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Volumn 156, Issue 1, 2010, Pages 14-22

New insights into the regulatory networks of paralogous genes in bacteria

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT; MESSENGER RNA; OUTER MEMBRANE PROTEIN C; OUTER MEMBRANE PROTEIN F; REGULATOR PROTEIN; RNA BINDING PROTEIN; SIGMA FACTOR; TRANS ACTING FACTOR; TRANSCRIPTION FACTOR; TRANSFER RNA;

EID: 76849091721     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/mic.0.033266-0     Document Type: Review
Times cited : (30)

References (60)
  • 1
    • 33751429178 scopus 로고    scopus 로고
    • The evolution of two-component systems in bacteria reveals different strategies for niche adaptation
    • Alm, E., Huang, K. & Arkin, A. (2006). The evolution of two-component systems in bacteria reveals different strategies for niche adaptation. PLOS Comput Biol 2, e143.
    • (2006) PLOS Comput Biol , vol.2
    • Alm, E.1    Huang, K.2    Arkin, A.3
  • 4
    • 33646113855 scopus 로고    scopus 로고
    • Evolutionary dynamics of prokaryotic transcriptional regulatory networks
    • Babu, M. 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
  • 5
    • 34548419328 scopus 로고    scopus 로고
    • Interplay between network structures, regulatory modes and sensing mechanisms of transcription factors in the transcriptional regulatory network of E. coli
    • Balaji, S., Babu, M. M. & Aravind, L. (2007). Interplay between network structures, regulatory modes and sensing mechanisms of transcription factors in the transcriptional regulatory network of E. coli. J Mol Biol 372, 1108-1122.
    • (2007) J Mol Biol , vol.372 , pp. 1108-1122
    • Balaji, S.1    Babu, M.M.2    Aravind, L.3
  • 6
    • 1342325448 scopus 로고    scopus 로고
    • Transcriptional organization and regulation of the L-idonic acid pathway (GntII system) in Escherichia coli
    • Bausch, C., Ramsey, M. & Conway, T. (2004). Transcriptional organization and regulation of the L-idonic acid pathway (GntII system) in Escherichia coli. J Bacteriol 186, 1388-1397.
    • (2004) J Bacteriol , vol.186 , pp. 1388-1397
    • Bausch, C.1    Ramsey, M.2    Conway, T.3
  • 7
    • 0026713398 scopus 로고
    • The effect of supercoiling on the in vitro transcription of the spoIIA operon from Bacillus subtilis
    • Bird, T., Burbulys, D., Wu, J. J., Strauch, M. A., Hoch, J. A. & Spiegelman, G. B. (1992). The effect of supercoiling on the in vitro transcription of the spoIIA operon from Bacillus subtilis. Biochimie 74, 627-634.
    • (1992) Biochimie , vol.74 , pp. 627-634
    • Bird, T.1    Burbulys, D.2    Wu, J.J.3    Strauch, M.A.4    Hoch, J.A.5    Spiegelman, G.B.6
  • 9
    • 0037316190 scopus 로고    scopus 로고
    • A microarray-based antibiotic screen identifies a regulatory role for supercoiling in the osmotic stress response of Escherichia coli
    • Cheung, K. J., Badarinarayana, V., Selinger, D. W., Janse, D. & Church, G. M. (2003). A microarray-based antibiotic screen identifies a regulatory role for supercoiling in the osmotic stress response of Escherichia coli. Genome Res 13, 206-215.
    • (2003) Genome Res , vol.13 , pp. 206-215
    • Cheung, K.J.1    Badarinarayana, V.2    Selinger, D.W.3    Janse, D.4    Church, G.M.5
  • 10
    • 0034444676 scopus 로고    scopus 로고
    • Coupling of flagellar gene expression to flagellar assembly in Salmonella enterica serovar typhimurium and Escherichia coli
    • Chilcott, G. S. & Hughes, K. T. (2000). Coupling of flagellar gene expression to flagellar assembly in Salmonella enterica serovar typhimurium and Escherichia coli. Microbiol Mol Biol Rev 64, 694-708.
    • (2000) Microbiol Mol Biol Rev , vol.64 , pp. 694-708
    • Chilcott, G.S.1    Hughes, K.T.2
  • 11
    • 38449095243 scopus 로고    scopus 로고
    • Trigger enzymes: Bifunctional proteins active in metabolism and in controlling gene expression
    • Commichau, F. M. & Stulke, J. (2008). Trigger enzymes: bifunctional proteins active in metabolism and in controlling gene expression. Mol Microbiol 67, 692-702.
    • (2008) Mol Microbiol , vol.67 , pp. 692-702
    • Commichau, F.M.1    Stulke, J.2
  • 12
    • 56549119570 scopus 로고    scopus 로고
    • Turning a hobby into a job: How duplicated genes find new functions
    • Conant, G. C. & Wolfe, K. H. (2008). Turning a hobby into a job: how duplicated genes find new functions. Nat Rev Genet 9, 938-950.
    • (2008) Nat Rev Genet , vol.9 , pp. 938-950
    • Conant, G.C.1    Wolfe, K.H.2
  • 13
    • 4344624948 scopus 로고    scopus 로고
    • Molecular evolution in the yeast transcriptional regulation network
    • Evangelisti, A. M. & Wagner, A. (2004). Molecular evolution in the yeast transcriptional regulation network. J Exp Zool B Mol Dev Evol 302, 392-411.
    • (2004) J Exp Zool B Mol Dev Evol , vol.302 , pp. 392-411
    • Evangelisti, A.M.1    Wagner, A.2
  • 14
    • 33750992443 scopus 로고    scopus 로고
    • Flipping the switch: Bringing order to flagellar assembly
    • Ferris, H. U. & Minamino, T. (2006). Flipping the switch: bringing order to flagellar assembly. Trends Microbiol 14, 519-526.
    • (2006) Trends Microbiol , vol.14 , pp. 519-526
    • Ferris, H.U.1    Minamino, T.2
  • 15
    • 34648851384 scopus 로고    scopus 로고
    • The primordial metabolism: An ancestral interconnection between leucine, arginine, and lysine biosynthesis
    • Fondi, M., Brilli, M., Emiliani, G., Paffetti, D. & Fani, R. (2007). The primordial metabolism: an ancestral interconnection between leucine, arginine, and lysine biosynthesis. BMC Evol Biol 7 (Suppl 2), S3.
    • (2007) BMC Evol Biol , vol.7 , Issue.SUPPL. 2
    • Fondi, M.1    Brilli, M.2    Emiliani, G.3    Paffetti, D.4    Fani, R.5
  • 16
    • 38549140094 scopus 로고    scopus 로고
    • Gama-Castro, S, Jimenez-Jacinto, V, Peralta-Gil, M, Santos- Zavaleta, A, Penaloza-Spinola, M. I, Contreras-Moreira, B, Segura-Salazar, J, Muniz-Rascado, L, Martinez-Flores, I. & other authors (2008, RegulonDB (version 6.0, gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res 36, D120-D124
    • Gama-Castro, S., Jimenez-Jacinto, V., Peralta-Gil, M., Santos- Zavaleta, A., Penaloza-Spinola, M. I., Contreras-Moreira, B., Segura-Salazar, J., Muniz-Rascado, L., Martinez-Flores, I. & other authors (2008). RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res 36, D120-D124.
  • 18
    • 33744780700 scopus 로고    scopus 로고
    • Evolution of transcriptional regulatory networks in microbial genomes
    • Gelfand, M. S. (2006). Evolution of transcriptional regulatory networks in microbial genomes. Curr Opin Struct Biol 16, 420-429.
    • (2006) Curr Opin Struct Biol , vol.16 , pp. 420-429
    • Gelfand, M.S.1
  • 19
    • 20644462362 scopus 로고    scopus 로고
    • Micros for microbes: Non-coding regulatory RNAs in bacteria
    • Gottesman, S. (2005). Micros for microbes: non-coding regulatory RNAs in bacteria. Trends Genet 21, 399-404.
    • (2005) Trends Genet , vol.21 , pp. 399-404
    • Gottesman, S.1
  • 21
    • 0028264505 scopus 로고
    • DNA supercoiling and thermal regulation of unsaturated fatty acid synthesis in Bacillus subtilis
    • Grau, R., Gardiol, D., Glikin, G. C. & de Mendoza, D. (1994). DNA supercoiling and thermal regulation of unsaturated fatty acid synthesis in Bacillus subtilis. Mol Microbiol 11, 933-941.
    • (1994) Mol Microbiol , vol.11 , pp. 933-941
    • Grau, R.1    Gardiol, D.2    Glikin, G.C.3    de Mendoza, D.4
  • 22
    • 0036890022 scopus 로고    scopus 로고
    • Rapid divergence in expression between duplicate genes inferred from microarray data
    • Gu, Z., Nicolae, D., Lu, H. H. & Li, W. H. (2002). Rapid divergence in expression between duplicate genes inferred from microarray data. Trends Genet 18, 609-613.
    • (2002) Trends Genet , vol.18 , pp. 609-613
    • Gu, Z.1    Nicolae, D.2    Lu, H.H.3    Li, W.H.4
  • 23
    • 14144255920 scopus 로고    scopus 로고
    • Rapid evolution of expression and regulatory divergences after yeast gene duplication
    • Gu, X., Zhang, Z. & Huang, W. (2005). Rapid evolution of expression and regulatory divergences after yeast gene duplication. Proc Natl Acad Sci U S A 102, 707-712.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 707-712
    • Gu, X.1    Zhang, Z.2    Huang, W.3
  • 24
    • 33748257975 scopus 로고    scopus 로고
    • Modulating the outer membrane with small RNAs
    • Guillier, M., Gottesman, S. & Storz, G. (2006). Modulating the outer membrane with small RNAs. Genes Dev 20, 2338-2348.
    • (2006) Genes Dev , vol.20 , pp. 2338-2348
    • Guillier, M.1    Gottesman, S.2    Storz, G.3
  • 25
    • 68249084505 scopus 로고    scopus 로고
    • Guo, X., Zhang, Z., Gerstein, M. B. & Zheng, D. (2009). Small RNAs originated from pseudogenes: cis- or trans-acting? PLOS Comput Biol 5, e1000449.
    • Guo, X., Zhang, Z., Gerstein, M. B. & Zheng, D. (2009). Small RNAs originated from pseudogenes: cis- or trans-acting? PLOS Comput Biol 5, e1000449.
  • 26
    • 22144489471 scopus 로고    scopus 로고
    • New insights into regulation of the tryptophan biosynthetic operon in Gram-positive bacteria
    • Gutierrez-Preciado, A., Jensen, R. A., Yanofsky, C. & Merino, E. (2005). New insights into regulation of the tryptophan biosynthetic operon in Gram-positive bacteria. Trends Genet 21, 432-436.
    • (2005) Trends Genet , vol.21 , pp. 432-436
    • Gutierrez-Preciado, A.1    Jensen, R.A.2    Yanofsky, C.3    Merino, E.4
  • 28
    • 0036953237 scopus 로고    scopus 로고
    • DNA topology-mediated control of global gene expression in Escherichia coli
    • Hatfield, G. W. & Benham, C. J. (2002). DNA topology-mediated control of global gene expression in Escherichia coli. Annu Rev Genet 36, 175-203.
    • (2002) Annu Rev Genet , vol.36 , pp. 175-203
    • Hatfield, G.W.1    Benham, C.J.2
  • 29
    • 35848954992 scopus 로고    scopus 로고
    • SigB-dependent general stress response in Bacillus subtilis and related gram-positive bacteria
    • Hecker, M., Pane-Farre, J. & Volker, U. (2007). SigB-dependent general stress response in Bacillus subtilis and related gram-positive bacteria. Annu Rev Microbiol 61, 215-236.
    • (2007) Annu Rev Microbiol , vol.61 , pp. 215-236
    • Hecker, M.1    Pane-Farre, J.2    Volker, U.3
  • 30
    • 0036714331 scopus 로고    scopus 로고
    • S (RpoS) subunit of RNA polymerase
    • table
    • S (RpoS) subunit of RNA polymerase. Microbiol Mol Biol Rev 66, 373-395 (table).
    • (2002) Microbiol Mol Biol Rev , vol.66 , pp. 373-395
    • Hengge-Aronis, R.1
  • 31
    • 0025777765 scopus 로고
    • Bacterial DNA supercoiling and [ATP]/[ADP]. Changes associated with a transition to anaerobic growth
    • Hsieh, L. S., Burger, R. M. & Drlica, K. (1991). Bacterial DNA supercoiling and [ATP]/[ADP]. Changes associated with a transition to anaerobic growth. J Mol Biol 219, 443-450.
    • (1991) J Mol Biol , vol.219 , pp. 443-450
    • Hsieh, L.S.1    Burger, R.M.2    Drlica, K.3
  • 32
    • 0031564639 scopus 로고    scopus 로고
    • Gene organization and transcriptional regulation of the gntRKU operon involved in gluconate uptake and catabolism of Escherichia coli
    • Izu, H., Adachi, O. & Yamada, M. (1997). Gene organization and transcriptional regulation of the gntRKU operon involved in gluconate uptake and catabolism of Escherichia coli. J Mol Biol 267, 778-793.
    • (1997) J Mol Biol , vol.267 , pp. 778-793
    • Izu, H.1    Adachi, O.2    Yamada, M.3
  • 34
    • 25444448797 scopus 로고    scopus 로고
    • Spontaneous evolution of modularity and network motifs
    • Kashtan, N. & Alon, U. (2005). Spontaneous evolution of modularity and network motifs. Proc Natl Acad Sci U S A 102, 13773-13778.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 13773-13778
    • Kashtan, N.1    Alon, U.2
  • 35
    • 0033659766 scopus 로고    scopus 로고
    • Regulation of sigma factor activity during Bacillus subtilis development
    • Kroos, L. & Yu, Y. T. (2000). Regulation of sigma factor activity during Bacillus subtilis development. Curr Opin Microbiol 3, 553-560.
    • (2000) Curr Opin Microbiol , vol.3 , pp. 553-560
    • Kroos, L.1    Yu, Y.T.2
  • 36
    • 26444488575 scopus 로고    scopus 로고
    • Expression divergence between duplicate genes
    • Li, W. H., Yang, J. & Gu, X. (2005). Expression divergence between duplicate genes. Trends Genet 21, 602-607.
    • (2005) Trends Genet , vol.21 , pp. 602-607
    • Li, W.H.1    Yang, J.2    Gu, X.3
  • 38
    • 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. (2004). Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 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
  • 39
    • 0034634395 scopus 로고    scopus 로고
    • The evolutionary fate and consequences of duplicate genes
    • Lynch, M. & Conery, J. S. (2000). The evolutionary fate and consequences of duplicate genes. Science 290, 1151-1155.
    • (2000) Science , vol.290 , pp. 1151-1155
    • Lynch, M.1    Conery, J.S.2
  • 40
    • 0242386460 scopus 로고    scopus 로고
    • Identifying global regulators in transcriptional regulatory networks in bacteria
    • Martinez-Antonio, A. & Collado-Vides, J. (2003). Identifying global regulators in transcriptional regulatory networks in bacteria. Curr Opin Microbiol 6, 482-489.
    • (2003) Curr Opin Microbiol , vol.6 , pp. 482-489
    • Martinez-Antonio, A.1    Collado-Vides, J.2
  • 41
    • 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
  • 43
    • 0000451424 scopus 로고
    • Covalent modification of the glnG product, NRI, by the glnL product, NRII, regulates the transcription of the glnALG operon in Escherichia coli
    • Ninfa, A. J. & Magasanik, B. (1986). Covalent modification of the glnG product, NRI, by the glnL product, NRII, regulates the transcription of the glnALG operon in Escherichia coli. Proc Natl Acad Sci U S A 83, 5909-5913.
    • (1986) Proc Natl Acad Sci U S A , vol.83 , pp. 5909-5913
    • Ninfa, A.J.1    Magasanik, B.2
  • 44
    • 34347374095 scopus 로고    scopus 로고
    • Genomic SELEX search for target promoters under the control of the PhoQP-RstBA signal relay cascade
    • Ogasawara, H., Hasegawa, A., Kanda, E., Miki, T., Yamamoto, K. & Ishihama, A. (2007). Genomic SELEX search for target promoters under the control of the PhoQP-RstBA signal relay cascade. J Bacteriol 189, 4791-4799.
    • (2007) J Bacteriol , vol.189 , pp. 4791-4799
    • Ogasawara, H.1    Hasegawa, A.2    Kanda, E.3    Miki, T.4    Yamamoto, K.5    Ishihama, A.6
  • 46
    • 0029992419 scopus 로고    scopus 로고
    • From acids to osmZ: Multiple factors influence synthesis of the OmpF and OmpC porins in Escherichia coli
    • Pratt, L. A., Hsing, W., Gibson, K. E. & Silhavy, T. J. (1996). From acids to osmZ: multiple factors influence synthesis of the OmpF and OmpC porins in Escherichia coli. Mol Microbiol 20, 911-917.
    • (1996) Mol Microbiol , vol.20 , pp. 911-917
    • Pratt, L.A.1    Hsing, W.2    Gibson, K.E.3    Silhavy, T.J.4
  • 48
    • 33845660440 scopus 로고    scopus 로고
    • Keeping signals straight in transcription regulation: Specificity determinants for the interaction of a family of conserved bacterial RNA-protein couples
    • Schilling, O., Herzberg, C., Hertrich, T., Vorsmann, H., Jessen, D., Hubner, S., Titgemeyer, F. & Stulke, J. (2006). Keeping signals straight in transcription regulation: specificity determinants for the interaction of a family of conserved bacterial RNA-protein couples. Nucleic Acids Res 34, 6102-6115.
    • (2006) Nucleic Acids Res , vol.34 , pp. 6102-6115
    • Schilling, O.1    Herzberg, C.2    Hertrich, T.3    Vorsmann, H.4    Jessen, D.5    Hubner, S.6    Titgemeyer, F.7    Stulke, J.8
  • 49
    • 0036578795 scopus 로고    scopus 로고
    • Network motifs in the transcriptional regulation network of Escherichia coli
    • Shen-Orr, S. S., Milo, R., Mangan, S. & Alon, U. (2002). Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 31, 64-68.
    • (2002) Nat Genet , vol.31 , pp. 64-68
    • Shen-Orr, S.S.1    Milo, R.2    Mangan, S.3    Alon, U.4
  • 50
    • 38549162091 scopus 로고    scopus 로고
    • DBTBS: A database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information
    • 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, D93-D96.
    • (2008) Nucleic Acids Res , vol.36
    • Sierro, N.1    Makita, Y.2    de Hoon, M.3    Nakai, K.4
  • 51
    • 2442537233 scopus 로고    scopus 로고
    • Gene regulatory network growth by duplication
    • Teichmann, S. A. & Babu, M. M. (2004). Gene regulatory network growth by duplication. Nat Genet 36, 492-496.
    • (2004) Nat Genet , vol.36 , pp. 492-496
    • Teichmann, S.A.1    Babu, M.M.2
  • 53
    • 0026576546 scopus 로고
    • Is cross regulation by phosphorylation of two-component response regulator proteins important in bacteria?
    • Wanner, B. L. (1992). Is cross regulation by phosphorylation of two-component response regulator proteins important in bacteria? J Bacteriol 174, 2053-2058.
    • (1992) J Bacteriol , vol.174 , pp. 2053-2058
    • Wanner, B.L.1
  • 54
    • 0034065133 scopus 로고    scopus 로고
    • Escherichia coli response to hydrogen peroxide: A role for DNA supercoiling, topoisomerase I and Fis
    • Weinstein-Fischer, D., Elgrably-Weiss, M. & Altuvia, S. (2000). Escherichia coli response to hydrogen peroxide: a role for DNA supercoiling, topoisomerase I and Fis. Mol Microbiol 35, 1413-1420.
    • (2000) Mol Microbiol , vol.35 , pp. 1413-1420
    • Weinstein-Fischer, D.1    Elgrably-Weiss, M.2    Altuvia, S.3
  • 55
    • 27144527479 scopus 로고    scopus 로고
    • Regulation of bacterial gene expression by riboswitches
    • Winkler, W. C. & Breaker, R. R. (2005). Regulation of bacterial gene expression by riboswitches. Annu Rev Microbiol 59, 487-517.
    • (2005) Annu Rev Microbiol , vol.59 , pp. 487-517
    • Winkler, W.C.1    Breaker, R.R.2
  • 56
    • 16244398023 scopus 로고    scopus 로고
    • Transcriptional response of Escherichia coli to external copper
    • Yamamoto, K. & Ishihama, A. (2005a). Transcriptional response of Escherichia coli to external copper. Mol Microbiol 56, 215-227.
    • (2005) Mol Microbiol , vol.56 , pp. 215-227
    • Yamamoto, K.1    Ishihama, A.2
  • 57
    • 24944583149 scopus 로고    scopus 로고
    • Transcriptional response of Escherichia coli to external zinc
    • Yamamoto, K. & Ishihama, A. (2005b). Transcriptional response of Escherichia coli to external zinc. J Bacteriol 187, 6333-6340.
    • (2005) J Bacteriol , vol.187 , pp. 6333-6340
    • Yamamoto, K.1    Ishihama, A.2
  • 59
    • 0032584099 scopus 로고    scopus 로고
    • Positive Darwinian selection after gene duplication in primate ribonuclease genes
    • Zhang, J., Rosenberg, H. F. & Nei, M. (1998). Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc Natl Acad Sci U S A 95, 3708-3713.
    • (1998) Proc Natl Acad Sci U S A , vol.95 , pp. 3708-3713
    • Zhang, J.1    Rosenberg, H.F.2    Nei, M.3


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