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Volumn 12, Issue 5, 2005, Pages 269-280

Genome-wide survey of transcription factors in prokaryotes reveals many bacteria-specific families not found in archaea

Author keywords

Comparative genomics; DNA binding; Domain organization; Prokaryote; Transcription factor

Indexed keywords

DNA; TRANSCRIPTION FACTOR;

EID: 33646596266     PISSN: 13402838     EISSN: 13402838     Source Type: Journal    
DOI: 10.1093/dnares/dsi016     Document Type: Article
Times cited : (49)

References (46)
  • 1
    • 0033765113 scopus 로고    scopus 로고
    • Functional modulation of Escherichia coli RNA polymerase
    • Ishihama, A. 2000, Functional modulation of Escherichia coli RNA polymerase, Annu. Rev. Microbiol., 54, 499-518.
    • (2000) Annu. Rev. Microbiol. , vol.54 , pp. 499-518
    • Ishihama, A.1
  • 2
    • 1942535726 scopus 로고    scopus 로고
    • Transcriptional regulation in archaea
    • Ouhammouch, M. 2004, Transcriptional regulation in archaea, Curr. Opin. Genet. Dev., 14, 133-138.
    • (2004) Curr. Opin. Genet. Dev. , vol.14 , pp. 133-138
    • Ouhammouch, M.1
  • 3
    • 0034671865 scopus 로고    scopus 로고
    • Arabidopsis transcription factors: Genome-wide comparative analysis among eukaryotes
    • Riechmann, J. L., Heard, J., Martin, G., et al. 2000, Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes, Science, 290, 2105-2110.
    • (2000) Science , vol.290 , pp. 2105-2110
    • Riechmann, J.L.1    Heard, J.2    Martin, G.3
  • 4
    • 0037440195 scopus 로고    scopus 로고
    • The phylogenetic diversity of eukaryotic transcription
    • Coulson, R. M. and Ouzounis, C. A. 2003, The phylogenetic diversity of eukaryotic transcription, Nucleic Acids Res., 31, 653-660.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 653-660
    • Coulson, R.M.1    Ouzounis, C.A.2
  • 5
    • 0037208166 scopus 로고    scopus 로고
    • TRANSFAC: Transcriptional regulation, from patterns to profiles
    • Matys, V., Fricke, E., Geffers, R., et al. 2003, TRANSFAC: transcriptional regulation, from patterns to profiles, Nucleic Acids Res., 31, 374-378.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 374-378
    • Matys, V.1    Fricke, E.2    Geffers, R.3
  • 6
    • 0343963178 scopus 로고    scopus 로고
    • The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12
    • Perez-Rueda, E. and Collado-Vides, J. 2000, The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12, Nucleic Acids Res., 28, 1838-1847.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 1838-1847
    • Perez-Rueda, E.1    Collado-Vides, J.2
  • 7
    • 0033485460 scopus 로고    scopus 로고
    • DNA-binding proteins and evolution of transcription regulation in the archaea
    • Aravind, L. and Koonin, E. V. 1999, DNA-binding proteins and evolution of transcription regulation in the archaea, Nucleic Acids Res., 27, 4658-4670.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 4658-4670
    • Aravind, L.1    Koonin, E.V.2
  • 9
    • 0037665941 scopus 로고    scopus 로고
    • Transcription regulation and environmental adaptation in bacteria
    • Cases, I., de Lorenzo, V., and Ouzounis, C. A. 2003, Transcription regulation and environmental adaptation in bacteria, Trends Microbiol., 11, 248-253.
    • (2003) Trends Microbiol. , vol.11 , pp. 248-253
    • Cases, I.1    De Lorenzo, V.2    Ouzounis, C.A.3
  • 10
    • 1042298811 scopus 로고    scopus 로고
    • Evolution of protein superfamilies and bacterial genome size
    • Ranea, J. A., Buchan, D. W., Thornton, J. M., and Orengo, C. A. 2004, Evolution of protein superfamilies and bacterial genome size, J. Mol. Biol., 336, 871-887.
    • (2004) J. Mol. Biol. , vol.336 , pp. 871-887
    • Ranea, J.A.1    Buchan, D.W.2    Thornton, J.M.3    Orengo, C.A.4
  • 12
    • 8844258763 scopus 로고    scopus 로고
    • BacTregulators: A database of transcriptional regulators in bacteria and archaea
    • Martinez-Bueno, M., Molina-Henares, A. J., Pareja, E., Ramos, J. L., and Tobes, R. 2004, BacTregulators: a database of transcriptional regulators in bacteria and archaea, Bioinformatics, 20, 2787-2791.
    • (2004) Bioinformatics , vol.20 , pp. 2787-2791
    • Martinez-Bueno, M.1    Molina-Henares, A.J.2    Pareja, E.3    Ramos, J.L.4    Tobes, R.5
  • 13
    • 0037440734 scopus 로고    scopus 로고
    • Evolution of transcription factors and the gene regulatory network in Escherichia coli
    • Babu, M. M. and Teichmann, S. A. 2003, Evolution of transcription factors and the gene regulatory network in Escherichia coli, Nucleic Acids Res., 31, 1234-1244.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 1234-1244
    • Babu, M.M.1    Teichmann, S.A.2
  • 14
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin, A. G., Brenner, S. E., Hubbard, T., and Chothia, C. 1995, SCOP: a structural classification of proteins database for the investigation of sequences and structures, J. Mol. Biol., 247, 536-540.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 15
    • 0036084143 scopus 로고    scopus 로고
    • GTOP: A database of protein structures predicted from genome sequences
    • Kawabata, T., Fukuchi, S., Homma, K., et al. 2002, GTOP: a database of protein structures predicted from genome sequences, Nucleic Acids Res., 30, 294-298.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 294-298
    • Kawabata, T.1    Fukuchi, S.2    Homma, K.3
  • 16
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul, S. F., Madden, T. L., Schaffer, A. A., et al. 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 25, 3389-3402.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3
  • 18
    • 13444273448 scopus 로고    scopus 로고
    • The Universal Protein Resource (UniProt)
    • Bairoch, A., Apweiler, R., Wu, C. H., et al. 2005, The Universal Protein Resource (UniProt), Nucleic Acids Res., 33, D154-D159.
    • (2005) Nucleic Acids Res. , vol.33
    • Bairoch, A.1    Apweiler, R.2    Wu, C.H.3
  • 19
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy, S. R. 1998, Profile hidden Markov models, Bioinformatics, 14, 755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 21
    • 0038575389 scopus 로고    scopus 로고
    • Archaeal chromatin and transcription
    • Reeve, J. N. 2003, Archaeal chromatin and transcription, Mol. Microbiol., 48, 587-598.
    • (2003) Mol. Microbiol. , vol.48 , pp. 587-598
    • Reeve, J.N.1
  • 22
    • 0141504155 scopus 로고    scopus 로고
    • Rho factor: Transcription termination in four steps
    • Kaplan, D. L. and O'Donnell, M. 2003, Rho factor: transcription termination in four steps, Curr. Biol., 13, R714-R716.
    • (2003) Curr. Biol. , vol.13
    • Kaplan, D.L.1    O'Donnell, M.2
  • 23
    • 1942467448 scopus 로고    scopus 로고
    • Recent developments in bacterial cold-shock response
    • Phadtare, S. 2004, Recent developments in bacterial cold-shock response, Curr. Issues Mol. Biol., 6, 125-36.
    • (2004) Curr. Issues Mol. Biol. , vol.6 , pp. 125-136
    • Phadtare, S.1
  • 24
    • 14044250534 scopus 로고    scopus 로고
    • Structure analysis of PH1161 protein, a transcriptional activator TenA homologue from the hyperthermophilic archaeon Pyrococcus horikoshii
    • Itou, H., Yao, M., Watanabe, N., and Tanaka, I. 2004, Structure analysis of PH1161 protein, a transcriptional activator TenA homologue from the hyperthermophilic archaeon Pyrococcus horikoshii, Acta Crystallogr. D Biol. Crystallogr., 60, 1094-1100.
    • (2004) Acta Crystallogr. D Biol. Crystallogr. , vol.60 , pp. 1094-1100
    • Itou, H.1    Yao, M.2    Watanabe, N.3    Tanaka, I.4
  • 25
    • 0042902833 scopus 로고    scopus 로고
    • The COG database: An updated version includes eukaryotes
    • Tatusov, R. L., Fedorova, N. D., Jackson, J. D., et al. 2003, The COG database: an updated version includes eukaryotes, BMC Bioinformatics, 4, 41.
    • (2003) BMC Bioinformatics , vol.4 , pp. 41
    • Tatusov, R.L.1    Fedorova, N.D.2    Jackson, J.D.3
  • 26
    • 0842268045 scopus 로고    scopus 로고
    • Supra-domains: Evolutionary units larger than single protein domains
    • Vogel, C., Berzuini, C., Bashton, M., et al. 2004, Supra-domains: evolutionary units larger than single protein domains, J. Mol. Biol., 336, 809-823.
    • (2004) J. Mol. Biol. , vol.336 , pp. 809-823
    • Vogel, C.1    Berzuini, C.2    Bashton, M.3
  • 27
    • 0035798398 scopus 로고    scopus 로고
    • Protein family and fold occurrence in genomes: Power-law behaviour and evolutionary model
    • Qian, J., Luscombe, N. M., and Gerstein, M. 2001, Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model, J. Mol. Biol., 313, 673-681.
    • (2001) J. Mol. Biol. , vol.313 , pp. 673-681
    • Qian, J.1    Luscombe, N.M.2    Gerstein, M.3
  • 28
    • 0030888558 scopus 로고    scopus 로고
    • DnaA initiator - Also a transcription factor
    • Messer, W. and Weigel, C. 1997, DnaA initiator - also a transcription factor, Mol. Microbiol., 24, 1-6.
    • (1997) Mol. Microbiol. , vol.24 , pp. 1-6
    • Messer, W.1    Weigel, C.2
  • 29
    • 0037478650 scopus 로고    scopus 로고
    • Complete genome sequence of the marine planctomycete Pirellula sp. strain 1
    • Glockner, F. O., Kube, M., Bauer, M., et al. 2003, Complete genome sequence of the marine planctomycete Pirellula sp. strain 1, Proc. Natl Acad. Sci. USA, 100, 8298-8303.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 8298-8303
    • Glockner, F.O.1    Kube, M.2    Bauer, M.3
  • 30
    • 0035981243 scopus 로고    scopus 로고
    • Characterization of genes encoding multi-domain proteins in the genome of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120
    • Ohmori, M., Ikeuchi, M., Sato, N., et al. 2001, Characterization of genes encoding multi-domain proteins in the genome of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120, DNA Res., 8, 271-284.
    • (2001) DNA Res. , vol.8 , pp. 271-284
    • Ohmori, M.1    Ikeuchi, M.2    Sato, N.3
  • 32
    • 1542267826 scopus 로고    scopus 로고
    • The archaeal feast/famine regulatory protein: Potential roles of its assembly forms for regulating transcription
    • Koike, H., Ishijima, S. A., Clowney, L., and Suzuki, M. 2004, The archaeal feast/famine regulatory protein: potential roles of its assembly forms for regulating transcription, Proc. Natl Acad. Sci. USA, 101, 2840-2845.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 2840-2845
    • Koike, H.1    Ishijima, S.A.2    Clowney, L.3    Suzuki, M.4
  • 33
    • 0035109743 scopus 로고    scopus 로고
    • Transcription-associated protein families are primarily taxon-specific
    • Coulson, R. M. R., Enright, A. J., and Ouzounis, C. A. 2001, Transcription-associated protein families are primarily taxon-specific, Bioinformatics, 17, 95-97.
    • (2001) Bioinformatics , vol.17 , pp. 95-97
    • Coulson, R.M.R.1    Enright, A.J.2    Ouzounis, C.A.3
  • 34
    • 0034618559 scopus 로고    scopus 로고
    • Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS
    • Shigenobu, S., Watanabe, H., Hattori, M., Sakaki, Y., and Ishikawa, H. 2000, Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS, Nature, 407, 81-86.
    • (2000) Nature , vol.407 , pp. 81-86
    • Shigenobu, S.1    Watanabe, H.2    Hattori, M.3    Sakaki, Y.4    Ishikawa, H.5
  • 35
    • 20444492834 scopus 로고    scopus 로고
    • Regulation of transcription in a reduced bacterial genome: Nutrient-provisioning genes of the obligate symbiont Buchnera aphidicola
    • Moran, N. A., Dunbar, H. E., and Wilcox, J. L. 2005, Regulation of transcription in a reduced bacterial genome: nutrient-provisioning genes of the obligate symbiont Buchnera aphidicola, J. Bacteriol., 187, 4229-4237.
    • (2005) J. Bacteriol. , vol.187 , pp. 4229-4237
    • Moran, N.A.1    Dunbar, H.E.2    Wilcox, J.L.3
  • 36
    • 0036225678 scopus 로고    scopus 로고
    • The genome of M. acetivorans reveals extensive metabolic and physiological diversity
    • Galagan, J. E., Nusbaum, C., Roy, A., et al. 2002, The genome of M. acetivorans reveals extensive metabolic and physiological diversity, Genome Res., 12, 532-542.
    • (2002) Genome Res. , vol.12 , pp. 532-542
    • Galagan, J.E.1    Nusbaum, C.2    Roy, A.3
  • 37
    • 0031458333 scopus 로고    scopus 로고
    • The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus
    • Klenk, H. P., Clayton, R. A., Tomb, J. F., et al. 1997, The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus, Nature, 390, 364-370.
    • (1997) Nature , vol.390 , pp. 364-370
    • Klenk, H.P.1    Clayton, R.A.2    Tomb, J.F.3
  • 38
    • 0037046560 scopus 로고    scopus 로고
    • Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)
    • Bentley, S. D., Chater, K. F., Cerdeno-Tarraga, A. M., et al. 2002, Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2), Nature, 417, 141-147.
    • (2002) Nature , vol.417 , pp. 141-147
    • Bentley, S.D.1    Chater, K.F.2    Cerdeno-Tarraga, A.M.3
  • 39
    • 0037195083 scopus 로고    scopus 로고
    • The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract
    • Schell, M. A., Karmirantzou, M., Snel, B., et al. 2002, The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract, Proc. Natl Acad. Sci. USA, 99, 14422-14427.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 14422-14427
    • Schell, M.A.1    Karmirantzou, M.2    Snel, B.3
  • 40
    • 0030731108 scopus 로고    scopus 로고
    • The complete genome sequence of the gram-positive bacterium Bacillus subtilis
    • Kunst, F., Ogasawara, N., Moszer, I., et al. 1997, The complete genome sequence of the gram-positive bacterium Bacillus subtilis, Nature, 390, 249-256.
    • (1997) Nature , vol.390 , pp. 249-256
    • Kunst, F.1    Ogasawara, N.2    Moszer, I.3
  • 41
    • 0034902930 scopus 로고    scopus 로고
    • Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum
    • Nolling, J., Breton, G., Omelchenko, M. V., et al. 2001, Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum, J. Bacteriol., 183, 4823-4838.
    • (2001) J. Bacteriol. , vol.183 , pp. 4823-4838
    • Nolling, J.1    Breton, G.2    Omelchenko, M.V.3
  • 42
    • 10744220624 scopus 로고    scopus 로고
    • The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens
    • Duchaud, E., Rusniok, C., Frangeul, L., et al. 2003, The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens, Nat. Biotechnol., 21, 1307-1313.
    • (2003) Nat. Biotechnol. , vol.21 , pp. 1307-1313
    • Duchaud, E.1    Rusniok, C.2    Frangeul, L.3
  • 43
    • 10744220291 scopus 로고    scopus 로고
    • The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533
    • Pridmore, R. D., Berger, B., Desiere, F., et al. 2004, The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533, Proc. Natl Acad. Sci. USA, 101, 2512-2517.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 2512-2517
    • Pridmore, R.D.1    Berger, B.2    Desiere, F.3
  • 44
    • 0035021812 scopus 로고    scopus 로고
    • The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403
    • Bolotin, A., Wincker, P., Mauger, S., et al. 2001, The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403, Genome Res., 11, 731-753.
    • (2001) Genome Res. , vol.11 , pp. 731-753
    • Bolotin, A.1    Wincker, P.2    Mauger, S.3
  • 45
    • 0036206041 scopus 로고    scopus 로고
    • Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586
    • Kapatral, V., Anderson, I., Ivanova, N., et al. 2002, Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586, J. Bacteriol., 184, 2005-2018.
    • (2002) J. Bacteriol. , vol.184 , pp. 2005-2018
    • Kapatral, V.1    Anderson, I.2    Ivanova, N.3
  • 46
    • 0348103717 scopus 로고    scopus 로고
    • Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris
    • Larimer, F. W., Chain, P., Hauser, L., et al. 2004, Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris, Nat. Biotechnol., 22, 55-61.
    • (2004) Nat. Biotechnol. , vol.22 , pp. 55-61
    • Larimer, F.W.1    Chain, P.2    Hauser, L.3


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