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Volumn 61, Issue , 2012, Pages 1-36

Signal Correlations in Ecological Niches Can Shape the Organization and Evolution of Bacterial Gene Regulatory Networks

Author keywords

Chromatin immunoprecipitation; Gene expression; Genomics; Network evolution; Phylogenetic footprinting; Regulatory network; Regulon; Signal transduction; Stress response; Transcription; Transcription factor; Transcription factor binding site; Transcription profiling

Indexed keywords

BACTERIAL DNA; SIGMA FACTOR; TRANSCRIPTION FACTOR;

EID: 84867151554     PISSN: 00652911     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-394423-8.00001-9     Document Type: Chapter
Times cited : (6)

References (116)
  • 1
    • 34249079154 scopus 로고    scopus 로고
    • Network motifs: Theory and experimental approaches
    • Alon U. Network motifs: Theory and experimental approaches. Nature Reviews. Genetics 2007, 8:450-461.
    • (2007) Nature Reviews. Genetics , vol.8 , pp. 450-461
    • Alon, U.1
  • 3
    • 7744226739 scopus 로고    scopus 로고
    • Increased motility of Escherichia coli by insertion sequence element integration into the regulatory region of the flhD operon
    • Barker C.S., Prüß B.M., Matsumura P. Increased motility of Escherichia coli by insertion sequence element integration into the regulatory region of the flhD operon. Journal of Bacteriology 2004, 186:7529-7537.
    • (2004) Journal of Bacteriology , vol.186 , pp. 7529-7537
    • Barker, C.S.1    Prüß, B.M.2    Matsumura, P.3
  • 4
    • 1842506160 scopus 로고    scopus 로고
    • Regulation at complex bacterial promoters: How bacteria use different promoter organizations to produce different regulatory outcomes
    • Barnard A., Wolfe A., Busby S. Regulation at complex bacterial promoters: How bacteria use different promoter organizations to produce different regulatory outcomes. Current Opinion in Microbiology 2004, 7:102-108.
    • (2004) Current Opinion in Microbiology , vol.7 , pp. 102-108
    • Barnard, A.1    Wolfe, A.2    Busby, S.3
  • 5
    • 78650497790 scopus 로고    scopus 로고
    • On the power and limits of evolutionary conservation-Unraveling bacterial gene regulatory networks
    • Baumbach J. On the power and limits of evolutionary conservation-Unraveling bacterial gene regulatory networks. Nucleic Acids Research 2010, 38:7877.
    • (2010) Nucleic Acids Research , vol.38 , pp. 7877
    • Baumbach, J.1
  • 6
    • 22344449669 scopus 로고    scopus 로고
    • Constructing transcriptional regulatory networks
    • Blais A., Dynlacht B.D. Constructing transcriptional regulatory networks. Genes & Development 2005, 19:1499.
    • (2005) Genes & Development , vol.19 , pp. 1499
    • Blais, A.1    Dynlacht, B.D.2
  • 7
    • 0036107903 scopus 로고    scopus 로고
    • Discovery of regulatory elements by a computational method for phylogenetic footprinting
    • Blanchette M., Tompa M. Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Research 2002, 12:739-748.
    • (2002) Genome Research , vol.12 , pp. 739-748
    • Blanchette, M.1    Tompa, M.2
  • 8
    • 37349099750 scopus 로고    scopus 로고
    • A predictive model for transcriptional control of physiology in a free living cell
    • Bonneau R., Facciotti M.T., Reiss D.J., Schmid A.K., Pan M., Kaur A., et al. A predictive model for transcriptional control of physiology in a free living cell. Cell 2007, 131:1354-1365.
    • (2007) Cell , vol.131 , pp. 1354-1365
    • Bonneau, R.1    Facciotti, M.T.2    Reiss, D.J.3    Schmid, A.K.4    Pan, M.5    Kaur, A.6
  • 13
    • 1242316281 scopus 로고    scopus 로고
    • ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments
    • Buck M.J., Lieb J.D. ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 2004, 83:349-360.
    • (2004) Genomics , vol.83 , pp. 349-360
    • Buck, M.J.1    Lieb, J.D.2
  • 14
    • 13444302680 scopus 로고    scopus 로고
    • Promoters in the environment: Transcriptional regulation in its natural context
    • Cases I., de Lorenzo V. Promoters in the environment: Transcriptional regulation in its natural context. Nature Reviews. Microbiology 2005, 3:105-118.
    • (2005) Nature Reviews. Microbiology , vol.3 , pp. 105-118
    • Cases, I.1    de Lorenzo, V.2
  • 15
    • 0037665941 scopus 로고    scopus 로고
    • Transcription regulation and environmental adaptation in bacteria
    • Cases I., de Lorenzo V., Ouzounis C.A. Transcription regulation and environmental adaptation in bacteria. Trends in Microbiology 2003, 11:248-253.
    • (2003) Trends in Microbiology , vol.11 , pp. 248-253
    • Cases, I.1    de Lorenzo, V.2    Ouzounis, C.A.3
  • 16
    • 20344370764 scopus 로고    scopus 로고
    • Allosteric mechanisms of signal transduction
    • Changeux J.P., Edelstein S.J. Allosteric mechanisms of signal transduction. Science 2005, 308:1424-1428.
    • (2005) Science , vol.308 , pp. 1424-1428
    • Changeux, J.P.1    Edelstein, S.J.2
  • 17
    • 37849023306 scopus 로고    scopus 로고
    • Assessing performance of orthology detection strategies applied to eukaryotic genomes
    • Chen F., Mackey A.J., Vermunt J.K., Roos D.S. Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS One 2007, 2:e383.
    • (2007) PLoS One , vol.2
    • Chen, F.1    Mackey, A.J.2    Vermunt, J.K.3    Roos, D.S.4
  • 18
    • 0038724989 scopus 로고    scopus 로고
    • Finding functional features in Saccharomyces genomes by phylogenetic footprinting
    • Cliften P., Sudarsanam P., Desikan A., Fulton L., Fulton B., Majors J., et al. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 2003, 301:71-76.
    • (2003) Science , vol.301 , pp. 71-76
    • Cliften, P.1    Sudarsanam, P.2    Desikan, A.3    Fulton, L.4    Fulton, B.5    Majors, J.6
  • 19
    • 40149109210 scopus 로고    scopus 로고
    • Expression profiles reveal parallel evolution of epistatic interactions involving the CRP regulon in Escherichia coli
    • Cooper T.F., Remold S.K., Lenski R.E., Schneider D. Expression profiles reveal parallel evolution of epistatic interactions involving the CRP regulon in Escherichia coli. PLoS Genetics 2008, 4:e35.
    • (2008) PLoS Genetics , vol.4
    • Cooper, T.F.1    Remold, S.K.2    Lenski, R.E.3    Schneider, D.4
  • 20
    • 42049092081 scopus 로고    scopus 로고
    • The mechanisms of carbon catabolite repression in bacteria
    • Deutscher J. The mechanisms of carbon catabolite repression in bacteria. Current Opinion in Microbiology 2008, 11:87-93.
    • (2008) Current Opinion in Microbiology , vol.11 , pp. 87-93
    • Deutscher, J.1
  • 21
    • 77954143123 scopus 로고    scopus 로고
    • Impact of recombination on bacterial evolution
    • Didelot X., Maiden M.C.J. Impact of recombination on bacterial evolution. Trends in Microbiology 2010, 18:315-322.
    • (2010) Trends in Microbiology , vol.18 , pp. 315-322
    • Didelot, X.1    Maiden, M.C.J.2
  • 22
    • 34249723155 scopus 로고    scopus 로고
    • Frequent gain and loss of functional transcription factor binding sites
    • Doniger S.W., Fay J.C. Frequent gain and loss of functional transcription factor binding sites. PLoS Computational Biology 2007, 3:e99.
    • (2007) PLoS Computational Biology , vol.3
    • Doniger, S.W.1    Fay, J.C.2
  • 23
    • 77957325735 scopus 로고    scopus 로고
    • Reconstruction of the core and extended regulons of global transcription factors
    • Dufour Y.S., Kiley P.J., Donohue T.J. Reconstruction of the core and extended regulons of global transcription factors. PLoS Genetics 2010, 6:e1001027.
    • (2010) PLoS Genetics , vol.6
    • Dufour, Y.S.1    Kiley, P.J.2    Donohue, T.J.3
  • 24
    • 52949112607 scopus 로고    scopus 로고
    • Organization and evolution of the biological response to singlet oxygen stress
    • Dufour Y.S., Landick R., Donohue T.J. Organization and evolution of the biological response to singlet oxygen stress. Journal of Molecular Biology 2008, 383:713-730.
    • (2008) Journal of Molecular Biology , vol.383 , pp. 713-730
    • Dufour, Y.S.1    Landick, R.2    Donohue, T.J.3
  • 25
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy S.R. Profile hidden Markov models. Bioinformatics 1998, 14:755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 26
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar R.C. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 2004, 32:1792-1797.
    • (2004) Nucleic Acids Research , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 27
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • Enright A.J., van Dongen S., Ouzounis C.A. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Research 2002, 30:1575-1584.
    • (2002) Nucleic Acids Research , vol.30 , pp. 1575-1584
    • Enright, A.J.1    van Dongen, S.2    Ouzounis, C.A.3
  • 28
    • 13544260858 scopus 로고    scopus 로고
    • Differences in LexA regulon structure among proteobacteria through in vivo assisted comparative genomics
    • Erill I., Jara M., Salvador N., Escribano M., Campoy S., Barbé J. Differences in LexA regulon structure among proteobacteria through in vivo assisted comparative genomics. Nucleic Acids Research 2004, 32:6617-6626.
    • (2004) Nucleic Acids Research , vol.32 , pp. 6617-6626
    • Erill, I.1    Jara, M.2    Salvador, N.3    Escribano, M.4    Campoy, S.5    Barbé, J.6
  • 30
    • 27144533653 scopus 로고    scopus 로고
    • Reconstructing the metabolic network of a bacterium from its genome
    • Francke C., Siezen R.J., Teusink B. Reconstructing the metabolic network of a bacterium from its genome. Trends in Microbiology 2005, 13:550-558.
    • (2005) Trends in Microbiology , vol.13 , pp. 550-558
    • Francke, C.1    Siezen, R.J.2    Teusink, B.3
  • 31
    • 40749125240 scopus 로고    scopus 로고
    • Selection against spurious promoter motifs correlates with translational efficiency across bacteria
    • Froula J.L., Francino M.P. Selection against spurious promoter motifs correlates with translational efficiency across bacteria. PLoS One 2007, 2:e745.
    • (2007) PLoS One , vol.2
    • Froula, J.L.1    Francino, M.P.2
  • 32
    • 33744780700 scopus 로고    scopus 로고
    • Evolution of transcriptional regulatory networks in microbial genomes
    • Gelfand M.S. Evolution of transcriptional regulatory networks in microbial genomes. Current Opinion in Structural Biology 2006, 16:420-429.
    • (2006) Current Opinion in Structural Biology , vol.16 , pp. 420-429
    • Gelfand, M.S.1
  • 33
    • 33748648583 scopus 로고    scopus 로고
    • II , a second member of the heat shock sigma factor family
    • II , a second member of the heat shock sigma factor family. Journal of Bacteriology 2006, 188:5712.
    • (2006) Journal of Bacteriology , vol.188 , pp. 5712
    • Green, H.A.1    Donohue, T.J.2
  • 34
    • 0242692671 scopus 로고    scopus 로고
    • Multiple sigma subunits and the partitioning of bacterial transcription space
    • Gruber T.M., Gross C.A. Multiple sigma subunits and the partitioning of bacterial transcription space. Annual Review of Microbiology 2003, 57:441-466.
    • (2003) Annual Review of Microbiology , vol.57 , pp. 441-466
    • Gruber, T.M.1    Gross, C.A.2
  • 35
    • 13844266109 scopus 로고    scopus 로고
    • Genome properties: A system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics
    • Haft D.H., Selengut J.D., Brinkac L.M., Zafar N., White O. Genome properties: A system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics. Bioinformatics 2005, 21:293-306.
    • (2005) Bioinformatics , vol.21 , pp. 293-306
    • Haft, D.H.1    Selengut, J.D.2    Brinkac, L.M.3    Zafar, N.4    White, O.5
  • 36
    • 0038586484 scopus 로고    scopus 로고
    • The effects of selection against spurious transcription factor binding sites
    • Hahn M.W., Stajich J.E., Wray G.A. The effects of selection against spurious transcription factor binding sites. Molecular Biology and Evolution 2003, 20:901-906.
    • (2003) Molecular Biology and Evolution , vol.20 , pp. 901-906
    • Hahn, M.W.1    Stajich, J.E.2    Wray, G.A.3
  • 39
    • 0035985580 scopus 로고    scopus 로고
    • The extracytoplasmic function (ECF) sigma factors
    • Helmann J.D. The extracytoplasmic function (ECF) sigma factors. Advances in Microbial Physiology 2002, 46:47-110.
    • (2002) Advances in Microbial Physiology , vol.46 , pp. 47-110
    • Helmann, J.D.1
  • 40
    • 1342325451 scopus 로고    scopus 로고
    • Transcriptional profiling of Caulobacter crescentus during growth on complex and minimal media
    • Hottes A.K., Meewan M., Yang D., Arana N., Romero P., McAdams H.H., et al. Transcriptional profiling of Caulobacter crescentus during growth on complex and minimal media. Journal of Bacteriology 2004, 186:1448-1461.
    • (2004) Journal of Bacteriology , vol.186 , pp. 1448-1461
    • Hottes, A.K.1    Meewan, M.2    Yang, D.3    Arana, N.4    Romero, P.5    McAdams, H.H.6
  • 41
    • 42949147755 scopus 로고    scopus 로고
    • Phylogenetic simulation of promoter evolution: Estimation and modeling of binding site turnover events and assessment of their impact on alignment tools
    • Huang W., Nevins J.R., Ohler U. Phylogenetic simulation of promoter evolution: Estimation and modeling of binding site turnover events and assessment of their impact on alignment tools. Genome Biology 2007, 8:R225.
    • (2007) Genome Biology , vol.8
    • Huang, W.1    Nevins, J.R.2    Ohler, U.3
  • 42
    • 0043163746 scopus 로고    scopus 로고
    • Transcription increases multiple spontaneous point mutations in Salmonella enterica
    • Hudson R.E., Bergthorsson U., Ochman H. Transcription increases multiple spontaneous point mutations in Salmonella enterica. Nucleic Acids Research 2003, 31:4517-4522.
    • (2003) Nucleic Acids Research , vol.31 , pp. 4517-4522
    • Hudson, R.E.1    Bergthorsson, U.2    Ochman, H.3
  • 43
    • 28644447550 scopus 로고    scopus 로고
    • Ecological perspectives on the sequenced genome collection
    • Hughes Martiny J.B., Field D. Ecological perspectives on the sequenced genome collection. Ecology Letters 2005, 8:1334-1345.
    • (2005) Ecology Letters , vol.8 , pp. 1334-1345
    • Hughes Martiny, J.B.1    Field, D.2
  • 45
    • 36849063165 scopus 로고    scopus 로고
    • Structure and evolution of gene regulatory networks in microbial genomes
    • Janga S.C., Collado-Vides J. Structure and evolution of gene regulatory networks in microbial genomes. Research in Microbiology 2007, 158:787-794.
    • (2007) Research in Microbiology , vol.158 , pp. 787-794
    • Janga, S.C.1    Collado-Vides, J.2
  • 46
    • 0020724096 scopus 로고
    • Insertion of IS2 creates a novel ampC promoter in Escherichia coli
    • Jaurin B., Normark S. Insertion of IS2 creates a novel ampC promoter in Escherichia coli. Cell 1983, 32:809-816.
    • (1983) Cell , vol.32 , pp. 809-816
    • Jaurin, B.1    Normark, S.2
  • 47
    • 40849138085 scopus 로고    scopus 로고
    • Diverse two-dimensional input functions control bacterial sugar genes
    • Kaplan S., Bren A., Zaslaver A., Dekel E., Alon U. Diverse two-dimensional input functions control bacterial sugar genes. Molecular Cell 2008, 29:786-792.
    • (2008) Molecular Cell , vol.29 , pp. 786-792
    • Kaplan, S.1    Bren, A.2    Zaslaver, A.3    Dekel, E.4    Alon, U.5
  • 50
    • 33846914726 scopus 로고    scopus 로고
    • The regulatory roles and mechanism of transcriptional pausing
    • Landick R. The regulatory roles and mechanism of transcriptional pausing. Biochemical Society Transactions 2006, 34:1062-1066.
    • (2006) Biochemical Society Transactions , vol.34 , pp. 1062-1066
    • Landick, R.1
  • 51
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: Identification of ortholog groups for eukaryotic genomes
    • Li L., Stoeckert C.J., Roos D.S. OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Research 2003, 13:2178-2189.
    • (2003) Genome Research , vol.13 , pp. 2178-2189
    • Li, L.1    Stoeckert, C.J.2    Roos, D.S.3
  • 52
    • 0035189042 scopus 로고    scopus 로고
    • Roles of DNA adenine methylation in regulating bacterial gene expression and virulence
    • Low D.A., Weyand N.J., Mahan M.J. Roles of DNA adenine methylation in regulating bacterial gene expression and virulence. Infection and Immunity 2001, 69:7197-7204.
    • (2001) Infection and Immunity , vol.69 , pp. 7197-7204
    • Low, D.A.1    Weyand, N.J.2    Mahan, M.J.3
  • 54
    • 4644326931 scopus 로고    scopus 로고
    • Genomic analysis of regulatory network dynamics reveals large topological changes
    • Luscombe N.M., Babu M.M., Yu H., Snyder M., Teichmann S.A., Gerstein M. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 2004, 431:308-312.
    • (2004) Nature , vol.431 , pp. 308-312
    • Luscombe, N.M.1    Babu, M.M.2    Yu, H.3    Snyder, M.4    Teichmann, S.A.5    Gerstein, M.6
  • 55
    • 33646113855 scopus 로고    scopus 로고
    • Evolutionary dynamics of prokaryotic transcriptional regulatory networks
    • Madan Babu M., Teichmann S.A., Aravind L. Evolutionary dynamics of prokaryotic transcriptional regulatory networks. Journal of Molecular Biology 2006, 358:614-633.
    • (2006) Journal of Molecular Biology , vol.358 , pp. 614-633
    • Madan Babu, M.1    Teichmann, S.A.2    Aravind, L.3
  • 57
    • 34547630151 scopus 로고    scopus 로고
    • ChIP-seq: Welcome to the new frontier
    • Mardis E.R. ChIP-seq: Welcome to the new frontier. Nature Methods 2007, 4:613-614.
    • (2007) Nature Methods , vol.4 , pp. 613-614
    • Mardis, E.R.1
  • 63
    • 79955565307 scopus 로고    scopus 로고
    • A mathematical model for adaptive prediction of environmental changes by microorganisms
    • Mitchell A., Pilpel Y. A mathematical model for adaptive prediction of environmental changes by microorganisms. Proceedings of the National Academy of Sciences 2011, 108:7271.
    • (2011) Proceedings of the National Academy of Sciences , vol.108 , pp. 7271
    • Mitchell, A.1    Pilpel, Y.2
  • 64
    • 67650376275 scopus 로고    scopus 로고
    • Adaptive prediction of environmental changes by microorganisms
    • Mitchell A., Romano G.H., Groisman B., Yona A., Dekel E., Kupiec M., et al. Adaptive prediction of environmental changes by microorganisms. Nature 2009, 460:220-224.
    • (2009) Nature , vol.460 , pp. 220-224
    • Mitchell, A.1    Romano, G.H.2    Groisman, B.3    Yona, A.4    Dekel, E.5    Kupiec, M.6
  • 65
    • 38849135019 scopus 로고    scopus 로고
    • Choosing BLAST options for better detection of orthologs as reciprocal best hits
    • Moreno-Hagelsieb G., Latimer K. Choosing BLAST options for better detection of orthologs as reciprocal best hits. Bioinformatics 2008, 24:319-324.
    • (2008) Bioinformatics , vol.24 , pp. 319-324
    • Moreno-Hagelsieb, G.1    Latimer, K.2
  • 66
    • 33747816168 scopus 로고    scopus 로고
    • MicroFootPrinter: A tool for phylogenetic footprinting in prokaryotic genomes
    • Neph S., Tompa M. MicroFootPrinter: A tool for phylogenetic footprinting in prokaryotic genomes. Nucleic Acids Research 2006, 34:W366-W368.
    • (2006) Nucleic Acids Research , vol.34
    • Neph, S.1    Tompa, M.2
  • 67
    • 27244440541 scopus 로고    scopus 로고
    • Scaling laws in the functional content of genomes
    • Springer, New York, NY, USA, W.Y. Koonin, E.V.G.P. Karev (Eds.)
    • Nimwegen E. Scaling laws in the functional content of genomes. Power Laws, Scale-Free Networks and Genome Biology 2006, 236-253. Springer, New York, NY, USA. W.Y. Koonin, E.V.G.P. Karev (Eds.).
    • (2006) Power Laws, Scale-Free Networks and Genome Biology , pp. 236-253
    • Nimwegen, E.1
  • 69
    • 58149503635 scopus 로고    scopus 로고
    • II activates oxidative-stress defense systems and is controlled by RpoE in the singlet oxygen-dependent response in Rhodobacter sphaeroides
    • II activates oxidative-stress defense systems and is controlled by RpoE in the singlet oxygen-dependent response in Rhodobacter sphaeroides. Journal of Bacteriology 2009, 191:220-230.
    • (2009) Journal of Bacteriology , vol.191 , pp. 220-230
    • Nuss, A.M.1    Glaeser, J.2    Klug, G.3
  • 70
    • 0034682335 scopus 로고    scopus 로고
    • Lateral gene transfer and the nature of bacterial innovation
    • Ochman H., Lawrence J.G., Groisman E.A. Lateral gene transfer and the nature of bacterial innovation. Nature 2000, 405:299-304.
    • (2000) Nature , vol.405 , pp. 299-304
    • Ochman, H.1    Lawrence, J.G.2    Groisman, E.A.3
  • 71
    • 77954289636 scopus 로고    scopus 로고
    • B has a small core regulon and a conserved role in virulence but makes differential contributions to stress tolerance across a diverse collection of strains
    • B has a small core regulon and a conserved role in virulence but makes differential contributions to stress tolerance across a diverse collection of strains. Applied and Environmental Microbiology 2010, 76:4216.
    • (2010) Applied and Environmental Microbiology , vol.76 , pp. 4216
    • Oliver, H.1    Orsi, R.2    Wiedmann, M.3    Boor, K.4
  • 73
    • 0037261948 scopus 로고    scopus 로고
    • The sigma70 family of sigma factors
    • Paget M., Helmann J.D. The sigma70 family of sigma factors. Genome Biology 2003, 4:203.
    • (2003) Genome Biology , vol.4 , pp. 203
    • Paget, M.1    Helmann, J.D.2
  • 75
    • 67650601963 scopus 로고    scopus 로고
    • Evolution of transcriptional regulatory circuits in bacteria
    • Perez J.C., Groisman E.A. Evolution of transcriptional regulatory circuits in bacteria. Cell 2009, 138:233-244.
    • (2009) Cell , vol.138 , pp. 233-244
    • Perez, J.C.1    Groisman, E.A.2
  • 76
    • 63149115913 scopus 로고    scopus 로고
    • Transcription factor function and promoter architecture govern the evolution of bacterial regulons
    • Perez J.C., Groisman E.A. Transcription factor function and promoter architecture govern the evolution of bacterial regulons. Proceedings of the National Academy of Sciences 2009, 106:4319.
    • (2009) Proceedings of the National Academy of Sciences , vol.106 , pp. 4319
    • Perez, J.C.1    Groisman, E.A.2
  • 78
    • 0028304807 scopus 로고
    • Insertion of a novel DNA sequence, IS 1186, upstream of the silent carbapenemase gene cfiA, promotes expression of carbapenem resistance in clinical isolates of Bacteroides fragilis
    • Podglajen I., Breuil J., Collatz E. Insertion of a novel DNA sequence, IS 1186, upstream of the silent carbapenemase gene cfiA, promotes expression of carbapenem resistance in clinical isolates of Bacteroides fragilis. Molecular Microbiology 1994, 12:105-114.
    • (1994) Molecular Microbiology , vol.12 , pp. 105-114
    • Podglajen, I.1    Breuil, J.2    Collatz, E.3
  • 79
    • 34848865681 scopus 로고    scopus 로고
    • Orthologous transcription factors in bacteria have different functions and regulate different genes
    • Price M.N., Dehal P.S., Arkin A.P. Orthologous transcription factors in bacteria have different functions and regulate different genes. PLoS Computational Biology 2007, 3:e175.
    • (2007) PLoS Computational Biology , vol.3
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 80
    • 40149098889 scopus 로고    scopus 로고
    • Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli
    • Price M.N., Dehal P.S., Arkin A.P. Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli. Genome Biology 2008, 9:R4.
    • (2008) Genome Biology , vol.9
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 81
    • 22444441190 scopus 로고    scopus 로고
    • Operon formation is driven by co-regulation and not by horizontal gene transfer
    • Price M.N., Huang K.H., Arkin A.P., Alm E.J. Operon formation is driven by co-regulation and not by horizontal gene transfer. Genome Research 2005, 15:809-819.
    • (2005) Genome Research , vol.15 , pp. 809-819
    • Price, M.N.1    Huang, K.H.2    Arkin, A.P.3    Alm, E.J.4
  • 82
    • 0035375137 scopus 로고    scopus 로고
    • Computational analysis of microarray data
    • Quackenbush J. Computational analysis of microarray data. Nature Reviews. Genetics 2001, 2:418-427.
    • (2001) Nature Reviews. Genetics , vol.2 , pp. 418-427
    • Quackenbush, J.1
  • 83
    • 0036180002 scopus 로고    scopus 로고
    • The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons
    • Rajewsky N., Socci N.D., Zapotocky M., Siggia E.D. The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons. Genome Research 2002, 12:298-308.
    • (2002) Genome Research , vol.12 , pp. 298-308
    • Rajewsky, N.1    Socci, N.D.2    Zapotocky, M.3    Siggia, E.D.4
  • 85
    • 55049138544 scopus 로고    scopus 로고
    • Evolutionary patterns in prokaryotic genomes
    • Rocha E.P.C. Evolutionary patterns in prokaryotic genomes. Current Opinion in Microbiology 2008, 11:454-460.
    • (2008) Current Opinion in Microbiology , vol.11 , pp. 454-460
    • Rocha, E.P.C.1
  • 86
    • 34548219522 scopus 로고    scopus 로고
    • Comparative genomic reconstruction of transcriptional regulatory networks in bacteria
    • Rodionov D.A. Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chemical Reviews 2007, 107:3467-3497.
    • (2007) Chemical Reviews , vol.107 , pp. 3467-3497
    • Rodionov, D.A.1
  • 87
    • 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. Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria. Genome Biology 2004, 5:R90.
    • (2004) Genome Biology , vol.5
    • Rodionov, D.A.1    Dubchak, I.2    Arkin, A.3    Alm, E.4    Gelfand, M.S.5
  • 88
    • 85044710067 scopus 로고    scopus 로고
    • Dissimilatory metabolism of nitrogen oxides in bacteria: Comparative reconstruction of transcriptional networks
    • Rodionov D.A., Dubchak I.L., Arkin A.P., Alm E.J., Gelfand M.S. Dissimilatory metabolism of nitrogen oxides in bacteria: Comparative reconstruction of transcriptional networks. PLoS Computational Biology 2005, 1:e55.
    • (2005) PLoS Computational Biology , vol.1
    • Rodionov, D.A.1    Dubchak, I.L.2    Arkin, A.P.3    Alm, E.J.4    Gelfand, M.S.5
  • 89
    • 34247587012 scopus 로고    scopus 로고
    • GENETICS: Getting closer to the whole picture
    • Sauer U., Heinemann M., Zamboni N. GENETICS: Getting closer to the whole picture. Science's STKE 2007, 316:550.
    • (2007) Science's STKE , vol.316 , pp. 550
    • Sauer, U.1    Heinemann, M.2    Zamboni, N.3
  • 90
    • 34848928442 scopus 로고    scopus 로고
    • Genes induced late in infection increase fitness of Vibrio cholerae after release into the environment
    • Schild S., Tamayo R., Nelson E.J., Qadri F., Calderwood S.B., Camilli A. Genes induced late in infection increase fitness of Vibrio cholerae after release into the environment. Cell Host & Microbe 2007, 2:264-277.
    • (2007) Cell Host & Microbe , vol.2 , pp. 264-277
    • Schild, S.1    Tamayo, R.2    Nelson, E.J.3    Qadri, F.4    Calderwood, S.B.5    Camilli, A.6
  • 92
    • 36549078564 scopus 로고    scopus 로고
    • PhyME: A software tool for finding motifs in sets of orthologous sequences
    • Sinha S. PhyME: A software tool for finding motifs in sets of orthologous sequences. Methods in Molecular Biology (Clifton, NJ) 2007, 395:309.
    • (2007) Methods in Molecular Biology (Clifton, NJ) , vol.395 , pp. 309
    • Sinha, S.1
  • 94
    • 0036899286 scopus 로고    scopus 로고
    • From patterns to pathways: Gene expression data analysis comes of age
    • Slonim D.K. From patterns to pathways: Gene expression data analysis comes of age. Nature Genetics 2002, 32:502-508.
    • (2002) Nature Genetics , vol.32 , pp. 502-508
    • Slonim, D.K.1
  • 95
    • 70350432754 scopus 로고    scopus 로고
    • The third pillar of bacterial signal transduction: Classification of the extracytoplasmic function (ECF) σ factor protein family
    • Staroń A., Sofia H.J., Dietrich S., Ulrich L.E., Liesegang H., Mascher T. The third pillar of bacterial signal transduction: Classification of the extracytoplasmic function (ECF) σ factor protein family. Molecular Microbiology 2009, 74:557-581.
    • (2009) Molecular Microbiology , vol.74 , pp. 557-581
    • Staroń, A.1    Sofia, H.J.2    Dietrich, S.3    Ulrich, L.E.4    Liesegang, H.5    Mascher, T.6
  • 97
    • 42549102413 scopus 로고    scopus 로고
    • Characterization of the PvdS-regulated promoter motif in Pseudomonas syringae pv. tomato DC3000 reveals regulon members and insights regarding PvdS function in other pseudomonads
    • Swingle B., Thete D., Moll M., Myers C.R., Schneider D.J., Cartinhour S. Characterization of the PvdS-regulated promoter motif in Pseudomonas syringae pv. tomato DC3000 reveals regulon members and insights regarding PvdS function in other pseudomonads. Molecular Microbiology 2008, 68:871-889.
    • (2008) Molecular Microbiology , vol.68 , pp. 871-889
    • Swingle, B.1    Thete, D.2    Moll, M.3    Myers, C.R.4    Schneider, D.J.5    Cartinhour, S.6
  • 99
    • 45549085296 scopus 로고    scopus 로고
    • Predictive behavior within microbial genetic networks
    • Tagkopoulos I., Liu Y.C., Tavazoie S. Predictive behavior within microbial genetic networks. Science 2008, 320:1313.
    • (2008) Science , vol.320 , pp. 1313
    • Tagkopoulos, I.1    Liu, Y.C.2    Tavazoie, S.3
  • 100
    • 22444450760 scopus 로고    scopus 로고
    • Escherichia coli mutator ΔpolA is defective in base mismatch correction: The nature of in vivo DNA replication errors
    • Tago Y., Imai M., Ihara M., Atofuji H., Nagata Y., Yamamoto K. Escherichia coli mutator ΔpolA is defective in base mismatch correction: The nature of in vivo DNA replication errors. Journal of Molecular Biology 2005, 351:299-308.
    • (2005) Journal of Molecular Biology , vol.351 , pp. 299-308
    • Tago, Y.1    Imai, M.2    Ihara, M.3    Atofuji, H.4    Nagata, Y.5    Yamamoto, K.6
  • 101
    • 0030660581 scopus 로고    scopus 로고
    • A genomic perspective on protein families
    • Tatusov R.L., Koonin E.V., Lipman D.J. A genomic perspective on protein families. Science 1997, 278:631-637.
    • (1997) Science , vol.278 , pp. 631-637
    • Tatusov, R.L.1    Koonin, E.V.2    Lipman, D.J.3
  • 102
    • 2442537233 scopus 로고    scopus 로고
    • Gene regulatory network growth by duplication
    • Teichmann S.A., Babu M.M. Gene regulatory network growth by duplication. Nature Genetics 2004, 36:492-496.
    • (2004) Nature Genetics , vol.36 , pp. 492-496
    • Teichmann, S.A.1    Babu, M.M.2
  • 103
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 1994, 22:4673-4680.
    • (1994) Nucleic Acids Research , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 104
    • 79851505378 scopus 로고    scopus 로고
    • Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes
    • Treangen T.J., Rocha E.P.C. Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLoS Genetics 2011, 7:e1001284.
    • (2011) PLoS Genetics , vol.7
    • Treangen, T.J.1    Rocha, E.P.C.2
  • 106
    • 12944325784 scopus 로고    scopus 로고
    • One-component systems dominate signal transduction in prokaryotes
    • Ulrich L.E., Koonin E.V., Zhulin I.B. One-component systems dominate signal transduction in prokaryotes. Trends in Microbiology 2005, 13:52-56.
    • (2005) Trends in Microbiology , vol.13 , pp. 52-56
    • Ulrich, L.E.1    Koonin, E.V.2    Zhulin, I.B.3
  • 108
    • 77249100734 scopus 로고    scopus 로고
    • Network inference and network response identification: Moving genome-scale data to the next level of biological discovery
    • Veiga D.F.T., Dutta B., Balázsi G. Network inference and network response identification: Moving genome-scale data to the next level of biological discovery. Molecular BioSystems 2010, 6:469-480.
    • (2010) Molecular BioSystems , vol.6 , pp. 469-480
    • Veiga, D.F.T.1    Dutta, B.2    Balázsi, G.3
  • 109
    • 79960469948 scopus 로고    scopus 로고
    • Evolutionary rewiring and reprogramming of bacterial transcription regulation
    • Wang L., Wang F.F., Qian W. Evolutionary rewiring and reprogramming of bacterial transcription regulation. Journal of Genetics and Genomics 2011, 38:279-288.
    • (2011) Journal of Genetics and Genomics , vol.38 , pp. 279-288
    • Wang, L.1    Wang, F.F.2    Qian, W.3
  • 110
    • 79960961566 scopus 로고    scopus 로고
    • Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches
    • Wiedenbeck J., Cohan F.M. Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches. FEMS Microbiology Reviews 2011, 35:957-976.
    • (2011) FEMS Microbiology Reviews , vol.35 , pp. 957-976
    • Wiedenbeck, J.1    Cohan, F.M.2
  • 111
    • 27144527479 scopus 로고    scopus 로고
    • Regulation of bacterial gene expression by riboswitches
    • Winkler W.C., Breaker R.R. Regulation of bacterial gene expression by riboswitches. Annual Review of Microbiology 2005, 59:487-517.
    • (2005) Annual Review of Microbiology , vol.59 , pp. 487-517
    • Winkler, W.C.1    Breaker, R.R.2
  • 112
    • 0039820099 scopus 로고    scopus 로고
    • Eubacterial sigma-factors
    • Wösten M. Eubacterial sigma-factors. FEMS Microbiology Reviews 1998, 22:127-150.
    • (1998) FEMS Microbiology Reviews , vol.22 , pp. 127-150
    • Wösten, M.1
  • 113
    • 16244398023 scopus 로고    scopus 로고
    • Transcriptional response of Escherichia coli to external copper
    • Yamamoto K., Ishihama A. Transcriptional response of Escherichia coli to external copper. Molecular Microbiology 2005, 56:215-227.
    • (2005) Molecular Microbiology , vol.56 , pp. 215-227
    • Yamamoto, K.1    Ishihama, A.2
  • 114
    • 24944583149 scopus 로고    scopus 로고
    • Transcriptional response of Escherichia coli to external zinc
    • Yamamoto K., Ishihama A. Transcriptional response of Escherichia coli to external zinc. Journal of Bacteriology 2005, 187:6333.
    • (2005) Journal of Bacteriology , vol.187 , pp. 6333
    • Yamamoto, K.1    Ishihama, A.2
  • 115
    • 59649095559 scopus 로고    scopus 로고
    • Coordinated regulation of virulence during systemic infection of Salmonella enterica serovar Typhimurium
    • Yoon H., McDermott J.E., Porwollik S., McClelland M., Heffron F. Coordinated regulation of virulence during systemic infection of Salmonella enterica serovar Typhimurium. PLoS Pathogens 2009, 5:e1000306.
    • (2009) PLoS Pathogens , vol.5
    • Yoon, H.1    McDermott, J.E.2    Porwollik, S.3    McClelland, M.4    Heffron, F.5
  • 116
    • 33750459412 scopus 로고    scopus 로고
    • Global analysis of gene transcription regulation in prokaryotes
    • Zhou D., Yang R. Global analysis of gene transcription regulation in prokaryotes. Cellular and Molecular Life Sciences 2006, 63:2260-2290.
    • (2006) Cellular and Molecular Life Sciences , vol.63 , pp. 2260-2290
    • Zhou, D.1    Yang, R.2


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