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Volumn 155, Issue 1, 2009, Pages 186-197

Experimental determination of translational start sites resolves uncertainties in genomic open reading frame predictions - Application to Mycobacterium tuberculosis

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; LEXA PROTEIN; PROTEIN RV1955; PROTEIN SIGC; UNCLASSIFIED DRUG; DNA BINDING PROTEIN; EPITOPE; LEXA PROTEIN, BACTERIA; SERINE PROTEINASE; SIGC PROTEIN, BACTERIA; SIGMA FACTOR;

EID: 61449122153     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/mic.0.022889-0     Document Type: Article
Times cited : (34)

References (38)
  • 2
    • 0035875343 scopus 로고    scopus 로고
    • GeneMarkS: A self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
    • Besemer, J., Lomsadze, A. & 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.
    • (2001) Nucleic Acids Res , vol.29 , pp. 2607-2618
    • Besemer, J.1    Lomsadze, A.2    Borodovsky, M.3
  • 3
    • 0036270739 scopus 로고    scopus 로고
    • Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling
    • Betts, J. C., Lukey, P. T., Robb, L. C., McAdam, R. A. & Duncan, K. (2002). Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling. Mol Microbiol 43, 717-731.
    • (2002) Mol Microbiol , vol.43 , pp. 717-731
    • Betts, J.C.1    Lukey, P.T.2    Robb, L.C.3    McAdam, R.A.4    Duncan, K.5
  • 5
    • 0036774642 scopus 로고    scopus 로고
    • Reannotation of the genome sequence of Mycobacterium tuberculosis H37Rv
    • Camus, J. C., Pryor, M. J., Medigue, C. & Cole, S. T. (2002). Reannotation of the genome sequence of Mycobacterium tuberculosis H37Rv. Microbiology 148, 2967-2973.
    • (2002) Microbiology , vol.148 , pp. 2967-2973
    • Camus, J.C.1    Pryor, M.J.2    Medigue, C.3    Cole, S.T.4
  • 6
    • 0035477134 scopus 로고    scopus 로고
    • A computational approach to identify genes for functional RNAs in genomic sequences
    • Carter, R. J., Dubchak, I. & Holbrook, S. R. (2001). A computational approach to identify genes for functional RNAs in genomic sequences. Nucleic Acids Res 29, 3928-3938.
    • (2001) Nucleic Acids Res , vol.29 , pp. 3928-3938
    • Carter, R.J.1    Dubchak, I.2    Holbrook, S.R.3
  • 7
    • 0023916543 scopus 로고
    • Mechanism of expression of the overlapping genes of Bacillus subtilis aspartokinase II
    • Chen, N. Y. & Paulus, H. (1988). Mechanism of expression of the overlapping genes of Bacillus subtilis aspartokinase II. J Biol Chem 263, 9526-9532.
    • (1988) J Biol Chem , vol.263 , pp. 9526-9532
    • Chen, N.Y.1    Paulus, H.2
  • 10
    • 0036267340 scopus 로고    scopus 로고
    • Definition of the mycobacterial SOS box and use to identify LexA-regulated genes in Mycobacterium tuberculosis
    • Davis, E. O., Dullaghan, E. M. & Rand, L. (2002). Definition of the mycobacterial SOS box and use to identify LexA-regulated genes in Mycobacterium tuberculosis. J Bacteriol 184, 3287-3295.
    • (2002) J Bacteriol , vol.184 , pp. 3287-3295
    • Davis, E.O.1    Dullaghan, E.M.2    Rand, L.3
  • 12
    • 0030683590 scopus 로고    scopus 로고
    • SOS induction in mycobacteria: Analysis of the DNA-binding activity of a LexA-like repressor and its role in DNA damage induction of the recA gene from Mycobacterium smegmatis
    • Durbach, S. I., Andersen, S. J. & Mizrahi, V. (1997). SOS induction in mycobacteria: analysis of the DNA-binding activity of a LexA-like repressor and its role in DNA damage induction of the recA gene from Mycobacterium smegmatis. Mol Microbiol 26, 643-653.
    • (1997) Mol Microbiol , vol.26 , pp. 643-653
    • Durbach, S.I.1    Andersen, S.J.2    Mizrahi, V.3
  • 13
    • 0001433809 scopus 로고
    • Method for determination of the amino acid sequence in peptides
    • Edman, P. J. (1950). Method for determination of the amino acid sequence in peptides. Acta Chem Scand 4, 283-293.
    • (1950) Acta Chem Scand , vol.4 , pp. 283-293
    • Edman, P.J.1
  • 15
    • 0027201142 scopus 로고
    • Gene structure and expression of the Corynebacterium flavum N13 ask-asd operon
    • Follettie, M. T., Peoples, O. P., Agoropoulou, C. & Sinskey, A. J. (1993). Gene structure and expression of the Corynebacterium flavum N13 ask-asd operon. J Bacteriol 175, 4096-4103.
    • (1993) J Bacteriol , vol.175 , pp. 4096-4103
    • Follettie, M.T.1    Peoples, O.P.2    Agoropoulou, C.3    Sinskey, A.J.4
  • 16
    • 4444220904 scopus 로고    scopus 로고
    • Identification of a promoter motif regulating the major DNA damage response mechanism of Mycobacterium tuberculosis
    • Gamulin, V., Cetkovic, H. & Ahel, I. (2004). Identification of a promoter motif regulating the major DNA damage response mechanism of Mycobacterium tuberculosis. FEMS Microbiol Lett 238, 57-63.
    • (2004) FEMS Microbiol Lett , vol.238 , pp. 57-63
    • Gamulin, V.1    Cetkovic, H.2    Ahel, I.3
  • 17
    • 33745288760 scopus 로고    scopus 로고
    • Examination of Mycobacterium tuberculosis sigma factor mutants using low-dose aerosol infection of guinea pigs suggests a role for SigC in pathogenesis
    • Karls, R. K., Guarner, J., McMurray, D. N., Birkness, K. A. & Quinn, F. D. (2006). Examination of Mycobacterium tuberculosis sigma factor mutants using low-dose aerosol infection of guinea pigs suggests a role for SigC in pathogenesis. Microbiology 152, 1591-1600.
    • (2006) Microbiology , vol.152 , pp. 1591-1600
    • Karls, R.K.1    Guarner, J.2    McMurray, D.N.3    Birkness, K.A.4    Quinn, F.D.5
  • 18
    • 33847643705 scopus 로고    scopus 로고
    • Hon-yaku: A biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes
    • Makita, Y., de Hoon, M. & Danchin, A. (2007). Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes. BMC Bioinformatics 8, 47.
    • (2007) BMC Bioinformatics , vol.8 , pp. 47
    • Makita, Y.1    de Hoon, M.2    Danchin, A.3
  • 19
    • 0036198887 scopus 로고    scopus 로고
    • Leaderless mRNAs in bacteria: Surprises in ribosomal recruitment and translational control
    • Moll, I., Grill, S., Gualerzi, C. O. & Blasi, U. (2002). Leaderless mRNAs in bacteria: surprises in ribosomal recruitment and translational control. Mol Microbiol 43, 239-246.
    • (2002) Mol Microbiol , vol.43 , pp. 239-246
    • Moll, I.1    Grill, S.2    Gualerzi, C.O.3    Blasi, U.4
  • 20
    • 0001291140 scopus 로고    scopus 로고
    • A powerful non-homology method for the prediction of operons in prokaryotes
    • Moreno-Hagelsieb, G. & Collado-Vides, J. (2002). A powerful non-homology method for the prediction of operons in prokaryotes. Bioinformatics 18, S329-S336.
    • (2002) Bioinformatics , vol.18
    • Moreno-Hagelsieb, G.1    Collado-Vides, J.2
  • 21
    • 0030999727 scopus 로고    scopus 로고
    • Characterization of Mycobacterium tuberculosis LexA: Recognition of a Cheo (Bacillus-type SOS) box
    • Movahedzadeh, F., Colston, M. J. & Davis, E. O. (1997). Characterization of Mycobacterium tuberculosis LexA: recognition of a Cheo (Bacillus-type SOS) box. Microbiology 143, 929-936.
    • (1997) Microbiology , vol.143 , pp. 929-936
    • Movahedzadeh, F.1    Colston, M.J.2    Davis, E.O.3
  • 22
    • 28944435815 scopus 로고    scopus 로고
    • Large-scale prokaryotic gene prediction and comparison to genome annotation
    • Nielsen, P. & Krogh, A. (2005). Large-scale prokaryotic gene prediction and comparison to genome annotation. Bioinformatics 21, 4322-4329.
    • (2005) Bioinformatics , vol.21 , pp. 4322-4329
    • Nielsen, P.1    Krogh, A.2
  • 24
    • 0021947560 scopus 로고
    • Two translational initiation sites in the infB gene are used to express initiation factor IF2 alpha and IF2 beta in Escherichia coli
    • Plumbridge, J. A., Deville, F., Sacerdot, C., Petersen, H. U., Cenatiempo, Y., Cozzone, A., Grunberg-Manago, M. & Hershey, J. W. (1985). Two translational initiation sites in the infB gene are used to express initiation factor IF2 alpha and IF2 beta in Escherichia coli. EMBO J 4, 223-229.
    • (1985) EMBO J , vol.4 , pp. 223-229
    • Plumbridge, J.A.1    Deville, F.2    Sacerdot, C.3    Petersen, H.U.4    Cenatiempo, Y.5    Cozzone, A.6    Grunberg-Manago, M.7    Hershey, J.W.8
  • 26
    • 0242690139 scopus 로고    scopus 로고
    • The majority of inducible DNA repair genes in Mycobacterium tuberculosis are induced independently of RecA
    • Rand, L., Hinds, J., Springer, B., Sander, P., Buxton, R. S. & Davis, E. O. (2003). The majority of inducible DNA repair genes in Mycobacterium tuberculosis are induced independently of RecA. Mol Microbiol 50, 1031-1042.
    • (2003) Mol Microbiol , vol.50 , pp. 1031-1042
    • Rand, L.1    Hinds, J.2    Springer, B.3    Sander, P.4    Buxton, R.S.5    Davis, E.O.6
  • 27
    • 33847208190 scopus 로고    scopus 로고
    • Experimental determination of translational starts using peptide mass mapping and tandem mass spectrometry within the proteome of Mycobacterium tuberculosis
    • Rison, S. C. G., Mattow, J., Jungblut, P. R. & 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.
    • (2007) Microbiology , vol.153 , pp. 521-528
    • Rison, S.C.G.1    Mattow, J.2    Jungblut, P.R.3    Stoker, N.G.4
  • 30
    • 0025081151 scopus 로고
    • Isolation and characterization of efficient plasmid transformation mutants of Mycobacterium smegmatis
    • Snapper, S. B., Melton, R. E., Mustafa, S., Kieser, T. & Jacobs, W. R., Jr (1990). Isolation and characterization of efficient plasmid transformation mutants of Mycobacterium smegmatis. Mol Microbiol 4, 1911-1919.
    • (1990) Mol Microbiol , vol.4 , pp. 1911-1919
    • Snapper, S.B.1    Melton, R.E.2    Mustafa, S.3    Kieser, T.4    Jacobs Jr, W.R.5
  • 31
    • 17444361941 scopus 로고    scopus 로고
    • Epitope-tagging vectors for the expression and detection of recombinant proteins in mycobacteria
    • Spratt, J. M., Ryan, A. A., Britton, W. J. & Triccas, J. A. (2005). Epitope-tagging vectors for the expression and detection of recombinant proteins in mycobacteria. Plasmid 53, 269-273.
    • (2005) Plasmid , vol.53 , pp. 269-273
    • Spratt, J.M.1    Ryan, A.A.2    Britton, W.J.3    Triccas, J.A.4
  • 33
    • 33846054258 scopus 로고    scopus 로고
    • Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer
    • Stinear, T. P., Seemann, T., Pidot, S., Frigui, W., Reysset, G., Garnier, T., Meurice, G., Simon, D., Bouchier, C. & other authors (2007). Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer. Genome Res 17, 192-200.
    • (2007) Genome Res , vol.17 , pp. 192-200
    • Stinear, T.P.1    Seemann, T.2    Pidot, S.3    Frigui, W.4    Reysset, G.5    Garnier, T.6    Meurice, G.7    Simon, D.8    Bouchier, C.9
  • 34
    • 0025922291 scopus 로고    scopus 로고
    • Stover, C. K., de la Cruz, V. F., Fuerst, T. R., Burlein, J. E., Benson, L. A., Bennett, L. T., Bansal, G. P., Young, J. F., Lee, M. H. & other authors (1991). New use of BCG for recombinant vaccines. Nature 351, 456-460.
    • Stover, C. K., de la Cruz, V. F., Fuerst, T. R., Burlein, J. E., Benson, L. A., Bennett, L. T., Bansal, G. P., Young, J. F., Lee, M. H. & other authors (1991). New use of BCG for recombinant vaccines. Nature 351, 456-460.
  • 35
    • 1942455731 scopus 로고    scopus 로고
    • Mycobacterium tuberculosis ECF sigma factor sigC is required for lethality in mice and for the conditional expression of a defined gene set
    • Sun, R., Converse, P. J., Ko, C., Tyagi, S., Morrison, N. E. & Bishai, W. R. (2004). Mycobacterium tuberculosis ECF sigma factor sigC is required for lethality in mice and for the conditional expression of a defined gene set. Mol Microbiol 52, 25-38.
    • (2004) Mol Microbiol , vol.52 , pp. 25-38
    • Sun, R.1    Converse, P.J.2    Ko, C.3    Tyagi, S.4    Morrison, N.E.5    Bishai, W.R.6
  • 37
    • 0036468504 scopus 로고    scopus 로고
    • Mycobacterium smegmatis and tuberculosis
    • Tyagi, J. S. & Sharma, D. (2002). Mycobacterium smegmatis and tuberculosis. Trends Microbiol 10, 68-69.
    • (2002) Trends Microbiol , vol.10 , pp. 68-69
    • Tyagi, J.S.1    Sharma, D.2
  • 38
    • 27144447762 scopus 로고    scopus 로고
    • Identifying sigma factors in Mycobacterium smegmatis by comparative genomic analysis
    • Waagmeester, A., Thompson, J. & Reyrat, J.-M. (2005). Identifying sigma factors in Mycobacterium smegmatis by comparative genomic analysis. Trends Microbiol 13, 505-509.
    • (2005) Trends Microbiol , vol.13 , pp. 505-509
    • Waagmeester, A.1    Thompson, J.2    Reyrat, J.-M.3


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