| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
Molecular Genetics and Immunobiology of Mycobacteria |
Unité de Génétique Moléculaire Bactérienne, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex, France1
Annotation-Bases de Données (PT4), Génopole, Institut Pasteur, Paris, France2
Génoscope/UMR 8030, Atelier de Génomique Comparative, 2 rue Gaston Crémieux, 91006 Evry Cedex, France3
Author for correspondence: Stewart T. Cole. Tel: +33 1 45688446. Fax: +33 1 40613583. e-mail: stcole{at}pasteur.fr
Original genome annotations need to be regularly updated if the information they contain is to remain accurate and relevant. Here the complete re-annotation of the genome sequence of Mycobacterium tuberculosis strain H37Rv is presented almost 4 years after the first submission. Eighty-two new protein-coding sequences (CDS) have been included and 22 of these have a predicted function. The majority were identified by manual or automated re-analysis of the genome and most of them were shorter than the 100 codon cut-off used in the initial genome analysis. The functional classification of 643 CDS has been changed based principally on recent sequence comparisons and new experimental data from the literature. More than 300 gene names and over 1000 targeted citations have been added and the lengths of 60 genes have been modified. Presently, it is possible to assign a function to 2058 proteins (52% of the 3995 proteins predicted) and only 376 putative proteins share no homology with known proteins and thus could be unique to M. tuberculosis.
Keywords: mycobacteria, tuberculosis, genomics
Abbreviations: CDS, protein-coding sequences
This article has been cited by other articles:
|
|
 |
|
  J. J. Vecchione, B. Alexander Jr., and J. K. Sello Two Distinct Major Facilitator Superfamily Drug Efflux Pumps Mediate Chloramphenicol Resistance in Streptomyces coelicolor Antimicrob. Agents Chemother., November 1, 2009; 53(11): 4673 - 4677. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. A. Leversen, G. A. de Souza, H. Malen, S. Prasad, I. Jonassen, and H. G. Wiker Evaluation of signal peptide prediction algorithms for identification of mycobacterial signal peptides using sequence data from proteomic methods Microbiology, July 1, 2009; 155(7): 2375 - 2383. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. S. Mathurin, G. W. Martens, H. Kornfeld, and R. M. Welsh CD4 T-Cell-Mediated Heterologous Immunity between Mycobacteria and Poxviruses J. Virol., April 15, 2009; 83(8): 3528 - 3539. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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, January 1, 2009; 155(1): 186 - 197. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Baumbach, A. Tauch, and S. Rahmann Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks Brief Bioinform, January 1, 2009; 10(1): 75 - 83. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Gallien, E. Perrodou, C. Carapito, C. Deshayes, J.-M. Reyrat, A. Van Dorsselaer, O. Poch, C. Schaeffer, and O. Lecompte Ortho-proteogenomics: Multiple proteomes investigation through orthology and a new MS-based protocol Genome Res., January 1, 2009; 19(1): 128 - 135. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. A. McDonough, J. R. McCann, E. M. Tekippe, J. S. Silverman, N. W. Rigel, and M. Braunstein Identification of Functional Tat Signal Sequences in Mycobacterium tuberculosis Proteins J. Bacteriol., October 1, 2008; 190(19): 6428 - 6438. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I. Borodina, J. Siebring, J. Zhang, C. P. Smith, G. van Keulen, L. Dijkhuizen, and J. Nielsen Antibiotic Overproduction in Streptomyces coelicolor A3(2) Mediated by Phosphofructokinase Deletion J. Biol. Chem., September 12, 2008; 283(37): 25186 - 25199. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. K. Ward, E. A. Hoye, and A. M. Talaat The Global Responses of Mycobacterium tuberculosis to Physiological Levels of Copper J. Bacteriol., April 15, 2008; 190(8): 2939 - 2946. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Lechat, L. Hummel, S. Rousseau, and I. Moszer GenoList: an integrated environment for comparative analysis of microbial genomes Nucleic Acids Res., January 11, 2008; 36(suppl_1): D469 - D474. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Z. Schneider, T. Parish, L. A. Basso, and D. S. Santos The Two Chorismate Mutases from both Mycobacterium tuberculosis and Mycobacterium smegmatis: Biochemical Analysis and Limited Regulation of Promoter Activity by Aromatic Amino Acids J. Bacteriol., January 1, 2008; 190(1): 122 - 134. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I. Rajan, S. Aravamuthan, and S. S. Mande Identification of compositionally distinct regions in genomes using the centroid method Bioinformatics, October 15, 2007; 23(20): 2672 - 2677. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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., August 1, 2007; 35(15): 5085 - 5095. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Becq, M. C. Gutierrez, V. Rosas-Magallanes, J. Rauzier, B. Gicquel, O. Neyrolles, and P. Deschavanne Contribution of Horizontally Acquired Genomic Islands to the Evolution of the Tubercle Bacilli Mol. Biol. Evol., August 1, 2007; 24(8): 1861 - 1871. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. M. Talaat, S. K. Ward, C.-W. Wu, E. Rondon, C. Tavano, J. P. Bannantine, R. Lyons, and S. A. Johnston Mycobacterial Bacilli Are Metabolically Active during Chronic Tuberculosis in Murine Lungs: Insights from Genome-Wide Transcriptional Profiling J. Bacteriol., June 1, 2007; 189(11): 4265 - 4274. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Parish, G. Roberts, F. Laval, M. Schaeffer, M. Daffe, and K. Duncan Functional Complementation of the Essential Gene fabG1 of Mycobacterium tuberculosis by Mycobacterium smegmatis fabG but Not Escherichia coli fabG J. Bacteriol., May 15, 2007; 189(10): 3721 - 3728. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. J. Alteri, J. Xicohtencatl-Cortes, S. Hess, G. Caballero-Olin, J. A. Giron, and R. L. Friedman Mycobacterium tuberculosis produces pili during human infection PNAS, March 20, 2007; 104(12): 5145 - 5150. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Ranguelova, S. Girotto, G. J. Gerfen, S. Yu, J. Suarez, L. Metlitsky, and R. S. Magliozzo Radical Sites in Mycobacterium tuberculosis KatG Identified Using Electron Paramagnetic Resonance Spectroscopy, the Three-dimensional Crystal Structure, and Electron Transfer Couplings J. Biol. Chem., March 2, 2007; 282(9): 6255 - 6264. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. G. Thakur, A. M. Joshi, and B. Gopal Structural and Biophysical Studies on Two Promoter Recognition Domains of the Extra-cytoplasmic Function {sigma} Factor {sigma}C from Mycobacterium tuberculosis J. Biol. Chem., February 16, 2007; 282(7): 4711 - 4718. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. C. G. 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, February 1, 2007; 153(2): 521 - 528. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S.-K. Kim, S. K. Reddy, B. C. Nelson, G. B. Vasquez, A. Davis, A. J. Howard, S. Patterson, G. L. Gilliland, J. E. Ladner, and P. T. Reddy Biochemical and Structural Characterization of the Secreted Chorismate Mutase (Rv1885c) from Mycobacterium tuberculosis H37Rv: an *AroQ Enzyme Not Regulated by the Aromatic Amino Acids J. Bacteriol., December 15, 2006; 188(24): 8638 - 8648. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
U. H. Manjunatha, R. Lahiri, B. Randhawa, C. S. Dowd, J. L. Krahenbuhl, and C. E. Barry III Mycobacterium leprae Is Naturally Resistant to PA-824. Antimicrob. Agents Chemother., October 1, 2006; 50(10): 3350 - 3354. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Benabdesselem, D. M. Fathallah, R. C. Huard, H. Zhu, M. A. Jarboui, K. Dellagi, J. L. Ho, and R. M. Barbouche Enhanced Patient Serum Immunoreactivity to Recombinant Mycobacterium tuberculosis CFP32 Produced in the Yeast Pichia pastoris Compared to Escherichia coli and Its Potential for Serodiagnosis of Tuberculosis. J. Clin. Microbiol., September 1, 2006; 44(9): 3086 - 3093. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. M. Joshi, A. K. Pandey, N. Capite, S. M. Fortune, E. J. Rubin, and C. M. Sassetti Characterization of mycobacterial virulence genes through genetic interaction mapping PNAS, August 1, 2006; 103(31): 11760 - 11765. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. T. Madsen, L. Jakobsen, K. Buriankova, F. Doucet-Populaire, J.-L. Pernodet, and S. Douthwaite Methyltransferase Erm(37) Slips on rRNA to Confer Atypical Resistance in Mycobacterium tuberculosis J. Biol. Chem., November 25, 2005; 280(47): 38942 - 38947. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Gao and R. S. Gupta Conserved indels in protein sequences that are characteristic of the phylum Actinobacteria Int J Syst Evol Microbiol, November 1, 2005; 55(6): 2401 - 2412. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. E. Maus, B. B. Plikaytis, and T. M. Shinnick Molecular Analysis of Cross-Resistance to Capreomycin, Kanamycin, Amikacin, and Viomycin in Mycobacterium tuberculosis Antimicrob. Agents Chemother., August 1, 2005; 49(8): 3192 - 3197. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P.-E. Jacques, A. L. Gervais, M. Cantin, J.-F. Lucier, G. Dallaire, G. Drouin, L. Gaudreau, J. Goulet, and R. Brzezinski MtbRegList, a database dedicated to the analysis of transcriptional regulation in Mycobacterium tuberculosis Bioinformatics, May 15, 2005; 21(10): 2563 - 2565. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. B. Sable, I. Verma, D. Behera, and G. K. Khuller Human immune recognition-based multicomponent subunit vaccines against tuberculosis Eur. Respir. J., May 1, 2005; 25(5): 902 - 910. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. E. Maus, B. B. Plikaytis, and T. M. Shinnick Mutation of tlyA Confers Capreomycin Resistance in Mycobacterium tuberculosis Antimicrob. Agents Chemother., February 1, 2005; 49(2): 571 - 577. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Weldingh, I. Rosenkrands, L. M. Okkels, T. M. Doherty, and P. Andersen Assessing the Serodiagnostic Potential of 35 Mycobacterium tuberculosis Proteins and Identification of Four Novel Serological Antigens J. Clin. Microbiol., January 1, 2005; 43(1): 57 - 65. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. G. Mawuenyega, C. V. Forst, K. M. Dobos, J. T. Belisle, J. Chen, E. M. Bradbury, A. R.M. Bradbury, and X. Chen Mycobacterium tuberculosis Functional Network Analysis by Global Subcellular Protein Profiling Mol. Biol. Cell, January 1, 2005; 16(1): 396 - 404. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. G. Tsolaki, A. E. Hirsh, K. DeRiemer, J. A. Enciso, M. Z. Wong, M. Hannan, Y.-O. L. G. de la Salmoniere, K. Aman, M. Kato-Maeda, and P. M. Small From the Cover: Functional and evolutionary genomics of Mycobacterium tuberculosis: Insights from genomic deletions in 100 strains PNAS, April 6, 2004; 101(14): 4865 - 4870. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. C. Onwueme, J. A. Ferreras, J. Buglino, C. D. Lima, and L. E. N. Quadri Mycobacterial polyketide-associated proteins are acyltransferases: Proof of principle with Mycobacterium tuberculosis PapA5 PNAS, March 30, 2004; 101(13): 4608 - 4613. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Marmiesse, P. Brodin, C. Buchrieser, C. Gutierrez, N. Simoes, V. Vincent, P. Glaser, S. T. Cole, and R. Brosch Macro-array and bioinformatic analyses reveal mycobacterial 'core' genes, variation in the ESAT-6 gene family and new phylogenetic markers for the Mycobacterium tuberculosis complex Microbiology, February 1, 2004; 150(2): 483 - 496. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. B. D. LaMarca, W. Zhu, J. E. L. Arceneaux, B. R. Byers, and M. D. Lundrigan Participation of fad and mbt Genes in Synthesis of Mycobactin in Mycobacterium smegmatis J. Bacteriol., January 15, 2004; 186(2): 374 - 382. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Buriankova, F. Doucet-Populaire, O. Dorson, A. Gondran, J.-C. Ghnassia, J. Weiser, and J.-L. Pernodet Molecular Basis of Intrinsic Macrolide Resistance in the Mycobacterium tuberculosis Complex Antimicrob. Agents Chemother., January 1, 2004; 48(1): 143 - 150. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. C. Huard, S. Chitale, M. Leung, L. C. O. Lazzarini, H. Zhu, E. Shashkina, S. Laal, M. B. Conde, A. L. Kritski, J. T. Belisle, et al. The Mycobacterium tuberculosis Complex-Restricted Gene cfp32 Encodes an Expressed Protein That Is Detectable in Tuberculosis Patients and Is Positively Correlated with Pulmonary Interleukin-10 Infect. Immun., December 1, 2003; 71(12): 6871 - 6883. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Saxena, G. Yadav, D. Mohanty, and R. S. Gokhale A New Family of Type III Polyketide Synthases in Mycobacterium tuberculosis J. Biol. Chem., November 7, 2003; 278(45): 44780 - 44790. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Bocs, S. Cruveiller, D. Vallenet, G. Nuel, and C. Medigue AMIGene: Annotation of MIcrobial Genes Nucleic Acids Res., July 1, 2003; 31(13): 3723 - 3726. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Liu, T. I. Bonner, T. Nguyen, J. L. Lyons, S. L. Christian, and E. S. Gershon DNannotator: annotation software tool kit for regional genomic sequences Nucleic Acids Res., July 1, 2003; 31(13): 3729 - 3735. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. B. Young Mycobacteria research in the post-genomic era Microbiology, October 1, 2002; 148(10): 2915 - 2917. [Full Text] [PDF]
|
|
|
|
|
|
S. T. Cole Comparative and functional genomics of the Mycobacterium tuberculosis complex Microbiology, October 1, 2002; 148(10): 2919 - 2928. [Full Text] [PDF]
|
|
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
| INT J SYST EVOL MICROBIOL | MICROBIOLOGY | J GEN VIROL |
| J MED MICROBIOL | ALL SGM JOURNALS | |
