Reannotation of translational start sites in the genome of Mycobacterium tuberculosis

Tuberculosis

Volumn 93, Issue 1, 2013, Pages 18-25

  Dejesus, Michael A ^a   Sacchettini, James C ^a   Ioerger, Thomas R ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

Author keywords

Actinobacteria; Orthologs; Reannotation; Translational start sites

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENOME; HIDDEN MARKOV MODEL; MASS SPECTROMETRY; MOLECULAR GENETICS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; START CODON; STOP CODON; STRUCTURAL GENOMICS;

ACTINOBACTERIA; AMINO ACID SEQUENCE; CODON, INITIATOR; COMPUTATIONAL BIOLOGY; GENOME, BACTERIAL; HUMANS; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; MYCOBACTERIUM TUBERCULOSIS; OPEN READING FRAMES; PROTEIN BIOSYNTHESIS; RIBOSOMES; SEQUENCE ALIGNMENT;

EID: 84874519947     PISSN: 14729792     EISSN: 1873281X     Source Type: Journal    
DOI: 10.1016/j.tube.2012.11.012     Document Type: Article

References (28)

1. 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 doi: 10.1038/31159
2. J.C. Camus, M.J. Pryor, C. Medigue, and S.T. Cole Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv Microbiology 148 2002 2967 2973
3. S.C. Rison, J. Mattow, P.R. Jungblut, and N.G. Stoker Experimental determination of translational starts using peptide mass mapping and tandem mass spectrometry within the proteome of Mycobacterium tuberculosis Microbiology 153 2007 521 528
4. K.L. Smollett, A.S. Fivian-Hughes, J.E. Smith, A. Chang, T. Rao, and E.O. Davis Experimental determination of translational start sites resolves uncertainties in genomic open reading frame predictions-application to Mycobacterium tuberculosis Microbiology 155 2009 186 197 doi: 155/1/186 [pii] 10.1099/mic.0.022889-0
5. M. Strong, P. Mallick, M. Pellegrini, M.J. Thompson, and D. Eisenberg Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach Genome Biol 4 2003 R59 10.1186/gb-2003-4-9-r59
6. A.L. Delcher, D. Harmon, S. Kasif, O. White, and S.L. Salzberg Improved microbial gene identification with GLIMMER Nucleic Acids Res 27 1999 4636 4641 doi: gkc675 [pii]
7. S.L. Salzberg, A.L. Delcher, S. Kasif, and O. White Microbial gene identification using interpolated Markov models Nucleic Acids Res 26 1998 544 548 doi: gkb128 [pii]
8. M. Borodovsky, R. Mills, J. Besemer, and A. Lomsadze Prokaryotic gene prediction using GeneMark and GeneMark.hmm Curr Protoc Bioinform 2003 10.1002/0471250953.bi0405s01 [Chapter 4:Unit4 5]
9. J. Besemer, and M. Borodovsky GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses Nucleic Acids Res 33 2005 W451 W454 doi: 33/suppl-2/W451 [pii] 10.1093/nar/gki487
10. R.K. Aziz, D. Bartels, A.A. Best, M. DeJongh, T. Disz, R.A. Edwards, K. Formsma, S. Gerdes, E.M. Glass, M. Kubal, F. Meyer, G.J. Olsen, R. Olson, A.L. Osterman, R.A. Overbeek, L.K. McNeil, D. Paarmann, T. Paczian, B. Parrello, G.D. Pusch, C. Reich, R. Stevens, O. Vassieva, V. Vonstein, A. Wilke, and O. Zagnitko The RAST server: rapid annotations using subsystems technology BMC Genomics 9 2008 75 doi: 1471-2164-9-75 [pii] 10.1186/1471-2164-9-75
11. P. Bakke, N. Carney, W. Deloache, M. Gearing, K. Ingvorsen, M. Lotz, J. McNair, P. Penumetcha, S. Simpson, L. Voss, M. Win, L.J. Heyer, and A.M. Campbell Evaluation of three automated genome annotations for Halorhabdus utahensis PLoS One 4 2009 e6291 10.1371/journal.pone.0006291
12. D.S. Kelkar, D. Kumar, P. Kumar, L. Balakrishnan, B. Muthusamy, A.K. Yadav, P. Shrivastava, A. Marimuthu, S. Anand, H. Sundaram, R. Kingsbury, H.C. Harsha, B. Nair, T.S. Prasad, D.S. Chauhan, K. Katoch, V.M. Katoch, R. Chaerkady, S. Ramachandran, D. Dash, and A. Pandey Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry Mol Cell Proteomics 10 2011 M111 011627. doi: M111.011445 [pii] 10.1074/mcp.M111.011445
13. M. Kozak Initiation of translation in prokaryotes and eukaryotes Gene 234 1999 187 208 doi: S0378111999002103 [pii]
14. A. La Teana, C.L. Pon, and C.O. Gualerzi Translation of mRNAs with degenerate initiation triplet AUU displays high initiation factor 2 dependence and is subject to initiation factor 3 repression Proc Natl Acad Sci U S A 90 1993 4161 4165
15. J. Shine, and L. Dalgarno Determinant of cistron specificity in bacterial ribosomes Nature 254 1975 34 38
16. S. Ringquist, S. Shinedling, D. Barrick, L. Green, J. Binkley, G.D. Stormo, and L. Gold Translation initiation in Escherichia coli: sequences within the ribosome-binding site Mol Microbiol 6 1992 1219 1229
17. M.H. de Smit, and J. van Duin Secondary structure of the ribosome binding site determines translational efficiency: a quantitative analysis Proc Natl Acad Sci U S A 87 1990 7668 7672
18. J. Ma, A. Campbell, and S. Karlin Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures J Bacteriol 184 2002 5733 5745
19. M.Y. Lobanov, S.O. Garbuzynskiy, and O.V. Galzitskaya Statistical analysis of unstructured amino acid residues in protein structures Biochemistry (Mosc) 75 2010 192 200 doi: BCM75020236 [pii]
20. S.F. Altschul, W. Gish, W. Miller, E.W. Myers, and D.J. Lipman Basic local alignment search tool J Mol Biol 215 1990 403 410 doi: 10.1016/S0022-2836(05)80360-2 S0022-2836(05)80360-2 [pii]
21. M.A. Larkin, G. Blackshields, N.P. Brown, R. Chenna, P.A. McGettigan, H. McWilliam, F. Valentin, I.M. Wallace, A. Wilm, R. Lopez, J.D. Thompson, T.J. Gibson, and D.G. Higgins Clustal W and Clustal X version 2.0 Bioinformatics 23 2007 2947 2948 doi: btm404 [pii] 10.1093/bioinformatics/btm404
22. T. Liu, A. Ramesh, Z. Ma, S.K. Ward, L. Zhang, G.N. George, A.M. Talaat, J.C. Sacchettini, and D.P. Giedroc CsoR is a novel Mycobacterium tuberculosis copper-sensing transcriptional regulator Nat Chem Biol 3 2007 60 68 doi: nchembio844 [pii] 10.1038/nchembio844
23. M.D. Ermolaeva, O. White, and S.L. Salzberg Prediction of operons in microbial genomes Nucleic Acids Res 29 2001 1216 1221
24. H. Salgado, G. Moreno-Hagelsieb, T.F. Smith, and J. Collado-Vides Operons in Escherichia coli: genomic analyses and predictions Proc Natl Acad Sci U S A 97 2000 6652 6657 doi: 10.1073/pnas.110147297 110147297 [pii]
25. L.E. Quadri, J. Sello, T.A. Keating, P.H. Weinreb, and C.T. Walsh Identification of a Mycobacterium tuberculosis gene cluster encoding the biosynthetic enzymes for assembly of the virulence-conferring siderophore mycobactin Chem Biol 5 1998 631 645 doi: S1074-5521(98)90291-5 [pii]
26. M.D. McMahon, J.S. Rush, and M.G. Thomas Analyses of MbtB, MbtE, and MbtF suggest revisions to the mycobactin biosynthesis pathway in Mycobacterium tuberculosis J Bacteriol 194 2012 2809 2818 doi: JB.00088-12 [pii] 10.1128/JB.00088-12
27. P. Roback, J. Beard, D. Baumann, C. Gille, K. Henry, S. Krohn, H. Wiste, M.I. Voskuil, C. Rainville, and R. Rutherford A predicted operon map for Mycobacterium tuberculosis Nucleic Acids Res 35 2007 5085 5095 doi: gkm518 [pii] 10.1093/nar/gkm518
28. G.A. de Souza, H. Malen, T. Softeland, G. Saelensminde, S. Prasad, I. Jonassen, and H.G. Wiker High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example BMC Genomics 9 2008 316 doi: 1471-2164-9-316 [pii] 10.1186/1471-2164-9- 316