메뉴 건너뛰기




Volumn 2, Issue 12, 2006, Pages 1552-1560

Transcriptional regulation by competing transcription factor modules

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; COMPLEX NETWORKS; ENZYME ACTIVITY; NETWORK ARCHITECTURE; TRANSCRIPTION;

EID: 33846002036     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0020164     Document Type: Article
Times cited : (99)

References (55)
  • 2
    • 17044396348 scopus 로고    scopus 로고
    • Gene regulatory networks special feature: Logic functions of the genomic cis-regulatory code
    • doi:10.1073/pnas.0409624102
    • Istrail S, Davidson EH (2005) Gene regulatory networks special feature: Logic functions of the genomic cis-regulatory code. Proc Natl Acad Sci U S A 102: 4954-4959. doi:10.1073/pnas.0409624102
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 4954-4959
    • Istrail, S.1    Davidson, E.H.2
  • 3
    • 0032549745 scopus 로고    scopus 로고
    • Genomic cis-regulatory logic: Experimental and computational analysis of a sea urchin gene
    • doi:10.1126/science.279.5358.1896
    • Yuh CH, Bolouri H, Davidson EH (1998) Genomic cis-regulatory logic: Experimental and computational analysis of a sea urchin gene. Science 279: 1896-1902. doi:10.1126/science.279.5358.1896
    • (1998) Science , vol.279 , pp. 1896-1902
    • Yuh, C.H.1    Bolouri, H.2    Davidson, E.H.3
  • 4
    • 54249116230 scopus 로고
    • Genetic regulatory mechanisms in the synthesis of proteins
    • Jacob F, Monod J (1961) Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 3: 318-356.
    • (1961) J Mol Biol , vol.3 , pp. 318-356
    • Jacob, F.1    Monod, J.2
  • 6
    • 0004211673 scopus 로고    scopus 로고
    • New York: Cold Spring Harbor Laboratory Press. 208 p
    • Ptashne M, Gann A (2002) Genes and signals. New York: Cold Spring Harbor Laboratory Press. 208 p.
    • (2002) Genes and signals
    • Ptashne, M.1    Gann, A.2
  • 9
    • 0032034820 scopus 로고    scopus 로고
    • Some repressors of bacterial transcription
    • Müller-Hill B (1998) Some repressors of bacterial transcription. Curr Opin Micobiol 1: 145-151.
    • (1998) Curr Opin Micobiol , vol.1 , pp. 145-151
    • Müller-Hill, B.1
  • 10
    • 0347635508 scopus 로고    scopus 로고
    • Design of genetic networks with specified functions by evolution in silico
    • Francois P, Hakim Y (2004) Design of genetic networks with specified functions by evolution in silico. Proc Natl Acad Sci U S A 101: 580-585.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 580-585
    • Francois, P.1    Hakim, Y.2
  • 12
    • 0022429106 scopus 로고
    • The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation
    • Shea MA, Ackers GK (1985) The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation. J Mol Biol 181: 211-230.
    • (1985) J Mol Biol , vol.181 , pp. 211-230
    • Shea, M.A.1    Ackers, G.K.2
  • 15
    • 0027230594 scopus 로고    scopus 로고
    • Lisser S, Margalit H (1993) Compilation of E. coli mRNA promoter sequences. NAR 21: 1507-1516.
    • Lisser S, Margalit H (1993) Compilation of E. coli mRNA promoter sequences. NAR 21: 1507-1516.
  • 16
    • 0023147228 scopus 로고
    • Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters
    • Berg OG, von Hippel PH (1987) Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J Mol Biol 193: 723-750.
    • (1987) J Mol Biol , vol.193 , pp. 723-750
    • Berg, O.G.1    von Hippel, P.H.2
  • 17
    • 0023774773 scopus 로고
    • Selection of DNA binding sites by regulatory proteins. Functional specificity and pseudosite competition
    • Berg OG (1988) Selection of DNA binding sites by regulatory proteins. Functional specificity and pseudosite competition. J Biomol Struc Dynam 6: 275-297.
    • (1988) J Biomol Struc Dynam , vol.6 , pp. 275-297
    • Berg, O.G.1
  • 18
    • 0023147228 scopus 로고
    • Selection of DNA binding sites by regulatory proteins ii. The binding specificity of Cyclic AMP receptor protein to recognition sites
    • Berg OG, von Hippel PH (1987) Selection of DNA binding sites by regulatory proteins ii. The binding specificity of Cyclic AMP receptor protein to recognition sites. J Mol Biol 193: 723-750.
    • (1987) J Mol Biol , vol.193 , pp. 723-750
    • Berg, O.G.1    von Hippel, P.H.2
  • 19
    • 0242574990 scopus 로고    scopus 로고
    • A biophysical approach to transcription factor binding site discovery
    • Djordjevic M, Sengupta AM, Shraiman BI (2003) A biophysical approach to transcription factor binding site discovery. Genome Res 13: 2381-2390.
    • (2003) Genome Res , vol.13 , pp. 2381-2390
    • Djordjevic, M.1    Sengupta, A.M.2    Shraiman, B.I.3
  • 21
    • 0032032780 scopus 로고    scopus 로고
    • Specificity, free energy and information content in protein-DNA interactions
    • Stormo GD, Fields DS (1998) Specificity, free energy and information content in protein-DNA interactions. Trends Biochem Sci 23: 109-113.
    • (1998) Trends Biochem Sci , vol.23 , pp. 109-113
    • Stormo, G.D.1    Fields, D.S.2
  • 22
    • 0036787402 scopus 로고    scopus 로고
    • On the selection and evolution of regulatory DNA motifs
    • Gerland U, Hwa T (2002) On the selection and evolution of regulatory DNA motifs. J Mol Evol 55: 386-400.
    • (2002) J Mol Evol , vol.55 , pp. 386-400
    • Gerland, U.1    Hwa, T.2
  • 23
    • 0037126028 scopus 로고    scopus 로고
    • Physical constraints and functional characteristics of transcription factor-DNA interaction
    • Gerland U, Moroz DJ, Hwa T (2002) Physical constraints and functional characteristics of transcription factor-DNA interaction. Proc Natl Acad Sci U S A 99: 12015-12020.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 12015-12020
    • Gerland, U.1    Moroz, D.J.2    Hwa, T.3
  • 24
    • 0028061282 scopus 로고
    • Promoter structure, promoter recognition, and transcription activation in prokaryotes
    • Busby S, Ebright RH (1994) Promoter structure, promoter recognition, and transcription activation in prokaryotes. Cell 79: 743-746.
    • (1994) Cell , vol.79 , pp. 743-746
    • Busby, S.1    Ebright, R.H.2
  • 25
    • 0034597003 scopus 로고    scopus 로고
    • Synergistic transcription activation: A dual role for CRP in the activation of an Escherichia coli promoter depending on MalT and CRP
    • Richet E (2000) Synergistic transcription activation: A dual role for CRP in the activation of an Escherichia coli promoter depending on MalT and CRP. EMBO J 19: 5222-5232.
    • (2000) EMBO J , vol.19 , pp. 5222-5232
    • Richet, E.1
  • 26
    • 0037126615 scopus 로고    scopus 로고
    • A simple mechanism for co-dependence on two activators at an Escherichia coli promoter
    • Wade J, Belyaeva T, Hyde E, Busby S (2001) A simple mechanism for co-dependence on two activators at an Escherichia coli promoter. EMBO J 20: 7160-7167.
    • (2001) EMBO J , vol.20 , pp. 7160-7167
    • Wade, J.1    Belyaeva, T.2    Hyde, E.3    Busby, S.4
  • 27
    • 33744821614 scopus 로고    scopus 로고
    • Transcript analysis reveals an extended regulon and the importance of protein-protein co-operativity for the Escherichia coli methionine repressor
    • Marincs F, Manfield IW, Stead JA, McDowall KJ, Stockley PG (2006) Transcript analysis reveals an extended regulon and the importance of protein-protein co-operativity for the Escherichia coli methionine repressor. Biochem J 396: 227-234.
    • (2006) Biochem J , vol.396 , pp. 227-234
    • Marincs, F.1    Manfield, I.W.2    Stead, J.A.3    McDowall, K.J.4    Stockley, P.G.5
  • 28
    • 0027461910 scopus 로고
    • Lrp, a global regulatory protein of Escherichia coli, binds co-operatively to multiple sites and activates transcription of ilvih
    • Wang Q, Calvo JM (1993) Lrp, a global regulatory protein of Escherichia coli, binds co-operatively to multiple sites and activates transcription of ilvih. J Mol Biol 229: 306-318.
    • (1993) J Mol Biol , vol.229 , pp. 306-318
    • Wang, Q.1    Calvo, J.M.2
  • 29
    • 0034637480 scopus 로고    scopus 로고
    • Evidence of an unusually long operator for the Fur repressor in the aerobactin promoter of Escherichia coli
    • Escolar L, Perez-Martin J, de Lorenzo V (2000) Evidence of an unusually long operator for the Fur repressor in the aerobactin promoter of Escherichia coli. J Biol Chem 275: 24709-24714.
    • (2000) J Biol Chem , vol.275 , pp. 24709-24714
    • Escolar, L.1    Perez-Martin, J.2    de Lorenzo, V.3
  • 30
    • 0029858049 scopus 로고    scopus 로고
    • Transcriptional control mediated by the ArcA two-component response regulator protein of Escherichia coli: Characterization of DNA binding at target promoters
    • Lynch A, Lin E (1996) Transcriptional control mediated by the ArcA two-component response regulator protein of Escherichia coli: Characterization of DNA binding at target promoters. J Bacteriol 178: 6238-6249.
    • (1996) J Bacteriol , vol.178 , pp. 6238-6249
    • Lynch, A.1    Lin, E.2
  • 31
    • 0030609130 scopus 로고    scopus 로고
    • Role of multiple ArcA recognition sites in anaerobic regulation of succinate dehydrogenase (sdhCDAB) gene expression in Escherichia coli
    • Shen J, Gunsalus R (1997) Role of multiple ArcA recognition sites in anaerobic regulation of succinate dehydrogenase (sdhCDAB) gene expression in Escherichia coli. Mol Microbiol 26: 223-236.
    • (1997) Mol Microbiol , vol.26 , pp. 223-236
    • Shen, J.1    Gunsalus, R.2
  • 32
    • 13444283630 scopus 로고    scopus 로고
    • Interaction network containing conserved and essential protein complexes in Escherichia coli
    • Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433: 531-537.
    • (2005) Nature , vol.433 , pp. 531-537
    • Butland, G.1    Peregrin-Alvarez, J.M.2    Li, J.3    Yang, W.4    Yang, X.5
  • 33
    • 33845503073 scopus 로고    scopus 로고
    • Adaptive evolution of transcription factor binding sites. BCM
    • Berg J, Willmann S, Lässig M (2004) Adaptive evolution of transcription factor binding sites. BCM Evol Biol 4: 42.
    • (2004) Evol Biol , vol.4 , pp. 42
    • Berg, J.1    Willmann, S.2    Lässig, M.3
  • 36
    • 0027446708 scopus 로고
    • Molecular biology of the LysR family of transcriptional regulators
    • Schell MA (1993) Molecular biology of the LysR family of transcriptional regulators. Ann Rev Microbiol 47: 597-626.
    • (1993) Ann Rev Microbiol , vol.47 , pp. 597-626
    • Schell, M.A.1
  • 37
    • 0029080491 scopus 로고
    • DNA binding sites of the LysR-type regulator GcvA in the gcv and gcvA control regions of Escherichia coli
    • Wilson R, Urbanowski M, Stauffer G (1995) DNA binding sites of the LysR-type regulator GcvA in the gcv and gcvA control regions of Escherichia coli. J Bacteriol 177: 4940-4946.
    • (1995) J Bacteriol , vol.177 , pp. 4940-4946
    • Wilson, R.1    Urbanowski, M.2    Stauffer, G.3
  • 38
    • 0028109899 scopus 로고
    • Functional analysis of the Escherichia coli K-12 cyn operon transcriptional regulation
    • Lamblin A, Fuchs J (1994) Functional analysis of the Escherichia coli K-12 cyn operon transcriptional regulation. J Bacteriol 176: 6613-6622.
    • (1994) J Bacteriol , vol.176 , pp. 6613-6622
    • Lamblin, A.1    Fuchs, J.2
  • 39
    • 0035072749 scopus 로고    scopus 로고
    • Mechanisms of transcriptional repression
    • Rojo F (2001) Mechanisms of transcriptional repression. Curr Opin Micobiol 4: 145-151.
    • (2001) Curr Opin Micobiol , vol.4 , pp. 145-151
    • Rojo, F.1
  • 40
    • 0040075183 scopus 로고    scopus 로고
    • Occlusion of RNA polymerase by oligomerization of DnaA protein over the dnaA promoter of Escherichia coli
    • Lee YS, Hwang DS (1997) Occlusion of RNA polymerase by oligomerization of DnaA protein over the dnaA promoter of Escherichia coli. J Biol Chem 272: 83-88.
    • (1997) J Biol Chem , vol.272 , pp. 83-88
    • Lee, Y.S.1    Hwang, D.S.2
  • 41
    • 0012099926 scopus 로고    scopus 로고
    • Studies of the Escherichia coli Trp repressor binding to its five operators and to variant operator sequences
    • Jeeves M, Evans PD, Parslow RA, Jaseja M, Hyde EI (1999) Studies of the Escherichia coli Trp repressor binding to its five operators and to variant operator sequences. Eur J Biochem 265: 919-928.
    • (1999) Eur J Biochem , vol.265 , pp. 919-928
    • Jeeves, M.1    Evans, P.D.2    Parslow, R.A.3    Jaseja, M.4    Hyde, E.I.5
  • 42
    • 0029010741 scopus 로고
    • aldB, an RpoS-dependent gene in Escherichia coli encoding an aldehyde dehydrogenase that is repressed by Fis and activated by Crp
    • Xu J, Johnson R (1995) aldB, an RpoS-dependent gene in Escherichia coli encoding an aldehyde dehydrogenase that is repressed by Fis and activated by Crp. J Bacteriol 177: 3166-3175.
    • (1995) J Bacteriol , vol.177 , pp. 3166-3175
    • Xu, J.1    Johnson, R.2
  • 43
    • 0027983641 scopus 로고
    • CRP induces the repositioning of MalT at the Escherichia coli malKp promoter primarily through DNA bending
    • Richet E, Sogaard-Andersen L (1994) CRP induces the repositioning of MalT at the Escherichia coli malKp promoter primarily through DNA bending. EMBO J 13: 4558-4567.
    • (1994) EMBO J , vol.13 , pp. 4558-4567
    • Richet, E.1    Sogaard-Andersen, L.2
  • 44
    • 0029865234 scopus 로고    scopus 로고
    • Analysis of CRP-CytR interactions at the Escherichia coli udp promoter
    • Brikun I, Suziedelis K, Stemmann O, Zhong R, Alikhanian L, et al. (1996) Analysis of CRP-CytR interactions at the Escherichia coli udp promoter. J Bacteriol 178: 1614-1622.
    • (1996) J Bacteriol , vol.178 , pp. 1614-1622
    • Brikun, I.1    Suziedelis, K.2    Stemmann, O.3    Zhong, R.4    Alikhanian, L.5
  • 45
    • 0028828823 scopus 로고
    • Gene-regulatory modules in Escherichia coli: Nucleoprotein complexes formed by cAMP-CRP and CytR at the nupG promoter
    • Pedersen H, Dall J, Dandanell G, Valentin-Hansen P (1995) Gene-regulatory modules in Escherichia coli: Nucleoprotein complexes formed by cAMP-CRP and CytR at the nupG promoter. Mol Microbiol 17: 843-853.
    • (1995) Mol Microbiol , vol.17 , pp. 843-853
    • Pedersen, H.1    Dall, J.2    Dandanell, G.3    Valentin-Hansen, P.4
  • 46
    • 0026000281 scopus 로고
    • The cyclic AMP (cAMP)-cAMP receptor protein complex functions both as an activator and as a corepressor at the tsx-p2 promoter of Escherichia coli k-12
    • Gerlach P, Sogaard-Andersen L, Pedersen H, Martinussen J, Valentin-Hansen P, et al. (1991) The cyclic AMP (cAMP)-cAMP receptor protein complex functions both as an activator and as a corepressor at the tsx-p2 promoter of Escherichia coli k-12. J Bacteriol 173: 5419-5430.
    • (1991) J Bacteriol , vol.173 , pp. 5419-5430
    • Gerlach, P.1    Sogaard-Andersen, L.2    Pedersen, H.3    Martinussen, J.4    Valentin-Hansen, P.5
  • 47
    • 0035476678 scopus 로고    scopus 로고
    • Repression of deoP2 in Escherichia coli by CytR: Conversion of a transcription activator into a repressor
    • Shin M, Kang S, Hyun S, Fujita N, Ishihama A, et al. (2001) Repression of deoP2 in Escherichia coli by CytR: Conversion of a transcription activator into a repressor. EMBO J 20: 5392-5399.
    • (2001) EMBO J , vol.20 , pp. 5392-5399
    • Shin, M.1    Kang, S.2    Hyun, S.3    Fujita, N.4    Ishihama, A.5
  • 48
    • 0036300938 scopus 로고    scopus 로고
    • Thermodynamics of E. coli cytidine repressor interactions with DNA: Distinct modes of binding to different operators suggests a role in differential gene regulation
    • Tretyachenko-Ladokhina V, Ross J, Senear D (2002) Thermodynamics of E. coli cytidine repressor interactions with DNA: Distinct modes of binding to different operators suggests a role in differential gene regulation. J Mol Biol 316: 531-546.
    • (2002) J Mol Biol , vol.316 , pp. 531-546
    • Tretyachenko-Ladokhina, V.1    Ross, J.2    Senear, D.3
  • 49
    • 0032956969 scopus 로고    scopus 로고
    • Dissection of a surface-exposed portion of the cAMP-CRP complex that mediates transcription activation and repression
    • Meibom K, Sogaard-Andersen L, Mironov A, Valentin-Hansen P (1999) Dissection of a surface-exposed portion of the cAMP-CRP complex that mediates transcription activation and repression. Mol Microbiol 32: 497-504.
    • (1999) Mol Microbiol , vol.32 , pp. 497-504
    • Meibom, K.1    Sogaard-Andersen, L.2    Mironov, A.3    Valentin-Hansen, P.4
  • 50
    • 27444437323 scopus 로고    scopus 로고
    • LRP and H-NS - Cooperative partners for transcription regulation at Escherichia coli rrna promoters
    • Pul U, Wurm R, Lux B, Meltzer M, Menzel A, et al. (2005) LRP and H-NS - Cooperative partners for transcription regulation at Escherichia coli rrna promoters. Mol Microbiol 58: 864-876.
    • (2005) Mol Microbiol , vol.58 , pp. 864-876
    • Pul, U.1    Wurm, R.2    Lux, B.3    Meltzer, M.4    Menzel, A.5
  • 51
    • 0004210529 scopus 로고    scopus 로고
    • 7th edition. Sunderland Massachusetts, Sinauer
    • Gilbert SF (2003) Developmental biology. 7th edition. Sunderland (Massachusetts): Sinauer.
    • (2003) Developmental biology
    • Gilbert, S.F.1
  • 52
    • 0036578795 scopus 로고    scopus 로고
    • Network motifs in the transcriptional regulation network of Escherichia coli
    • Shen-Orr SS, 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
  • 54
    • 0037303198 scopus 로고    scopus 로고
    • Functional determinants of transcription factors in Escherichia coli: Protein families and binding sites
    • Madan Babu M, Teichmann SA (2003) Functional determinants of transcription factors in Escherichia coli: Protein families and binding sites. Trends Genet 19: 75-79.
    • (2003) Trends Genet , vol.19 , pp. 75-79
    • Madan Babu, M.1    Teichmann, S.A.2
  • 55
    • 0343963178 scopus 로고    scopus 로고
    • The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12
    • Pérez-Rueda E, Collado-Vides J (2003) The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12. Nucl Acids Res 28: 1838-1847.
    • (2003) Nucl Acids Res , vol.28 , pp. 1838-1847
    • Pérez-Rueda, E.1    Collado-Vides, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.