Differential gene repertoire in Mycobacterium ulcerans identifies candidate genes for patho-adaptation

PLoS Neglected Tropical Diseases

Volumn 2, Issue 12, 2008, Pages

  Käser, Michael ^a   Pluschke, Gerd ^a  

^a SWISS TROPICAL AND PUBLIC HEALTH INSTITUTE   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTATION; AFRICA; ARTICLE; AUSTRALIA; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL VIRULENCE; BACTERIUM ISOLATE; BURULI ULCER; COMPARATIVE GENOMIC HYBRIDIZATION; DNA MICROARRAY; FRAMESHIFT MUTATION; GENE CONVERSION; GENE IDENTIFICATION; GENE INACTIVATION; GENE LOCATION; GENE LOSS; GENE SEQUENCE; HAPLOTYPE; MICROBIAL DIVERSITY; MYCOBACTERIUM ULCERANS; NONHUMAN; PATHOGENICITY; PSEUDOGENE; ANIMAL; CHEMISTRY; FISH; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; HUMAN; ISOLATION AND PURIFICATION; MICROBIOLOGY; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION;

BACTERIAL DNA; PRIMER DNA;

ANIMALS; BASE SEQUENCE; BURULI ULCER; DNA PRIMERS; DNA, BACTERIAL; FISHES; GENETIC VARIATION; GENOME, BACTERIAL; GEOGRAPHY; HAPLOTYPES; HUMANS; MYCOBACTERIUM ULCERANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION;

EID: 65549152272     PISSN: None     EISSN: None     Source Type: Journal    
DOI: 10.1371/journal.pntd.0000353     Document Type: Article

References (55)

1. Alland D, Lacher DW, Hazbon MH, Motiwala AS, Qi W, et al. (2007) Role of large sequence polymorphisms (LSPs) in generating genomic diversity among clinical isolates of Mycobacterium tuberculosis and the utility of LSPs in phylogenetic analysis. J Clin Microbiol 45: 39-46.
2. Brosch R, Gordon SV, Marmiesse M, Brodin P, Buchrieser C, et al. (2002) A newx evolutionary scenario for the Mycobacterium tuberculosis complex. Proc Natl Acad Sci U S A 99: 3684-3689.
3. Cole ST (2002) Comparative and functional genomics of the Mycobacterium tuberculosis complex. Microbiology 148: 2919-2928.
4. Filliol I, Motiwala AS, Cavatore M, Qi W, Hazbon MH, et al. (2006) Global phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis: insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP set. J Bacteriol 188: 759-772.
5. Behr MA, Wilson MA, Gill WP, Salamon H, Schoolnik GK, et al. (1999) Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science 284: 1520-1523.
6. Gagneux S, Small PM (2007) Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development. Lancet Infect Dis 7: 328-337.
7. Hirsh AE, Tsolaki AG, DeRiemer K, Feldman MW, Small PM (2004) Stable association between strains of Mycobacterium tuberculosis and their human host populations. Proc Natl Acad Sci U S A 101: 4871-4876.
8. Rondini S, Käser M, Stinear T, Tessier M, Mangold C, et al. (2007) Ongoing genome reduction in Mycobacterium ulcerans. Emerg Infect Dis 13: 1008-1015.
9. Kaser M, Rondini S, Naegeli M, Stinear T, Portaels F, et al. (2007) Evolution of two distinct phylogenetic lineages of the emerging human pathogen Mycobacterium ulcerans. BMC Evol Biol 7: 177.
10. Stinear TP, Jenkin GA, Johnson PD, Davies JK (2000) Comparative genetic analysis of Mycobacterium ulcerans and Mycobacterium marinum reveals evidence of recent divergence. J Bacteriol 182: 6322-6330.
11. Stinear TP, Seemann T, Pidot S, Frigui W, Reysset G, et al. (2007) Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer. Genome Research 17: 192-200.
12. Stinear TP, Seemann T, Harrison PF, Jenkin GA, Davies JK, et al. (2008) Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis. Genome Research 18: 729-741.
13. Huber CA, Ruf MT, Pluschke G, Kaser M (2008) Independent loss of immunogenic proteins in Mycobacterium ulcerans suggests immune evasion. Clin Vaccine Immunol 15: 598-606.
14. WHO (2008) Buruli ulcer: progress report, 2004-2008, Weekly epidemiological record. 17, 83: 145-156.
15. Guerra H, Palomino JC, Falconi E, Bravo F, Donaires N, et al. (2008) Mycobacterium ulcerans Disease, Peru. Emerg Infect Dis 14: 373-377.
16. Mve-Obiang A, Lee RE, Portaels F, Small PL (2003) Heterogeneity of mycolactones produced by clinical isolates of Mycobacterium ulcerans: implications for virulence. Infect Immun 71: 774-783.
17. Stinear TP, Mve-Obiang A, Small PL, Frigui W, Pryor MJ, et al. (2004) Giant plasmid-encoded polyketide synthases produce the macrolide toxin of Mycobacterium ulcerans. Proc Natl Acad Sci U S A 101: 1345-1349.
18. Stinear TP, Pryor MJ, Porter JL, Cole ST (2005) Functional analysis and annotation of the virulence plasmid pMUM001 from Mycobacterium ulcerans. Microbiology 151: 683-692.
19. Maurelli AT (2007) Black holes, antivirulence genes, and gene inactivation in the evolution of bacterial pathogens. FEMS Microbiol Lett 267: 1-8.
20. Sokurenko EV, Hasty DL, Dykhuizen DE (1999) Pathoadaptive mutations: gene loss and variation in bacterial pathogens. Trends Microbiol 7: 191-195.
21. Chain PS, Carniel E, Larimer FW, Lamerdin J, Stoutland PO, et al. (2004) Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis. Proc Natl Acad Sci U S A 101: 13826-13831.
22. Maurelli AT, Fernandez RE, Bloch CA, Rode CK, Fasano A (1998) "Black holes" and bacterial pathogenicity: a large genomic deletion that enhances the virulence of Shigella spp. and enteroinvasive Escherichia coli. Proc Natl Acad Sci U S A 95: 3943-3948.
23. Torres AG, Vazquez-Juarez RC, Tutt CB, Garcia-Gallegos JG (2005) Pathoadaptive mutation that mediates adherence of shiga toxin-producing Escherichia coli O111. Infect Immun 73: 4766-4776.
24. Moore RA, Reckseidler-Zenteno S, Kim H, Nierman W, Yu Y, et al. (2004) Contribution of gene loss to the pathogenic evolution of Burkholderia pseudomallei and Burkholderia mallei. Infect Immun 72: 4172-4187.
25. Prunier AL, Schuch R, Fernandez RE, Mumy KL, Kohler H, et al. (2007) nadA and nadB of Shigella flexneri 5a are antivirulence loci responsible for the synthesis of quinolinate, a small molecule inhibitor of Shigella pathogenicity. Microbiology 153: 2363-2372.
26. Papavinasasundaram KG, Chan B, Chung JH, Colston MJ, Davis EO, et al. (2005) Deletion of the Mycobacterium tuberculosis pknH gene confers a higher bacillary load during the chronic phase of infection in BALB/c mice. J Bacteriol 187: 5751-5760.
27. Parish T, Smith DA, Kendall S, Casali N, Bancroft GJ, et al. (2003) Deletion of two-component regulatory systems increases the virulence of Mycobacterium tuberculosis. Infect Immun 71: 1134-1140.
28. Shimono N, Morici L, Casali N, Cantrell S, Sidders B, et al. (2003) Hypervirulent mutant of Mycobacterium tuberculosis resulting from disruption of the mce1 operon. Proc Natl Acad Sci U S A 100: 15918-15923.
29. Ten Bokum AM, Movahedzadeh F, Frita R, Bancroft GJ, Stoker NG (2008) The case for hypervirulence through gene deletion in Mycobacterium tuberculosis. Trends Microbiol 16: 436-441.
30. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, et al. (2000) Artemis: sequence visualization and annotation. Bioinformatics 16: 944-945.
31. Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, et al. (2005) ACT: the Artemis Comparison Tool. Bioinformatics 21: 3422-3423.
32. Yip MJ, Porter JL, Fyfe JA, Lavender CJ, Portaels F, et al. (3007) Evolution of Mycobacterium ulcerans and other mycolactone-producing mycobacteria from a common Mycobacterium marinum progenitor. J Bacteriol 189: 2021-2029.
33. Smith NH, Gordon SV, Rua-Domenech R, Clifton-Hadley RS, Hewinson RG (2006) Bottlenecks and broomsticks: the molecular evolution of Mycobacterium bovis. Nat Rev Microbiol 4: 670-681.
34. de Jong BC, Hill PC, Brookes RH, Gagneux S, Jeffries DJ, et al. (2006) Mycobacterium africanum elicits an attenuated T cell response to early secreted antigenic target, 6 kDa, in patients with tuberculosis and their household contacts. J Infect Dis 193: 1279-1286.
35. Uchida Y, Casali N, White A, Morici L, Kendall LV, et al. (2007) Accelerated immunopathological response of mice infected with Mycobacterium tuberculosis disrupted in the mce1 operon negative transcriptional regulator. Cell Microbiol 9: 1275-1283.
36. Sharma K, Gupta M, Krupa A, Srinivasan N, Singh Y (2006) EmbR, a regulatory protein with ATPase activity, is a substrate of multiple serine/threonine kinases and phosphatase in Mycobacterium tuberculosis. FEBS J 273: 2711-2721.
37. Petrini B (2006) Mycobacterium marinum: ubiquitous agent of waterborne granulomatous skin infections. Eur J Clin Microbiol Infect Dis 25: 609-613.
38. Ranger BS, Mahrous EA, Mosi L, Adusumilli S, Lee RE, et al. (2006) Globally distributed mycobacterial fish pathogens produce a novel plasmid-encoded toxic macrolide, mycolactone f. Infect Immun 74: 6037-6045.
39. Ucko M, Colorni A, Kvitt H, Diamant A, Zlotkin A, et al. (2002) Strain variation in Mycobacterium marinum fish isolates. Appl Environ Microbiol 68: 5281-5287.
40. The Wellcome Trust Sanger Institute Mycobacterium marinum sequencing project [http://www.sanger.ac.uk/Projects/M_marinum/].
41. Jaeger T (2007) Peroxiredoxin systems in mycobacteria. Subcell Biochem 44: 207-217.
42. Nusrath UA, Selvakumar N, Narayanan S, Narayanan PR (2008) Molecular analysis of isoniazid-resistant clinical isolates of Mycobacterium tuberculosis from India. Int J Antimicrob Agents 31: 71-75.
43. Brodin P, Rosenkrands I, Andersen P, Cole ST, Brosch R (2004) ESAT-6 proteins: protective antigens and virulence factors? Trends Microbiol 12: 500-508.
44. Collins DM, Skou B, White S, Bassett S, Collins L, et al. (2005) Generation of attenuated Mycobacterium bovis strains by signature-tagged mutagenesis for discovery of novel vaccine candidates. Infect Immun 73: 2379-2386.
45. Roupie V, Romano M, Zhang L, Korf H, Lin MY, et al. (2007) Immunogenicity of eight dormancy regulon-encoded proteins of Mycobacterium tuberculosis in DNA-vaccinated and tuberculosis-infected mice. Infect Immun 75: 941-949.
46. Stewart GR, Newton SM, Wilkinson KA, Humphreys IR, Murphy HN, et al. (2005) The stress-responsive chaperone alpha-crystallin 2 is required for pathogenesis of Mycobacterium tuberculosis. Mol Microbiol 55: 1127-1137.
47. Gioffre A, Infante E, Aguilar D, Santangelo MP, Klepp L, et al. (2005) Mutation in mce operons attenuates Mycobacterium tuberculosis virulence. Microbes Infect 7: 325-334.
48. Brosch R, Pym AS, Gordon SV, Cole ST (2001) The evolution of mycobacterial pathogenicity: clues from comparative genomics. Trends Microbiol 9: 452-458.
49. Fleischmann RD, Alland D, Eisen JA, Carpenter L, White O, et al. (2002) Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J Bacteriol 184: 5479-5490.
50. Lyashchenko K, Colangeli R, Houde M, Al Jahdali H, Menzies D, et al. (1998) Heterogeneous antibody responses in tuberculosis. Infect Immun 66: 3936-3940.
51. Kantardjieff KA, Kim CY, Naranjo C, Waldo GS, Lekin T, et al. (2004) Mycobacterium tuberculosis RmlC epimerase (Rv3465): a promising drug-target structure in the rhamnose pathway. Acta Crystallogr D Biol Crystallogr 60: 895-902.
52. Wu JH, Wu AM, Tsai CG, Chang XY, Tsai SF, et al. (2008) Contribution of fucose-containing capsules in Klebsiella pneumoniae to bacterial virulence in mice. Exp Biol Med (Maywood) 233: 64-70.
53. Chang JC, Harik NS, Liao RP, Sherman DR (2007) Identification of mycobacterial genes that alter growth and pathology in macrophages and in mice. J Infect Dis 196: 788-795.
54. Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, et al. (1998) Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393: 537-544.
55. Stewart GR, Wernisch L, Stabler R, Mangan JA, Hinds J, et al. (2002) Dissection of the heat-shock response in Mycobacterium tuberculosis using mutants and microarrays. Microbiology 148: 3129-3138.