Publication Type:

Journal Article

Source:

Molecular and Cellular Proteomics, Volume 10, Number 12 (2011)

URL:

http://www.scopus.com/inward/record.url?eid=2-s2.0-83055173265&partnerID=40&md5=d86e7a2e46b0b4a5ddc8b8952182852e

Keywords:

amino terminal sequence, article, bacterial genome, bacterial protein, 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, pyruvate dehydrogenase, sequence analysis, tandem mass spectrometry

Abstract:

The genome sequencing of H37Rv strain of Mycobacterium tuberculosis was completed in 1998 followed by the whole genome sequencing of a clinical isolate, CDC1551 in 2002. Since then, the genomic sequences of a number of other strains have become available making it one of the better studied pathogenic bacterial species at the genomic level. However, annotation of its genome remains challenging because of high GC content and dissimilarity to other model prokaryotes. To this end, we carried out an in-depth proteogenomic analysis of the M. tuberculosis H37Rv strain using Fourier transform mass spectrometry with high resolution at both MS and tandem MS levels. In all, we identified 3176 proteins from Mycobacterium tuberculosis representing ∼80% of its total predicted gene count. In addition to protein database search, we carried out a genome database search, which led to identification of ∼250 novel peptides. Based on these novel genome search-specific peptides, we discovered 41 novel protein coding genes in the H37Rv genome. Using peptide evidence and alternative gene prediction tools, we also corrected 79 gene models. Finally, mass spectrometric data from N terminus-derived peptides confirmed 727 existing annotations for translational start sites while correcting those for 33 proteins. We report creation of a high confidence set of protein coding regions in Mycobacterium tuberculosis genome obtained by high resolution tandem mass-spectrometry at both precursor and fragment detection steps for the first time. This proteogenomic approach should be generally applicable to other organisms whose genomes have already been sequenced for obtaining a more accurate catalogue of protein-coding genes. © 2011 by The American Society for Biochemistry and Molecular Biology, Inc.

Notes:

cited By (since 1996)23

Cite this Research Publication

D. Sab Kelkar, Kumar, Dc, Kumar, Pa, Balakrishnan, Lad, Muthusamy, Bae, Yadav, A. Kc, Shrivastava, Pc, Marimuthu, Aaf, Anand, Sg, Sundaram, Hg, Kingsbury, Rg, Harsha, H. Ca, Nair, Bb, Prasad, T. S. Kae f, Chauhan, D. Sh, Katoch, Kh, Katoch, V. Mi, Kumar, Pg, Chaerkady, Raj, Ramachandran, Sc, Dash, Dc, and Pandey, Aaj, “Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry”, Molecular and Cellular Proteomics, vol. 10, 2011.