Complete genome sequence of the frog pathogen Mycobacterium ulcerans ecovar Liflandii

Journal of Bacteriology

Volumn 195, Issue 3, 2013, Pages 556-564

  Tobias, Nicholas J ^a,b   Doig, Kenneth D ^a   Medema, Marnix H ^c   Chen, Honglei ^d   Haring, Volker ^d   Moore, Robert ^d,e   Seemann, Torsten ^b   Stinear, Timothy P ^a  

^a UNIVERSITY OF MELBOURNE   (Australia)

^b MONASH UNIVERSITY   (Australia)

^c UNIVERSITY OF GRONINGEN   (Netherlands)

^d CSIRO   (Australia)

^e Australian Government Australian Research Council   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

PHENYLALANINE; TRYPTOPHAN; TYROSINE;

ANURA; ARTICLE; BACTERIAL STRAIN; CHROMOSOME; ECOTYPE; GENE SEQUENCE; GENOME ANALYSIS; METABOLOME; MYCOBACTERIUM; MYCOBACTERIUM LIFLANDII; MYCOBACTERIUM ULCERANS; NONHUMAN; PATHOGENESIS; PLASMID; PRIORITY JOURNAL;

ANIMALS; ANTI-BACTERIAL AGENTS; CHROMOSOME MAPPING; CHROMOSOMES, BACTERIAL; DRUG RESISTANCE, BACTERIAL; GENOME, BACTERIAL; MULTIGENE FAMILY; MYCOBACTERIUM INFECTIONS, NONTUBERCULOUS; MYCOBACTERIUM ULCERANS; RANIDAE;

EID: 84873052039     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.02132-12     Document Type: Article

References (52)

1. Trott KA, Stacy BA, Lifland BD, Diggs HE, Harland RM, Khokha MK, Grammer TC, Parker JM. 2004. Characterization of a Mycobacterium ulcerans-like infection in a colony of African tropical clawed frogs (Xenopus tropicalis). Comp. Med. 54:309-317.
2. Nigou J, Gilleron M, Puzo G. 2003. Lipoarabinomannans: from structure to biosynthesis. Biochimie 85:153-166.
3. Fremont-Rahl JJ, Ek C, Williamson HR, Small PL, Fox JG, Muthupalani S. 2011. Mycobacterium liflandii outbreak in a research colony of Xenopus (Silurana) tropicalis frogs. Vet. Pathol. 48:856-867.
4. Chai N, Bronchain O, Panteix G, Godreuil S, de Medeiros C, Saunders R, Bouts T, de Luze A. 2012. Propagation method of saving valuable strains from a Mycobacterium liflandii infection in Western clawed frogs (Silurana tropicalis). J. Zoo Wildl. Med. 43:15-19.
5. Hong H, Stinear T, Skelton P, Spencer JB, Leadlay PF. 2005. Structure elucidation of a novel family of mycolactone toxins from the frog pathogen Mycobacterium sp. MU128FXT by mass spectrometry. Chem. Commun. (Camb.) 34:4306-4308.
6. Mve-Obiang A, Lee RE, Umstot ES, Trott KA, Grammer TC, Parker JM, Ranger BS, Grainger R, Mahrous EA, Small PL. 2005. A newly discovered mycobacterial pathogen isolated from laboratory colonies of Xenopus species with lethal infections produces a novel form of mycolactone, the Mycobacterium ulcerans macrolide toxin. Infect. Immun. 73:3307-3312.
7. Kaser M, Rondini S, Naegeli M, Stinear T, Portaels F, Certa U, Pluschke G. 2007. Evolution of two distinct phylogenetic lineages of the emerging human pathogen Mycobacterium ulcerans. BMC Evol. Biol. 7:177. doi:10 .1186/1471-2148-7-177.
8. Doig KD, Holt KE, Fyfe JA, Lavender CJ, Eddyani M, Portaels F, Yeboah-Manu D, Pluschke G, Seemann T, Stinear TP. 2012. On the origin of Mycobacterium ulcerans, the causative agent of Buruli ulcer.BMC Genomics 13:258. doi:10.1186/1471-2164-13-258.
9. Yip MJ, Porter JL, Fyfe JA, Lavender CJ, Portaels F, Rhodes M, Kator H, Colorni A, Jenkin GA, Stinear T. 2007. Evolution of Mycobacterium ulcerans and other mycolactone-producing mycobacteria from a common Mycobacterium marinum progenitor. J. Bacteriol. 189:2021-2029.
10. Pidot SJ, Asiedu K, Kaser M, Fyfe JA, Stinear TP. 2010. Mycobacterium ulcerans and other mycolactone-producing mycobacteria should be considered a single species. PLoS Negl. Trop. Dis. 4:e663. doi:10.1371/journal .pntd.0000663.
11. Suykerbuyk P, Vleminckx K, Pasmans F, Stragier P, Ablordey A, Tran HT, Hermans K, Fleetwood M, Meyers WM, Portaels F. 2007. Mycobacterium liflandii infection in European colony of Silurana tropicalis. Emerg. Infect. Dis. 13:743-746.
12. Stinear TP, Seemann T, Pidot S, Frigui W, Reysset G, Garnier T, Meurice G, Simon D, Bouchier C, Ma L, Tichit M, Porter JL, Ryan J, Johnson PD, Davies JK, Jenkin GA, Small PL, Jones LM, Tekaia F, Laval F, Daffe M, Parkhill J, Cole ST. 2007. Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer. Genome Res. 17:192-200.
13. Stinear TP, Seemann T, Harrison PF, Jenkin GA, Davies JK, Johnson PD, Abdellah Z, Arrowsmith C, Chillingworth T, Churcher C, Clarke K, Cronin A, Davis P, Goodhead I, Holroyd N, Jagels K, Lord A, Moule S, Mungall K, Norbertczak H, Quail MA, Rabbinowitsch E, Walker D, White B, Whitehead S, Small PL, Brosch R, Ramakrishnan L, Fischbach MA, Parkhill J, Cole ST. 2008. Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis. Genome Res. 18:729-741.
14. Heysell SK, Mtabho C, Mpagama S, Mwaigwisya S, Pholwat S, Ndusilo N, Gratz J, Aarnoutse RE, Kibiki GS, Houpt ER. 2011. Plasma drug activity assay for treatment optimization in tuberculosis patients. Antimicrob. Agents Chemother. 55:5819-5825.
15. van Hijum SA, Zomer AL, Kuipers OP, Kok J. 2005. Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies. Nucleic Acids Res. 33:W560-W566.
16. Bonfield JK, Smith K, Staden R. 1995. A new DNA sequence assembly program. Nucleic Acids Res. 23:4992-4999.
17. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. 2009. Circos: an information aesthetic for comparative genomics. Genome Res. 19:1639-1645.
18. Darling AE, Mau B, Perna NT. 2010. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5:e11147. doi:10.1371/journal.pone.0011147.
19. Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, Parkhill J. 2005. ACT: the Artemis Comparison Tool. Bioinformatics 21:3422-3423.
20. Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P, Fischbach MA, Weber T, Takano E, Breitling R. 2011. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res. 39:W339-W346.
21. Pidot SJ, Hong H, Seemann T, Porter JL, Yip MJ, Men A, Johnson M, Wilson P, Davies JK, Leadlay PF, Stinear TP. 2008. Deciphering the genetic basis for polyketide variation among mycobacteria producing mycolactones. BMC Genomics 9:462. doi:10.1186/1471-2164-9-462.
22. Kaser M, Pluschke G. 2008. Differential gene repertoire in Mycobacterium ulcerans identifies candidate genes for patho-adaptation. PLoS Negl. Trop. Dis. 2:e353. doi:10.1371/journal.pntd.0000353.
23. Mahillon J, Chandler M. 1998. Insertion sequences. Microbiol. Mol. Biol. Rev. 62:725-774.
24. Stinear T, Ross BC, Davies JK, Marino L, Robins-Browne RM, Oppedisano F, Sievers A, Johnson PD. 1999. Identification and characterization of IS2404 and IS2606: two distinct repeated sequences for detection of Mycobacterium ulcerans by PCR. J. Clin. Microbiol. 37:1018-1023.
25. Voskuil MI, Schnappinger D, Visconti KC, Harrell MI, Dolganov GM, Sherman DR, Schoolnik GK. 2003. Inhibition of respiration by nitric oxide induces a Mycobacterium tuberculosis dormancy program. J. Exp. Med. 198:705-713.
26. Moran NA. 2002. Microbial minimalism: genome reduction in bacterial pathogens. Cell 108:583-586.
27. Ramakrishnan L, Federspiel NA, Falkow S. 2000. Granuloma-specific expression of Mycobacterium virulence proteins from the glycine-rich PE-PGRS family. Science 288:1436-1439.
28. Bottai D, Brosch R. 2009. Mycobacterial PE, PPE and ESX clusters: novel insights into the secretion of these most unusual protein families. Mol. Microbiol. 73:325-328.
29. Delogu G, Brennan MJ. 2001. Comparative immune response to PE and PE_PGRS antigens of Mycobacterium tuberculosis. Infect. Immun. 69: 5606-5611.
30. Cole ST, Eiglmeier K, Parkhill J, James KD, Thomson NR, Wheeler PR, Honore N, Garnier T, Churcher C, Harris D, Mungall K, Basham D, Brown D, Chillingworth T, Connor R, Davies RM, Devlin K, Duthoy S, Feltwell T, Fraser A, Hamlin N, Holroyd S, Hornsby T, Jagels K, Lacroix C, Maclean J, Moule S, Murphy L, Oliver K, Quail MA, Rajandream MA, Rutherford KM, Rutter S, Seeger K, Simon S, Simmonds M, Skelton J, Squares R, Squares S, Stevens K, Taylor K, Whitehead S, Woodward JR, Barrell BG. 2001. Massive gene decay in the leprosy bacillus. Nature 409:1007-1011.
31. Shi L, Sohaskey CD, Kana BD, Dawes S, North RJ, Mizrahi V, Gennaro ML. 2005. Changes in energy metabolism of Mycobacterium tuberculosis in mouse lung and under in vitro conditions affecting aerobic respiration. Proc. Natl. Acad. Sci. U. S. A. 102:15629-15634.
32. Hsu T, Hingley-Wilson SM, Chen B, Chen M, Dai AZ, Morin PM, Marks CB, Padiyar J, Goulding C, Gingery M, Eisenberg D, Russell RG, Derrick SC, Collins FM, Morris SL, King CH, and Jacobs WR, Jr. 2003. The primary mechanism of attenuation of bacillus Calmette-Guerin is a loss of secreted lytic function required for invasion of lung interstitial tissue. Proc. Natl. Acad. Sci. U. S. A. 100:12420-12425.
33. Brodin P, Majlessi L, Marsollier L, de Jonge MI, Bottai D, Demangel C, Hinds J, Neyrolles O, Butcher PD, Leclerc C, Cole ST, Brosch R. 2006. Dissection of ESAT-6 system 1 of Mycobacterium tuberculosis and impact on immunogenicity and virulence. Infect. Immun. 74:88-98.
34. Steyn AJ, Joseph J, Bloom BR. 2003. Interaction of the sensor module of Mycobacterium tuberculosis H37Rv KdpD with members of the Lpr family. Mol. Microbiol. 47:1075-1089.
35. Casali N, Riley LW. 2007. A phylogenomic analysis of the Actinomycetales mce operons. BMC Genomics 8:60. doi:10.1186/1471-2164-8-60.
36. Camacho LR, Ensergueix D, Perez E, Gicquel B, Guilhot C. 1999. Identification of a virulence gene cluster of Mycobacterium tuberculosis by signature-tagged transposon mutagenesis. Mol. Microbiol. 34:257-267.
37. Kovacs-Simon A, Titball RW, Michell SL. 2011. Lipoproteins of bacterial pathogens. Infect. Immun. 79:548-561.
38. Hussain M, Ozawa Y, Ichihara S, Mizushima S. 1982. Signal peptide digestion in Escherichia coli. Effect of protease inhibitors on hydrolysis of the cleaved signal peptide of the major outer-membrane lipoprotein. Eur. J. Biochem. 129:233-239.
39. Okuda S, Tokuda H. 2011. Lipoprotein sorting in bacteria. Annu. Rev. Microbiol. 65:239-259.
40. Ichihara S, Beppu N, Mizushima S. 1984. Protease IV, a cytoplasmic membrane protein of Escherichia coli, has signal peptide peptidase activity. J. Biol. Chem. 259:9853-9857.
41. Henneke P, Dramsi S, Mancuso G, Chraibi K, Pellegrini E, Theilacker C, Hubner J, Santos-Sierra S, Teti G, Golenbock DT, Poyart C, Trieu- Cuot P. 2008. Lipoproteins are critical TLR2 activating toxins in group B streptococcal sepsis. J. Immunol. 180:6149-6158.
42. Machata S, Tchatalbachev S, Mohamed W, Jansch L, Hain T, Chakraborty T. 2008. Lipoproteins of Listeria monocytogenes are critical for virulence and TLR2-mediated immune activation. J. Immunol. 181:2028-2035.
43. Pittard AJ. 1987. Biosynthesis of the aromatic amino acids, p 368-394. In Ingraham JL, Low KB, Magasanik B, Schaechter M, Umbarger HE (ed), Escherichia coli and Salmonella typhimurium: cellular and molecular biology. American Society for Microbiology, Washington, DC.
44. Barker C, Lewis D. 1974. Impaired regulation of aromatic amino acid synthesis in a mutant resistant to p-fluorophenylalanine. J. Gen. Microbiol. 82:337-343.
45. Parish T, Stoker NG. 2002. The common aromatic amino acid biosynthesis pathway is essential in Mycobacterium tuberculosis. Microbiology 148:3069-3077.
46. Alland D, Steyn AJ, Weisbrod T, Aldrich K, and Jacobs WR, Jr. 2000. Characterization of the Mycobacterium tuberculosis iniBAC promoter, a promoter that responds to cell wall biosynthesis inhibition. J. Bacteriol. 182:1802-1811.
47. Colangeli R, Helb D, Sridharan S, Sun J, Varma-Basil M, Hazbon MH, Harbacheuski R, Megjugorac NJ, Jacobs WR, Jr, Holzenburg A, Sacchettini JC, Alland D. 2005. The Mycobacterium tuberculosis iniA gene is essential for activity of an efflux pump that confers drug tolerance to both isoniazid and ethambutol. Mol. Microbiol. 55:1829-1840.
48. Chopra T, Gokhale RS. 2009. Polyketide versatility in the biosynthesis of complex mycobacterial cell wall lipids. Methods Enzymol. 459:259-294.
49. Rocha EP, Fralick J, Vediyappan G, Danchin A, Norris V. 2003. A strand-specific model for chromosome segregation in bacteria. Mol. Microbiol. 49:895-903.
50. Konstantinidis KT, Tiedje JM. 2005. Genomic insights that advance the species definition for prokaryotes. Proc. Natl. Acad. Sci. U. S. A. 102:2567-2572.
51. Rumble SM, Lacroute P, Dalca AV, Fiume M, Sidow A, Brudno M. 2009. SHRiMP: accurate mapping of short color-space reads. PLoS Comput. Biol. 5:e1000386.
52. Wu CH, Tsai-Wu JJ, Huang YT, Lin CY, Lioua GG, Lee FJ. 1998. Identification and subcellular localization of a novel Cu, Zn superoxide dismutase of Mycobacterium tuberculosis. FEBS Lett 439:192-196.