Comparative analysis of microbial genomes to study unique and expanded gene families in Mycobacterium tuberculosis

Infection, Genetics and Evolution

Volumn 9, Issue 3, 2009, Pages 314-321

  Mulder, Nicola ^a   Rabiu, Halimah ^a   Jamieson, Gordon ^a   Vuppu, Venu ^a  

^a UNIVERSITY OF CAPE TOWN   (South Africa)

Author keywords

Comparative genomics; Duplication; Mycobacteria; Pathogen; Tuberculosis

Indexed keywords

ADENOSINE TRIPHOSPHATASE (POTASSIUM SODIUM); ADHESIN; ALDEHYDE DEHYDROGENASE; CELL SURFACE PROTEIN; CYTOTOXIN; DNA BINDING PROTEIN; HEMAGGLUTININ; HEMOLYSIN; HEPARIN BINDING PROTEIN; PHOSPHOLIPASE C; PROTEOME; SIGMA FACTOR RPON; SULFATASE; VIRULENCE FACTOR;

ARTICLE; BACTERIAL GENETICS; BACTERIAL VIRULENCE; COMPUTER PROGRAM; DEATH; EVOLUTION; GENE DUPLICATION; GENE FUNCTION; GENETIC ANALYSIS; MULTIGENE FAMILY; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PATHOGENESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; SEQUENCE ALIGNMENT; TUBERCULOSIS;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENOME, BACTERIAL; HUMANS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; MYCOBACTERIUM TUBERCULOSIS; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, PROTEIN; TUBERCULOSIS, PULMONARY; VIRULENCE FACTORS;

CORYNEBACTERINEAE; MYCOBACTERIUM TUBERCULOSIS;

EID: 64549103427     PISSN: 15671348     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.meegid.2007.12.006     Document Type: Article

References (46)

1. Böttger E.C., Springer B., Pletschette M., and Sander P. Fitness of antibiotic resistant microorganisms and compensatory mutations. Nat. Med. 4 (1998) 1343-1344
2. Bridges C.B. The bar 'gene' a duplication. Science 83 (1936) 210-211
3. Brosch R., Pym A.S., Gordon S.V., and Cole S.T. The evolution of mycobacterial pathogenicity: clues from comparative genomics. Trends Microbiol. 9 (2001) 452-458
4. Camon E., Magrane M., Barrell D., Lee V., Dimmer E., Maslen J., Binns D., Harte N., Lopez R., and Apweiler R. The gene ontology annotation (GOA) database: sharing knowledge in Uniprot with gene ontology. Nucleic Acids Res. 32 (2004) D262-D266
5. Camus J.C., Pryor M.J., Medigue C., and Cole S.T. Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv. Microbiology 148 (2002) 2967-2973
6. Chitale S., Ehrt S., Kawamura I., Fujimura T., Shimono N., Anand N., Lu S., Cohen-Gould L., and Riley L.W. Recombinant Mycobacterium tuberculosis protein associated with mammalian cell entry. Cell Microbiol. 3 4 (2001) 247-254
7. Cole S.T. Learning from the genome sequence of Mycobacterium tuberculosis H37Rv. FEBS Lett. 452 1/2 (1999) 7-10
8. Cole S.T. Comparative mycobacterial genomics as a tool for drug target and antigen discovery. Eur. Respir. J. 20 36 (2002) 78s-86s
9. Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C., Harris D., Gordon S.V., Eiglmeier K., Gas S., Barry C.E., Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T., Connor R., Davies R., Devlin K., Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S., Murphy L., Oliver K., Osborne J., Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton J., Squares R., Squares S., Sulston J.E., Taylor K., Whitehead S., and Barrell B.G. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393 (1998) 537-544
10. Cole S.T., Eiglmeier K., Parkhill J., James K.D., Thomson N.R., Wheeler P.R., Honoré N., Garnier T., Churcher C., Harris D., Mungall K., Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., 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 M.A., Rajandream M.A., Rutherford K.M., Rutter S., Seeger K., Simon S., Simmonds M., Skelton J., Squares R., Squares S., Stevens K., Taylor K., Whitehead S., Woodward J.R., and Barrell B.G. Massive gene decay in the leprosy bacillus. Nature 409 (2001) 1007-1011
11. Cooksey R.C., Morlock G.P., McQueen A., Glickman S.E., and Crawford J.T. Characterization of streptomycin resistance mechanisms among M. tuberculosis isolates from patients in New York City. Antimicrob. Agents Chemother. 40 (1996) 1186-1188
12. Domenech P., Reed M.B., and Barry III C.E. Contribution of the Mycobacterium tuberculosis MmpL protein family to virulence and drug resistance. Infect. Immun. 73 6 (2005) 3492-3501
13. Fleischmann R.D., Alland D., Eisen J.A., Carpenter L., White O., Peterson J., DeBoy R., Dodson R., Gwinn M., Haft D., Hickey E., Kolonay J.F., Nelson W.C., Umayam L.A., Ermolaeva M., Salzberg S.L., Delcher A., Utterback T., Weidman J., Khouri H., Gill J., Mikula A., Bishai W., Jacobs Jr. W.R., Venter J.C., and Fraser C.M. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J. Bacteriol. 184 (2002) 5479-5490
14. Force A., Lynch M., Pickett F.B., Amores A., Yan Y.L., and Postlethwait J. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151 4 (1999) 1531-1545
15. Gene Ontology Consortium. The gene ontology (GO) project in 2006. Nucleic Acids Res. 34 (2006) D322-D326
16. Gevers D., Vandepoele K., Simillon C., and Van de Peer Y. Gene duplication and biased functional retention of paralogs in bacterial genomes. Trends Microbiol. 12 4 (2004) 48-154
17. Gey van Pittius N.C., Sampson S.L., Lee H., Kim Y., van Helden P.D., and Warren R.M. 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 (2006) 95-124
18. Glickman M.S., and Jacobs W.R. Microbial pathogenesis of Mycobacterium tuberculosis: dawn of a discipline. Cell 104 4 (2001) 477-485
19. Gordon S.V., Heym B., Parkhill J., Barrell B., and Cole S.T. New insertion sequences and a novel repeated sequence in the genome of Mycobacterium tuberculosis H37Rv. Microbiology 145 (1999) 881-892
20. Gordon S.V., Eiglmeier K., Garnier T., Brosch R., Parkhill J., Barrell B., Cole T., and Hewinson R.G. Genomics of Mycobacterium bovis. Tuberculosis (Edinb.) 81 1/2 (2001) 157-163
21. Harboe M., Christensen A., Ahmad S., Ulvund G., Harkness R.E., Mustafa A.S., and Wiker H.G. Cross-reaction between mammalian cell entry (Mce) proteins of Mycobacterium tuberculosis. Scand. J. Immunol. 56 6 (2002) 580-587
22. Hooper S.D., and Berg O.G. On the nature of gene innovation: duplication patterns in microbial genomes. Mol. Biol. Evol. 20 6 (2003) 945-954
23. Hughes A.L. Gene duplication and the origin of novel proteins. Proc. Natl. Acad. Sci. U.S.A. 102 25 (2005) 8791-8792
24. Jensen R.A. Enzyme recruitment in the evolution of new function. Annu. Rev. Microbiol. 30 (1976) 409-425
25. Kondrashov F.A., Rogozin I.B., Wolf Y.I., and Koonin E.V. Selection in the evolution of gene duplications. Genome Biol. 3 2 (2002) research0008.1-0008.9
26. Lara-Tejero M., Sutterwala F.S., Ogura Y., Grant E.P., Bertin J., Coyle A.J., Flavell R.A., and Galan J.E. Role of the caspase-1 inflammasome in Salmonella typhimurium pathogenesis. J. Exp. Med. 203 (2006) 1407-1412
27. Lowrie D.B. DNA vaccines for therapy of tuberculosis: where are we now?. Vaccine 24 12 (2006) 1983-1989
28. Mulder N.J., Apweiler R., Attwood T.K., Bairoch A., Bateman A., Binns D., Bork P., Buillard V., Cerutti L., Copley R., Courcelle E., Das U., Daugherty L., Dibley M., Finn R., Fleischmann W., Gough J., Haft D., Hulo N., Hunter S., Kahn D., Kanapin A., Kejariwal A., Labarga A., Langendijk-Genevaux P.S., Lonsdale D., Lopez R., Letunic I., Madera M., Maslen J., McAnulla C., McDowall J., Mistry J., Mitchell A., Nikolskaya A.N., Orchard S., Orengo C., Petryszak R., Selengut J.D., Sigrist C.J., Thomas P.D., Valentin F., Wilson D., Wu C.H., and Yeats C. New developments in the InterPro database. Nucleic Acids Res. 35 (2007) D224-D228
29. Murray M., and Nardell E. Molecular epidemiology of tuberculosis: achievements and challenges to current knowledge. Bull. World Health Organ. 80 6 (2002) 477-482
30. Nair J., Rouse D.A., Bai G.H., and Morris S.L. The rpsL gene and streptomycin resistance in single and multiple drug-resistant strains of Mycobacterium tuberculosis. Mol. Microbiol. 10 (1993) 521-527
31. Namboori S., Srinivasan N., and Pandit S.B. Enhanced functional and structural domain assignments using remote similarity detection procedures for proteins encoded in the genome of Mycobacterium tuberculosis H37Rv. J. Biosci. 29 3 (2004) 245-259
32. Nei M. Gene duplication and nucleotide substitution in evolution. Nature 221 5175 (1969) 40-42
33. Ohno S. Evolution by Gene Duplication (1970), Springer-Verlag, New York
34. Orgel L.E. Gene duplication and the origin of proteins with novel functions. J. Theor. Biol. 67 4 (1977) 773
35. Pablos-Mendez A., Raviglione M.C., Laszlo A., Binkin N., Rieder H.L., Bustreo F., Cohn D.L., Lambregts-van C.S., Weezenbeek S., Kim J., Chaulet P., and Nunn P. Global surveillance for antituberculosis-drug resistance, 1994-1997. World health organization-international union against tuberculosis and lung disease working group on anti-tuberculosis drug resistance surveillance. N. Engl. J. Med. 338 (1998) 1641-1649
36. Riska P.F., Ya S., Bardarov S., Freundlich L., Sarkis G., Carrière C., Kumar V., Chan J., and Jacobs W.R. Rapid film-based determination of antibiotic susceptibilities of Mycobacterium tuberculosis strains by using a luciferase reporter phage and the bronx box. J. Clin. Microbiol. 37 4 (1999) 1144-1149
37. Robinson P.N., Wollstein A., Bohme U., and Beattie B. Ontologising gene-expression micro-array data: characterising clusters with gene ontology. Bioinformatics 20 6 (2004) 979-981
38. Sampson S.L., Lukey P., Warren R.M., van Helden P.D., Richardson M., and Everett M.J. Expression, characterization and subcellular localization of the Mycobacterium tuberculosis PPE gene Rv1917c. Tuberculosis (Edinb.) 81 5/6 (2001) 305-317
39. Sasetti C.M., and Rubin E.J. Genetic requirements for mycobacterial survival during infection. Proc. Natl. Acad. Sci. U.S.A. 100 22 (2003) 12989-12994
40. Spratt B.G. Antibiotic resistance: counting the cost. Curr. Biol. 6 (1996) 1219-1221
41. Tekaia F., Gordon S.V., Garnier T., Brosch R., Barrell B.G., and Cole S.T. Analysis of the proteome of Mycobacterium tuberculosis in silico. Tuber. Lung Dis. 79 (1999) 329-342
42. TØnjum T., Welty D.B., Jantzen E., and Small P.L. Differentiation of M. 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 (1998) 918-925
43. UniProt Consortium. The universal protein resource (UniProt). Nucleic Acids Res. 35 (2007) D193-D197
44. van den Braak N., Simons G., Gorkink R., Reijans M., Eadie K., Kremers K., van Soolingen D., Savelkoul P., Verbrugh H., and van Belkum A. A new highthroughput AFLP approach for identification of new genetic polymorphism in the genome of the clonal microorganism Mycobacterium tuberculosis. J. Microbiol. Methods 56 1 (2004) 49-62
45. Weinstock G.M., Smajs D., Hardham J., and Norris S.J. From microbial genome sequence to applications. Res. Microbiol. 151 2 (2000) 151-158
46. World Health Organization (WHO), 2006. Tuberculosis Fact Sheet No. 104-Global and regional incidence. http://www.who.int/whr/en.