purify M. tuberculosis topoisomerase I protein from natural sources or from material present when producing the protein by recombinant DNA methodology. The present invention relates to antibodies that bind to an epitope which is specific for M. tuberculosis topoisomerase I protein.
As used herein, the term "antibody" is meant to refer to complete, intact antibodies, and Fab fragments and F(ab).sub.2 fragments thereof. Complete, intact antibodies include monoclonal antibodies such as murine monoclonal antibodies, chimeric antibodies and humanized antibodies.
The production of antibodies and the protein structures of complete, intact antibodies, Fab fragments and F(ab).sub.2 fragments and the organization of the genetic sequences that encode such molecules are well known and are described, for example, in Harlow, E. and D. Lane (1988) ANTIBODIES: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., which is incorporated herein by reference. Briefly, for example, the M. tuberculosis protein, or an immunogenic fragment thereof is injected into mice. The spleen of the mouse is removed, the spleen cells are isolated and fused with immortalized mouse cells. The hybrid cells, or hybridomas, are cultured and those cells which secrete antibodies are selected. The antibodies are analyzed and, if found to specifically bind to M. tuberculosis protein that was injected into the mouse, the hybridoma which produces them is cultured to produce a continuous supply of antibodies.
Using standard techniques and readily available starting materials, a nucleic acid molecule that encodes an M. tuberculosis R2 protein may be isolated from a cDNA library, using probes which are designed using the nucleotide sequence information disclosed in SEQ ID NO:1 or SEQ ID NO:5. Likewise, a nucleic acid molecule that encodes M. tuberculosis topoisomerase I protein may be isolated from a cDNA library, using probes which are designed using the nucleotide sequence information disclosed in SEQ ID NO:3.
One aspect of the present invention relates to an isolated nucleic acid molecule that comprises a nucleotide sequence that encodes an M. tuberculosis R2 protein. In some embodiments, the nucleic acid molecules consist of a nucleotide sequence that encodes an M. tuberculosis R2 protein. In some embodiments, the nucleic acid molecules comprise the nucleotide sequence that consists of the coding sequence in SEQ ID NO:1. In some embodiments, the nucleic acid molecules consist of the nucleotide sequence set forth in SEQ ID NO:1. In some embodiments, the nucleic acid molecules comprise the nucleotide sequence that consists of the coding sequence in SEQ ID NO:5. In some embodiments, the nucleic acid molecules consist of the nucleotide sequence set forth in SEQ ID NO:5. The isolated nucleic acid molecules of the invention are useful to prepare constructs and recombinant expression systems for preparing isolated M. tuberculosis R2 protein.
One aspect of the present invention relates to an isolated nucleic acid molecule that comprises a nucleotide sequence that encodes M. tuberculosis topoisomerase I protein. In some embodiments, the nucleic acid molecules consist of a nucleotide sequence that encodes M. tuberculosis topoisomerase I protein. In some embodiments, the nucleic acid molecules comprise the nucleotide sequence that consists of the coding sequence in SEQ ID NO:3. In some embodiments, the nucleic acid molecules consist of the nucleotide sequence set forth in SEQ ID NO:3. The isolated nucleic acid molecules of the invention are useful to prepare constructs and recombinant expression systems for preparing isolated M. tuberculosis topoisomerase I protein.
A genomic or cDNA library may be generated by well known techniques. Clones of an M. tuberculosis R2 protein are identified using probes that comprise at least a portion of the nucleotide sequence disclosed in SEQ ID NO:1 or SEQ ID NO:5, respectively. Clones of the M. tuberculosis topoisomerase I protein are identified using probes that comprise at least a portion of the nucleotide sequence disclosed in SEQ ID NO:3. The probes have at least 16 nucleotides, preferably 24 nucleotides. The probes are used to screen the genomic or cDNA libraries using standard hybridization techniques.
The present invention relates to isolated nucleic acid molecules that comprises at least 10 nucleotides of a nucleotide sequence identical or complementary to a fragment of SEQ ID NO:1, SEQ ID NO:3 or SEQ ID NO:5.
In some embodiments, the isolated nucleic acid molecules consist of a nucleotide sequence identical or complementary to a fragment of SEQ ID NO:1 which is at least 10 nucleotides. In some embodiments, the isolated nucleic acid molecules comprise or consist of a nucleotide sequence identical or complementary to a fragment of SEQ ID NO:1 which is 15-150 nucleotides. In some embodiments, the isolated nucleic acid molecules comprise or consist of a nucleotide sequence identical or complementary to a fragment of SEQ ID NO:1 which is 15-30 nucleotides.
In some embodiments, the isolated nucleic acid molecules consist of a nucleotide sequence identical or complementary to a fragment of SEQ ID NO:5 which is at least 10 nucleotides. In some embodiments, the isolated nucleic acid molecules comprise or consist of a nucleotide sequence identical or complementary to a fragment of SEQ ID NO:5 which is 15-150 nucleotides. In some embodiments, the isolated nucleic acid molecules comprise or consist of a nucleotide sequence identical or complementary to a fragment of SEQ ID NO:5 which is 15-30 nucleotides.
In some embodiments, the isolated nucleic acid molecules consist of a nucleotide sequence identical or complementary to a fragment of SEQ ID NO:3 which is at least 10 nucleotides. In some embodiments, the isolated nucleic acid molecules comprise or consist of a nucleotide sequence identical or complementary to a fragment of SEQ ID NO:3 which is 15-150 nucleotides. In some embodiments, the isolated nucleic acid molecules comprise or consist of a nucleotide sequence identical or complementary to a fragment of SEQ ID NO:3 which is 15-30 nucleotides.
Isolated nucleic acid molecules that comprise or consist of a nucleotide sequence identical or complementary to a fragment of SEQ ID NO:1 which is at least 10 nucleotides are useful as probes for identifying genes and cDNA sequences that encodes M. tuberculosis R2 protein R2-2, PCR primers for amplifying genes and cDNA that encodes M. tuberculosis R2 protein R2-2, and antisense molecules for inhibiting transcription and translation of genes and cDNA, respectively, which encode M. tuberculosis R2 protein R2-2.
The nucleotide sequence in SEQ ID NO:1 may be used to design probes, primers and complimentary molecules which specifically hybridize to the unique nucleotide sequences of M. tuberculosis R2 protein. Probes, primers and complimentary molecules which specifically hybridize to nucleotide sequence that encodes M. tuberculosis R2 protein may be designed routinely by those having ordinary skill in the art.
Isolated nucleic acid molecules that comprise or consist of a nucleotide sequence identical or complementary to a fragment of SEQ ID NO:5 which is at least 10 nucleotides are useful as probes for identifying genes and cDNA sequences that encodes M. tuberculosis R2 protein R2-1, PCR primers for amplifying genes and cDNA that encodes M. tuberculosis R2 protein R2-1, and antisense molecules for inhibiting transcription and translation of genes and cDNA, respectively, which encode M. tuberculosis R2 protein R2-1.
The nucleotide sequence in SEQ ID NO:5 may be used to design probes, primers and complimentary molecules which specifically hybridize to the unique nucleotide sequences of M. tuberculosis R2 protein R2-1. Probes, primers and complimentary molecules which specifically hybridize to nucleotide sequence that encodes M. tuberculosis R2 protein R2-1 may be designed routinely by those having ordinary skill in the art.
Isolated nucleic acid molecules that comprise or consist of a nucleotide sequence identical or complementary to a fragment of SEQ ID NO:3 which is at least 10 nucleotides are useful as probes for identifying genes and cDNA sequences that encodes M. tuberculosis topoisomerase I protein, PCR primers for amplifying genes and cDNA that encodes M. tuberculosis topoisomerase I protein, and antisense molecules for inhibiting transcription and translation of genes and cDNA, respectively, which encode M. tuberculosis topoisomerase I protein.
The nucleotide sequence in SEQ ID NO:3 may be used to design probes, primers and complimentary molecules which specifically hybridize to the unique nucleotide sequences of M. tuberculosis topoisomerase I protein. Probes, primers and complimentary molecules which specifically hybridize to nucleotide sequence that encodes M. tuberculosis topoisomerase I protein may be designed routinely by those having ordinary skill in the art.
The present invention also includes labelled oligonucleotides which are useful as probes for performing oligonucleotide hybridization methods to identify clones that encode an M. tuberculosis R2 protein or topoisomerase I protein. Accordingly, the present invention includes probes that can be labelled and hybridized to unique nucleotide sequences of nucleic acid molecules that encode M. tuberculosis R2 protein or topoisomerase I protein. The labelled probes of the present invention are labelled with radiolabelled nucleotides or are otherwise detectable by readily available nonradioactive detection systems. In some preferred embodiments, probes comprise oligonucleotides consisting of between 10 and 100 nucleotides. In some preferred, probes comprise oligonucleotides consisting of between 10 and 50 nucleotides. In some preferred, probes comprise oligonucleotides consisting of between 12 and 20 nucleotides. The probes preferably contain nucleotide sequence completely identical or complementary to a fragment of a unique nucleotide sequences of nucleic acid molecules that encode an M. tuberculosis R2 protein or topoisomerase I protein.
PCR technology is practiced routinely by those having ordinary skill in the art and its uses in diagnostics are well known and accepted. Methods for practicing PCR technology are disclosed in "PCR Protocols: A Guide to Methods and Applications", Innis, M. A., et al. Eds. Academic Press, Inc. San Diego, Calif. (1990), which is incorporated herein by reference. Applications of PCR technology are disclosed in "Polymerase Chain Reaction" Erlich, H. A., et al., Eds. Cold Spring Harbor Press, Cold Spring Harbor, N.Y. (1989), which is incorporated herein by reference. Some simple rules aid in the design of efficient primers. Typical primers are 18-28 nucleotides in length having 50% to 60% g+c composition. The entire primer is preferably complementary to the sequence it must hybridize to. Preferably, primers generate PCR products 100 basepairs to 2000 base pairs. However, it is possible to generate products of 50 base pairs to up to 10 kb and more.
PCR technology allows for the rapid generation of multiple copies of nucleotide sequences by providing 5' and 3' primers that hybridize to sequences present in a nucleic acid molecule, and further providing free nucleotides and an enzyme which fills in the complementary bases to the nucleotide sequence between the primers with the free nucleotides to produce a complementary strand of DNA. The enzyme will fill in the complementary sequences adjacent to the primers. If both the 5' primer and 3' primer hybridize to nucleotide sequences on the complementary strands of the same fragment of nucleic acid, exponential amplification of a specific double-stranded product results. If only a single primer hybridizes to the nucleic acid molecule, linear amplification produces single-stranded products of variable length.
One having ordinary skill in the art can isolate the nucleic acid molecule that encodes M. tuberculosis ribonucleotide reductase protein or M. tuberculosis topoisomerase I protein and insert it into an expression vector using standard techniques and readily available starting materials.
The present invention relates to a recombinant expression vector that comprises a nucleotide sequence that encodes M. tuberculosis R2 protein R2-2 that comprises the amino acid sequence of SEQ ID NO:2.
The present invention relates to a recombinant expression vector that comprises a nucleotide sequence that encodes M. tuberculosis R2 protein R2-1 that comprises the amino acid sequence of SEQ ID NO:6.
The present invention relates to a recombinant expression vector that comprises a nucleotide sequence that encodes M. tuberculosis topoisomerase I protein that comprises the amino acid sequence of SEQ ID NO:4.
As used herein, the term "recombinant expression vector" is meant to refer to a plasmid, phage, viral particle or other vector which, when introduced into an appropriate host, contains the necessary genetic elements to direct expression of the coding sequence that encodes M. tuberculosis R2 or topoisomerase I protein. The coding sequence is operably linked to the necessary regulatory sequences. Expression vectors are well known and readily available. Examples of expression vectors include plasmids, phages, viral vectors and other nucleic acid molecules or nucleic acid molecule containing vehicles useful to transform host cells and facilitate expression of coding sequences.
In some embodiments, the recombinant expression vector comprises the nucleotide sequence set forth in SEQ ID NO:1. The recombinant expression vectors of the invention are useful for transforming hosts to prepare recombinant expression systems for preparing the M. tuberculosis R2-2 protein.
In some embodiments, the recombinant expression vector comprises the nucleotide sequence set forth in SEQ ID NO:5. The recombinant expression vectors of the invention are useful for transforming hosts to prepare recombinant expression systems for preparing the M. tuberculosis R2-1 protein.
In some embodiments, the recombinant expression vector comprises the nucleotide sequence set forth in SEQ ID NO:3. The recombinant expression vectors of the invention are useful for transforming hosts to prepare recombinant expression systems for preparing the M. tuberculosis topoisomerase I protein.
The present invention relates to a host cell that comprises the recombinant expression vector that includes a nucleotide sequence that encodes M. tuberculosis R2 protein R2-2 having SEQ ID NO:2. In some embodiments, the host cell comprises a recombinant expression vector that comprises SEQ ID NO:1.
The present invention relates to a host cell that comprises the recombinant expression vector that includes a nucleotide sequence that encodes M. tuberculosis R2 protein R2-1 having SEQ ID NO:6. In some embodiments, the host cell comprises a recombinant expression vector that comprises SEQ ID NO:5.
The present invention relates to a host cell that comprises the recombinant expression vector that includes a nucleotide sequence that encodes M. tuberculosis topoisomerase I protein having SEQ ID NO:4. In some embodiments, the host cell comprises a recombinant expression vector that comprises SEQ ID NO:3.
Host cells for use in well known recombinant expression systems for production of proteins are well known and readily available. Examples of host cells include bacteria cells such as E. coli, yeast cells such as S. cerevisiae, insect cells such as S. frugiperda, non-human mammalian tissue culture cells chinese hamster ovary (CHO) cells and human tissue culture cells such as HeLa cells.
The present invention relates to a transgenic, non-human mammal that comprises the recombinant expression vector that includes a nucleic acid sequence that encodes an M. tuberculosis R2 protein or the M. tuberculosis topoisomerase I protein. Transgenic, non-human mammals useful to produce recombinant proteins are well known as are the expression vectors necessary and the techniques for generating transgenic animals. Generally, the transgenic animal comprises a recombinant expression vector in which the nucleotide sequence that encodes the M. tuberculosis protein operably linked to a mammary cell specific promoter whereby the coding sequence is only expressed in mammary cells and the recombinant protein so expressed is recovered from the animal's milk. In some embodiments, the coding sequence that encodes M. tuberculosis R2 protein R2-2 is SEQ ID NO:1. In some embodiments, the coding sequence that encodes M. tuberculosis R2 protein R2-1 is SEQ ID NO:5. In some embodiments, the coding sequence that encodes M. tuberculosis topoisomerase 1 protein is SEQ ID NO:3.
In some embodiments, for example, one having ordinary skill in the art can, using well known techniques, insert such DNA molecules into a commercially available expression vector for use in well known expression systems. For example, the commercially available plasmid pSE420 (Invitrogen, San Diego, Calif.) may be used for production of the M. tuberculosis protein in E. coli. The commercially available plasmid pYES2 (Invitrogen, San Diego, Calif.) may, for example, be used for production in S. cerevisiae strains of yeast. The commercially available MAXBAC.TM. complete baculovirus expression system (Invitrogen, San Diego, Calif.) may, for example, be used for production in insect cells. The commercially available plasmid pcDNA I (Invitrogen, San Diego, Calif.) may, for example, be used for production in mammalian cells such as CHO cells. One having ordinary skill in the art can use these commercial expression vectors and systems or others to produce M. tuberculosis proteins using routine techniques and readily available starting materials. (See e.g., Sambrook et al., Molecular Cloning a Laboratory Manual, Second Ed. Cold Spring Harbor Press (1989), which is incorporated herein by reference.) Thus, the desired proteins can be prepared in both prokaryotic and eukaryotic systems, resulting in a spectrum of processed forms of the protein.
One having ordinary skill in the art may use other commercially available expression vectors and systems or produce vectors using well known methods and readily available starting materials. Expression systems containing the requisite control sequences, such as promoters and polyadenylation signals, and preferably enhancers, are readily available and known in the art for a variety of hosts. See e.g., Sambrook et al., Molecular Cloning a Laboratory Manual, Second Ed. Cold Spring Harbor Press (1989).
A wide variety of eukaryotic hosts are also now available for production of recombinant foreign proteins. As in bacteria, eukaryotic hosts may be transformed with expression systems which produce the desired protein directly, but more commonly signal sequences are provided to effect the secretion of the protein.
Commonly used eukaryotic systems include, but is not limited to, yeast, fungal cells, insect cells, mammalian cells, avian cells, and cells of higher plants. Suitable promoters are available which are compatible and operable for use in each of these host types as well as are termination sequences and enhancers, e.g. the baculovirus polyhedron promoter. As above, promoters can be either constitutive or inducible. For example, in mammalian systems, the mouse metallothionein promoter can be induced by the addition of heavy metal ions.
The particulars for the construction of expression systems suitable for desired hosts are known to those in the art. Briefly, for recombinant production of the protein, the DNA encoding the polypeptide is suitably ligated into the expression vector of choice. The DNA is operably linked to all regulatory elements which are necessary for expression of the DNA in the selected host. One having ordinary skill in the art can, using well known techniques, prepare expression vectors for recombinant production of the polypeptide.
The expression vector including the DNA that encodes an M. tuberculosis R2 or topoisomerase I protein is used to transform the compatible host which is then cultured and maintained under conditions wherein expression of the foreign DNA takes place. The protein of the present invention thus produced is recovered from the culture, either by lysing the cells or from the culture medium as appropriate and known to those in the art. One having ordinary skill in the art can, using well known techniques, isolate the M. tuberculosis R2 or topoisomerase I protein that is produced using such expression systems. The methods of purifying M. tuberculosis proteins from natural sources using antibodies which specifically bind to M. tuberculosis R2 or topoisomerase I protein as described above, may be equally applied to purifying M. tuberculosis protein produced by recombinant DNA methodology.
Examples of genetic constructs include the M. tuberculosis protein coding sequence operably linked to a promoter that is functional in the cell line into which the constructs are transfected. Examples of constitutive promoters include promoters from cytomegalovirus or SV40. Examples of inducible promoters include mouse mammary leukemia virus or metallothionein promoters. Those having ordinary skill in the art can readily produce genetic constructs useful for transfecting with cells with DNA that encodes M. tuberculosis R2 or topoisomerase I protein from readily available starting materials.
In some embodiments of the invention, transgenic non-human animals are generated. The transgenic animals according to the invention contain coding sequences that encodes either an M. tuberculosis R2 or topoisomerase I protein under the regulatory control of a mammary specific promoter. One having ordinary skill in the art using standard techniques, such as those taught in U.S. Pat. No. 4,873,191 issued Oct. 10, 1989 to Wagner and U.S. Pat. No. 4,736,866 issued Apr. 12, 1988 to Leder, both of which are incorporated herein by reference, can produce transgenic animals which produce the M. tuberculosis protein. Preferred animals are goats and rodents, particularly rats and mice.
In addition to producing these proteins by recombinant techniques, automated peptide synthesizers may also be employed to produce an M. tuberculosis R2 protein or M. tuberculosis topoisomerase I protein.

EXAMPLES
Example 1
Ribonucleotide reductase (RR) of the Class I form is a cell cycle regulated, two subunit, oxygen and iron dependent, radical mediated, allosteric enzyme that catalyzes the reduction of nucleoside diphosphates to deoxynucleoside diphosphates. This enzymatic activity is regulated at the protein level by 1) subunit interaction, 2) formation and maintenance of an .mu.-oxo bridged iron (III)/tyrosyl radical redox center, and 3) positive and negative nucleotide allosteric effectors. There are additional regulatory features at the level of transcription, translation and post-translational modifications. Given its central role in the cell cycle, human ribonucleotide reductase is a well recognized target in the design of cancer chemotherapeutic agents. Furthermore, ribonucleotide reductase is gaining wide acceptance as a target for antivirals and antiparasitic chemotherapy.
Inhibition of ribonucleotide reductase in a variety of mycobacterial species has been reported to substantially alter the growth patterns of the organisms. Studies in the 1960s and 1970s showed that M. smegmatis, cultured in iron depleted media, displayed elongated morphology with decreased DNA synthesis and increased activity of DNA repair enzymes. When grown in the presence of 200 .mu.g/ml of the radical scavenger hydroxyurea, growth of M. smegmatic was completely inhibited. At lower concentrations the organisms contained a decreased DNA/protein ratio with an increase in DNA polymerase and ATP-dependent DNAase activities as measured in crude extracts. Heterocyclic hydrazone inhibitors of ribonucleotide reductase have been reported to have minimum inhibitory concentrations against the virulent H37Rv strain of M. tuberculosis in the range of 40-80 .mu.M.
Both subunits of ribonucleotide reductase have been cloned from a number of species including mammals, clam, yeast, bacteria, viruses and protozoa. Most of the biochemical characterization has been carried out on the E. coli or the mammalian species. However, recent work and work on E. coli and Salmonella typhimurium ribonucleotide reductase has important consequences for the relevance of the M. tuberculosis work.
S. typhimurium contains a ribonucleotide reductase system highly related to that encoded by the nrdA (large subunit) and nrdB (small subunit) genes found in E. coli, with 96.5% and 98.4% homology to the R1 and R2 subunits respectively. However, both S. typhimurium and E. coli contain a second set of chromosomal genes, nrdE and nrdF, that encode a ribonucleotide reductase that is not expressed under normal growth conditions. When purified and analyzed using a recombinant expression plasmid system, nrdE/nrdF has properties similar to those of the nrdA/nrdB systems, yet there are important differences in the allosteric effectors of the enzyme, in the character of the Fe/tyrosyl radical and in the R1-R2 subunit interaction surfaces. dATP is a positive allosteric activator up to 1 mM for the nrdE/nrdF system whereas dATP activates the nrdA/nrdB system only up to 1 uM and is negative effector at higher concentrations. ATP, dTTP, dGTP are activators of the nrdA/nrdB system but show only minimal activation of the nrdE/nrdF system. The EPR signal arising from the radical is more like the photosystem II signal that the ribonucleotide reductase signal. The C-terminal tail of the nrdF encoded small subunit is different from the C-terminal tail of the nrdB encoded small subunit. The interaction between subunits is dependent on the recognition of specific residues found at the C-terminal tail of R2 and residues in the R1 structure. Therefore, there is no complementation between a nrdE large subunit and a nrdB small subunit.
Given that E. coli, Salmonella typhimurium, and yeast contain genes encoding one or both ribonucleotide reductase subunits that are not expressed except under very unusual circumstances, and that mammalian cells possibly contain ribonucleotide reductase pseudogenes, active ribonucleotide reductase enzyme was purified from the Erdman strain of M. tuberculosis and the gene encoding the large subunit was cloned using information from the amino acid sequence. This strategy ensured that the genes so isolated would encode the actively transcribed and translated message.
M. tuberculosis R1 unexpectedly represents a nrdE-type R1. The gene encoding the small subunit has been cloned utilizing PCR primers homologous to the sequence of nrdF from Salmonella. In order to investigate the possibility that M. tuberculosis contains a non-coding nrdA/nrdB-type ribonucleotide reductase, extensive PCR experiments were carried out using a wide variety of primers. No sequences homologous to a nrdA/nrdB system could be found even at low stringency. Southern blots using E. coli nrdA and nrdB genes as probes did not reveal any positive bands. Furthermore, Western blots of M. tuberculosis extracts developed with anti-E. coli nrdA R1 and anti-E. coli nrdB R2 antibodies showed no cross reaction.
Two complete M. tuberculosis R2 genes, R2-1 and R2-2, were isolated by PCR amplification of conserved regions followed by screening of size selected M. tuberculosis libraries. Alignment of the M. tuberculosis R2 polypeptides encoded by the two genes with S. typhimurium human and E. coli R2 indicated that both of the M. tuberculosis R2 proteins contains the active site tyrosine and the iron binding residues corresponding to Asp84, Glu115, His118, Glu204, Glu238 and His241 in E. coli R2. The C termini, as expected, was different from that of human and E. coli R2.
Both M. tuberculosis R2-1 and R2-2 were cloned and expressed in E. coli. M. tuberculosis R2-1 was insoluble and biochemically inactive. M. tuberculosis R2-2 yielded soluble, biochemically active recombinant protein.
The recombinant M. tuberculosis R2, derived from R2-2, has now been purified to greater than 90% as estimated by SDS-PAGE with a yield of more than 20 mg/liter of culture. The purified recombinant R2 has a typical tyrosine radical absorbance at 408 nm which was abolished when the sample was treated with 15 mM of hydroxyurea for 10 min. The activity of the recombinant M. tuberculosis R2 was determined by the rate of dCDP production in the presence of recombinant M. tuberculosis R1. The specific activity of R2 was 200 nmol/mg protein/min when assayed in the presence of excess R1 and DTT as reductant, comparable with that of mouse R2. The reduction of CDP requires ATP as activator with an optimum concentration of 1 to 2 mM. Concentrations higher than 2 mM inhibited the activity. dATP stimulated CDP reduction even at concentrations as high as 1 mM, with inhibition found at higher concentrations. This pattern of dATP stimulation and inhibition is similar to that observed in S. typhimurium nrdEF ribonucleotide reductase yet quite different from the mammalian system where inhibition is seen at concentrations greater than 0.1 mM dATP.
MATERIALS AND METHODS
All restriction enzymes were purchased from NEBioLab. pET-11a and BL21(DE3) competent cells were from Novagen. DEAE-cellulose was from Sigma. Protein concentrations were determined using the method of Bradford M. M. 1996 Anal. Biochem. 72:248-251, which is incorporated herein by reference). Partially purified wild type M. tuberculosis ribonucleotide reductase holoenzyme and pure recombinant R1 were prepared as described in Yang, F.-D., et al. 1990 FEBS 272(1,2):61-64 which is incorporated herein by reference. Heptapeptides Acetyl-TDTDWDF-OH (SEQ ID NO:7) and Acetyl-EDDDWDF-OH (SEQ ID NO:8) identical to M. tuberculosis R2-1 and M. tuberculosis R2-2 C-terminal sequences, called R2P7-1 and R2P7-2, were purchased from SynPep (P.O.Box 2999, Dublin, Calif. 94568).
Isolation of partial R2 sequences
Two sets of PCR primers were used in PCR reactions to isolate the first fragments of M. tuberculosis R2 genes. The first set of primers (N and C1 primers) was: N-terminal primer 5'-TTCATGGAGGC(G/C)GT(G/C)CA-3' (SEQ ID NO:9) and C-terminal primer 5'-TAGAACAGGAA(G/C)GACTC-3' (SEQ ID NO:10). The second set of primers (N and C2 primers) was: N-primer, the same as the N-primer in first set, and C-primer 5'-TG(G/C)AC(G/C)GCCTCGTC (SEQ ID NO:11). The PCR reactions were carried out in separate tubes in 100 .mu.l which contained 0.25 .mu.g of M. tuberculosis genomic DNA, 100 pmol of primers, all four dNTPs (each 0.2 mM), 10 .mu.l 10.times.PCR buffer (Perkin-Elmer) and 2.5 U Taq polymerase (Perkin-Elmer). The reactions were conducted in 30 cycles with the following program: 20 s at 94.degree. C., 30 s at 48.degree. C., and 30 s at 72.degree. C. The two PCR products, 200 bp oligonucleotide from the first set of primers and 300 bp oligonucleotide from the second set of primers, were purified from an agarose gel using Qiaex silica gel particles (Qiagen), subcloned and sequenced.
Southern Analysis
M. tuberculosis DNA (1 mg for each reaction) was digested with EcoRI, Not I, Sac I and Xba I in a final volume of 10 ml at 37.degree. C. overnight. The digested mixture was separated on a 0.7% agarose gel (20 cm) at 70 V for 6 hrs in 1.times.TBE buffer. The DNA was transferred onto a nylon membrane (MSI), dried at 80.degree. C. for 2 hrs and pre-hybridized with 25 ml of hybridization mixture (50% formamide, 5.times.SSPE, 0.1% SDS, and 0.25% dry milk) at 42.degree. C. for 1 hr in a hybridization bag. .sup.32 P labeled oligonucleotide probe, representing the 200 bp PCR product obtained with the first set of primers (probe 1) was added directly to the hybridization bag and hybridization was continued for 48 hrs at 42.degree. C. After the film was developed, the membrane was stripped and reprobed with the .sup.32 P labeled 300 bp PCR product obtained with the second set of primers as discussed above (probe 2).
Construction of a size selected M. tuberculosis R2-1 or R2-2 library in Lambda ZAP II
M. tuberculosis DNA (10 mg) was digested with Sac I (for R2-1) or EcoR I (for R2-2) in the corresponding buffer in a final volume of 100 ml at 37.degree. C. overnight. The digested DNA was then separated by agarose gel electrophoresis using the same conditions as described for the Southern analysis. The 4 kb SacI fragment, and the 6 kb EcoR I fragment were purified with Qiaex, ligated to the correspondingly prepared Lambda ZAP II (Stratagene). XL1-Blue were infected with the recombinant phage preparations and screened with either probe 1 or probe 2. Positive plaques were picked and the recombinant phagemids were excised and used to transform XL1-Blue. The phagemids were purified and the sequences of the inserts were determined.
Expression of M. tuberculosis R2-1 and M. tuberculosis R2-2
Full length M. tuberculosis R2-1 was isolated from genomic M. tuberculosis DNA by PCR using primers with Xba I cloning sites (underline) (N-primer, TCTAGAATGACCGGCAAGCTCGTTG SEQ ID NO:12; C-primer, TCTAGATTAGAAGTCCCAGTCGGTG SEQ ID NO:13). Full length M. tuberculosis R2-2 was isolated from the 6 kb insert containing recombinant phagemid DNA containing by PCR using primers containing Nhe I cloning sites (underline) (N primer, 5'-GCTAGCGTGACTGGAAACGCAAAG SEQ ID NO:14; C primer, 5'-GCTAGCCTAGAAGTCCCAGTCATC SEQ ID NO:15). The PCR reaction mixture, in a total volume of 100 ml, contained 0.25 mg of genomic or phagemid DNA, 100 pmol of each primer, all four dNTPs (each at 0.2 mM), and 3.0 U of Taq polymerase. The reaction was carried out in 30 cycles of the following program: 20 s at 94.degree. C., 20 s at 54.degree. C., 3 min at 72.degree. C. The PCR product was gel purified with GenElute Agarose Spin Column (Supelco) and cloned into the pCR vector (Invitrogen). The recombinant plasmid was then transformed into OneShot bacteria, purified and digested with XbaI (M. tuberculosis R2-1) or NheI (M. tuberculosis R2-2). The excised M. tuberculosis R2-1 or M. tuberculosis R2-2 gene was again gel purified and cloned into the NheI linearized pET-11a plasmid. BL21(DE3) competent cells were transformed, induced with 0.4 mM IPTG and grown at 37.degree. C. for 2.5 hours.
Purification of the Recombinant M. tuberculosis R2-2
Recombinant E. coli cell paste (3 g) was suspended in 30 ml of 50 mM Tris-HCl, 0.1 mM DTT, pH 7.5 (buffer A) containing 2 mM PMSF and disintegrated with French press. The cell debris was removed by centrifugation at 23,000.times.g for 20 min. A solution of 10% streptomycin sulfate in buffer A was added to the supernatant to a final concentration of 0.5% with stirring to precipitate DNA and ribosomal RNA. The precipitate was removed by centrifugation (23,000.times.g, 20 min). Solid ammonium sulfate was slowly added to the supernatant to 60% saturation with stirring. After the addition was complete, the suspension was stirred for 10 min and the precipitate was collected by centrifugation (23,000.times.g, 20 min). The pellet was resuspended in 5 ml of buffer A and dialyzed against the same buffer for 5 hrs with one buffer change. After removal of insoluble protein by centrifugation (5,000.times.g, 10 min), the dialysate was loaded onto a DE52 column (1.times.6 cm) which was pre-equilibrated with buffer A. The column was washed with 20 ml of buffer A containing 100 mM KCl, and 15 ml of buffer A containing 200 mM KCl subsequently. R2 was then eluted with 20 ml of buffer A containing 300 mM KCl and concentrated in an Amicon concentrator. Concentrated R2 was diluted 3 fold with buffer A to reduce the concentration of salt, concentrated one more time and stored at -70.degree. C. M. tuberculosis rR2-2 remained soluble throughout the purification process while, under the same conditions, M. tuberculosis rR2-1 was insoluble.
Activity assays of the recombinant M. tuberculosis ribonucleotide reductase
Activities were determined from the rate of reduction of �.sup.3 H!CDP as described previously in Yang et al. 1990 SUPRA. 5 mg of holoenzyme was generated from an equimolar ratio of recombinant R1 and R2-2 in order to determine the effects of ATP and dATP on CDP reduction and to measure inhibition of activity by peptides R2P7-1 and R2P7-2.
The effect of ATP and dATP on CDP reduction was examined. 5 mg recombinant ribonucleotide reductase (1 to 1 molar ratio of R1 to R2) was used in each assay in a final volume of 100 ml in the presence of 6 mM CDP. Reactions were carried out at 37.degree. C. for 20 min.
Nucleotide sequence accession numbers
The GenBank accession number for M. tuberculosis R2-1 is U41099 and for M. tuberculosis R2-2 U41100, which are incorporated herein by reference.
RESULTS
Isolation of M. tuberculosis R2-1 and R2-2 genes
Using high molecular weight DNA extracted from the Erdman strain of M. tuberculosis as template, the N and C1 set of PCR primers (SEQ ID NO:9 and SEQ ID NO:10) generated 200 bp PCR product and the N and C2 set of PCR primers (SEQ ID NO:9 and SEQ ID NO:11) generated 300 bp PCR product were not identical in the region of overlap. Nevertheless, both fragments contained an open reading frame and both were homologous with S. typhimurium R2F. This result led to the postulate that there may be two R2 genes in M. tuberculosis. In fact, the Southern blot hybridization pattern of Sac I, Not I and EcoRI digested M. tuberculosis DNA was different when probed with the two PCR products.
Sequence analysis of the complete coding region of the two genes confirmed the hypothesis. There is 71% homology at the DNA level between the two genes and 71% identity in the derived amino acid sequence. M. tuberculosis R2-1 is 64%, and M. tuberculosis R2-2 is 71% identical to the S. typhimurium nrdF gene product. This is in contrast to 21-23% identity to the E.coli nrdB gene product and approximately 16% identity with the human R2 subunit.
Alignment of the two M. tuberculosis R2 polypeptides with S. typhimurium, human and E. coli R2 demonstrated that both M. tuberculosis R2s contain the conserved free radical tyrosine corresponding to Tyr122; the iron binding residues corresponding to Asp 84, Glu115, His118, Glu204, Glu238 and His241 in E. coli R2 and Trp34 and Asp44; and the hydrophobic pocket forming residues corresponding to Phe 208, Phe 212 and Ile 234 in E. coli R2 proposed to be essential to mediate electron transfer to the large subunit.
The C-terminal residues of the M. tuberculosis R2 genes differ significantly from any other R2 gene thus far identified. Differences between the human R2 C-terminus and M. tuberculosis R2 C-terminus include Phe383 replaced by threonine (in R2-1) or glutamic acid (in R2-2), Thr384 replaced by Asp, Lue385 replaced by Thr (in R2-1) or Asp (in R2-2), and Ala387 replaced by Trp. The existence of a phenylalanine in position 383 in the mammalian system has been shown to be essential for the binding of peptide inhibitors to the large subunit. Residues Leu385 and Ala387 are also critical residues in mammalian R2-R1 binding. Clearly, the C-termini of M. tuberculosis R2s are more hydrophilic and more negatively charged than that of human R2. There are 5 residues with their side chains negatively charged in R2-2. Plus the carboxyl group of Phe324, there are 6 negatively charged carboxyl groups among the seven C-terminal residues, indicating that the binding domain on R1 must be more positively charged. The observed divergence at the C-terminus between human and M. tuberculosis may have important impact on antituberculous drug development given the potential to develop species specific inhibitors of ribonucleotide reductase based on the differences between their C-terminal amino acids.
Gene organization of M. tuberculosis R2
A search of Genbank revealed an exact match starting 48 nucleotides following the stop codon of M. tuberculosis R2-1 which corresponded to the 5' non-coding region of the gene encoding MPT64, a secreted protein from M. tuberculosis, identified recently to be thioredoxin. This sequence includes the -35 and -10 promoter region of MPT64. Further sequence analysis showed that the entire 5' non-coding, the coding and 3'-non-coding region of MPT64 is found downstream from the M. tuberculosis R2-1 gene. The 3' non-coding sequences of the salmonella nrdF gene correspond to the upstream sequences of the proV gene in the proU operon. ProV is involved in the osmotic regulation in salmonella and does not appear to be related in sequence to the MPT64 gene in mycobacteria. Extensive sequence analysis of the 5' and 3' flanking regions of M. tuberculosis R2-2 did not reveal adjacent coding regions.
Unlike other bacterial ribonucleotide reductase systems, R1 was not found to form an operon with either M. tuberculosis R2-1, or M. tuberculosis R2-2.
Expression, purification and activity of recombinant M. tuberculosis R2
When M. tuberculosis R2-1 and M. tuberculosis R2-2 were cloned and expressed in E. coli, only recombinant M. tuberculosis R2-2 was soluble. Preliminary work on unfolding and refolding the insoluble M. tuberculosis R2-1 did not yield biologically active R2.
Recombinant M. tuberculosis R2-2 purified to greater than 90% as estimated by SDS-PAGE. Using this expression system, more than 20 mg of pure M. tuberculosis rR2-2 was obtained from 1 liter culture.
The activity of the recombinant M. tuberculosis ribonucleotide reductase was determined by the rate of dCDP production using DTT as reductant. In all activity assays an equi-molar ratio of R1 and R2 was used to reconstitute the enzyme. dATP stimulated CDP reduction at concentrations as high as 1 mM and showed more efficient than ATP at low concentration while ATP was a more potent positive effector for CDP reduction at higher concentration than dATP. ATP stimulated CDP reduction up to 45 pmoles dCDP in 20 min, while dATP can only to 13 pmoles under same assay condition.
Inhibition of CDP reduction activities of reconstituted M. tuberculosis ribonucleotide reductase by R2P7-1 and R2P7-2 was evaluated. 5 mg reconstituted ribonucleotide reductase (1 to 1 molar ratio of R1 to R2-2) was used in each assays in final volume of 100 ml in the presence of 6 mM CDP, 2 mM ATP and 0.0-0.5 mM amount of the inhibitors. The activity of recombinant M. tuberculosis was inhibited by R2P7-2 with an IC.sub.50 of 15-20 mM and by R2P7-1 with an IC.sub.50 of 100 mM. The IC.sub.50 of R2P7-2 is consistent with that found in other ribonucleotide reductase systems. For example, for the mammalian enzyme, the IC.sub.50 for a heptamer corresponding to the R2 C-terminal tail of the mammalian R2 is 20 mM and for the herpes simplex virus enzyme, the IC.sub.50 is 20 mM for the nonapeptide corresponding to the herpes simplex virus R2 C-terminal tail. By contrast, IC.sub.50 's in the range of 20 mM are not obtained for the nrdAB system until the length of the peptide reaches approximately 37 residues. The differential inhibition of M. tuberculosis ribonucleotide reductase activity by the two peptides, reflecting the relatively weak binding of the C-terminal tail corresponding M. tuberculosis R2-1 to M. tuberculosis R1 indicates that it is unlikely that M. tuberculosis R2-1 would form an active holoenzyme with M. tuberculosis R1 in vivo under normal growth conditions. This suggests that under conditions where M. tuberculosis R2 is expressed, another, as yet unidentified M. tuberculosis R1 is expressed. Comparison of partially purified ribonucleotide reductase holoenzyme from M. tuberculosis extracts with the two recombinant R2s clearly showed that one band of the holoenzyme corresponded R2-2 and no protein component could be identified that corresponded to R2-1.
Absorption spectra of recombinant M. tuberculosis R2-2 and hydroxyurea treated M. tuberculosis R2-2 was evaluated. 12 mM R2-2 in 50 mM tris-HCl, 0.1 mM DTT, pH 7.6 was tested as was 12 mM R2-2 in 50 mM tris-HCl, 0.1 mM DTT, pH 7.6 after 5 min incubation with 15 mM hydroxyurea, and 12 mM R2-2 in 50 mM tris-HCl, 0.1 mM DTT, pH 7.6 was test after 10 min incubation with 15 mM hydroxyurea. The spectra were taken from a Shimadzu UV-Visible spectrophotometer UV-160.
The UV spectrum of M. tuberculosis rR2-2 showed a typical tyrosyl radical absorbance band at 408 nm that could be abolished upon incubation with 15 mM of hydroxyurea for 10 min. In addition, hydroxyurea inhibited the activity of CDP reduction with an IC.sub.50 of 2 mM which is slightly higher than that found for calf thymus (IC90 of 1 mM) and Salmonella ribonucleotide reductase (IC.sub.50 approx. 0.5 mM) and may reflect structural differences in the enzyme from different species.
Example 2
In vitro assays are performed to identify inhibitors of M. tuberculosis ribonucleotide reductase activity using the recombinant M. tuberculosis ribonucleotide reductase (R1 and R2-1). The activity is measured by determining by the rate of deoxyribonucleotide production using DTT as reductant. An equimolar ratio of R1 and R2 is used to reconstitute the enzyme.
�5-.sup.3 H! CDP, �8,5-.sup.3 H! GDP, �8-.sup.3 H! ADP and �.alpha.-.sup.32 P!dATP were purchased from Amersham. All cold NDPs and NTPs were from Sigma. Sepharose 4B was purchased from Pharmacia. Phenylboronate sepharose (PBA-60) was purchased from Amicon.
dATP stimulates ribonucleotide diphosphate reduction at concentrations as high as 1 mM and is more efficient than ATP at low concentration while ATP was a more potent positive effector for ribonucleotide reduction at higher concentration than dATP. ATP stimulates ribonucleotide reduction up to 45 pmoles deoxyribonucleotide in 20 min, while dATP can only to 13 pmoles under same assay condition.
Inhibition of ribonucleotide reduction activities of reconstituted M. tuberculosis ribonucleotide reductase by using 5 mg reconstituted ribonucleotide reductase (1 to 1 molar ratio of R1 to R2-2) in each assays in final volume of 100 ml in the presence of 6 mM NDP, 2 mM ATP and 0.0 .mu.M-1 nM amount of candidate inhibitors.
The ribonucleotide reductase assay used directly separates the deoxyribonucleotide product from the reaction mixture over a phenylboronate agarose gel (PBA-60). The reaction mixture, made up in a final volume of 100 ml of 60 mM Hepes, pH 7.6 buffer, contained 8 mM Mg(OAc).sub.2, 8.75 mM NaF, 0.05 mM FeCl.sub.3, 25 mM DTT and varying amounts of effector and �.sup.3 H! NDP substrate. The reaction was started by the addition of the enzyme (either partially purified or highly purified), carried out at 37.degree. C. and stopped by heating in a boiling water bath for 3 minutes. The denatured protein was removed by centrifugation. The supernatant was diluted with equal volume of 50 mM tris-HCl buffer, pH 8.5 containing 50 mM magnesium chloride and applied onto a 0.5.times.6.0 cm PBA-60 column which was pre-equilibrated with the same buffer. The column was then washed with 5 ml of the same buffer. The quantity of deoxyribonucleotide was determined by liquid scintillation. The column was regenerated by washing with 10 ml of 50 mM sodium citrate buffer, pH 6.5 and double deionized water. All assays were carried out in triplicate.
Example 3
Construction of the ts complementation system--the drug screening system
The genes encoding M. tuberculosis ribonucleotide reductase are not contained in an operon as they are in E. coli and Salmonella. Therefore, two systems were designed to express M. tuberculosis ribonucleotide reductase: 1) where the genes are arrayed in a mini-operon construct and 2) where each gene is arrayed on a separate expression plasmid.
The mini-operon was inserted into the commercially available IPTG inducible expression vector pTrc99A as follows. The M. tuberculosis R1 gene was inserted into the multiple cloning site of pTrc99A using a PCR primer generated NcoI site at the N-terminus and a SacI site at the C-terminus. The M. tuberculosis R2 gene was inserted using a PCR primer generated KpnI restriction site, a ribosome binding site and 7 nucleotide spacing before the first coding triplet (ATG), at the N-terminus. The ribosome binding site found in the Salmonella operon which has been shown to work in E. coli (Jordan, A., et al. 1994 J. Bact. 176(11):3420-3427 and Jordan, A., et al. 1994 Proc. Natl. Acad. Sci. USA 91:12892-12896 which are incorporated herein by reference) was utilized. While the M. tuberculosis R2 start codon is valine, a methionine start codon was chosen in order to maximize the likelihood of expression in E. coli. The TbR2 C-terminal primer was designed to add a HindIII site to the end of the gene for cloning purposes. pTrc99A containing this mini-operon construct was denoted pTrcMTbRRop. pTreMTbRRop was electroporated into nrdA E. coli using the BioRad Gene Pulser.
To generate the vectors for the second system, M. tuberculosis R1 was PCR amplified with an NcoI site at the N-terminus, and a SacI site at the C-terminus and ligated into pTrc99A. This expression vector was denoted pTrcMTbR1. In order to avoid the problem of plasmid exclusion in E. coli, a compatible second hybrid plasmid vector was constructed containing the transcriptional machinery and lacI repressor gene of pTrc99A, the origin of replication, p15A, from the plasmid pACYC177 and kanamycin resistance gene. This hybrid plasmid was denoted pSC. M. tuberculosis R2 was inserted into pSC using PCR generated cloning sites and the resultant expression plasmid denoted pSCMTbR2. pTrcMTbR1 and pSCMTbR2 were then electroporated into ts nrdA E. coli.
Electroporation and complementation were carried out as follows. Frozen nrdA cells were grown overnight at 30.degree. C. in 5 ml of 2YT media with streptomycin, a marker contained in this strain of nrdA. One ml of overnight culture was added to 50 ml of 2YT/Strep media, and grown at 30.degree. C. to Ab.sub.600 =1. The cells were washed twice with distilled water, once with 10% glycerol, and resuspended in 0.2 ml of 10% glycerol. The gene pulser apparatus was set at: 200 Ohms, 25 microfarrads, 2.5 kV. 2 ul of pTrcMTbRRop (20 ng/ul) or 2 ul of both pTrcMTbR1 (100 ng/ul) and pSCMTbR2 (100 ng/ul) wee mixed with 45 ul of nrdA E. coli (Ab.sub.600 =1) and subjected to electroporation. One ml of LB was then added and the cells were allowed to grow at 30.degree. C. for 1 hour. After 1 hour, the cells were induced with IPTG and grown at 30.degree. C. for 45 minutes then spread onto agar plates containing 50 microliters of 0.2M IPTG, and either ampicillin/streptomycin for pTrcMTbRRop selection or ampicillin/streptomycin/kanamycin for selection of the double plasmid system. Plates were incubated at 30.degree. C. and 42.degree. C. overnight. A protein extract was prepared from successful 42.degree. transformants from both systems and the presence of recombinant R1 and R2 was confirmed by SDS gel electrophoresis. The same set of expression vectors were created containing the mammalian ribonucleotide reductase genes which, upon electroporation and selection as above, generated no complementation.
Example 4
(a) Isolation of the gene of M. tuberculosis topoisomerase I
In our attempt to isolate the gene encoding the small subunit of ribonucleotide reductase (RR) from M. tuberculosis, a 288 bp fragment was isolated using N and C primers derived from the amino acid sequence of E. coli RR small subunit. Unexpectedly, sequence analysis of this fragment revealed a high degree of homology with Topo I from synechococcus rather than with the small subunit of ribonucleotide reductase. This fragment was subsequently used as a probe to isolate the complete gene encoding M. tuberculosis topoisomerase I (SEQ ID NO:3).
The gene was isolated in two steps. The 5' 2249 nucleotides contained in the DNA fragment between NotI cutting sites was first isolated by screening with Probe 1. The 3' 451 nucleotides contained in the DNA fragment between the two SacI cutting sites was isolated by screening with Probe 2.
Probe 1, the first 288 bp fragment of M. tuberculosis Topo I gene, was isolated by PCR using M. tuberculosis genomic DNA as template and primers (N primer, 5'-ATCGAGAACATCCA SEQ ID NO:14; C primer, 5'-AAGAAGATGCCCTC SEQ ID NO:15) which were designed for isolation of ribonucleotide reductase from M. tuberculosis. The PCR reaction was carried out in a total volume of 100 ml which contained 0.25 mg of M. tuberculosis genomic DNA, all four dNTPs (each at 0.2 mM), 10 ml of 10.times.PCR buffer (Perkin-Elmer), 2.5 U Taq polymerase and 100 pmol of each primer. The reaction was conducted in 20 cycles of the following program: 20 s at 94.degree. C., 30 s at 45.degree. C., and 60 s at 72.degree. C. The PCR product was purified from agarose gel with Qiaex silica gel particles (Qiagen) according to the manufacture's protocol.
Probe 2, a 300 bp oligonucleotide corresponding to the 3' end of the 3.7 kb fragment, was also prepared by PCR in the same way.
To isolate the whole gene, M. tuberculosis DNA was digested with restriction enzyme and then analyzed by Southern blot. Thus, M. tuberculosis DNA (1 mg) was digested with either 5 U of NotI or 10 U of SacI in a final volume of 10 ml at 37.degree. C. overnight. The digested fragments were separated by electrophoresis through a 0.7% agarose gel (20 cm) at 70 V for 6 hrs in 1.times.TBE buffer. The DNA was transferred onto a nylon membrane (MSI), dried at 80.degree. C. for 2 hrs and pre-hybridized with 25 ml of hybridization mixture (50% formamide, 5.times.SSPE, 0.1% SDS, and 0.25% dry milk) at 42.degree. C. for 1 hr. .sup.32 P labeled oligonucleotide probe was added directly to the hybridization bag and hybridization continued for 48 hrs at 42.degree. C. The hybridized band was visualized by autoradiography. Based on the result of Southern analysis, 10 mg of M. tuberculosis DNA was digested with either NotI or SacI in the corresponding buffer in a final volume of 100 ml at 37.degree. C. overnight. The digested DNA was then separated by agarose gel electrophoresis using the same conditions as used in the Southern analysis. The DNA fragment on the gel corresponding to the band shown on the Southern blot was purified with Qiaex and ligated to the correspondingly prepared Lambda ZAP II (Stratagene). The recombinant phage were used to infect XL1-Blue and screened with either Probe 1 or Probe 2. Positive plaques were picked and the recombinant phagemid excised by following the manufacture's protocol. The phagemid was then transformed XL1-Blue, purified, and sequenced.
After the complete gene sequence was determined, the explanation for selection of topoisomerase I using ribonucleotide reductase primers became clear. The DNA sequence used as the initial N-primer was identical to nucleotide positions 1662 to 1676 in M. tuberculosis topoisomerase I, except for two residues. Similarly, 9 of 14 C-primer residues were identical to nucleotide positions 1942 to 1950 in M. tuberculosis topoisomerase I.
The 3.7 kb fragment between the two Not I restriction sites was isolated from a size selected Not I library in Lambda Zap II screened with the original 288 bp PCR product. This fragment contained 2249 residues in the 5' region of the gene. The C-terminal region of the gene was isolated from a size selected Sac I digest library of genomic DNA screened with a 300 bp probe corresponding to the 3' end of the 3.7 kb fragment.
(b) Structure analysis of the gene and the enzyme
A 4.4 kb of M. tuberculosis genomic DNA was isolated and 3007 bp sequenced (SEQ ID NO:3). The GenBank accession number for the DNA sequence of M. tuberculosis topoisomerase I is U 40159. Within this region, an open reading frame of 2700 nucleotides was identified. The potential ATG start codon preceded by a plausible ribosome binding site, GGGATAA (underline) was identified. The gene encodes a polypeptide of 900 amino acids with a predicted molecular mass of 99353 Daltons. The coding region is 65.7% G+C, with third position of the codons 65.6% G or C rich.
The amino acid alignment of M. tuberculosis topoisomerase I with that of E. coli and synechococcus topoisomerase I shows that there is 20% and 30% overall identities respectively. Most of the identical residues are located in the N-terminal domain which include the active site tyrosine 347. Atomic resolution X-ray crystallographic analysis of the 67 kDa N-terminal fragment of E. coli topoisomerase I revealed a torus shaped structure with a 27.5 Angstrom average diameter hole. The structure indicates that the active site tyrosine 319 and its neighboring amino acids in the tertiary structure are involved in an extensive network of hydrogen bonds. This network consisting of Glu30, Lys34, Asp116, Asp118, Glu120, Gln337, Tyr340, Glu341, and Arg349 are all conserved in M. tuberculosis topoisomerase I. In contrast, there is no significant homology between M. tuberculosis topoisomerase I and E. coli topoisomerase III analyzed by computer.
The homology between M. tuberculosis, synechococcus and E. coli topoisomerase I breaks down in the C-terminal domain beyond amino acid residue 600. Activity studies of intact and C-terminal truncated E. coli topoisomerase I and topoisomerase III demonstrated that the C-terminal domain contains the DNA binding site. The DNA binding property largely comes from a zinc finger structure (E. coli topoisomerase I) or positively charged amino acid residues (E. coli topoisomerase III). M. tuberculosis topoisomerase I does not contain a zinc finger DNA binding motif in the C-terminal region of the protein. However, similar to E. coli topoisomerase III, there are short domains of residues that may contribute to the DNA binding property of this enzyme.
(c) Expression and activity of recombinant M. tuberculosis topoisomerase I
M. tuberculosis topoisomerase I was expressed in E. coli BL21(DE3) and purified nearly to homogeneity. To express M. tuberculosis topoisomerase I, the gene was isolated by PCR using M. tuberculosis genomic DNA as template and primers that contained NheI cloning sites (underline): N primer, 5'-GCTAGCATGGAGCGTGGGGCGCAGTTGGCTG SEQ ID NO:16; C primer, 5'-GCTAGCTTATGGAAGCCACGTCGTCGCCCT SEQ ID NO:17. The PCR reaction mixture, in a total volume of 100 ml, contained 0.25 mg of M. tuberculosis genomic DNA, 100 pmol of each primer, all four dNTPs (each at 0.2 mM), 3.0 U of Taq polymerase and 10% DMSO. The reaction was carried out in 30 cycles of the following program: 20 s at 94.degree. C., 20 s at 54.degree. C., 4 min at 72.degree. C. The PCR product was gel purified and cloned into pCR vector (Invitrogen). The recombinant plasmid was then transformed to OneShot cell, purified and digested with NheI. The excised topoisomerase I gene was again gel purified and cloned into the NheI linearized pET-11a plasmid. BL21(DE3) competent cells were transformed, induced with 0.1 mM IPTG and grown at 15.degree. C. overnight. The crude extracts from un-induced recombinant E. coli (15 mg), from induced recombinant E. coli (10 mg), and purified recombinant M. tuberculosis topoisomerase I (1 mg) were analyzed by 8% SDS-PAGE.
About 10 mg of pure recombinant M. tuberculosis topoisomerase I was obtained from 2 g of E. coli cell paste. The purification procedure was largely adopted from that for E. coli topoisomerase I purification except the final step of single stranded DNA-Agarose chromatography. The advantage of using this procedure was that the contaminate host E. coli topoisomerase I (10 mg in 2 g cell paste, about 0.1% of the total amount of recombinant M. tuberculosis topoisomerase I contained there) was able to be removed from the recombinant M. tuberculosis topoisomerase I in the step of phosphocellulose column chromatography, where E. coli topoisomerase I was absorbed on the column and the recombinant M. tuberculosis topoisomerase I directly flew through the column.
The recombinant M. tuberculosis topoisomerase I was purified as follows. Recombinant E. coli cell paste (2 g) was suspended in 20 ml of 50 mM Na/PO.sub.4, 100 mM KCl, 5% glycerol, 0.1 mM DTT, pH 7.5 (buffer A) containing 2 mM PMSF and disintegrated in a French press. The cell debris was removed by centrifugation at 23,000.times.g for 20 min. A solution of 10% streptomycin sulfate in buffer A was added to the supernatant to a final concentration of 0.5% with stirring to precipitate ribosomal RNA. The precipitate was removed by centrifugation (23,000.times.g, 20 min). Solid ammonium sulfate was slowly added to the supernatant to 60% saturation with stirring. After the addition was complete, the suspension was stirred for 10 min and the precipitate was collected by centrifugation (23,000.times.g, 20 min). The pellet was resuspended in 5 ml of buffer A and dialyzed against the same buffer for 4 hrs with one buffer change. After removal of insoluble protein by centrifugation (5,000.times.g, 10 min), the dialysate was loaded onto a phosphocellulose column (1.times.6 cm) which was pre-equilibrated with buffer A. The active M. tuberculosis topoisomerase I component in the breakthrough fraction was directly loaded onto a 2 ml ss-DNA agarose column. The column was washed with 10 ml of 50 mM Tris-HCL, 0.1 mM DTT, pH 7.6 (buffer B). M. tuberculosis topoisomerase I was eluted with 10 ml buffer B containing 1.0M KCl and then dialyzed against buffer B containing 0.1M KCl for 4 hrs with one buffer change. The dialysate was concentrated with a centriprep 10 (Amicon) and store at -70.degree. C.
The activity assays with equal amounts of the 60% ammonium sulfate fraction of extract prepared from un-induced and induced E. coli showed that the expressed protein was enzymatically active in relaxing negatively supercoiled plasmid DNA, while the activity of the host E. coli topoisomerase I was not detectable. There is a good correlation between the activity and the amount of purified enzyme used in each assay.
Activities were measured in a final volume of 10 ml contained 0.25 mg of negatively supercoiled pUC19 plasmid DNA, 50 mM Tris-HCl (pH 8.0), 20 mM KCl, 0.5 mM DTT, 10.0 mM MgCl.sub.2 and 30 mg/ml bovine serum albumin. The reaction was carried out at 37.degree. C. for 10 min and stopped by the addition of 5 ml of stop solution which contained 5% SDS, 10 mM EDTA, 5% glycerol and 0.25% bromophenol blue, followed by heating at 65.degree. C. for 10 min. The result was analyzed by electrophoresis on a 1.0% agarose gel (82 mm) in 1.times.TBE buffer at 100 V for about 1-2 hrs. The gel was then stained with ethidium bromide and photographed under UV light. Form I denotes supercoiled DNA and Form II completely relaxed or nicked circle DNA. Correlation between activity and amount of purified recombinant enzyme. Activities were measured at the same condition as that in panel A. The reaction was started by the addition of 0 ng, 30 ng, 150 ng, 300 ng, 600 ng, 1200 ng and 1800 ng of pure recombinant M. tuberculosis topoisomerase I.
The effect of magnesium ion on the activity was analyzed as follows. Activities were measured with 150 ng of purified recombinant M. tuberculosis topoisomerase I and in the presence of 0.0 mM, 0.1 mM, 0.5 mM, 1.0 mM, 5.0 mM, and 10.0 mM MgCl.sub.2.
The effect of ATP on the activity was also analyzed. Activities were measured under the same conditions as above with 150 ng of purified recombinant M. tuberculosis Topo I and 1.0 mM MgCl.sub.2 in the presence of 0.0 mM, 0.4 mM, 0.8mM, and 1.6 mM ATP.
Inhibition of enzymatic activity by spermidine was also evaluated. Inhibition of topoisomerase I activity was titrated with spermidine at 0.0 mM, 0.5 mM, 1.0 mM, 2.0 mM, and 4.0 mM in the presence of 150 ng of purified recombinant M. tuberculosis topoisomerase I. The assay condition were the same as that described above for testing the effect of ATP on activity.
The data indicated that DNA relaxing activity of the recombinant M. tuberculosis topoisomerase I required Mg.sup.2+ with an optimal concentration of 1.0 mM. Higher MgCl.sub.2 concentrations caused a more distributive than processive relaxation mechanism. In the presence of 4.0 mM spermidine, the enzymatic activity was almost completely inhibited. In all activity assay experiments, no ATP dependence was observed. On the contrary, ATP inhibited the reaction in agreement with the observation on type I DNA topoisomerase from Fervidobacterium islandicum.
(d) Conclusions
Our preliminary characterization of the expressed enzyme, together with the DNA alignment, strongly confirm that this enzyme is a type I DNA topoisomerase. Unlike the well characterized E. coli topoisomerase I, M. tuberculosis topoisomerase I does not contain a zinc finger DNA binding domain implying that there may be a difference in the enzyme-DNA binding mechanism. The availability of large amounts of recombinant M. tuberculosis topoisomerase I will facilitate a more complete characterization of the physical-chemical and biological properties of this enzyme.
Example 5
Ribonucleotide reductase, an allosterically regulated, cell cycle dependent enzyme catalyzing a unique step in the synthesis of DNA, the reduction of 2'-ribonucleotides to 2'-deoxyribonucleotides was purified 500 fold from M. tuberculosis Erdman strain through cell disruption, ammonium sulfate fractionation and dATP-sepharose affinity column chromatography. The enzyme consists of identical subunits R1 and R2, both of which are required for activity. R1 has a molecular weight of 84 Kd as identified by SDS-PAGE and photoaffinity labeling with dATP. The amino acid sequences of the N-terminal and two internal peptides were determined and a partial R1 gene was isolated by polymerase chain reaction (PCR) using primers designed from these amino acid sequences.
The coding sequences for a biologically active form of M. tuberculosis R1 were isolated by screening size selected libraries, regenerated by PCR amplification of high molecular weight M. tuberculosis DNA and expressed in E. coli. This coding sequence is 2169 nucleotides and contains no introns. The predicted molecular weight of R1 from the DNA sequence is 82244 Da. Recombinant M. tuberculosis R1, purified to homogeneity, was biologically active when assayed with extracts of M. tuberculosis enriched for R2.
MATERIALS AND METHODS
Materials
�5-.sup.3 H! CDP, �8,5-.sup.3 H! GDP, �8-.sup.3 ! ADP and �.alpha.-.sup.32 P!dATP were purchased from Amersham. All cold NDPs and NTPs were from Sigma. Sepharose 4B was purchased from Pharmacia. Phenylboronate sepharose (PBA-60) was purchased from Amicon. The molecular weight markers for SDS-PAGE were purchased from Bio-Rad.
Purification of M. tuberculosis Ribonucleotide Reductase
Twenty grams of M. tuberculosis cell paste was washed once with 100 ml of 50 mM Tris-HCl, 5 mM MgCl.sub.2, 0.1 mM DTT, pH 7.6 (Buffer A), resuspended in 200 ml of buffer A containing 2 mM phenylmethyl sulfonyl fluoride and subjected to two rounds of disruption in a pre-chilled French Press. The cell debris was removed by centrifugation at 23,000.times.g for 30 minutes. The supernatant was precipitated by addition of 10% streptomycin sulfate in buffer A to a final concentration of 0.5%. The resulting suspension was stirred for an additional 10 minutes, and the precipitate was removed by centrifugation (23,000.times.g, 20 min.). Solid ammonium sulfate was slowly added to the supernatant to 60% saturation with stirring. After the addition was completed, the suspension was stirred for 10 minutes and the precipitate was collected by centrifugation (23,000.times.g, 20 min.) and resuspended in 15 ml buffer A. The suspension was dialyzed against the same buffer for 5 hours with one buffer change. The dialysate (referred to hereafter as partially purified enzyme) was centrifuged at 13,800.times.g for 5 minutes and then applied onto a 1.0.times.3.0 cm dATP-sepharose column at room temperature in small aliquots. dATP-substituted sepharose gel was prepared by well known methods. Briefly, dADP was condensed with p-nitrophenyl phosphate which was activated with diphenylphosphorochloridate. After hydrogenation of the nitro group of the p-nitrophenyl ester of dATP, the p-aminophenyl ester of dATP was coupled to cyanogen bromide activated sepharose 4B. The column was then washed with 10 column volumes of buffer A. Ribonucleotide reductase was eluted with 10 ml of buffer A containing 10 mM ATP, concentrated to 200 ml with centriprep-10 (Amicon), and stored at -70.degree. C. (referred to hereafter as highly purified enzyme).
Ribonucleotide Reductase Activity Assay
The ribonucleotide reductase assay followed the method of Steeper, J. R. and C. D. Steuart, 1970. Analytical Biochem 34:123-130, which is incorporated herein by reference, modified to directly separate the deoxyribonucleotide product from the reaction mixture over a phenylboronate agarose gel (PBA-60). The reaction mixture, made up in a final volume of 100 ml of 60 mM Hepes, pH 7.6 buffer, contained 8 mM Mg(OAc).sub.2, 8.75 mM NaF, 0.05 mM FeCl.sub.3, 25 mM DTT and varying amounts of effector and �.sup.3 H! NDP substrate. The reaction was started by the addition of the enzyme (either partially purified or highly purified), carried out at 37.degree. C. and stopped by heating in a boiling water bath for 3 minutes. The denatured protein was removed by centrifugation. The supernatant was diluted with equal volume of 50 mM tris-HCl buffer, pH 8.5 containing 50 mM magnesium chloride and applied onto a 0.5.times.6.0 cm PBA-60 column which was pre-equilibrated with the same buffer. The column was then washed with 5 ml of the same buffer. The quantity of deoxyribonucleotide was determined by liquid scintillation. The column was regenerated by washing with 10 ml of 50 mM sodium citrate buffer, pH 6.5 and double deionized water. All assays were carried out in triplicate.
Photoaffinity Labeling of M. tuberculosis ribonucleotide reductase with �.alpha.-.sup.32 P!dATP
Partially purified ribonucleotide reductase (30 mg) or pure ribonucleotide reductase (3 mg) in 20 ml of buffer A was mixed with 16 pmoles �.alpha.-.sup.32 P!dATP (300 Ci/mmol) in the presence or absence of 5 mM ATP or 2.5 mM CDP and incubated on ice for 5 minutes. The mixture was placed as a drop on parafilm on dry ice and irradiated for 30 minutes using a UVP uv minerallight lamp, model UVGL-58. After irradiation, the protein was precipitated with 5% trichloroacetic acid and washed 2 times with buffer A containing 5% trichloroacetic acid. The protein was then dissolved in loading buffer and analyzed on 12% SDS slab gels. The stained and dried gel was autoradiographed at room temperature for 5 hours.
N-terminal and internal amino acid sequence analysis
Highly purified M. tuberculosis ribonucleotide reductase (30 mg) was subjected to preparative SDS-PAGE (12% gel) and blotted onto an Immoblon-P membrane (Millipore) in 12.5 mM tris, 95 mM glycine-10% MeOH, pH 8.6 at 4.degree. C. (100V, 1 hr). The membrane was washed with double distilled water and stained for 5 min with 0.25% coomassie blue R250 in 40% MeOH and destained for 10 min with 50% MeOH. The membrane was vacuum dried and N-terminal and internal sequence analysis was performed on the protein band.
Isolation of a partial sequence of the M. tuberculosis R1 gene
PCR using primers designed based on internal amino acid sequences was carried out in a total volume of 100 ml which contained 0.25 mg of M. tuberculosis genomic DNA, 100 pmoles of primers, all four dNTP (each at 0.2 mM), 10 ml of 10.times.PCR buffer (Perkin Elmer) and 2.5 units of Taq polymerase. The reaction was carried out in 20 cycles of the following program: 20 s at 94.degree. C., 30 s at 45.degree. C., and 60 s at 72.degree. C. The PCR product was purified from an agarose gel using Qiaex silicagel particles (Qiagen) according to the manufacturer's protocol.
Expression and activity of recombinant M. tuberculosis R1 produced in E. coli
The R1 gene was isolated from high molecular weight M. tuberculosis DNA by PCR using primers that contained Nhe1 cloning sites (underlined): N-primer, 5'-AAAAAAGCTAGCCCCACCGTGATCGCCGAGCCCGTAGCCTC SEQ ID NO:18; C-primer, 5'-AAAAAAGCTAGCCTACAGCATGCAGGA SEQ ID NO:19. The PCR reaction mixture in a total volume of 100 ml contained 0.25 mg of M. tuberculosis genomic DNA, 100 pmoles of each primer, all four dNTPs (each at 0.2 mM), and 2.5 units of Taq polymerase. The reaction was carried out in 30 cycles of the following program: 20 s at 94.degree. C., 20 s at 55.degree. C., and 90 s at 72.degree. C. The PCR product was gel purified with Qiaex silicagel particles, digested with Nhe 1, phenol extracted and precipitated with ethanol. The cloning vector containing the heat inducible pL promoter was prepared by digestion with Nhe 1, treated with alkaline phosphatase, phenol extracted and precipitated with ethanol. 28 ng of M. tuberculosis R1 DNA prepared as above was ligated with Nhe 1 digested pZMs (15 ng) in a final volume of 10 ml containing 400 units of T4 DNA ligase and 1 ml of 10.times.ligation buffer at 16.degree. C. overnight. The ligation mix was then used to transform N4830 (Pharmacia. New Jersey) competent cells and plated onto LB agar supplemented with ampicillin. M. tuberculosis R1 was expressed by heat induction at 42.degree. C. The purification of the recombinant R1 was essentially the same as that of the wild type R1 from M. tuberculosis.
RESULTS AND DISCUSSION
Purification of M. tuberculosis ribonucleotide reductase
Twenty grams of cell paste yielded 80 mg of protein with a specific activity of 1000 units (nmoles of product per mg protein per hour). Ribonucleotide reductase activity was not detected in the crude extract, however, it was detectable in the 60% ammonium sulfate fraction and was stimulated by addition of ATP and inhibited by dATP. Based on this, and the observation that mammalian as well as E. coli ribonucleotide reductase were purified by dATP affinity chromatography, M. tuberculosis ribonucleotide reductase was purified 500 fold usingribonucleotide se affinity column.
ribonucleotide reductase activity found in the 60% ammonium sulfate fraction was resolved into two components using DE52 column chromatography in Mg.sup.2+ free buffer A. The two fractions, one in the breakthrough (DE1) and a second in the 0.5M NaCl (DE2) fractions, lacked ribonucleotide reductase activity when assayed individually. The breakthrough fraction of dATP affinity chromatography (dA1) which contained no ribonucleotide reductase activity but is rich in R2 was able to restore ribonucleotide reductase activity to DE1, but not to the DE2 fraction, indicating that DE1 contains R1.
The enzyme was stable throughout the purification. However, activity decreased after one month storage at -70.degree. C. if the concentration of the protein was lower than 1 mg/ml. The partially purified enzyme was stable throughout the 4 hour incubation during the activity assay in the presence of substrate and effectors.
SDS-PAGE of the dATP-sepharose affinity purified material showed one major band with a molecular weight of 84,000 Da. This band was specifically labeled by �.alpha.-.sup.32 P!dATP in the presence of 2 mM CDP and was completely inhibited by 5 mM ATP which provided additional evidence that the protein was R1.
Activity of M. tuberculosis ribonucleotide reductase
M. tuberculosis ribonucleotide reductase utilized all four ribonucleoside diphosphates as substrate. The reduction of CDP and UDP could be detected in 60% ammonium sulfate precipitate, whereas reduction of ADP and GDP required the use of the dATP affinity purified material. Maximum activity (2 nmoles of dCDP/hr/mg protein) of partially purified enzyme for CDP reduction was obtained in the presence of 6 mM ATP. In the presence of dGTP (6 mM) and ATP (3 mM), 1.8 mg of the highly purified enzyme reduced 50 pmoles of dADP in 3 hours. The same amount of dGDP was produced by equal concentrations of highly purified enzyme in the presence of dTTP (1.5 mM) and ATP (3 mM) The reduction of all four NDPs was inhibited by dATP.
Identification of the gene encoding M. tuberculosis R1
Sufficient quantities of purified enzyme were generated to obtain N-terminal and internal amino acid sequence data in order to design PCR primers.
A fragment of 908 bp of R1 gene was isolated by polymerase chain reaction (PCR) using primers corresponding to peptide 2 (P2) (5'-GA(G/A)TTCTTCCA(G/A)AC SEQ ID NO:20) and peptide 3 (P3) (5'-GCGTAGGTGTCGATGAT SEQ ID NO:21). The 906 bp fragment was used to probe EcoR1 digested high molecular weight M. tuberculosis DNA. Two bands, 1.1 Kb and 2 Kb, were observed on the Southern blot. Two size selected libraries were generated in lambda ZAP II, one containing inserts of 1.1 Kb and one containing inserts of 2.0 Kb. Plaques were screened with the 908 bp fragment, positives were picked and the plasmid containing the insert was rescued. The 2 kb fragment contained 548 bp of coding region including a potential C-terminus, 358 bp of which overlapped with the 908 bp probe. The 1.1 kb fragment contained coding region 5' to that contained within the 2 Kb fragment but did not extend all the way to the N terminus. The N-terminal 522 bp fragment was isolated by PCR using primers corresponding to peptides 1 and 2: P1 (CCCACCGT(G/C)ATCGCCGAGCC(C/G)GT SEQ ID NO:22) and P2 (AGGGTCTGGAAGAACTC SEQ ID NO:23). Peptide 1 was the sequence determined from N-terminal analysis of highly purified M. tuberculosis R1 and therefore may represent a processed form of R1. In this regard, R1 with heterogeneous N-termini and identical activities have been isolated from E. coli suggesting that the N-terminus does not play a central role in either the catalytic or regulatory activity. The initial 908 bp fragment was generated by PCR from internal amino acid sequence data. Two EcoR1 fragments, 1.1 kB and 2 kB, provided all but the N-terminal region which was subsequently obtained as a PCR product using the results of amino acid analysis of the N-terminus and an internal site.
The nucleotide sequence of the 2169 base pair R1 gene (SEQ ID NO:24) encodes a protein of 723 amino acids with a calculated molecular weight of 82,244 Da. The coding region is 59% G+C with the third position of the codon 70% G/C rich. The 3' non-coding region is 63% G/C rich.
Expression and activity of recombinant M. tuberculosis R1
Recombinant M. tuberculosis R1 (M. tuberculosis rR1) was expressed in E. coli using a heat induced expression system. M. tuberculosis rR1 was soluble and had the same molecular weight as R1 purified from M. tuberculosis indicating little or no glycosylation. M. tuberculosis rR1 could also be photoaffinity labeled by �.alpha.-.sup.32 P!dATP in the presence of CDP. The activity of purified M. tuberculosis rR1 assayed with dA1 was comparable to that of partially purified wild type M. tuberculosis ribonucleotide reductase indicating the authenticity of the recombinant gene product.
__________________________________________________________________________SEQUENCE LISTING(1) GENERAL INFORMATION:(iii) NUMBER OF SEQUENCES: 25(2) INFORMATION FOR SEQ ID NO:1:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 1613 base pairs(B) TYPE: nucleic acid(C) STRANDEDNESS: double(D) TOPOLOGY: both(ii) MOLECULE TYPE: cDNA(ix) FEATURE:(A) NAME/KEY: CDS(B) LOCATION: 362..1333(xi) SEQUENCE DESCRIPTION: SEQ ID NO:1:GCGCAAGACCGGTTCAACCAGGAGCTGCAGCGCAGGCTGGCTGGGTCGGTGTGGAACAGT60GGCGGCTGCCGCAGCTGTATCTCGACGAGCACGCAAGAACACCGTGCTCTGGTGCGGCTA120CACCTGGCAATACTGGCTGACCACCCGCTCGGTCAACCCCGCCGAGTACCGGTTCTTCGG180GATCGGCAACGGTTTGTCGACGACCGCGCGACGGTCGCTGCGGCGAACTAGCCGGCGAAA240CAGGCGAGCGGATTCGCGACACGCAAACACAACTTCTTGTGTTGCAGTACCTTGTCGGAC300CCCAGGGGTAGTGTTTGAGGCCTAGCAAGGCAGCTTGTTGTCCTGGTGAAGTGGGGTTCT360GGTGACTGGAAACGCAAAGCTAATTGATCGAGTCTCAGCGATCAAC406ValThrGlyAsnAlaLysLeuIleAspArgValSerAlaIleAsn151015TGGAACCGACTGCAAGATGAGAAGGACGCCGAGGTCTGGGATCGGCTG454TrpAsnArgLeuGlnAspGluLysAspAlaGluValTrpAspArgLeu202530ACCGGAAACTTCTGGCTGCCCGAGAAGGTGCCGGTGTCCAATGACATC502ThrGlyAsnPheTrpLeuProGluLysValProValSerAsnAspIle354045CCGTCGTGGGGCACCCTGACCGCCGGCGAGAAGCAACTAACCATGCGG550ProSerTrpGlyThrLeuThrAlaGlyGluLysGlnLeuThrMetArg505560GTCTTCACCGGCCTGACCATGCTGGACACCATCCAGGGCACCGTTGGT598ValPheThrGlyLeuThrMetLeuAspThrIleGlnGlyThrValGly657075GCGGTCAGCCTGATTCCCGACGCGCTGACTCCGCATGAGGAGGCGGTG646AlaValSerLeuIleProAspAlaLeuThrProHisGluGluAlaVal80859095TTGACCAACATCGCGTTCATGGAGTCCGTGCACGCCAAGAGCTACAGC694LeuThrAsnIleAlaPheMetGluSerValHisAlaLysSerTyrSer100105110CAGATCTTCTCCACGCTGTGTTCCACCGCCGAGATCGACGACGCCTTC742GlnIlePheSerThrLeuCysSerThrAlaGluIleAspAspAlaPhe115120125CGCTGGTCGGAGGAAAATCGCAATCTGCAGCGCAAGGCCGAGATCGTG790ArgTrpSerGluGluAsnArgAsnLeuGlnArgLysAlaGluIleVal130135140CTGCAGTACTACCGCGGCGACGAGCCGCTCAAGCGCAAGGTGGCCTCC838LeuGlnTyrTyrArgGlyAspGluProLeuLysArgLysValAlaSer145150155ACCCTGCTGGAGAGCTTCCTGTTCTACTCTGGGTTCTACCTGCCGATG886ThrLeuLeuGluSerPheLeuPheTyrSerGlyPheTyrLeuProMet160165170175TACTGGTCGAGTCGGGCCAAGTTGACCAACACCGCCGACATGATCCGG934TyrTrpSerSerArgAlaLysLeuThrAsnThrAlaAspMetIleArg180185190CTGATCATCCGCGACGAGGCCGTGCACGGTTACTACATCGGCTATAAG982LeuIleIleArgAspGluAlaValHisGlyTyrTyrIleGlyTyrLys195200205TTCCAGCGTGGTCTGGCGTTGGTTGACGACGTCACGCGCGCCGAGCTC1030PheGlnArgGlyLeuAlaLeuValAspAspValThrArgAlaGluLeu210215220AAGGACTACACCTACGAGCTACTGTTCGAGCTCTACGACAACGAGGTG1078LysAspTyrThrTyrGluLeuLeuPheGluLeuTyrAspAsnGluVal225230235GAATACACCCAGGACCTCTACGACGAGGTCGGGCTAACCGAGGACGTC1126GluTyrThrGlnAspLeuTyrAspGluValGlyLeuThrGluAspVal240245250255AAGAAGTTCTTGCGCTACAACGCCAACAAGGCGCTGATGAACCTCGGC1174LysLysPheLeuArgTyrAsnAlaAsnLysAlaLeuMetAsnLeuGly260265270TATGAGGCGCTGTTCCCCCGCGATGAGACCGACGTGAACCCGGCCATC1222TyrGluAlaLeuPheProArgAspGluThrAspValAsnProAlaIle275280285CTGTCGGCGCTGTCACCCAACGCCGACGAGAACCATGACTTCTTCTCC1270LeuSerAlaLeuSerProAsnAlaAspGluAsnHisAspPhePheSer290295300GGATCCGGGTCGAGCTATGTGATCGGCAAGGCGGTCGTCACCGAGGAC1318GlySerGlySerSerTyrValIleGlyLysAlaValValThrGluAsp305310315GATGACTGGGACTTCTAGAGTCGCGGAAATCAGGCCATTGTTCGGCCGGACTCCG1373AspAspTrpAspPhe320AGGCCAGCAAACACTGACCTGATGCGGTAACTAGCTACTACGTCGAGTTGATCTTTGACA1433TGGGCGGACCGTTCGATGCGGACGCGGAGGCCATTTCGACGAGGTTGCCGAGGCATTCGC1493CAAGCTCACCAATGTGGACCGCGACGTCGGCGTAGACCTGGAGAAGGAGCTGTGCAGTGA1553CGGTGGAGGCCGATGACCGCTCTCGGACGCGCTCGTCACAAGGCGTTTGTTGCCGCGCGT1613(2) INFORMATION FOR SEQ ID NO:2:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 324 amino acids(B) TYPE: amino acid(D) TOPOLOGY: linear(ii) MOLECULE TYPE: protein(xi) SEQUENCE DESCRIPTION: SEQ ID NO:2:ValThrGlyAsnAlaLysLeuIleAspArgValSerAlaIleAsnTrp151015AsnArgLeuGlnAspGluLysAspAlaGluValTrpAspArgLeuThr202530GlyAsnPheTrpLeuProGluLysValProValSerAsnAspIlePro354045SerTrpGlyThrLeuThrAlaGlyGluLysGlnLeuThrMetArgVal505560PheThrGlyLeuThrMetLeuAspThrIleGlnGlyThrValGlyAla65707580ValSerLeuIleProAspAlaLeuThrProHisGluGluAlaValLeu859095ThrAsnIleAlaPheMetGluSerValHisAlaLysSerTyrSerGln100105110IlePheSerThrLeuCysSerThrAlaGluIleAspAspAlaPheArg115120125TrpSerGluGluAsnArgAsnLeuGlnArgLysAlaGluIleValLeu130135140GlnTyrTyrArgGlyAspGluProLeuLysArgLysValAlaSerThr145150155160LeuLeuGluSerPheLeuPheTyrSerGlyPheTyrLeuProMetTyr165170175TrpSerSerArgAlaLysLeuThrAsnThrAlaAspMetIleArgLeu180185190IleIleArgAspGluAlaValHisGlyTyrTyrIleGlyTyrLysPhe195200205GlnArgGlyLeuAlaLeuValAspAspValThrArgAlaGluLeuLys210215220AspTyrThrTyrGluLeuLeuPheGluLeuTyrAspAsnGluValGlu225230235240TyrThrGlnAspLeuTyrAspGluValGlyLeuThrGluAspValLys245250255LysPheLeuArgTyrAsnAlaAsnLysAlaLeuMetAsnLeuGlyTyr260265270GluAlaLeuPheProArgAspGluThrAspValAsnProAlaIleLeu275280285SerAlaLeuSerProAsnAlaAspGluAsnHisAspPhePheSerGly290295300SerGlySerSerTyrValIleGlyLysAlaValValThrGluAspAsp305310315320AspTrpAspPhe(2) INFORMATION FOR SEQ ID NO:3:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 3107 base pairs(B) TYPE: nucleic acid(C) STRANDEDNESS: double(D) TOPOLOGY: both(ii) MOLECULE TYPE: cDNA(ix) FEATURE:(A) NAME/KEY: CDS(B) LOCATION: 207..2909(xi) SEQUENCE DESCRIPTION: SEQ ID NO:3:GATCTCCGAGCGTCCTGAGCGGCCCGTTTGAGCCTTTGGTGTGGTAATCTGTTTGCAGCC60GGTTTGCGCAGGCCCGCCCTAGAGTGCGAGATTGTCAGTTGCCGACAGGCGAGGGAAACG120GCGGCGTACCGGAATTCACCTGGGATTCGGCAGTCGGCCGCGTCCTCTACCTACCGGGGC180GGTCTCGATAGGGGCCGGGATAAGAGATGGAGCGTGGGGCGCAGTTGGCTGAC233MetGluArgGlyAlaGlnLeuAlaAsp325330CCGAAAACGAAGGGCCGTGGCAGCGGCGGCAATGGCAGCGGCCGGCGA281ProLysThrLysGlyArgGlySerGlyGlyAsnGlySerGlyArgArg335340345CTGGTCATCGTCGAGTCGCCCACCAAGGCGCGCAAGCTGGCCTCCTAC329LeuValIleValGluSerProThrLysAlaArgLysLeuAlaSerTyr350355360365CTGGGCTCTGGCTACATCGTCGAGTCCTCCCGGGGGCACATCCGTGAC377LeuGlySerGlyTyrIleValGluSerSerArgGlyHisIleArgAsp370375380TTGCGCGGGCCGCGTCGATGTACCCGCAAGTACAAGTCGCAGCCGTGG425LeuArgGlyProArgArgCysThrArgLysTyrLysSerGlnProTrp385390395GCGCGGCTCGGGGTCAACGTCGACGCCGACTTCGAACCGCTCTACATC473AlaArgLeuGlyValAsnValAspAlaAspPheGluProLeuTyrIle400405410ATCAGCCCGGAGAAACGGAGCACCGTCAGCGAGCTCAGGGGCCTGCTC521IleSerProGluLysArgSerThrValSerGluLeuArgGlyLeuLeu415420425AAAGACGTGGACGAGCTGTATCTGGCCACGGATGGGGACCGTGAGGGC569LysAspValAspGluLeuTyrLeuAlaThrAspGlyAspArgGluGly430435440445GAAGCTATTGCCTGGCATCTGCTGGAAACCCTCAAACCGCGCATACCG617GluAlaIleAlaTrpHisLeuLeuGluThrLeuLysProArgIlePro450455460GTAAAGCGGATGGTCTTCCACGAGATCACCGAACCGGCGATCCGCGCC665ValLysArgMetValPheHisGluIleThrGluProAlaIleArgAla465470475GCCGCCGAGCATCCCCGCGACCTAGACATCGACCTGGTCGACGCGCAG713AlaAlaGluHisProArgAspLeuAspIleAspLeuValAspAlaGln480485490GAGACCCGGCGCATCCTGGACCGGCTGTACGGCTACGAAGTCAGCCCA761GluThrArgArgIleLeuAspArgLeuTyrGlyTyrGluValSerPro495500505GTGCTGTGGAAGAAGGTCGCCCCCAAGTTGTCGGCGGGCCGGGTGCAG809ValLeuTrpLysLysValAlaProLysLeuSerAlaGlyArgValGln510515520525TCGGTGGCCACCCGCATCATCGTGGCGCGCGAACGCGACCGCATGGCG857SerValAlaThrArgIleIleValAlaArgGluArgAspArgMetAla530535540TTCCGCAGCGCGGCCTACTGGGACATCCTTGCCAAGCTGGATGCCAGC905PheArgSerAlaAlaTyrTrpAspIleLeuAlaLysLeuAspAlaSer545550555GTGTCCGACCCGGACGCCGCGCCGCCCACCTTCAGCGCCCGGCTGACG953ValSerAspProAspAlaAlaProProThrPheSerAlaArgLeuThr560565570GCCGTGGCTGGCCGGCGGGTGGCCACTGGCGCGATTTCGACTCGCTGG1001AlaValAlaGlyArgArgValAlaThrGlyAlaIleSerThrArgTrp575580585GCACGCTGCGCAAAGGCGACGAAGTCATTGTGCTCGACGAGGGGAGCG1049AlaArgCysAlaLysAlaThrLysSerLeuCysSerThrArgGlyAla590595600605CGACCGCGTTGGCCGGCGGGCCTGGATGGCACGCAGCTGACCGTGGCC1097ArgProArgTrpProAlaGlyLeuAspGlyThrGlnLeuThrValAla610615620TCGGCCGAGGAGAAGCCCTACGCCCGGCGCCCGTACCCGCCGTTCATG1145SerAlaGluGluLysProTyrAlaArgArgProTyrProProPheMet625630635ACCTCCACGCTGCAGCAAGAGGCCAGCCGCAAGCTGCGGTTCTCCGCC1193ThrSerThrLeuGlnGlnGluAlaSerArgLysLeuArgPheSerAla640645650GAGCGGACGATGAGCATCGCCCAGCGGCTGTACGAAAACGGCTACATC1241GluArgThrMetSerIleAlaGlnArgLeuTyrGluAsnGlyTyrIle655660665ACCTATATGCGTACCGACTCCACCACGCTGTCGGAGTCGGCGATCAAC1289ThrTyrMetArgThrAspSerThrThrLeuSerGluSerAlaIleAsn670675680685GCCGCACGTACCCAGGCGCGCCAGCTCTACGGCGACGGAGTACGTCGG1337AlaAlaArgThrGlnAlaArgGlnLeuTyrGlyAspGlyValArgArg690695700CCGGCGCCGCGCCAATACACCCGCAAGGTGAAGAACGCCCAGGAAGCG1385ProAlaProArgGlnTyrThrArgLysValLysAsnAlaGlnGluAla705710715CACGAGGCTATCCGGCCCGCCGGTGAAACGTTTGCCACCCCGGACGCG1433HisGluAlaIleArgProAlaGlyGluThrPheAlaThrProAspAla720725730GTGCGTCGCGAACTCGACGGTCCCAACATTGATGATTTCCGGCTCTAT1481ValArgArgGluLeuAspGlyProAsnIleAspAspPheArgLeuTyr735740745GAGCTGATTTGGCAACGCACCGTAGCCTCGCAGATGGCCGATGCGCGG1529GluLeuIleTrpGlnArgThrValAlaSerGlnMetAlaAspAlaArg750755760765GGCATGACGCTGAGCCTGCGGATCACTGGCATGTCGGGGCACCAGGAG1577GlyMetThrLeuSerLeuArgIleThrGlyMetSerGlyHisGlnGlu770775780GTGGTGTTCTCCGCGACCGGACGCACCTTGACGTTCCCGGGCTTCCTC1625ValValPheSerAlaThrGlyArgThrLeuThrPheProGlyPheLeu785790795AAGGCCTACGTGGAGACGGTGGACGAGCTGGTCGGCGGCGAGGCTGAC1673LysAlaTyrValGluThrValAspGluLeuValGlyGlyGluAlaAsp800805810GATGCCGAGCGGCGACTGCCCCATCTGACCCCGGGTCAACGGTTGGAC1721AspAlaGluArgArgLeuProHisLeuThrProGlyGlnArgLeuAsp815820825ATCGTCGAGTTGACCCCAGACGGCCATGCCACCAACCCGCCGGCCCGC1769IleValGluLeuThrProAspGlyHisAlaThrAsnProProAlaArg830835840845TACACCGAGGCGTCGCTGGTCAAAGCGCTCGAGGAGCTGGGCATCGGC1817TyrThrGluAlaSerLeuValLysAlaLeuGluGluLeuGlyIleGly850855860CGCCCGTCGACCTACTCGTCGATCATCAAGACCATCCAGGATCGCGGC1865ArgProSerThrTyrSerSerIleIleLysThrIleGlnAspArgGly865870875TACGTGCACAAGAAGGGCAGTGCACTGGTGCCGTCATGGGTGGCGTTC1913TyrValHisLysLysGlySerAlaLeuValProSerTrpValAlaPhe880885890GCGGTAACCGGTCTGCTCGAGCAGCATTTCGGTCGGCTCGTCGACTAC1961AlaValThrGlyLeuLeuGluGlnHisPheGlyArgLeuValAspTyr895900905GACTTCACCGCGGCGATGGAAGACGAGCTCGACGAGATCGCCGCCGGC2009AspPheThrAlaAlaMetGluAspGluLeuAspGluIleAlaAlaGly910915920925AACGAGCGCCGCACCAACTGGCTCAACAACTTCTACTTTGGTGGCGAT2057AsnGluArgArgThrAsnTrpLeuAsnAsnPheTyrPheGlyGlyAsp930935940CACGGTGTGCCCGATTCGGTAGCCCGATCGGGTGGCCTCAAGAAGCTT2105HisGlyValProAspSerValAlaArgSerGlyGlyLeuLysLysLeu945950955GTCGGGATCAATCTCGAGGGCATCGACGCACGAGAAGTAAACTCTATC2153ValGlyIleAsnLeuGluGlyIleAspAlaArgGluValAsnSerIle960965970AAGCTTTTTGACGACACCCACGGACGCCCCATATATGTTCGGGTGGGC2201LysLeuPheAspAspThrHisGlyArgProIleTyrValArgValGly975980985AAGAACGGTCCCTACCTGGAACGTTTGGTGGCCGGCGACACCGGTGAG2249LysAsnGlyProTyrLeuGluArgLeuValAlaGlyAspThrGlyGlu99099510001005CCCACGCCGCAGCGGGCCAACCTCAGCGACTCGATTACCCCGGACGAG2297ProThrProGlnArgAlaAsnLeuSerAspSerIleThrProAspGlu101010151020CTGACTCTACAGGTGGCCGAAGAGCTCTTTGCCACACCGCAACAGGGA2345LeuThrLeuGlnValAlaGluGluLeuPheAlaThrProGlnGlnGly102510301035CGGACTTTGGGCTTGGACCCAGAAACCGGCCACGAGATCGTGGCCAGG2393ArgThrLeuGlyLeuAspProGluThrGlyHisGluIleValAlaArg104010451050GAAGGCCGGTTTGGGCCGTATGTGACCGAGATCCTGCCGGAGCCTGCG2441GluGlyArgPheGlyProTyrValThrGluIleLeuProGluProAla105510601065GCTGATGCGGCCGCGGCCGCTCAGGGAGTCAAGAAACGCCAGAAGGCC2489AlaAspAlaAlaAlaAlaAlaGlnGlyValLysLysArgGlnLysAla1070107510801085GCCGGGCCCAAACCGCGCACCGGTTCGTTGCTGCGGAGCATGGACCTA2537AlaGlyProLysProArgThrGlySerLeuLeuArgSerMetAspLeu109010951100CAGACGGTCACCCTCGAAGACGCGCTGAGGCTGCTGTCACTGCCGCGC2585GlnThrValThrLeuGluAspAlaLeuArgLeuLeuSerLeuProArg110511101115GTGGTCGGAGTGGACCCCGCCTCGGTCGAGGAGATCACCGCGCAGAAC2633ValValGlyValAspProAlaSerValGluGluIleThrAlaGlnAsn112011251130GGGCGCTACGGACCGTATCTAAAGCGCGGCAACGATTCTCGATCACTG2681GlyArgTyrGlyProTyrLeuLysArgGlyAsnAspSerArgSerLeu113511401145GTCACCGAAGACCAGATATTCACCATCACGCTCGACGAAGCCCTGAAG2729ValThrGluAspGlnIlePheThrIleThrLeuAspGluAlaLeuLys1150115511601165ATCTACGCAGAGCCGAAACGTCGTGGCCGGCAAAGCGCTTCGGCTCCG2777IleTyrAlaGluProLysArgArgGlyArgGlnSerAlaSerAlaPro117011751180GCCTGCGCGAGCTGGGAACAGATCCGGCGTCGGGCAAGCCAATGGTCA2825AlaCysAlaSerTrpGluGlnIleArgArgArgAlaSerGlnTrpSer118511901195TCAAGGACGGCCGATTCGGGCCGTACGTCACCGACGGTGAGACCAATG2873SerArgThrAlaAspSerGlyArgThrSerProThrValArgProMet120012051210CCAGCCTGCGTAAGGGCGACGACGTGGCTTCCATAACCGACGAGCG2919ProAlaCysValArgAlaThrThrTrpLeuPro*121512201225CGCCGCCGAGCTGTTGGCCGATCGCCGAGCCGGGGTCCGGCAAAACGGCCAGCCAGGAAA2979GCTGCCCGGAAGGTGCCGGCGAAGAAGGCAGCCAAGGCGACTAGCCGCGTACTTCGCTGG3039AAACCTCTTCGGGTGCAGCCAGATTCATTGGCCTGGCTAGTTGGGTGGTGCAGCACGTCG3099CGGAGCTC3107(2) INFORMATION FOR SEQ ID NO:4:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 900 amino acids(B) TYPE: amino acid(D) TOPOLOGY: linear(ii) MOLECULE TYPE: protein(xi) SEQUENCE DESCRIPTION: SEQ ID NO:4:MetGluArgGlyAlaGlnLeuAlaAspProLysThrLysGlyArgGly151015SerGlyGlyAsnGlySerGlyArgArgLeuValIleValGluSerPro202530ThrLysAlaArgLysLeuAlaSerTyrLeuGlySerGlyTyrIleVal354045GluSerSerArgGlyHisIleArgAspLeuArgGlyProArgArgCys505560ThrArgLysTyrLysSerGlnProTrpAlaArgLeuGlyValAsnVal65707580AspAlaAspPheGluProLeuTyrIleIleSerProGluLysArgSer859095ThrValSerGluLeuArgGlyLeuLeuLysAspValAspGluLeuTyr100105110LeuAlaThrAspGlyAspArgGluGlyGluAlaIleAlaTrpHisLeu115120125LeuGluThrLeuLysProArgIleProValLysArgMetValPheHis130135140GluIleThrGluProAlaIleArgAlaAlaAlaGluHisProArgAsp145150155160LeuAspIleAspLeuValAspAlaGlnGluThrArgArgIleLeuAsp165170175ArgLeuTyrGlyTyrGluValSerProValLeuTrpLysLysValAla180185190ProLysLeuSerAlaGlyArgValGlnSerValAlaThrArgIleIle195200205ValAlaArgGluArgAspArgMetAlaPheArgSerAlaAlaTyrTrp210215220AspIleLeuAlaLysLeuAspAlaSerValSerAspProAspAlaAla225230235240ProProThrPheSerAlaArgLeuThrAlaValAlaGlyArgArgVal245250255AlaThrGlyAlaIleSerThrArgTrpAlaArgCysAlaLysAlaThr260265270LysSerLeuCysSerThrArgGlyAlaArgProArgTrpProAlaGly275280285LeuAspGlyThrGlnLeuThrValAlaSerAlaGluGluLysProTyr290295300AlaArgArgProTyrProProPheMetThrSerThrLeuGlnGlnGlu305310315320AlaSerArgLysLeuArgPheSerAlaGluArgThrMetSerIleAla325330335GlnArgLeuTyrGluAsnGlyTyrIleThrTyrMetArgThrAspSer340345350ThrThrLeuSerGluSerAlaIleAsnAlaAlaArgThrGlnAlaArg355360365GlnLeuTyrGlyAspGlyValArgArgProAlaProArgGlnTyrThr370375380ArgLysValLysAsnAlaGlnGluAlaHisGluAlaIleArgProAla385390395400GlyGluThrPheAlaThrProAspAlaValArgArgGluLeuAspGly405410415ProAsnIleAspAspPheArgLeuTyrGluLeuIleTrpGlnArgThr420425430ValAlaSerGlnMetAlaAspAlaArgGlyMetThrLeuSerLeuArg435440445IleThrGlyMetSerGlyHisGlnGluValValPheSerAlaThrGly450455460ArgThrLeuThrPheProGlyPheLeuLysAlaTyrValGluThrVal465470475480AspGluLeuValGlyGlyGluAlaAspAspAlaGluArgArgLeuPro485490495HisLeuThrProGlyGlnArgLeuAspIleValGluLeuThrProAsp500505510GlyHisAlaThrAsnProProAlaArgTyrThrGluAlaSerLeuVal515520525LysAlaLeuGluGluLeuGlyIleGlyArgProSerThrTyrSerSer530535540IleIleLysThrIleGlnAspArgGlyTyrValHisLysLysGlySer545550555560AlaLeuValProSerTrpValAlaPheAlaValThrGlyLeuLeuGlu565570575GlnHisPheGlyArgLeuValAspTyrAspPheThrAlaAlaMetGlu580585590AspGluLeuAspGluIleAlaAlaGlyAsnGluArgArgThrAsnTrp595600605LeuAsnAsnPheTyrPheGlyGlyAspHisGlyValProAspSerVal610615620AlaArgSerGlyGlyLeuLysLysLeuValGlyIleAsnLeuGluGly625630635640IleAspAlaArgGluValAsnSerIleLysLeuPheAspAspThrHis645650655GlyArgProIleTyrValArgValGlyLysAsnGlyProTyrLeuGlu660665670ArgLeuValAlaGlyAspThrGlyGluProThrProGlnArgAlaAsn675680685LeuSerAspSerIleThrProAspGluLeuThrLeuGlnValAlaGlu690695700GluLeuPheAlaThrProGlnGlnGlyArgThrLeuGlyLeuAspPro705710715720GluThrGlyHisGluIleValAlaArgGluGlyArgPheGlyProTyr725730735ValThrGluIleLeuProGluProAlaAlaAspAlaAlaAlaAlaAla740745750GlnGlyValLysLysArgGlnLysAlaAlaGlyProLysProArgThr755760765GlySerLeuLeuArgSerMetAspLeuGlnThrValThrLeuGluAsp770775780AlaLeuArgLeuLeuSerLeuProArgValValGlyValAspProAla785790795800SerValGluGluIleThrAlaGlnAsnGlyArgTyrGlyProTyrLeu805810815LysArgGlyAsnAspSerArgSerLeuValThrGluAspGlnIlePhe820825830ThrIleThrLeuAspGluAlaLeuLysIleTyrAlaGluProLysArg835840845ArgGlyArgGlnSerAlaSerAlaProAlaCysAlaSerTrpGluGln850855860IleArgArgArgAlaSerGlnTrpSerSerArgThrAlaAspSerGly865870875880ArgThrSerProThrValArgProMetProAlaCysValArgAlaThr885890895ThrTrpLeuPro900(2) INFORMATION FOR SEQ ID NO:5:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 1391 base pairs(B) TYPE: nucleic acid(C) STRANDEDNESS: double(D) TOPOLOGY: both(ii) MOLECULE TYPE: cDNA(ix) FEATURE:(A) NAME/KEY: CDS(B) LOCATION: 289..1254(xi) SEQUENCE DESCRIPTION: SEQ ID NO:5:AAGACTTCCCGCAAACCGACCATGAGTTCCGCGGCGTCGTCGGCTACTGGCCAGGCGTCG60CGTAACTGTATGCGCGGTGATCGCTGTTTGTAATGAGTTCAGCGACACGAAGAATAAAAT120ATGGTAGCCGAAATCACTAAGCTACAGTGCTGGTGCACGCCATGAAAGACCGTCAATGAC180AAGGAGGACGGCCGAAATGCCCAAGGACCGACTGCCGGACTTGACGCCCACAGGAGCGTA240CGCACCGGCCAACAGCGGCATGACCATGGCAAGGCAGGACGGCCCTCGATGACCGGC297MetThrGlyAAGCTCGTTGAGCGGGTGCACGCAATCAATTGGAACCGGTTGCTCGAT345LysLeuValGluArgValHisAlaIleAsnTrpAsnArgLeuLeuAsp51015GCTAAAGATTTGCAGGTCTGGGAACGTTTGACCGGTAACTTTTGGTTG393AlaLysAspLeuGlnValTrpGluArgLeuThrGlyAsnPheTrpLeu20253035CCGGAAAAGATTCCGCTCTCCAACGACCTGGCATCTTGGCAAACGTTG441ProGluLysIleProLeuSerAsnAspLeuAlaSerTrpGlnThrLeu404550AGTTCCACCGAGCAGCAGACGACGATCCGGGTGTTCACCGGCTTGACC489SerSerThrGluGlnGlnThrThrIleArgValPheThrGlyLeuThr556065CTGCTCGACACCGCGCAGGCGACGGTGGGAGCAGTGGCCATGATCGAC537LeuLeuAspThrAlaGlnAlaThrValGlyAlaValAlaMetIleAsp707580GACGCGGTCACCCCCCACGAAGAGGCGGTCCTGACCAACATGGCGTTC585AspAlaValThrProHisGluGluAlaValLeuThrAsnMetAlaPhe859095ATGGAGTCAGTGCACGCCAAGAGCTACAGCTCGATCTTCTCGACCCTG633MetGluSerValHisAlaLysSerTyrSerSerIlePheSerThrLeu100105110115TGCTCGACCAAGCAGATCGACGATGCCTTCGACTGGTCGGAACAGAAC681CysSerThrLysGlnIleAspAspAlaPheAspTrpSerGluGlnAsn120125130CCTTACCTGCAGCGAAAAGCGCAGATCATCGTCGACTACTACCGCGGT729ProTyrLeuGlnArgLysAlaGlnIleIleValAspTyrTyrArgGly135140145GACGACGCTCAAGCGCAAAGATCGTCGGTAATGCTGGAGTCCTTCCTG777AspAspAlaGlnAlaGlnArgSerSerValMetLeuGluSerPheLeu150155160TTCTACTCCGGCTTCTACCTGCCCATGTACTGGTCGTCGCGGGGTAAG825PheTyrSerGlyPheTyrLeuProMetTyrTrpSerSerArgGlyLys165170175CTCACCAACACCGCCGATCTGATCCGGCTGATCATCCGAGATGAAGCC873LeuThrAsnThrAlaAspLeuIleArgLeuIleIleArgAspGluAla180185190195GTCCACGGCTACTACATCGGCTACAAATGTCAACGAGGTTTGGCCGAC921ValHisGlyTyrTyrIleGlyTyrLysCysGlnArgGlyLeuAlaAsp200205210CTGACCGACGCCGAGCGGGCCGACCACCGCGAATACACCTGCGAGCTG969LeuThrAspAlaGluArgAlaAspHisArgGluTyrThrCysGluLeu215220225CTGCACACGCTCTACGCGAACGAGATCGACTATGCGCACGACTTGTAC1017LeuHisThrLeuTyrAlaAsnGluIleAspTyrAlaHisAspLeuTyr230235240GACGAGTTGGGCTGGACCGACGACGTTTTGCCCTACATGCGTTACAAC1065AspGluLeuGlyTrpThrAspAspValLeuProTyrMetArgTyrAsn245250255GCCAACAAGGCGCTAGCCAACCTGGGATACCAGCCTGCATTCGATCGT1113AlaAsnLysAlaLeuAlaAsnLeuGlyTyrGlnProAlaPheAspArg260265270275GACACCTGCCAGGTGAACCCGGCCGTGCGCGCAGCTCTCGACCCCGGT1161AspThrCysGlnValAsnProAlaValArgAlaAlaLeuAspProGly280285290GCAGGGGAGAACCACGACTTTTTCTCCGGCTCCGGAAGCTCATACGTA1209AlaGlyGluAsnHisAspPhePheSerGlySerGlySerSerTyrVal295300305ATGGGCACCCACCAACCCACCACCGACACCGACTGGGACTTCTAA1254MetGlyThrHisGlnProThrThrAspThrAspTrpAspPhe*310315320CCGCCCAGCGCGTCGGGGGCGTCGAGCACCACGCGACACCGGGCCCGATCGATCTGCTAG1314CTTGAGTCTGGTCAGGCATCGTCGTCAGCAGCCATGCCCTATGTTTGTCGTCGACTCAGA1374TATGCGGCAATCCAATC1391(2) INFORMATION FOR SEQ ID NO:6:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 321 amino acids(B) TYPE: amino acid(D) TOPOLOGY: linear(ii) MOLECULE TYPE: protein(xi) SEQUENCE DESCRIPTION: SEQ ID NO:6:MetThrGlyLysLeuValGluArgValHisAlaIleAsnTrpAsnArg151015LeuLeuAspAlaLysAspLeuGlnValTrpGluArgLeuThrGlyAsn202530PheTrpLeuProGluLysIleProLeuSerAsnAspLeuAlaSerTrp354045GlnThrLeuSerSerThrGluGlnGlnThrThrIleArgValPheThr505560GlyLeuThrLeuLeuAspThrAlaGlnAlaThrValGlyAlaValAla65707580MetIleAspAspAlaValThrProHisGluGluAlaValLeuThrAsn859095MetAlaPheMetGluSerValHisAlaLysSerTyrSerSerIlePhe100105110SerThrLeuCysSerThrLysGlnIleAspAspAlaPheAspTrpSer115120125GluGlnAsnProTyrLeuGlnArgLysAlaGlnIleIleValAspTyr130135140TyrArgGlyAspAspAlaGlnAlaGlnArgSerSerValMetLeuGlu145150155160SerPheLeuPheTyrSerGlyPheTyrLeuProMetTyrTrpSerSer165170175ArgGlyLysLeuThrAsnThrAlaAspLeuIleArgLeuIleIleArg180185190AspGluAlaValHisGlyTyrTyrIleGlyTyrLysCysGlnArgGly195200205LeuAlaAspLeuThrAspAlaGluArgAlaAspHisArgGluTyrThr210215220CysGluLeuLeuHisThrLeuTyrAlaAsnGluIleAspTyrAlaHis225230235240AspLeuTyrAspGluLeuGlyTrpThrAspAspValLeuProTyrMet245250255ArgTyrAsnAlaAsnLysAlaLeuAlaAsnLeuGlyTyrGlnProAla260265270PheAspArgAspThrCysGlnValAsnProAlaValArgAlaAlaLeu275280285AspProGlyAlaGlyGluAsnHisAspPhePheSerGlySerGlySer290295300SerTyrValMetGlyThrHisGlnProThrThrAspThrAspTrpAsp305310315320Phe(2) INFORMATION FOR SEQ ID NO:7:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 7 amino acids(B) TYPE: amino acid(C) STRANDEDNESS: Not Relevant(D) TOPOLOGY: linear(ii) MOLECULE TYPE: peptide(ix) FEATURE:(A) NAME/KEY: Modified-site(B) LOCATION: Thr(1)(D) OTHER INFORMATION: /product="OTHER"/note= "TERMINAL IS ACETYLATED"(xi) SEQUENCE DESCRIPTION: SEQ ID NO:7:ThrAspThrAspTrpAspPhe15(2) INFORMATION FOR SEQ ID NO:8:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 7 amino acids(B) TYPE: amino acid(C) STRANDEDNESS: Not Relevant(D) TOPOLOGY: linear(ii) MOLECULE TYPE: peptide(ix) FEATURE:(A) NAME/KEY: Modified-site(B) LOCATION: Thr(1)(D) OTHER INFORMATION: /product="OTHER"/note= "TERMINAL IS ACETYLATED"(xi) SEQUENCE DESCRIPTION: SEQ ID NO:8:GluAspAspAspTrpAspPhe15(2) INFORMATION FOR SEQ ID NO:9:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 17 base pairs(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) MOLECULE TYPE: DNA(xi) SEQUENCE DESCRIPTION: SEQ ID NO:9:TTCATGGAGGCSGTSCA17(2) INFORMATION FOR SEQ ID NO:10:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 17 base pairs(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) MOLECULE TYPE: DNA(xi) SEQUENCE DESCRIPTION: SEQ ID NO:10:TAGAACAGGAASGACTC17(2) INFORMATION FOR SEQ ID NO:11:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 14 base pairs(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) MOLECULE TYPE: DNA(xi) SEQUENCE DESCRIPTION: SEQ ID NO:11:TGSACSGCCTCGTC14(2) INFORMATION FOR SEQ ID NO:12:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 25 base pairs(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) MOLECULE TYPE: DNA(xi) SEQUENCE DESCRIPTION: SEQ ID NO:12:TCTAGAATGACCGGCAAGCTCGTTG25(2) INFORMATION FOR SEQ ID NO:13:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 25 base pairs(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) MOLECULE TYPE: DNA(xi) SEQUENCE DESCRIPTION: SEQ ID NO:13:TCTAGATTAGAAGTCCCAGTCGGTG25(2) INFORMATION FOR SEQ ID NO:14:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 14 base pairs(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) MOLECULE TYPE: DNA(xi) SEQUENCE DESCRIPTION: SEQ ID NO:14:ATCGAGAACATCCA14(2) INFORMATION FOR SEQ ID NO:15:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 14 base pairs(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) MOLECULE TYPE: DNA(xi) SEQUENCE DESCRIPTION: SEQ ID NO:15:AAGAAGATGCCCTC14(2) INFORMATION FOR SEQ ID NO:16:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 31 base pairs(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) MOLECULE TYPE: DNA(xi) SEQUENCE DESCRIPTION: SEQ ID NO:16:GCTAGCATGGAGCGTGGGGCGCAGTTGGCTG31(2) INFORMATION FOR SEQ ID NO:17:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 30 base pairs(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) MOLECULE TYPE: DNA(xi) SEQUENCE DESCRIPTION: SEQ ID NO:17:GCTAGCTTATGGAAGCCACGTCGTCGCCCT30(2) INFORMATION FOR SEQ ID NO:18:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 41 base pairs(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) MOLECULE TYPE: DNA(xi) SEQUENCE DESCRIPTION: SEQ ID NO:18:AAAAAAGCTAGCCCCACCGTGATCGCCGAGCCCGTAGCCTC41(2) INFORMATION FOR SEQ ID NO:19:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 27 base pairs(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) MOLECULE TYPE: DNA(xi) SEQUENCE DESCRIPTION: SEQ ID NO:19:AAAAAAGCTAGCCTACAGCATGCAGGA27(2) INFORMATION FOR SEQ ID NO:20:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 14 base pairs(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) MOLECULE TYPE: DNA(xi) SEQUENCE DESCRIPTION: SEQ ID NO:20:GARTTCTTCCARAC14(2) INFORMATION FOR SEQ ID NO:21:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 17 base pairs(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) MOLECULE TYPE: DNA(xi) SEQUENCE DESCRIPTION: SEQ ID NO:21:GCGTAGGTGTCGATGAT17(2) INFORMATION FOR SEQ ID NO:22:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 23 base pairs(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) MOLECULE TYPE: DNA(xi) SEQUENCE DESCRIPTION: SEQ ID NO:22:CCCACCGTSATCGCCGAGCCSGT23(2) INFORMATION FOR SEQ ID NO:23:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 17 base pairs(B) TYPE: nucleic acid(C) STRANDEDNESS: single(D) TOPOLOGY: linear(ii) MOLECULE TYPE: DNA(xi) SEQUENCE DESCRIPTION: SEQ ID NO:23:AGGGTCTGGAAGAACTC17(2) INFORMATION FOR SEQ ID NO:24:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 4107 base pairs(B) TYPE: nucleic acid(C) STRANDEDNESS: double(D) TOPOLOGY: both(ii) MOLECULE TYPE: cDNA(ix) FEATURE:(A) NAME/KEY: CDS(B) LOCATION: 446..2620(xi) SEQUENCE DESCRIPTION: SEQ ID NO:24:TAGATAAGGAAGATTGCGGTGCCATGGATTACTCGCGGGCGCAGCCTGGTCTATTTCTCC60AGCGTGTCGGAGAACACCCACCGCTTTGTGCAGAAACTGGGTATTCCCGCCACGCGGATA120CCGCTGCATGGCCGGATCGAGGTCGACGAGCCGTACGTGCTGATACTGCCCACCTACGGT180GGCGGCCGGGCCAACCCGGGTCTCGATGCCGGCGGATACGTCCCCAAACAGGTCATTGCC240TTCTTGAACAACGACCACAATCGACGCACGTGCGCGGGGTCATCGCTGCCGGCAATACCA300ACTTCGGTGCCGAGTTCTCGTACGCCGGCGACGTCGTCTCCCGAAAATGTAGCGTTCCCT360ACCTATACCGCTTCGAACTGATGGGCACCGAGGACGACGTCGCCGCCGTCCGCACCGGTC420TCGCTGAATTCTGGAAGGAACAGACGTGCCACCAACCGTCATTGCAGAGCCC472ValProProThrValIleAlaGluPro15GTAGCCTCCGGCGCGCACGCCTCTTACTCTGGGGGGCCGGGCGAAACG520ValAlaSerGlyAlaHisAlaSerTyrSerGlyGlyProGlyGluThr10152025GACTATCACGCGCTGAACGCGATGCTGAACCTGTACGACGCGGACGGC568AspTyrHisAlaLeuAsnAlaMetLeuAsnLeuTyrAspAlaAspGly303540AAGATCCAGTTCGACAAGGATCGGGAAGCAGCCCACCAGTACTTTTTG616LysIleGlnPheAspLysAspArgGluAlaAlaHisGlnTyrPheLeu455055CAGCATGTCAATCAGAACACGGTCTTCTTCCATAATCAGGACGAGAAG664GlnHisValAsnGlnAsnThrValPhePheHisAsnGlnAspGluLys606570CTCGACTACCTGATCCGCGAGAATTACTACGAGCGTGAGGTTCTCGAC712LeuAspTyrLeuIleArgGluAsnTyrTyrGluArgGluValLeuAsp758085CAGTACTCGCGCAACTTCGTCAAGACGCTGCTAGACCGCGCCTACGCC760GlnTyrSerArgAsnPheValLysThrLeuLeuAspArgAlaTyrAla9095100105AAAAAGTTCCGGTTTCCGACGTTTTTGGGTGCGTTCAAGTACTACACC808LysLysPheArgPheProThrPheLeuGlyAlaPheLysTyrTyrThr110115120TCCTACACGCTGAAAACCTTTGACGGGAAGCGCTATCTGGAGCGCTTC856SerTyrThrLeuLysThrPheAspGlyLysArgTyrLeuGluArgPhe125130135GAGGACCGCGTGGTCATGGTGGCGCTAACGTTGGCCGCCGGCGATACC904GluAspArgValValMetValAlaLeuThrLeuAlaAlaGlyAspThr140145150GCACTTGCCGAGCTGCTGGTCGACGAGATCATCGACGGCCGCTTCCAG952AlaLeuAlaGluLeuLeuValAspGluIleIleAspGlyArgPheGln155160165CCCGCCACACCGACGTTTTTGAATTCTGGCAAGAAGCAGCGCGGGGAG1000ProAlaThrProThrPheLeuAsnSerGlyLysLysGlnArgGlyGlu170175180185CCCGTGAGCTGTTTTTTGCTTCGCGTCGAAGATAACATGGAGTCGATC1048ProValSerCysPheLeuLeuArgValGluAspAsnMetGluSerIle190195200GGACGGTCGATCAACTCCGCGCTGCAGCTATCCAAGCGTGGCGGGGGA1096GlyArgSerIleAsnSerAlaLeuGlnLeuSerLysArgGlyGlyGly205210215GTGGCGTTGCTGCTGACCAACATTCGCGAGCACGGCGGCGCCATCAAG1144ValAlaLeuLeuLeuThrAsnIleArgGluHisGlyGlyAlaIleLys220225230AACATCGAGAACCAGTCCTCGGGCGTCATCCCCATCATGAAGTTGCTG1192AsnIleGluAsnGlnSerSerGlyValIleProIleMetLysLeuLeu235240245GAGGATGCGTTCTCCTACGCCAACCAGCTGGGCGCTCGTCAAGGTGCC1240GluAspAlaPheSerTyrAlaAsnGlnLeuGlyAlaArgGlnGlyAla250255260265GGCGCGGTGTACCTGCACGCCCATCACCCCGACATCTACCGATTCCTG1288GlyAlaValTyrLeuHisAlaHisHisProAspIleTyrArgPheLeu270275280GACACCAAGCGTGAGAACGCCGACGAGAAGATCCGGATCAAGACGCTG1336AspThrLysArgGluAsnAlaAspGluLysIleArgIleLysThrLeu285290295AGTCTGGGGGTGGTGATCCCCGACATCACCTTCGAGTTGGCCAAGCGC1384SerLeuGlyValValIleProAspIleThrPheGluLeuAlaLysArg300305310AACGATGACATGTACCTGTTCTCGCCCTACGATGTCGAGCGGGTCTAC1432AsnAspAspMetTyrLeuPheSerProTyrAspValGluArgValTyr315320325GGTGTGCCGTTCGCTGACATCTCGGTCACCGAGAAGTACTACGAAATG1480GlyValProPheAlaAspIleSerValThrGluLysTyrTyrGluMet330335340345GTCGATGACGCGCGCATCCGCAAGACCAAGATCAAGGCACGGGAGTTC1528ValAspAspAlaArgIleArgLysThrLysIleLysAlaArgGluPhe350355360TTCCAGACGCTGGCCGAGCTGCAGTTCGAGTCCGGCTACCCCTATATC1576PheGlnThrLeuAlaGluLeuGlnPheGluSerGlyTyrProTyrIle365370375ATGTTCGAAGACACCGTCAATCGCGCTAATCCAATTGATGGCAAGATC1624MetPheGluAspThrValAsnArgAlaAsnProIleAspGlyLysIle380385390ACGCACAGCAACCTGTGCTCGGAGATCCTGCAAGTGTCTACGCCGTCA1672ThrHisSerAsnLeuCysSerGluIleLeuGlnValSerThrProSer395400405TTGTTCAACGAGGACTTGTCGTATGCCAAAGTGGGCAAAGACATTTCG1720LeuPheAsnGluAspLeuSerTyrAlaLysValGlyLysAspIleSer410415420425TGCAACCTGGGGTCGCTGAACATCGCCAAGACGATGGACTCGCCGGAC1768CysAsnLeuGlySerLeuAsnIleAlaLysThrMetAspSerProAsp430435440TTCGCGCAGACGATCGAGGTGGCGATCCGCGCGTTGACCGCGGTGAGG1816PheAlaGlnThrIleGluValAlaIleArgAlaLeuThrAlaValArg445450455CACCAAACCCATATCAAGTCGGTGCCCTCAATCGAGCAGGGCAACAAC1864HisGlnThrHisIleLysSerValProSerIleGluGlnGlyAsnAsn460465470GACTCCCACGCGATCGGGCTAGGACAGATGAACCTGCACGGCTACCTG1912AspSerHisAlaIleGlyLeuGlyGlnMetAsnLeuHisGlyTyrLeu475480485GCCCGGGAACGCATCTTCTACGGATCCGACGAAGGCATCGACTTCACC1960AlaArgGluArgIlePheTyrGlySerAspGluGlyIleAspPheThr490495500505AACATCTACTTCTATACGGTGCTGTATCACGCGTTGCGGGCATCCAAC2008AsnIleTyrPheTyrThrValLeuTyrHisAlaLeuArgAlaSerAsn510515520CGCATCGCGATCGAACGCGGCACGCACTTCAAGGGTTTCGAGCGGTCC2056ArgIleAlaIleGluArgGlyThrHisPheLysGlyPheGluArgSer525530535AAGTACGCGTCCGGGGAATTCTTCGACAAGTACACCGACCAGATTTGG2104LysTyrAlaSerGlyGluPhePheAspLysTyrThrAspGlnIleTrp540545550GAGCCGAAGACCCAGAAGGTACGCCAGCTGTTCGCCGACGCCGGCATC2152GluProLysThrGlnLysValArgGlnLeuPheAlaAspAlaGlyIle555560565CGCATCCCAACGCAGGACGACTGGCGTCGGCTCAAGGAGTCGGTGCAA2200ArgIleProThrGlnAspAspTrpArgArgLeuLysGluSerValGln570575580585GCGCACGGCATCTACAACCAGAACCTGCAGGCGGTGCCGCCGACCGGG2248AlaHisGlyIleTyrAsnGlnAsnLeuGlnAlaValProProThrGly590595600TCGATTTCCTACATCAACCATTCGACGTCGTCGATTCACCCGATCGTG2296SerIleSerTyrIleAsnHisSerThrSerSerIleHisProIleVal605610615TCGAAGGTCGAGGTCCGCAAGGAAGGCAAGATCGGGCGGGTCTACTAC2344SerLysValGluValArgLysGluGlyLysIleGlyArgValTyrTyr620625630CCGGCGCCGTATATGACCAACGACAACCTGGAGTACTACGAAGACGCC2392ProAlaProTyrMetThrAsnAspAsnLeuGluTyrTyrGluAspAla635640645TACGAGATCGGTTACGAGAAGATCATCGACACCTACGCGGCGGCCACC2440TyrGluIleGlyTyrGluLysIleIleAspThrTyrAlaAlaAlaThr650655660665CAGCATGTGGATCAAGGGCTTTCGCTGACGTTGTTCTTCAAAGACACC2488GlnHisValAspGlnGlyLeuSerLeuThrLeuPhePheLysAspThr670675680GCCACCACCCGCGACGTGAACAAGGCGCAGATTTACGCCTGGCGCAAG2536AlaThrThrArgAspValAsnLysAlaGlnIleTyrAlaTrpArgLys685690695GGGATCAAGACGCTGTACTACATCCGGCTGCGGCAGATGGCGTTGGAG2584GlyIleLysThrLeuTyrTyrIleArgLeuArgGlnMetAlaLeuGlu700705710GGCACCGAGGTCGAGGGTTGCGTGTCCTGCATGCTGTAGCACCGGC2630GlyThrGluValGluGlyCysValSerCysMetLeu715720725GCGCCAGAGTGAAAGTGGCGACGGCTTCGCGGCGTGGTCGCGTCGTGAACCTCACATTCA2690ACCAAGCCTGGCGTGGCCAGTCTGCCCAGGTCAGCGCTTGCAACGCGGTAAGGTGCTTGA2750TGTGGTCAGAATCCCCCGACCCCACCCCAGTGCAAAGCCGGGGGTGAAAGTCGACGCCGC2810AGTGAACGGTGGCGTGACCGACCGCAAGAAGGTGCGCAACGAAATCGTCGACGCGGCGTT2870CCGCTATCGACCGGCTGGGCCCCGAGCTGAGTGTGCGCCAAATCGCCGAAGAGGCCGGCA2930CCGCCAAGCCCAAGATCTATCGGCATTTCACCGACAAGTCCGATTTGCTCGAGGCTATCG2990GGATGCGACTGCGTGACATGCTGTGGGCGGCGATCTTCCCGTCGCTCGACTTAGCCACCG3050ACTCTGCCCGCGAAGTTATCCGGCGCACGTCGAGGAGTACGTCAACCTCGTCGACCAGCA3110CCCCAACGTGCTGCGGGTGTTCATTCAGGGCCGCTCGCGAAAGCAGTCCGAGGCGACGGT3170ACGCACCCTCAACGAAGGCCGGGAGATCACGCTGGCCATGGCGAGATGTTCAACAACGAG3230CTGCGCAGATGGAGCTGAATCGAGCCGCGCTCGAACCATTCGGATCGGCCGCATCGGCAA3290CCGAGTGGTGGTTGGGCCCCGAACCCGACAGCCCGCGCGCATGCCGCGTGAGCAGTTCGT3350GGCGCATCTGACCACCATCATGATGGGCGTGATCGGTGCGCACCGCCGAAGCGCTGGGCA3410TCGCGGTCGACCCTGACCAACCGATCCACGACGCGGTACCCAACAAGTGCGCCGACACGT3470GCGTTGAGCGCGGCGGCCGTTGACATCGCTGCGGCAATCAACAACACTCGTCATATCCGA3530TACCCTGGGTACTGGGTATTTGCGCCGGCGAGGGTGACTGAAGCGCCAAACTCGCCGCTG3590AACAGGAACCGATCCATTGTGAGCATTGCCGATACGGCTGCCAAGCCGTCCACGCCAAGC3650CCGGCCAACCAGCCGCCGGTACGTACCCGCGCCGTCATCATCGGAACCGGATTCTCCGGT3710TTGGGCATGGCCATCGCACTGCAAAAGCAAGGAGTGACTTCGTCATATTGGAGAACGACG3770ACGTCGGCGGCACCTGGCGCGACAACAGGTACCCCGCTGCGCGCGACATCCCGTCGCACC3830TGTACTCCTTCTCGTTCGAGCCCAAGGCGGACTGGAAACACCTGTTTTCCTACTGGGACG3890AAATCTTGGGCTACCTCAAAGGGGTCACCGACAAGTAGCCCTGCGCCGCTACATCGAGTT3950CAATTCGCTCGTCGATCGCGGCTACTGGGACGACGACGAATGCCGCTGGCACGTGTTCAC4010CGCCGACGGGACGTGAATACGTCGCGCAGTTCCTGATCTCCGGGGCCGGTGCGTTGCACA4070TCCCGTCCTTCCCCGAGATCGCAGGTCGCGACGAATT4107(2) INFORMATION FOR SEQ ID NO:25:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 725 amino acids(B) TYPE: amino acid(D) TOPOLOGY: linear(ii) MOLECULE TYPE: protein(xi) SEQUENCE DESCRIPTION: SEQ ID NO:25:ValProProThrValIleAlaGluProValAlaSerGlyAlaHisAla151015SerTyrSerGlyGlyProGlyGluThrAspTyrHisAlaLeuAsnAla202530MetLeuAsnLeuTyrAspAlaAspGlyLysIleGlnPheAspLysAsp354045ArgGluAlaAlaHisGlnTyrPheLeuGlnHisValAsnGlnAsnThr505560ValPhePheHisAsnGlnAspGluLysLeuAspTyrLeuIleArgGlu65707580AsnTyrTyrGluArgGluValLeuAspGlnTyrSerArgAsnPheVal859095LysThrLeuLeuAspArgAlaTyrAlaLysLysPheArgPheProThr100105110PheLeuGlyAlaPheLysTyrTyrThrSerTyrThrLeuLysThrPhe115120125AspGlyLysArgTyrLeuGluArgPheGluAspArgValValMetVal130135140AlaLeuThrLeuAlaAlaGlyAspThrAlaLeuAlaGluLeuLeuVal145150155160AspGluIleIleAspGlyArgPheGlnProAlaThrProThrPheLeu165170175AsnSerGlyLysLysGlnArgGlyGluProValSerCysPheLeuLeu180185190ArgValGluAspAsnMetGluSerIleGlyArgSerIleAsnSerAla195200205LeuGlnLeuSerLysArgGlyGlyGlyValAlaLeuLeuLeuThrAsn210215220IleArgGluHisGlyGlyAlaIleLysAsnIleGluAsnGlnSerSer225230235240GlyValIleProIleMetLysLeuLeuGluAspAlaPheSerTyrAla245250255AsnGlnLeuGlyAlaArgGlnGlyAlaGlyAlaValTyrLeuHisAla260265270HisHisProAspIleTyrArgPheLeuAspThrLysArgGluAsnAla275280285AspGluLysIleArgIleLysThrLeuSerLeuGlyValValIlePro290295300AspIleThrPheGluLeuAlaLysArgAsnAspAspMetTyrLeuPhe305310315320SerProTyrAspValGluArgValTyrGlyValProPheAlaAspIle325330335SerValThrGluLysTyrTyrGluMetValAspAspAlaArgIleArg340345350LysThrLysIleLysAlaArgGluPhePheGlnThrLeuAlaGluLeu355360365GlnPheGluSerGlyTyrProTyrIleMetPheGluAspThrValAsn370375380ArgAlaAsnProIleAspGlyLysIleThrHisSerAsnLeuCysSer385390395400GluIleLeuGlnValSerThrProSerLeuPheAsnGluAspLeuSer405410415TyrAlaLysValGlyLysAspIleSerCysAsnLeuGlySerLeuAsn420425430IleAlaLysThrMetAspSerProAspPheAlaGlnThrIleGluVal435440445AlaIleArgAlaLeuThrAlaValArgHisGlnThrHisIleLysSer450455460ValProSerIleGluGlnGlyAsnAsnAspSerHisAlaIleGlyLeu465470475480GlyGlnMetAsnLeuHisGlyTyrLeuAlaArgGluArgIlePheTyr485490495GlySerAspGluGlyIleAspPheThrAsnIleTyrPheTyrThrVal500505510LeuTyrHisAlaLeuArgAlaSerAsnArgIleAlaIleGluArgGly515520525ThrHisPheLysGlyPheGluArgSerLysTyrAlaSerGlyGluPhe530535540PheAspLysTyrThrAspGlnIleTrpGluProLysThrGlnLysVal545550555560ArgGlnLeuPheAlaAspAlaGlyIleArgIleProThrGlnAspAsp565570575TrpArgArgLeuLysGluSerValGlnAlaHisGlyIleTyrAsnGln580585590AsnLeuGlnAlaValProProThrGlySerIleSerTyrIleAsnHis595600605SerThrSerSerIleHisProIleValSerLysValGluValArgLys610615620GluGlyLysIleGlyArgValTyrTyrProAlaProTyrMetThrAsn625630635640AspAsnLeuGluTyrTyrGluAspAlaTyrGluIleGlyTyrGluLys645650655IleIleAspThrTyrAlaAlaAlaThrGlnHisValAspGlnGlyLeu660665670SerLeuThrLeuPhePheLysAspThrAlaThrThrArgAspValAsn675680685LysAlaGlnIleTyrAlaTrpArgLysGlyIleLysThrLeuTyrTyr690695700IleArgLeuArgGlnMetAlaLeuGluGlyThrGluValGluGlyCys705710715720ValSerCysMetLeu725__________________________________________________________________________

Number	Name	Date	Kind
4736866	Leder et al.	Apr 1988
4873191	Wagner et al.	Oct 1989

Methods of identifying compounds that inhibit DNA synthesis in mycobacterium tuberculosis and compositions, reagents and kits for performing the same

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CPC

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US Referenced Citations (2)

Non-Patent Literature Citations (32)

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