Genes under positive selection in Mycobacterium tuberculosis

Computational Biology and Chemistry

Volumn 35, Issue 5, 2011, Pages 319-322

  Zhang, Yuan ^a   Zhang, Hong ^b   Zhou, Tianyin ^b   Zhong, Yang ^b   Jin, Qi ^a  

^a INSTITUTE OF PATHOGEN BIOLOGY   (China)

^b FUDAN UNIVERSITY   (China)

Author keywords

Evolutionary genomics; Mycobacterium tuberculosis; Positive selection

Indexed keywords

CLINICAL ISOLATES; GENOMICS; HYPOTHETICAL PROTEIN; MYCOBACTERIUM TUBERCULOSIS; MYCOBACTERIUM TUBERCULOSIS STRAINS; POSITIVE SELECTION; RNA POLYMERASE; SIGMA FACTOR;

PROTEINS; RNA;

GENES;

BACTERIAL ANTIGEN; BACTERIAL PROTEIN;

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BIOLOGICAL MODEL; CHEMISTRY; GENETIC ASSOCIATION; GENETIC SELECTION; GENETICS; HUMAN; ISOLATION AND PURIFICATION; LUNG TUBERCULOSIS; MICROBIOLOGY; MYCOBACTERIUM TUBERCULOSIS; PATHOGENICITY; VIRULENCE;

ANTIGENS, BACTERIAL; BACTERIAL PROTEINS; GENES, BACTERIAL; GENETIC ASSOCIATION STUDIES; GENOME, BACTERIAL; HUMANS; MODELS, GENETIC; MYCOBACTERIUM TUBERCULOSIS; SELECTION, GENETIC; TUBERCULOSIS, PULMONARY; VIRULENCE;

MYCOBACTERIUM TUBERCULOSIS;

EID: 80052699440     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2011.08.001     Document Type: Article

References (32)

1. N. Agarwal, S.C. Woolwine, S. Tyagi, and W.R. Bishai Characterization of the Mycobacterium tuberculosis sigma factor SigM by assessment of virulence and identification of SigM-dependent genes Infect. Immun. 75 2007 452 461 (Pubitemid 46047921)
2. G. Aguileta, G. Refregier, R. Yockteng, E. Fournier, and T. Giraud Rapidly evolving genes in pathogens: methods for detecting positive selection and examples among fungi, bacteria, viruses and protists Infect. Genet. Evol. 9 2009 656 670
3. S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 1997 3389 3402 (Pubitemid 27359211)
4. M. Anisimova, and Z. Yang Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites Mol. Biol. Evol. 24 2007 1219 1228 (Pubitemid 47343648)
5. R. Brosch, W.J. Philipp, E. Stavropoulos, M.J. Colston, S.T. Cole, and S.V. Gordon Genomic analysis reveals variation between Mycobacterium tuberculosis H37Rv and the attenuated M. tuberculosis H37Ra strain Infect. Immun. 67 1999 5768 5774 (Pubitemid 29508097)
6. J. Campuzano, D. Aguilar, K. Arriaga, J.C. Leon, L.P. Salas-Rangel, J. Gonzalez-y-Merchand, R. Hernandez-Pando, and C. Espitia The PGRS domain of Mycobacterium tuberculosis PE-PGRS Rv1759c antigen is an efficient subunit vaccine to prevent reactivation in a murine model of chronic tuberculosis Vaccine 25 2007 3722 3729
7. M.G. Chaitra, M.S. Shaila, N.R. Chandra, and R. Nayak HLA-A*0201-restricted cytotoxic T-cell epitopes in three PE/PPE family proteins of Mycobacterium tuberculosis Scand. J. Immunol. 67 2008 411 417 (Pubitemid 351392926)
8. M.G. Chaitra, M.S. Shaila, and R. Nayak Evaluation of T-cell responses to peptides with MHC class I-binding motifs derived from PE-PGRS 33 protein of Mycobacterium tuberculosis J. Med. Microbiol. 56 2007 466 474
9. M. Chen, H. Gan, and H.G. Remold A mechanism of virulence: virulent Mycobacterium tuberculosis strain H37Rv, but not attenuated H37Ra, causes significant mitochondrial inner membrane disruption in macrophages leading to necrosis J. Immunol. 176 2006 3707 3716 (Pubitemid 43364017)
10. S.T. Cole, R. Brosch, J. Parkhill, T. Garnier, C. Churcher, D. Harris, S.V. Gordon, K. Eiglmeier, S. Gas, C.E. Barry 3rd, F. Tekaia, K. Badcock, D. Basham, D. Brown, T. Chillingworth, R. Connor, R. Davies, K. Devlin, T. Feltwell, S. Gentles, N. Hamlin, S. Holroyd, T. Hornsby, K. Jagels, A. Krogh, J. McLean, S. Moule, L. Murphy, K. Oliver, J. Osborne, M.A. Quail, M.A. Rajandream, J. Rogers, S. Rutter, K. Seeger, J. Skelton, R. Squares, S. Squares, J.E. Sulston, K. Taylor, S. Whitehead, and B.G. Barrell Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence Nature 393 1998 537 544 (Pubitemid 28319235)
11. R.C. Edgar MUSCLE: a multiple sequence alignment method with reduced time and space complexity BMC Bioinformatics 5 2004 113
12. R.C. Edgar MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res. 32 2004 1792 1797 (Pubitemid 38832724)
13. R.D. Fleischmann, D. Alland, J.A. Eisen, L. Carpenter, O. White, J. Peterson, R. DeBoy, R. Dodson, M. Gwinn, D. Haft, E. Hickey, J.F. Kolonay, W.C. Nelson, L.A. Umayam, M. Ermolaeva, S.L. Salzberg, A. Delcher, T. Utterback, J. Weidman, H. Khouri, J. Gill, A. Mikula, W. Bishai, W.R. Jacobs Jr.; J.C. Venter, and C.M. Fraser Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains J. Bacteriol. 184 2002 5479 5490 (Pubitemid 35024395)
14. K.W. Koh, S.E. Soh, and G.T. Seah Strong antibody responses to Mycobacterium tuberculosis PE-PGRS62 protein are associated with latent and active tuberculosis Infect. Immun. 77 2009 3337 3343
15. A.S. Mustafa, R. Al-Attiyah, S.N. Hanif, and F.A. Shaban Efficient testing of large pools of Mycobacterium tuberculosis RD1 peptides and identification of major antigens and immunodominant peptides recognized by human Th1 cells Clin. Vaccine Immunol. 15 2008 916 924 (Pubitemid 351966995)
16. M. Nei Selectionism and neutralism in molecular evolution Mol. Biol. Evol. 22 2005 2318 2342 (Pubitemid 41662341)
17. L. Petersen, J.P. Bollback, M. Dimmic, M. Hubisz, and R. Nielsen Genes under positive selection in Escherichia coli Genome Res. 17 2007 1336 1343 (Pubitemid 47360908)
18. J.B. Plotkin, J. Dushoff, and H.B. Fraser Detecting selection using a single genome sequence of M. tuberculosis and P. falciparum Nature 428 2004 942 945 (Pubitemid 38560308)
19. K.D. Pruitt, T. Tatusova, and D.R. Maglott NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins Nucleic Acids Res. 35 2007 D61 D65
20. S. Raman, X. Puyang, T.Y. Cheng, D.C. Young, D.B. Moody, and R.N. Husson Mycobacterium tuberculosis SigM positively regulates Esx secreted protein and nonribosomal peptide synthetase genes and down regulates virulence-associated surface lipid synthesis J. Bacteriol. 188 2006 8460 8468 (Pubitemid 44894046)
21. L. Rindi, N. Lari, and C. Garzelli Genes of Mycobacterium tuberculosis H37Rv downregulated in the attenuated strain H37Ra are restricted to M. tuberculosis complex species New Microbiol. 24 2001 289 294 (Pubitemid 33633224)
22. R.F. Silver, J. Walrath, H. Lee, B.A. Jacobson, H. Horton, M.R. Bowman, K. Nocka, and J.P. Sypek Human alveolar macrophage gene responses to Mycobacterium tuberculosis strains H37Ra and H37Rv Am. J. Respir. Cell Mol. Biol. 40 2009 491 504
23. S. Talarico, M.D. Cave, B. Foxman, C.F. Marrs, L. Zhang, J.H. Bates, and Z. Yang Association of Mycobacterium tuberculosis PE PGRS33 polymorphism with clinical and epidemiological characteristics Tuberculosis (Edinb.) 87 2007 338 346 (Pubitemid 46936245)
24. S. Talarico, L. Zhang, C.F. Marrs, B. Foxman, M.D. Cave, M.J. Brennan, and Z. Yang Mycobacterium tuberculosis PE-PGRS16 and PE-PGRS26 genetic polymorphism among clinical isolates Tuberculosis (Edinb.) 88 2008 283 294
25. S. Tundup, N. Pathak, M. Ramanadham, S. Mukhopadhyay, K.J. Murthy, N.Z. Ehtesham, and S.E. Hasnain The co-operonic PE25/PPE41 protein complex of Mycobacterium tuberculosis elicits increased humoral and cell mediated immune response PLoS One 3 2008 e3586
26. Z.H. Yang Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A J. Mol. Evol. 51 2000 423 432
27. Z.H. Yang, and R. Nielsen Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages Mol. Biol. Evol. 19 2002 908 917
28. Z.H. Yang, W.S.W. Wong, and R. Nielsen Bayes empirical Bayes inference of amino acid sites under positive selection Mol. Biol. Evol. 22 2005 1107 1118 (Pubitemid 40471423)
29. Z.H. Yang PAML 4: phylogenetic analysis by maximum likelihood Mol. Biol. Evol. 24 2007 1586 1591
30. J. Zhang, and T.L. Madden PowerBLAST: a new network BLAST application for interactive or automated sequence analysis and annotation Genome Res. 7 1997 649 656 (Pubitemid 27313614)
31. J. Zhang, R. Nielsen, and Z. Yang Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level Mol. Biol. Evol. 22 2005 2472 2479 (Pubitemid 41661383)
32. H. Zheng, L. Lu, B. Wang, S. Pu, X. Zhang, G. Zhu, W. Shi, L. Zhang, H. Wang, S. Wang, G. Zhao, and Y. Zhang Genetic basis of virulence attenuation revealed by comparative genomic analysis of Mycobacterium tuberculosis strain H37Ra versus H37Rv PLoS One 11 2008 e2375