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Volumn 157, Issue 8, 2011, Pages 2308-2318

Diversity and distribution of transcription factors: Their partner domains play an important role in regulatory plasticity in bacteria

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; TRANSCRIPTION FACTOR; WINGED HELIX TRANSCRIPTION FACTOR;

EID: 79961045630     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/mic.0.050617-0     Document Type: Article
Times cited : (13)

References (57)
  • 1
    • 0033485460 scopus 로고    scopus 로고
    • DNA-binding proteins and evolution of transcription regulation in the archaea
    • Aravind, L. & 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
  • 2
    • 15944379232 scopus 로고    scopus 로고
    • The many faces of the helix-turn-helix domain: Transcription regulation and beyond
    • Aravind, L., Anantharaman, V., Balaji, S., Babu, M. M. & Iyer, L. M. (2005). The many faces of the helix-turn-helix domain: transcription regulation and beyond. FEMS Microbiol Rev 29, 231-262.
    • (2005) FEMS Microbiol Rev , vol.29 , pp. 231-262
    • Aravind, L.1    Anantharaman, V.2    Balaji, S.3    Babu, M.M.4    Iyer, L.M.5
  • 3
    • 38049144241 scopus 로고    scopus 로고
    • CoryneRegNet 4.0 - a reference database for corynebacterial gene regulatory networks
    • Baumbach, J. (2007). CoryneRegNet 4.0 - a reference database for corynebacterial gene regulatory networks. BMC Bioinformatics 8, 429.
    • (2007) BMC Bioinformatics , vol.8 , pp. 429
    • Baumbach, J.1
  • 4
    • 4544311326 scopus 로고    scopus 로고
    • Modelling the evolution of genomes with integrated external and internal functions
    • Bengtsson, B. O. (2004). Modelling the evolution of genomes with integrated external and internal functions. J Theor Biol 231, 271-278.
    • (2004) J Theor Biol , vol.231 , pp. 271-278
    • Bengtsson, B.O.1
  • 5
    • 0027275485 scopus 로고
    • The winged-helix DNA-binding motif: Another helix-turn-helix takeoff
    • Brennan, R. G. (1993). The winged-helix DNA-binding motif: another helix-turn-helix takeoff. Cell 74, 773-776.
    • (1993) Cell , vol.74 , pp. 773-776
    • Brennan, R.G.1
  • 6
    • 0024571640 scopus 로고
    • The helix-turn-helix DNA binding motif
    • Brennan, R. G. & Matthews, B. W. (1989a). The helix-turn-helix DNA binding motif. J Biol Chem 264, 1903-1906.
    • (1989) J Biol Chem , vol.264 , pp. 1903-1906
    • Brennan, R.G.1    Matthews, B.W.2
  • 7
    • 0024383444 scopus 로고
    • Structural basis of DNA-protein recognition
    • Brennan, R. G. & Matthews, B. W. (1989b). Structural basis of DNA-protein recognition. Trends Biochem Sci 14, 286-290.
    • (1989) Trends Biochem Sci , vol.14 , pp. 286-290
    • Brennan, R.G.1    Matthews, B.W.2
  • 9
    • 1842591130 scopus 로고    scopus 로고
    • The regulation of bacterial transcription initiation
    • Browning, D. F. & Busby, S. J. (2004). The regulation of bacterial transcription initiation. Nat Rev Microbiol 2, 57-65.
    • (2004) Nat Rev Microbiol , vol.2 , pp. 57-65
    • Browning, D.F.1    Busby, S.J.2
  • 10
    • 0037565104 scopus 로고    scopus 로고
    • The SmtB/ArsR family of metalloregulatory transcriptional repressors: Structural insights into prokaryotic metal resistance
    • Busenlehner, L. S., Pennella, M. A. & Giedroc, D. P. (2003). The SmtB/ArsR family of metalloregulatory transcriptional repressors: structural insights into prokaryotic metal resistance. FEMS Microbiol Rev 27, 131-143.
    • (2003) FEMS Microbiol Rev , vol.27 , pp. 131-143
    • Busenlehner, L.S.1    Pennella, M.A.2    Giedroc, D.P.3
  • 11
    • 0035822719 scopus 로고    scopus 로고
    • Universal scaling laws for hierarchical complexity in languages, organisms, behaviors and other combinatorial systems
    • Changizi, M. A. (2001). Universal scaling laws for hierarchical complexity in languages, organisms, behaviors and other combinatorial systems. J Theor Biol 211, 277-295.
    • (2001) J Theor Biol , vol.211 , pp. 277-295
    • Changizi, M.A.1
  • 12
    • 0035109743 scopus 로고    scopus 로고
    • Transcription-associated protein families are primarily taxon-specific
    • Coulson, R. M., Enright, A. J. & 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.1    Enright, A.J.2    Ouzounis, C.A.3
  • 13
    • 25444467951 scopus 로고    scopus 로고
    • Is prokaryotic complexity limited by accelerated growth in regulatory overhead
    • Croft, L. J., Lercher, M. J., Gagen, M. J. & Mattick, J. S. (2003). Is prokaryotic complexity limited by accelerated growth in regulatory overhead. Genome Biol 5, P2.
    • (2003) Genome Biol , vol.5
    • Croft, L.J.1    Lercher, M.J.2    Gagen, M.J.3    Mattick, J.S.4
  • 15
    • 33645858540 scopus 로고    scopus 로고
    • Regulation of virulence by members of the MarR/SlyA family
    • Ellison, D. W. & Miller, V. L. (2006). Regulation of virulence by members of the MarR/SlyA family. Curr Opin Microbiol 9, 153-159.
    • (2006) Curr Opin Microbiol , vol.9 , pp. 153-159
    • Ellison, D.W.1    Miller, V.L.2
  • 18
    • 0036225047 scopus 로고    scopus 로고
    • The FtsH protease is involved in development, stress response and heat shock control in Caulobacter crescentus
    • Fischer, B., Rummel, G., Aldridge, P. & Jenal, U. (2002). The FtsH protease is involved in development, stress response and heat shock control in Caulobacter crescentus. Mol Microbiol 44, 461-478.
    • (2002) Mol Microbiol , vol.44 , pp. 461-478
    • Fischer, B.1    Rummel, G.2    Aldridge, P.3    Jenal, U.4
  • 20
    • 29144475324 scopus 로고    scopus 로고
    • Complexity in regulation of tryptophan biosynthesis in Bacillus subtilis
    • Gollnick, P., Babitzke, P., Antson, A. & Yanofsky, C. (2005). Complexity in regulation of tryptophan biosynthesis in Bacillus subtilis. Annu Rev Genet 39, 47-68.
    • (2005) Annu Rev Genet , vol.39 , pp. 47-68
    • Gollnick, P.1    Babitzke, P.2    Antson, A.3    Yanofsky, C.4
  • 21
    • 0242692671 scopus 로고    scopus 로고
    • Multiple sigma subunits and the partitioning of bacterial transcription space
    • Gruber, T. M. & Gross, C. A. (2003). Multiple sigma subunits and the partitioning of bacterial transcription space. Annu Rev Microbiol 57, 441-466.
    • (2003) Annu Rev Microbiol , vol.57 , pp. 441-466
    • Gruber, T.M.1    Gross, C.A.2
  • 22
    • 47249165755 scopus 로고    scopus 로고
    • The hidden universal distribution of amino acid biosynthetic networks: A genomic perspective on their origins and evolution
    • Hernández-Montes, G., Díaz-Mejía, J. J., Pérez-Rueda, E. & Segovia, L. (2008). The hidden universal distribution of amino acid biosynthetic networks: a genomic perspective on their origins and evolution. Genome Biol 9, R95.
    • (2008) Genome Biol , vol.9
    • Hernández-Montes, G.1    Díaz-Mejía, J.J.2    Pérez-Rueda, E.3    Segovia, L.4
  • 23
    • 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
  • 24
    • 6044261571 scopus 로고    scopus 로고
    • Conservation of adjacency as evidence of paralogous operons
    • Janga, S. C. & Moreno-Hagelsieb, G. (2004). Conservation of adjacency as evidence of paralogous operons. Nucleic Acids Res 32, 5392-5397.
    • (2004) Nucleic Acids Res , vol.32 , pp. 5392-5397
    • Janga, S.C.1    Moreno-Hagelsieb, G.2
  • 25
    • 68749092014 scopus 로고    scopus 로고
    • Plasticity of transcriptional machinery in bacteria is increased by the repertoire of regulatory families
    • Janga, S. C. & Pé rez-Rueda, E. (2009). Plasticity of transcriptional machinery in bacteria is increased by the repertoire of regulatory families. Comput Biol Chem 33, 261-268.
    • (2009) Comput Biol Chem , vol.33 , pp. 261-268
    • Janga, S.C.1    Pérez-Rueda, E.2
  • 26
    • 0344153756 scopus 로고    scopus 로고
    • Phylogeny of the bacterial superfamily of Crp-Fnr transcription regulators: Exploiting the metabolic spectrum by controlling alternative gene programs
    • Körner, H., Sofia, H. J. & Zumft, W. G. (2003). Phylogeny of the bacterial superfamily of Crp-Fnr transcription regulators: exploiting the metabolic spectrum by controlling alternative gene programs. FEMS Microbiol Rev 27, 559-592.
    • (2003) FEMS Microbiol Rev , vol.27 , pp. 559-592
    • Körner, H.1    Sofia, H.J.2    Zumft, W.G.3
  • 27
    • 33644878620 scopus 로고    scopus 로고
    • DBD: A transcription factor prediction database
    • (Database issue),
    • Kummerfeld, S. K. & Teichmann, S. A. (2006). DBD: a transcription factor prediction database. Nucleic Acids Res 34 (Database issue), D74-D81.
    • (2006) Nucleic Acids Res , vol.34
    • Kummerfeld, S.K.1    Teichmann, S.A.2
  • 28
    • 0036066765 scopus 로고    scopus 로고
    • The role of lineage-specific gene family expansion in the evolution of eukaryotes
    • Lespinet, O., Wolf, Y. I., Koonin, E. V. & Aravind, L. (2002). The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res 12, 1048-1059.
    • (2002) Genome Res , vol.12 , pp. 1048-1059
    • Lespinet, O.1    Wolf, Y.I.2    Koonin, E.V.3    Aravind, L.4
  • 29
    • 0037819447 scopus 로고    scopus 로고
    • Transcription Regulation and Animal Diversity
    • Levine, M. & Tjian, R. (2003). Transcription regulation and animal diversity. Nature 424, 147-151.
    • (2003) Nature , vol.424 , pp. 147-151
    • Levine, M.1    Tjian, R.2
  • 30
    • 33750344923 scopus 로고    scopus 로고
    • Streamlining and simplification of microbial genome architecture
    • Lynch, M. (2006). Streamlining and simplification of microbial genome architecture. Annu Rev Microbiol 60, 327-349.
    • (2006) Annu Rev Microbiol , vol.60 , pp. 327-349
    • Lynch, M.1
  • 31
    • 0345306751 scopus 로고    scopus 로고
    • The origins of genome complexity
    • Lynch, M. & Conery, J. S. (2003). The origins of genome complexity. Science 302, 1401-1404.
    • (2003) Science , vol.302 , pp. 1401-1404
    • Lynch, M.1    Conery, J.S.2
  • 32
    • 0037440734 scopus 로고    scopus 로고
    • Evolution of transcription factors and the gene regulatory network in Escherichia coli
    • Madan Babu, M. & 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
  • 33
    • 33646113855 scopus 로고    scopus 로고
    • Evolutionary dynamics of prokaryotic transcriptional regulatory networks
    • Madan Babu, M., Teichmann, S. A. & Aravind, L. (2006). Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J Mol Biol 358, 614-633.
    • (2006) J Mol Biol , vol.358 , pp. 614-633
    • Babu, M.M.1    Teichmann, S.A.2    Aravind, L.3
  • 34
    • 58949097886 scopus 로고    scopus 로고
    • Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins
    • Maddocks, S. E. & Oyston, P. C. (2008). Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins. Microbiology 154, 3609-3623.
    • (2008) Microbiology , vol.154 , pp. 3609-3623
    • Maddocks, S.E.1    Oyston, P.C.2
  • 35
    • 30344484891 scopus 로고    scopus 로고
    • Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli
    • Martínez-Antonio, A., Janga, S. C., Salgado, H. & Collado-Vides, J. (2006). Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli. Trends Microbiol 14, 22-27.
    • (2006) Trends Microbiol , vol.14 , pp. 22-27
    • Martínez-Antonio, A.1    Janga, S.C.2    Salgado, H.3    Collado-Vides, J.4
  • 37
    • 17644366759 scopus 로고    scopus 로고
    • Transcription attenuation: A highly conserved regulatory strategy used by bacteria
    • Merino, E. & Yanofsky, C. (2005). Transcription attenuation: a highly conserved regulatory strategy used by bacteria. Trends Genet 21, 260-264.
    • (2005) Trends Genet , vol.21 , pp. 260-264
    • Merino, E.1    Yanofsky, C.2
  • 38
    • 33646828924 scopus 로고    scopus 로고
    • Investigations of the modular structure of bacterial promoters
    • Miroslavova, N. S. & Busby, S. J. (2006). Investigations of the modular structure of bacterial promoters. Biochem Soc Symp (73), 1-10.
    • (2006) Biochem Soc Symp , Issue.73 , pp. 1-10
    • Miroslavova, N.S.1    Busby, S.J.2
  • 39
    • 33748679406 scopus 로고    scopus 로고
    • Identification and analysis of DNA-binding transcription factors in Bacillus subtilis and other Firmicutes - a genomic approach
    • Moreno-Campuzano, S., Janga, S. C. & Perez-Rueda, E. (2006).Identification and analysis of DNA-binding transcription factors in Bacillus subtilis and other Firmicutes - a genomic approach. BMC Genomics 7, 147.
    • (2006) BMC Genomics , vol.7 , pp. 147
    • Moreno-Campuzano, S.1    Janga, S.C.2    Perez-Rueda, E.3
  • 41
    • 24944453275 scopus 로고    scopus 로고
    • Structural determinants of metal selectivity in prokaryotic metal-responsive transcriptional regulators
    • Pennella, M. A. & Giedroc, D. P. (2005). Structural determinants of metal selectivity in prokaryotic metal-responsive transcriptional regulators. Biometals 18, 413-428.
    • (2005) Biometals , vol.18 , pp. 413-428
    • Pennella, M.A.1    Giedroc, D.P.2
  • 42
    • 33845397687 scopus 로고    scopus 로고
    • BadM is a transcriptional repressor and one of three regulators that control benzoyl coenzyme A reductase gene expression in Rhodopseudomonas palustris
    • Peres, C. M. & Harwood, C. S. (2006). BadM is a transcriptional repressor and one of three regulators that control benzoyl coenzyme A reductase gene expression in Rhodopseudomonas palustris. J Bacteriol 188, 8662-8665.
    • (2006) J Bacteriol , vol.188 , pp. 8662-8665
    • Peres, C.M.1    Harwood, C.S.2
  • 43
    • 0034873196 scopus 로고    scopus 로고
    • Common history at the origin of the position-function correlation in transcriptional regulators in archaea and bacteria
    • Perez-Rueda, E. & Collado-Vides, J. (2001). Common history at the origin of the position-function correlation in transcriptional regulators in archaea and bacteria. J Mol Evol 53, 172-179.
    • (2001) J Mol Evol , vol.53 , pp. 172-179
    • Perez-Rueda, E.1    Collado-Vides, J.2
  • 44
    • 77952805130 scopus 로고    scopus 로고
    • Identification and genomic analysis of transcription factors in archaeal genomes exemplifies their functional architecture and evolutionary origin
    • Perez-Rueda, E. & Janga, S. C. (2010). Identification and genomic analysis of transcription factors in archaeal genomes exemplifies their functional architecture and evolutionary origin. Mol Biol Evol 27, 1449-1459.
    • (2010) Mol Biol Evol , vol.27 , pp. 1449-1459
    • Perez-Rueda, E.1    Janga, S.C.2
  • 45
    • 9544237144 scopus 로고    scopus 로고
    • Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea
    • Perez-Rueda, E., Collado-Vides, J. & Segovia, L. (2004).Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea. Comput Biol Chem 28, 341-350.
    • (2004) Comput Biol Chem , vol.28 , pp. 341-350
    • Perez-Rueda, E.1    Collado-Vides, J.2    Segovia, L.3
  • 46
    • 72949096572 scopus 로고    scopus 로고
    • Scaling relationship in the gene content of transcriptional machinery in bacteria
    • Perez-Rueda, E., Janga, S. C. & Martínez-Antonio, A. (2009). Scaling relationship in the gene content of transcriptional machinery in bacteria. MolBiosyst5, 1494-1501.
    • (2009) MolBiosyst , vol.5 , pp. 1494-1501
    • Perez-Rueda, E.1    Janga, S.C.2    Martínez-Antonio, A.3
  • 47
    • 0037066712 scopus 로고    scopus 로고
    • Subdivision of the helix-turn-helix GntR family of bacterial regulators in the FadR, HutC, MocR, and YtrA subfamilies
    • Rigali, S., Derouaux, A., Giannotta, F. & Dusart, J. (2002). Subdivision of the helix-turn-helix GntR family of bacterial regulators in the FadR, HutC, MocR, and YtrA subfamilies. J Biol Chem 277, 12507- 12515.
    • (2002) J Biol Chem , vol.277 , pp. 12507-12515
    • Rigali, S.1    Derouaux, A.2    Giannotta, F.3    Dusart, J.4
  • 48
    • 3242674438 scopus 로고    scopus 로고
    • Extending the classification of bacterial transcription factors beyond the helix-turn-helix motif as an alternative approach to discover new cis/trans relationships
    • Rigali, S., Schlicht, M., Hoskisson, P., Nothaft, H., Merzbacher, M., Joris, B. & Titgemeyer, F. (2004). Extending the classification of bacterial transcription factors beyond the helix-turn-helix motif as an alternative approach to discover new cis/trans relationships. Nucleic Acids Res 32, 3418-3426.
    • (2004) Nucleic Acids Res , vol.32 , pp. 3418-3426
    • Rigali, S.1    Schlicht, M.2    Hoskisson, P.3    Nothaft, H.4    Merzbacher, M.5    Joris, B.6    Titgemeyer, F.7
  • 49
    • 22544432327 scopus 로고    scopus 로고
    • Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria
    • Rodionov, D. A., Dubchak, I., Arkin, A., Alm, E. & Gelfand, M. S. (2004). Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria. Genome Biol 5, R90.
    • (2004) Genome Biol , vol.5
    • Rodionov, D.A.1    Dubchak, I.2    Arkin, A.3    Alm, E.4    Gelfand, M.S.5
  • 50
    • 65549141161 scopus 로고    scopus 로고
    • Stochastic analysis of the SOS response in Escherichia coli
    • Shimoni, Y., Altuvia, S., Margalit, H. & Biham, O. (2009). Stochastic analysis of the SOS response in Escherichia coli. PLoS ONE 4, e5363.
    • (2009) PLoS ONE , vol.e5363 , pp. 4
    • Shimoni, Y.1    Altuvia, S.2    Margalit, H.3    Biham, O.4
  • 51
    • 38549162091 scopus 로고    scopus 로고
    • DBTBS: A database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information
    • (Database issue)
    • Sierro, N., Makita, Y., de Hoon, M. & Nakai, K. (2008). DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res 36 (Database issue), D93-D96.
    • (2008) Nucleic Acids Res , vol.36
    • Sierro, N.1    Makita, Y.2    de Hoon, M.3    Nakai, K.4
  • 52
    • 38349193126 scopus 로고    scopus 로고
    • Ligand-induced conforma-tional changes and conformational dynamics in the solution structure of the lactose repressor protein
    • Taraban, M., Zhan, H., Whitten, A. E., Langley, D. B., Matthews, K. S., Swint-Kruse, L. & Trewhella, J. (2008). Ligand-induced conforma-tional changes and conformational dynamics in the solution structure of the lactose repressor protein. J Mol Biol 376, 466-481.
    • (2008) J Mol Biol , vol.376 , pp. 466-481
    • Taraban, M.1    Zhan, H.2    Whitten, A.E.3    Langley, D.B.4    Matthews, K.S.5    Swint-Kruse, L.6    Trewhella, J.7
  • 53
    • 26244442102 scopus 로고    scopus 로고
    • Modules, multidomain proteins and organismic complexity
    • Tordai, H., Nagy, A., Farkas, K., Bányai, L. & Patthy, L. (2005). Modules, multidomain proteins and organismic complexity. FEBS J 272, 5064-5078.
    • (2005) FEBS J , vol.272 , pp. 5064-5078
    • Tordai, H.1    Nagy, A.2    Farkas, K.3    Bányai, L.4    Patthy, L.5
  • 54
    • 0041828241 scopus 로고    scopus 로고
    • Scaling laws in the functional content of genomes
    • van Nimwegen, E. (2003). Scaling laws in the functional content of genomes. Trends Genet 19, 479-484.
    • (2003) Trends Genet , vol.19 , pp. 479-484
    • van Nimwegen, E.1
  • 55
    • 0346728474 scopus 로고    scopus 로고
    • Design of gene circuits: Lessons from bacteria
    • Wall, M. E., Hlavacek, W. S. & Savageau, M. A. (2004). Design of gene circuits: lessons from bacteria. Nat Rev Genet 5, 34-42.
    • (2004) Nat Rev Genet , vol.5 , pp. 34-42
    • Wall, M.E.1    Hlavacek, W.S.2    Savageau, M.A.3
  • 56
    • 18944386328 scopus 로고    scopus 로고
    • The origin of allometric scaling laws in biology from genomes to ecosystems: Towards a quantitative unifying theory of biological structure and organization
    • West, G. B. & Brown, J. H. (2005). The origin of allometric scaling laws in biology from genomes to ecosystems: towards a quantitative unifying theory of biological structure and organization. J Exp Biol 208, 1575-1592.
    • (2005) J Exp Biol , vol.208 , pp. 1575-1592
    • West, G.B.1    Brown, J.H.2
  • 57
    • 0039820099 scopus 로고    scopus 로고
    • Eubacterial sigma-factors
    • Wösten, M. M. (1998). Eubacterial sigma-factors. FEMS Microbiol Rev 22, 127-150.
    • (1998) FEMS Microbiol Rev , vol.22 , pp. 127-150
    • Wösten, M.M.1


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