Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry

Molecular and Cellular Proteomics

Volumn 10, Issue 12, 2011, Pages

  Kelkar, Dhanashree S ^a,b   Kumar, Dhirendra ^c   Kumar, Praveen ^a   Balakrishnan, Lavanya ^a,d   Muthusamy, Babylakshmi ^a,e   Yadav, Amit Kumar ^c   Shrivastava, Priyanka ^c   Marimuthu, Arivusudar ^a,f   Anand, Sridhar ^g   Sundaram, Hema ^g   Kingsbury, Reena ^g   Harsha, H C ^a   Nair, Bipin ^b   Prasad, T S Keshava ^a,e,f   Chauhan, Devendra Singh ^h   Katoch, Kiran ^h   Katoch, Vishwa Mohan ⁱ   Kumar, Prahlad ^g   Chaerkady, Raghothama ^a,j   Ramachandran, Srinivasan ^c   Dash, Debasis ^c   Pandey, Akhilesh ^a,j   more..

^a INSTITUTE OF BIOINFORMATICS   (India)

^b AMRITA UNIVERSITY   (India)

^c CSIR INSTITUTE OF GENOMICS AND INTEGRATIVE BIOLOGY   (India)

^d KUVEMPU UNIVERSITY   (India)

^e PONDICHERRY UNIVERSITY   (India)

^f MANIPAL UNIVERSITY   (India)

^g NATIONAL TUBERCULOSIS INSTITUTE   (India)

^h NATIONAL JALMA INSTITUTE FOR LEPROSY AND OTHER MYCOBACTERIAL DISEASES   (India)

ⁱ INDIAN COUNCIL OF MEDICAL RESEARCH   (India)

^j JOHNS HOPKINS UNIVERSITY   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; PYRUVATE DEHYDROGENASE;

AMINO TERMINAL SEQUENCE; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIUM CULTURE; BACTERIUM IDENTIFICATION; CODON; GENE SEQUENCE; GENETIC DATABASE; GENOME ANALYSIS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PEPTIDE ANALYSIS; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; SEQUENCE ANALYSIS; TANDEM MASS SPECTROMETRY;

EID: 83055173265     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: None     Document Type: Article

References (25)

1. Jungblut, P. R., Schaible, U. E., Mollenkopf, H. J., Zimny-Arndt, U., Raupach, B., Mattow, J., Halada, P., Lamer, S., Hagens, K., and Kaufmann, S. H. (1999) Comparative proteome analysis of Mycobacterium tuberculosis and Mycobacterium bovis BCG strains: towards functional genomics of microbial pathogens. Mol. Microbiol. 33, 1103-1117 (Pubitemid 29433617)
2. Jungblut, P. R., Müller, E. C., Mattow, J., and Kaufmann, S. H. (2001) Proteomics reveals open reading frames in Mycobacterium tuberculosis H37Rv not predicted by genomics. Infect. Immun. 69, 5905-5907 (Pubitemid 32786532)
3. Gu, S., Chen, J., Dobos, K. M., Bradbury, E. M., Belisle, J. T., and Chen, X. (2003) Comprehensive proteomic profiling of the membrane constituents of Mycobacterium tuberculosis strain. Mol. Cell. Proteomics 2, 1284-1296
4. Mawuenyega, K. G., Forst, C. V., Dobos, K. M., Belisle, J. T., Chen, J., Bradbury, E. M., Bradbury, A. R., and Chen, X. (2005) Mycobacterium tuberculosis functional network analysis by global subcellular protein profiling. Mol. Biol. Cell 16, 396-404 (Pubitemid 40024320)
5. Mattow, J., Siejak, F., Hagens, K., Becher, D., Albrecht, D., Krah, A., Schmidt, F., Jungblut, P. R., Kaufmann, S. H., and Schaible, U. E. (2006) Proteins unique to intraphagosomally grown Mycobacterium tuberculosis. Proteomics 6, 2485-2494
6. Målen, H., Berven, F. S., Fladmark, K. E., and Wiker, H. G. (2007) Comprehensive analysis of exported proteins from Mycobacterium tuberculosis H37Rv. Proteomics 7, 1702-1718 (Pubitemid 46841830)
7. Målen, H., Pathak, S., Softeland, T., de Souza, G. A., and Wiker, H. G. (2010) Definition of novel cell envelope associated proteins in Triton X-114 extracts of Mycobacterium tuberculosis H37Rv. BMC Microbiol. 10, 132
8. Cole, S. T., Brosch, R., Parkhill, J., Garnier, T., Churcher, C., Harris, D., Gordon, S. V., Eiglmeier, K., Gas, S., Barry, C. E., 3rd, 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. (1998) Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393, 537-544 (Pubitemid 28319235)
9. 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., Jr., Venter, J. C., and Fraser, C. M. (2002) Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J. Bacteriol. 184, 5479-5490 (Pubitemid 35024395)
10. Camus, J. C., Pryor, M. J., Médigue, C., and Cole, S. T. (2002) Reannotation of the genome sequence of Mycobacterium tuberculosis H37Rv. Microbiology 148, 2967-2973 (Pubitemid 35243696)
11. The Tuberculist Database [http://tuberculist.epfl.ch]
12. de Souza, G. A., Målen, H., Softeland, T., Saelensminde, G., Prasad, S., Jonassen, I., and Wiker, H. G. (2008) High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example. BMC Genomics 9, 316
13. Lew, J. M., Kapopoulou, A., Jones, L. M., and Cole, S. T. (2011) TubercuList - 10 years after. Tuberculosis 91, 1-7
14. Pandey, A., and Lewitter, F. (1999) Nucleotide sequence databases: a gold mine for biologists. Trends Biochem. Sci. 24, 276-280 (Pubitemid 29301692)
15. Mann, M., and Pandey, A. (2001) Use of mass spectrometry-derived data to annotate nucleotide and protein sequence databases. Trends Biochem. Sci. 26, 54-61 (Pubitemid 32124711)
16. Castellana, N., and Bafna, V. (2010) Proteogenomics to discover the full coding content of genomes: a computational perspective. J. Proteomics 73, 2124-2135
17. de Souza, G. A., Arntzen, M. Ø., Fortuin, S., Schürch, A. C., Målen, H., McEvoy, C. R., van Soolingen, D., Thiede, B., Warren, R. M., and Wiker, H. G. (2011) Proteogenomic analysis of polymorphisms and gene annotation divergences in prokaryotes using a clustered mass spectrometry-friendly database. Mol. Cell. Proteomics 10, M110.002527
18. 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 (Pubitemid 32600318)
19. FGENESB: Bacterial Operon and Gene Prediction [http://linux1.softberry. com/berry.phtml?topic=fgenesb&group=programs&subgroup=gfindb]
20. Amanchy, R., Kalume, D. E., and Pandey, A. (2005) Stable isotope labeling with amino acids in cell culture (SILAC) for studying dynamics of protein abundance and posttranslational modifications. Sci. STKE. 2005, pl2
21. Harsha, H. C., Molina, H., and Pandey, A. (2008) Quantitative proteomics using stable isotope labeling with amino acids in cell culture. Nat. Protoc. 3, 505-516 (Pubitemid 351372235)
22. Yadav, A. K., Kumar, D., and Dash, D. (2011) MassWiz: A Novel Scoring Algorithm with Target-Decoy Based Analysis Pipeline for Tandem Mass Spectrometry. J. Proteome. Res. 10, 2154-2160
23. Deutsch, E.W., Lam, H., and Aebersold, R. (2008) PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO. Rep. 9, 429-434 (Pubitemid 351627279)
24. Ioerger, T. R., Feng, Y., Ganesula, K., Chen, X., Dobos, K. M., Fortune, S., Jacobs, W. R., Jr., Mizrahi, V., Parish, T., Rubin, E., Sassetti, C., and Sacchettini, J. C. (2010) Variation among genome sequences of H37Rv strains of Mycobacterium tuberculosis from multiple laboratories. J. Bacteriol. 192, 3645-3653
25. Rison, S. C., Mattow, J., Jungblut, P. R., and Stoker, N. G. (2007) Experimental determination of translational starts using peptide mass mapping and tandem mass spectrometry within the proteome of Mycobacterium tuberculosis. Microbiology 153, 521-528