Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis

Genome Research

Volumn 18, Issue 5, 2008, Pages 729-741

  Stinear, Timothy P ^a   Seemann, Torsten ^a   Harrison, Paul F ^a   Jenkin, Grant A ^a   Davies, John K ^a   Johnson, Paul D R ^b   Abdellah, Zahra ^c   Arrowsmith, Claire ^c   Chillingworth, Tracey ^c   Churcher, Carol ^c   Clarke, Kay ^c   Cronin, Ann ^c   Davis, Paul ^c   Goodhead, Ian ^c   Holroyd, Nancy ^c   Jagels, Kay ^c   Lord, Angela ^c   Moule, Sharon ^c   Mungall, Karen ^c   Norbertczak, Halina ^c   Quail, Michael A ^c   Rabbinowitsch, Ester ^c   Walker, Danielle ^c   White, Brian ^c   Whitehead, Sally ^c   Small, Pamela L C ^d   Brosch, Roland ^e   Ramakrishnan, Lalita ^f   Fischbach, Michael A ^g   Parkhill, Julian ^c   Cole, Stewart T ^h   more..

^a MONASH UNIVERSITY   (Australia)

^b AUSTIN HOSPITAL   (Australia)

^c WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^d UNIVERSITY OF TENNESSEE   (United States)

^e INSTITUT PASTEUR   (France)

^f UNIVERSITY OF WASHINGTON   (United States)

^g MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^h EPFL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

GLUTAMIC ACID; PEPTIDE SYNTHASE; POLYKETIDE SYNTHASE; PROLINE;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; BACTERIAL GENOME; BACTERIAL SURVIVAL; COMPARATIVE STUDY; ECOLOGICAL NICHE; ENVIRONMENT; EVOLUTION; GENE LOCUS; GENE SEQUENCE; HORIZONTAL GENE TRANSFER; MOLECULAR PHYLOGENY; MYCOBACTERIUM; MYCOBACTERIUM AVIUM; MYCOBACTERIUM MARINUM; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PATHOGENESIS; PLASMID; PRIMATE; PRIORITY JOURNAL; PROPHAGE; TUBERCULOSIS;

BACTERIAL PROTEINS; CARRIER PROTEINS; CELL WALL; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; GENOMICS; MOLECULAR SEQUENCE DATA; MYCOBACTERIUM MARINUM; MYCOBACTERIUM TUBERCULOSIS; PHYLOGENY;

AMPHIBIA; CORYNEBACTERINEAE; MYCOBACTERIUM; MYCOBACTERIUM AVIUM; MYCOBACTERIUM MARINUM; MYCOBACTERIUM SMEGMATIS; MYCOBACTERIUM TUBERCULOSIS; PRIMATES;

EID: 42149102918     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.075069.107     Document Type: Article

References (105)

1. Abdallah, A.M., Verboom, T., Hannes, F., Safi, M., Strong, M., Eisenberg, D., Musters, R.J., Vandenbroucke-Grauls, C.M., Appelmelk, B.J., Luirink, J., et al. 2006. A specific secretion system mediates PPE41 transport in pathogenic mycobacteria. Mol. Microbiol. 62: 667-679.
2. Adekambi, T., Ben Salah, S., Khlif, M., Raoult, D., and Drancourt, M. 2006. Survival of environmental mycobacteria in Acanthamoeba polyphaga. Appl. Environ. Microbiol. 72: 5974-5981.
3. Alteri, C.J., Xicohténcatl-Cortes, J., Hess, S., Caballero-Olín, G., Girón, J.A., and Friedman, R.L. 2007. Mycobacterium tuberculosis produces pili during human infection. Proc. Natl. Acad. Sci. 104: 5145-5150.
4. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
5. Aronson, J.D. 1927. Spontaneous tuberculosis in salt water fish. J. Infect. Dis. 39: 315-320.
6. Aubry, A., Jarlier, V., Escolano, S., Truffot-Pernot, C., and Cambau, E. 2000. Antibiotic susceptibility pattern of Mycobacterium marinum. Antimicrob. Agents Chemother. 44: 3133-3136.
7. Aubry, A., Chosidow, O., Caumes, E., Robert, J., and Cambau, E. 2002. Sixty-three cases of Mycobacterium marinum infection: Clinical features, treatment, and antibiotic susceptibility of causative isolates. Arch. Intern. Med. 162: 1746-1752.
8. Bardouniotis, E., Ceri, H., and Olson, M.E. 2003. Biofilm formation and biocide susceptibility testing of Mycobacterium fortuitum and Mycobacterium marinum. Curr. Microbiol. 46: 28-32.
9. Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., Romero, D.A., and Horvath, P. 2007. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315: 1709-1712.
10. Becq, J., Gutierrez, M., Rosas-Magallanes, V., Rauzier, J., Gicquel, B., Neyrolles, O., and Deschavanne, P. 2007. Contribution of horizontally acquired genomic islands to the evolution of the tubercle bacilli. Mol. Biol. Evol. 24: 1867-1871.
11. Besemer, J., Lomsadze, A., and Borodovsky, M. 2001. GeneMarkS: A self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res. 29: 2607-2618.
12. Besra, G.S., McNeil, M.R., Rivoire, B., Khoo, K.H., Morris, H.R., Dell, A., and Brennan, P.J. 1993. Further structural definition of a new family of glycopeptidolipids from Mycobacterium xenopi. Biochemistry 32: 347-355.
13. Betts, J.C., Lukey, P.T., Robb, L.C., McAdam, R.A., and Duncan, K. 2002. Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling. Mol. Microbiol. 43: 717-731.
14. Bhatt, A., Fujiwara, N., Bhatt, K., Gurcha, S.S., Kremer, L., Chen, B., Chan, J., Porcelli, S.A., Kobayashi, K., Besra, G.S., et al. 2007a. Deletion of kasB in Mycobacterium tuberculosis causes loss of acid-fastness and subclinical latent tuberculosis in immunocompetent mice. Proc. Natl. Acad. Sci. 104: 5157-5162.
15. Bhatt, K., Gurcha, S.S., Bhatt, A., Besra, G.S., and Jacobs Jr., W.R. 2007b. Two polyketide-synthase-associated acyltransferases are required for sulfolipid biosynthesis in Mycobacterium tuberculosis. Microbiology 153: 513-520.
16. Billman-Jacobe, H., McConville, M.J., Haites, R.E., Kovacevic, S., and Coppel, R.L. 1999. Identification of a peptide synthetase involved in the biosynthesis of glycopeptidolipids of Mycobacterium smegmatis. Mol. Microbiol. 33: 1244-1253.
17. Brodin, P., Rosenkrands, I., Andersen, P., Cole, S.T., and Brosch, R. 2004. ESAT-6 proteins: Protective antigens and virulence factors? Trends Microbiol. 12: 500-508.
18. Brosch, R., Gordon, S.V., Billault, A., Garnier, T., Eiglmeier, K., Soravito, C., Barrell, B.G., and Cole, S.T. 1998. Use of a Mycobacterium tuberculosis H37Rv bacterial artificial chromosome library for genome mapping, sequencing, and comparative genomics. Infect. Immun. 66: 2221-2229.
19. Brosch, R., Gordon, S.V., Marmiesse, M., Brodin, P., Buchrieser, C., Eiglmeier, K., Garnier, T., Gutierrez, C., Hewinson, G., Kremer, K., et al. 2002. A new evolutionary scenario for the Mycobacterium tuberculosis complex. Proc. Natl. Acad. Sci. 99: 3684-3689.
20. Burguiere, A., Hitchen, P.G., Dover, L.G., Kremer, L., Ridell, M., Alexander, D.C., Liu, J., Morris, H.R., Minnikin, D.E., Dell, A., et al. 2005. LosA, a key glycosyltransferase involved in the biosynthesis of a novel family of glycosylated acyltrehalose lipooligosaccharides from Mycobacterium marinum. J. Biol. Chem. 280: 42124-42133.
21. Caimi, K. and Cataldi, A. 2004. A fragment of 21 ORFs around the direct repeat region of Mycobacterium tuberculosis is absent from the other sequenced mycobacterial genomes: Implications for the evolution of the DR region. Comp. Funct. Genomics 5: 116-122.
22. Carroll, P., Brown, A.C., Hartridge, A.R., and Parish, T. 2007. Expression of Mycobacterium tuberculosis Rv1991c using an arabinose-inducible promoter demonstrates its role as a toxin. FEMS Microbiol. Lett. 274: 73-82.
23. Carver, T.J., Rutherford, K.M., Berriman, M., Rajandream, M.A., Barrell, B.G., and Parkhill, J. 2005. ACT: The Artemis Comparison Tool. Bioinformatics 21: 3422-3423.
24. Clark, H.F. and Shepard, C.C. 1963. Effect of environmental temperatures on infection with Mycobacterium marinum (balnei) of mice and a number of poikilothermic species. J. Bacteriol. 86: 1057-1069.
25. Clay, H., Davis, J.M., Beery, D., Huttenlocher, A., Lyons, S.E., and Ramakrishnan, L. 2007. Dichotomous role of the macrophage in early Mycobacterium marinum infection of the zebrafish. Cell Host Microbe 2: 29-39.
26. Cole, S.T., Brosch, R., Parkhill, J., Garnier, T., Churcher, C., Harris, D., Gordon, S.V., Eiglmeier, K., Gas, S., Barry III, C.E., et al. 1998. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393: 537-544.
27. Constant, P., Perez, E., Malaga, W., Laneelle, M.A., Saurel, O., Daffe, M., and Guilhot, C. 2002. Role of the pks15/1 gene in the biosynthesis of phenolglycolipids in the Mycobacterium tuberculosis complex. Evidence that all strains synthesize glycosylated p-hydroxybenzoic methly esters and that strains devoid of phenolglycolipids harbor a frameshift mutation in the pks15/1 gene. J. Biol. Chem. 277: 38148-38158.
28. Converse, S.E., Mougous, J.D., Leavell, M.D., Leary, J.A., Bertozzi, C.R., and Cox, J.S. 2003. MmpL8 is required for sulfolipid-1 biosynthesis and Mycobacterium tuberculosis virulence. Proc. Natl. Acad. Sci. 100: 6121-6126.
29. Cosma, C.L., Sherman, D.R., and Ramakrishnan, L. 2003. The secret lives of the pathogenic mycobacteria. Annu. Rev. Microbiol. 57: 641-676.
30. Cosma, C.L., Humbert, O., and Ramakrishnan, L. 2004. Superinfecting mycobacteria home to established tuberculous granulomas. Nat. Immunol. 5: 828-835.
31. Cosma, C.L., Klein, K., Kim, R., Beery, D., and Ramakrishnan, L. 2006. Mycobacterium marinum Erp is a virulence determinant required for cell wall integrity and intracellular survival. Infect. Immun. 74: 3125-3133.
32. Daffe, M., Varnerot, A., and Levy-Frebault, V.V. 1992. The phenolic mycoside of Mycobacterium ulcerans: Structure and taxonomic implications. J. Gen. Microbiol. 138: 131-137.
33. Dailloux, M., Hartemann, P., and Beurey, J. 1980. Study on the relationship between isolation of mycobacteria and classical microbiological and chemical indicators of water quality in swimming pools. Zentralbl. Bakteriol. Mikrobiol. Hyg. [B] 171: 473-486.
34. Davis, J.M., Clay, H., Lewis, J.L., Ghori, N., Herbomel, P., and Ramakrishnan, L. 2002. Real-time visualization of mycobacterium-macrophage interactions leading to initiation of granuloma formation in zebrafish embryos. Immunity 17: 693-702.
35. Delcher, A.L., Harmon, D., Kasif, S., White, O., and Salzberg, S.L. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 27: 4636-4641.
36. Devulder, G., Perouse de Montclos, M., and Flandrois, J.P. 2005. A multigene approach to phylogenetic analysis using the genus Mycobacterium as a model. Int. J. Syst. Evol. Microbiol. 55: 293-302.
37. Domenech, P., Reed, M.B., Dowd, C.S., Manca, C., Kaplan, G., and Barry III, C.E. 2004. The role of MmpL8 in sulfatide biogenesis and virulence of Mycobacterium tuberculosis. J. Biol. Chem. 279: 21257-21265.
38. Fischbach, M.A. and Walsh, C.T. 2006. Assembly-line enzymology for polyketide and nonribosomal peptide antibiotics: Logic, machinery, and mechanisms. Chem. Rev. 106: 3468-3496.
39. Fortune, S.M., Jaeger, A., Sarracino, D.A., Chase, M.R., Sassetti, C.M., Sherman, D.R., Bloom, B.R., and Rubin, E.J. 2005. Mutually dependent secretion of proteins required for mycobacterial virulence. Proc. Natl. Acad. Sci. 102: 10676-10681.
40. Frishman, D., Mironov, A., Mewes, H.W., and Gelfand, M. 1998. Combining diverse evidence for gene recognition in completely sequenced bacterial genomes. Nucleic Acids Res. 26: 2941-2947.
41. Gao, L.Y., Groger, R., Cox, J.S., Beverley, S.M., Lawson, E.H., and Brown, E.J. 2003. Transposon mutagenesis of Mycobacterium marinum identifies a locus linking pigmentation and intracellular survival. Infect. Immun. 71: 922-929.
42. Gao, L.Y., Guo, S., McLaughlin, B., Morisaki, H., Engel, J.N., and Brown, E.J. 2004. A mycobacterial virulence gene cluster extending RD1 is required for cytolysis, bacterial spreading and ESAT-6 secretion. Mol. Microbiol. 53: 1677-1693.
43. Gao, L.Y., Pak, M., Kish, R., Kajihara, K., and Brown, E.J. 2006. A mycobacterial operon essential for virulence in vivo and invasion and intracellular persistence in macrophages. Infect. Immun. 74: 1757-1767.
44. Garnier, T., Eiglmeier, K., Camus, J.C., Medina, N., Mansoor, H., Pryor, M., Duthoy, S., Grondin, S., Lacroix, C., Monsempe, C., et al. 2003. The complete genome sequence of Mycobacterium bovis. Proc. Natl. Acad. Sci. 100: 7877-7882.
45. George, K.M., Chatterjee, D., Gunawardana, G., Welty, D., Hayman, J., Lee, R., and Small, P.L. 1999. Mycolactone: A polyketide toxin from Mycobacterium ulcerans required for virulence. Science 283: 854-857.
46. Gey Van Pittius, N.C., Gamieldien, J., Hide, W., Brown, G.D., Siezen, R.J., and Beyers, A.D. 2001. The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria. Genome Biol. 2: RESEARCH0044. doi: 10.1186/gb-2001-2-10-research0044.
47. Gey van Pittius, N.C., Sampson, S.L., Lee, H., Kim, Y., van Helden, P.D., and Warren, R.M. 2006. Evolution and expansion of the Mycobacterium tuberculosis PE and PPE multigene families and their association with the duplication of the ESAT-6 (esx) gene cluster regions. BMC Evol. Biol. 6: 95. doi: 10.1186/1471-2148-6-95.
48. Gokhale, R.S., Saxena, P., Chopra, T., and Mohanty, D. 2007. Versatile polyketide enzymatic machinery for the biosynthesis of complex mycobacterial lipids. Nat. Prod. Rep. 24: 267-277.
49. Guinn, K.M., Hickey, M.J., Mathur, S.K., Zakel, K.L., Grotzke, J.E., Lewinsohn, D.M., Smith, S., and Sherman, D.R. 2004. Individual RD1-region genes are required for export of ESAT-6/CFP-10 and for virulence of Mycobacterium tuberculosis. Mol. Microbiol. 51: 359-370.
50. Gutierrez, M.C., Brisse, S., Brosch, R., Fabre, M., Omais, B., Marmiesse, M., Supply, P., and Vincent, V. 2005. Ancient origin and gene mosaicism of the progenitor of Mycobacterium tuberculosis. PLoS Pathog. 1: e5. doi: 10.1371/journal.ppat.0010005.
51. Hagedorn, M. and Soldati, T. 2007. Flotillin and RacH modulate the intracellular immunity of Dictyostelium to Mycobacterium marinum infection. Cell. Microbiol. 9: 2984.
52. Hall-Stoodley, L., Brun, O.S., Polshyna, G., and Barker, L.P. 2006. Mycobacterium marinum biofilm formation reveals cording morphology. FEMS Microbiol. Lett. 257: 43-49.
53. Kinsella, R.J., Fitzpatrick, D.A., Creevey, C.J., and McInerney, J.O. 2003. Fatty acid biosynthesis in Mycobacterium tuberculosis: Lateral gene transfer, adaptive evolution, and gene duplication. Proc. Natl. Acad. Sci. 100: 10320-10325.
54. Krubasik, P. and Sandmann, G. 2000. A carotenogenic gene cluster from Brevibacterium linens with novel lycopene cyclase genes involved in the synthesis of aromatic carotenoids. Mol. Gen. Genet. 263: 423-432.
55. Leoni, E., Legnani, P., Mucci, M.T., and Pirani, R. 1999. Prevalence of mycobacteria in a swimming pool environment. J. Appl. Microbiol. 87: 683-688.
56. Lewis, K.N., Liao, R., Guinn, K.M., Hickey, M.J., Smith, S., Behr, M.A., and Sherman, D.R. 2003. Deletion of RD1 from Mycobacterium tuberculosis mimics bacille Calmette-Guerin attenuation. J. Infect. Dis. 187: 117-123.
57. Li, M.S., Waddell, S.J., Monahan, I.M., Mangan, J.A., Martin, S.L., Everett, M.J., and Butcher, P.D. 2004. Increased transcription of a potential sigma factor regulatory gene Rv1364c in Mycobacterium bovis BCG while residing in macrophages indicates use of alternative promoters. FEMS Microbiol. Lett. 233: 333-339.
58. Linell, F. and Norden, A. 1954. Mycobacterium balnei, a new acid-fast bacillus occurring in swimming pools and capable of producing skin lesions in humans. Acta Tuberc. Scand. Suppl. 33: 1-84.
59. Lobry, J.R. 1996. Asymmetric substitution patterns in the two DNA strands of bacteria. Mol. Biol. Evol. 13: 660-665.
60. MacGregor, R.R. 1995. Cutaneous tuberculosis. Clin. Dermatol. 13: 245-255.
61. MacGurn, J.A. and Cox, J.S. 2007. A genetic screen for Mycobacterium tuberculosis mutants defective for phagosome maturation arrest identifies components of the ESX-1 secretion system. Infect. Immun. 75: 2668-2678.
62. MacGurn, J.A., Raghavan, S., Stanley, S.A., and Cox, J.S. 2005. A non-RD1 gene cluster is required for Snm secretion in Mycobacterium tuberculosis. Mol. Microbiol. 57: 1653-1663.
63. Maciag, A., Dainese, E., Rodriguez, G.M., Milano, A., Provvedi, R., Pasca, M.R., Smith, I., Palu, G., Riccardi, G., and Manganelli, R. 2007. Global analysis of the Mycobacterium tuberculosis Zur (FurB) regulon. J. Bacteriol. 189: 730-740.
64. Matsunaga, I., Bhatt, A., Young, D.C., Cheng, T.Y., Eyles, S.J., Besra, G.S., Briken, V., Porcelli, S.A., Costello, C.E., Jacobs Jr., W.R., et al. 2004. Mycobacterium tuberculosis pks12 produces a novel polyketide presented by CD1c to T cells. J. Exp. Med. 200: 1559-1569.
65. Mehta, P.K., Pandey, A.K., Subbian, S., El-Etr, S.H., Cirillo, S.L., Samrakandi, M.M., and Cirillo, J.D. 2006. Identification of Mycobacterium marinum macrophage infection mutants. Microb. Pathog. 40: 139-151.
66. Okamoto, Y., Fujita, Y., Naka, T., Hirai, M., Tomiyasu, I., and Yano, I. 2006. Mycobacterial sulfolipid shows a virulence by inhibiting cord factor induced granuloma formation and TNF-alpha release. Microb. Pathog. 40: 245-253.
67. Onwueme, K.C., Vos, C.J., Zurita, J., Ferreras, J.A., and Quadri, L.E. 2005. The dimycocerosate ester polyketide virulence factors of mycobacteria. Prog. Lipid Res. 44: 259-302.
68. Parkhill, J., Sebaihia, M., Preston, A., Murphy, L.D., Thomson, N., Harris, D.E., Holden, M.T., Churcher, C.M., Bentley, S.D., Mungall, K.L., et al. 2003. Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nat. Genet. 35: 32-40.
69. Petrini, B. 2006. Mycobacterium marinum: Ubiquitous agent of waterborne granulomatous skin infections. Eur. J. Clin. Microbiol. Infect. Dis. 25: 609-613.
70. Portevin, D., De Sousa-D'Auria, C., Houssin, C., Grimaldi, C., Chami, M., Daffe, M., and Guilhot, C. 2004. A polyketide synthase catalyzes the last condensation step of mycolic acid biosynthesis in mycobacteria and related organisms. Proc. Natl. Acad. Sci. 101: 314-319.
71. Pozos, T.C. and Ramakrishnan, L. 2004. New models for the study of Mycobacterium-host interactions. Curr. Opin. Immunol. 16: 499-505.
72. Ramakrishnan, L. and Falkow, S. 1994. Mycobacterium marinum persists in cultured mammalian cells in a temperature-restricted fashion. Infect. Immun. 62: 3222-3229.
73. Ramakrishnan, L., Tran, H.T., Federspiel, N.A., and Falkow, S. 1997. A crtB homolog essential for photochromogenicity in Mycobacterium marinum: Isolation, characterization, and gene disruption via homologous recombination. J. Bacteriol. 179: 5862-5868.
74. Ramakrishnan, L., Federspiel, N.A., and Falkow, S. 2000. Granuloma-specific expression of mycobacterium virulence proteins from the glycine-rich PE-PGRS family. Science 288: 1436-1439.
75. Reed, M.B., Domenech, P., Manca, C., Su, H., Barczak, A.K., Kreiswirth, B.N., Kaplan, G., and Barry III, C.E. 2004. A glycolipid of hypervirulent tuberculosis strains that inhibits the innate immune response. Nature 431: 84-87.
76. Ren, H., Dover, L.G., Islam, S.T., Alexander, D.C., Chen, J.M., Besra, G.S., and Liu, J. 2007. Identification of the lipooligosaccharide biosynthetic gene cluster from Mycobacterium marinum. Mol. Microbiol. 63: 1345-1359.
77. Rezwan, M., Grau, T., Tschumi, A., and Sander, P. 2007. Lipoprotein synthesis in mycobacteria. Microbiology 153: 652-658.
78. Robinson, N., Wolke, M., Ernestus, K., and Plum, G. 2007. A mycobacterial gene involved in synthesis of an outer cell envelope lipid is a key factor in prevention of phagosome maturation. Infect. Immun. 75: 581-591.
79. Rohdich, F., Bacher, A., and Eisenreich, W. 2004. Perspectives in anti-infective drug design. The late steps in the biosynthesis of the universal terpenoid precursors, isopentenyl diphosphate and dimethylallyl diphosphate. Bioorg. Chem. 32: 292-308.
80. Rosas-Magallanes, V., Deschavanne, P., Quintana-Murci, L., Brosch, R., Gicquel, B., and Neyrolles, O. 2006. Horizontal transfer of a virulence operon to the ancestor of Mycobacterium tuberculosis. Mol. Biol. Evol. 23: 1129-1135.
81. Saad, M.H., Fonseca, L.D., Ferrazoli, L., Fandinho, F., Palaci, M., Grinsztejn, B., Kritski, A., Werneck, A., Poltoratskaia, N., Johnson Jr., W.D., et al. 1999. IS1245 genotypic analysis of Mycobacterium avium isolates from patients in Brazil. Int. J. Infect. Dis. 3: 192-196.
82. Saitou, N. and Nei, M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
83. Sassetti, C.M., Boyd, D.H., and Rubin, E.J. 2001. Comprehensive identification of conditionally essential genes in mycobacteria. Proc. Natl. Acad. Sci. 98: 12712-12717.
84. Singh, R., Singh, A., and Tyagi, A.K. 2005. Deciphering the genes involved in pathogenesis of Mycobacterium tuberculosis. Tuberculosis (Edinb.) 85: 325-335.
85. Slosarek, M., Kubin, M., and Pokorny, J. 1994. Water as a possible factor of transmission in mycobacterial infections. Cent. Eur. J. Public Health 2: 103-105.
86. Solomon, J.M., Leung, G.S., and Isberg, R.R. 2003. Intracellular replication of Mycobacterium marinum within Dictyostelium discoideum: Efficient replication in the absence of host coronin. Infect. Immun. 71: 3578-3586.
87. Stamm, L.M. and Brown, E.J. 2004. Mycobacterium marinum: The generalization and specialization of a pathogenic mycobacterium. Microbes Infect. 6: 1418-1428.
88. Stinear, T.P., Jenkin, G.A., Johnson, P.D.R., and Davies, J.K. 2000. Comparative genetic analysis of Mycobacterium ulcerans and Mycobacterium marinum reveals evidence of recent divergence. J. Bacteriol. 182: 6322-6330.
89. Stinear, T.P., Mve-Obiang, A., Small, P.L., Frigui, W., Pryor, M.J., Brosch, R., Jenkin, G.A., Johnson, P.D., Davies, J.K., Lee, R.E., et al. 2004. Giant plasmid-encoded polyketide synthases produce the macrolide toxin of Mycobacterium ulcerans. Proc. Natl. Acad. Sci. 101: 1345-1349.
90. Stinear, T.P., Seemann, T., Pidot, S., Frigui, W., Reysset, G., Garnier, T., Meurice, G., Simon, D., Bouchier, C., Ma, L., et al. 2007. Reductive evolution and niche-adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer. Genome Res. 7: 192-200.
91. Swaim, L.E., Connolly, L.E., Volkman, H.E., Humbert, O., Born, D.E., and Ramakrishnan, L. 2006. Mycobacterium marinum infection of adult zebrafish causes caseating granulomatous tuberculosis and is moderated by adaptive immunity. Infect. Immun. 74: 6108-6117.
92. Tekaia, F., Gordon, S.V., Garnier, T., Brosch, R., Barrell, B.G., and Cole, S.T. 1999. Analysis of the proteome of Mycobacterium tuberculosis in silico. Tuber. Lung Dis. 79: 329-342.
93. Tian, J., Bryk, R., Itoh, M., Suematsu, M., and Nathan, C. 2005. Variant tricarboxylic acid cycle in Mycobacterium tuberculosis: Identification of alpha-ketoglutarate decarboxylase. Proc. Natl. Acad. Sci. 102: 10670-10675.
94. Toma, F. 1998. [Nontuberculous mycobacteria in the hospital environment]. Bacteriol. Virusol. Parazitol. Epidemiol. 43: 229-235.
95. Tønjum, T., Welty, D.B., Jantzen, E., and Small, P.L. 1998. Differentiation of Mycobacterium ulcerans, M. marinum, and M. haemophilum: Mapping of their relationships to M. tuberculosis by fatty acid profile analysis, DNA-DNA hybridization, and 16S rRNA gene sequence analysis. J. Clin. Microbiol. 36: 918-925.
96. Travis, W.D., Travis, L.B., Roberts, G.D., Su, D.W., and Weiland, L.W. 1985. The histopathologic spectrum in Mycobacterium marinum infection. Arch. Pathol. Lab. Med. 109: 1109-1113.
97. Trivedi, O.A., Arora, P., Sridharan, V., Tickoo, R., Mohanty, D., and Gokhale, R.S. 2004. Enzymic activation and transfer of fatty acids as acyl-adenylates in mycobacteria. Nature 428: 441-445.
98. Tsukamura, M. 1983. Numerical classification of 280 strains of slowly growing mycobacteria. Proposal of Mycobacterium tuberculosis series, Mycobacterium avium series, and Mycobacterium nonchromogenicum series. Microbiol. Immunol. 27: 315-334.
99. van Embden, J.D., van Gorkom, T., Kremer, K., Jansen, R., van Der Zeijst, B.A., and Schouls, L.M. 2000. Genetic variation and evolutionary origin of the direct repeat locus of Mycobacterium tuberculosis complex bacteria. J. Bacteriol. 182: 2393-2401.
100. Vernikos, G.S. and Parkhill, J. 2006. Interpolated variable order motifs for identification of horizontally acquired DNA: Revisiting the Salmonella pathogenicity islands. Bioinformatics 22: 2196-2203.
101. Volkman, H.E., Clay, H., Beery, D., Chang, J.C., Sherman, D.R., and Ramakrishnan, L. 2004. Tuberculous granuloma formation is enhanced by a Mycobacterium virulence determinant. PLoS Biol. 2: e367. doi: 10.1371/journal.pbio.0020367.
102. Wehenkel, A., Bellinzoni, M., Grana, M., Duran, R., Villarino, A., Fernandez, P., Andre-Leroux, G., England, P., Takiff, H., Cervenansky, C., et al. 2007. Mycobacterial Ser/Thr protein kinases and phosphatases: Physiological roles and therapeutic potential. Biochim. Biophys. Acta 1784: 193-202. doi: 10.1016/j.bbapap.2007.08.006.
103. Wei, J., Dahl, J.L., Moulder, J.W., Roberts, E.A., O'Gaora, P., Young, D.B., and Friedman, R.L. 2000. Identification of a Mycobacterium tuberculosis gene that enhances mycobacterial survival in macrophages. J. Bacteriol. 182: 377-384.
104. Yip, M.J., Porter, J.L., Fyfe, J.A., Lavender, C.J., Portaels, F., Rhodes, M., Kator, H., Colorni, A., Jenkin, G.A., and Stinear, T. 2007. Evolution of Mycobacterium ulcerans and other mycolactone-producing mycobacteria from a common Mycobacterium marinum progenitor. J. Bacteriol. 189: 2021-2029.
105. Zhu, L., Zhang, Y., Teh, J.S., Zhang, J., Connell, N., Rubin, H., and Inouye, M. 2006. Characterization of mRNA interferases from Mycobacterium tuberculosis. J. Biol. Chem. 281: 18638-18643.