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Volumn 8, Issue 3, 2012, Pages

Probing the informational and regulatory plasticity of a transcription factor DNA-binding domain

Author keywords

[No Author keywords available]

Indexed keywords

DNA; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR MARA; UNCLASSIFIED DRUG; DNA BINDING PROTEIN; ESCHERICHIA COLI PROTEIN; HELIX LOOP HELIX PROTEIN; MARA PROTEIN, E COLI;

EID: 84859241581     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1002614     Document Type: Article
Times cited : (22)

References (54)
  • 1
    • 0023042012 scopus 로고
    • Information content of binding sites on nucleotide sequences
    • Schneider TD, Stormo GD, Gold L, Ehrenfeucht A, (1986) Information content of binding sites on nucleotide sequences. J Mol Biol 188: 415-431.
    • (1986) J Mol Biol , vol.188 , pp. 415-431
    • Schneider, T.D.1    Stormo, G.D.2    Gold, L.3    Ehrenfeucht, A.4
  • 2
    • 33749451228 scopus 로고    scopus 로고
    • Coding limits on the number of transcription factors
    • Itzkovitz S, Tlusty T, Alon U, (2006) Coding limits on the number of transcription factors. BMC genomics 7: 239.
    • (2006) BMC Genomics , vol.7 , pp. 239
    • Itzkovitz, S.1    Tlusty, T.2    Alon, U.3
  • 3
    • 0034923498 scopus 로고    scopus 로고
    • Design and selection of novel Cys2His2 zinc finger proteins
    • Pabo CO, Peisach E, Grant RA, (2001) Design and selection of novel Cys2His2 zinc finger proteins. Annu Rev Biochem 70: 313-340.
    • (2001) Annu Rev Biochem , vol.70 , pp. 313-340
    • Pabo, C.O.1    Peisach, E.2    Grant, R.A.3
  • 4
    • 0036977044 scopus 로고    scopus 로고
    • Probabilistic code for DNA recognition by proteins of the EGR family
    • Benos PV, Lapedes AS, Stormo GD, (2002) Probabilistic code for DNA recognition by proteins of the EGR family. J Mol Biol 323: 701-727.
    • (2002) J Mol Biol , vol.323 , pp. 701-727
    • Benos, P.V.1    Lapedes, A.S.2    Stormo, G.D.3
  • 5
    • 73249134379 scopus 로고    scopus 로고
    • Experimental determination of the evolvability of a transcription factor
    • Maerkl S, Quake S, (2009) Experimental determination of the evolvability of a transcription factor. Proceedings of the National Academy of Sciences 106: 18650.
    • (2009) Proceedings of the National Academy of Sciences , vol.106 , pp. 18650
    • Maerkl, S.1    Quake, S.2
  • 6
    • 0034682882 scopus 로고    scopus 로고
    • Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition?
    • Pabo CO, Nekludova L, (2000) Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition? J Mol Biol 301: 597-624.
    • (2000) J Mol Biol , vol.301 , pp. 597-624
    • Pabo, C.O.1    Nekludova, L.2
  • 7
    • 0141630791 scopus 로고
    • On the specificity of DNA-protein interactions
    • von Hippel PH, Berg OG, (1986) On the specificity of DNA-protein interactions. Proc Natl Acad Sci USA 83: 1608-1612.
    • (1986) Proc Natl Acad Sci USA , vol.83 , pp. 1608-1612
    • von Hippel, P.H.1    Berg, O.G.2
  • 8
    • 33846467150 scopus 로고    scopus 로고
    • A systems approach to measuring the binding energy landscapes of transcription factors
    • Maerkl SJ, Quake SR, (2007) A systems approach to measuring the binding energy landscapes of transcription factors. Science 315: 233-237.
    • (2007) Science , vol.315 , pp. 233-237
    • Maerkl, S.J.1    Quake, S.R.2
  • 9
    • 34548755108 scopus 로고    scopus 로고
    • Correlation between binding rate constants and individual information of E. coli Fis binding sites
    • Shultzaberger RK, Roberts LR, Lyakhov IG, Sidorov IA, Stephen AG, et al. (2007) Correlation between binding rate constants and individual information of E. coli Fis binding sites. Nucleic Acids Res 35: 5275-5283.
    • (2007) Nucleic Acids Res , vol.35 , pp. 5275-5283
    • Shultzaberger, R.K.1    Roberts, L.R.2    Lyakhov, I.G.3    Sidorov, I.A.4    Stephen, A.G.5
  • 10
    • 84856043672 scopus 로고
    • A Mathematical Theory of Communication
    • Shannon CE, (1948) A Mathematical Theory of Communication. Bell System Tech J 27: 379-423 623-656.
    • (1948) Bell System Tech J , vol.27 , pp. 379-423
    • Shannon, C.E.1
  • 11
    • 0034661690 scopus 로고    scopus 로고
    • Evolution of biological information
    • Schneider TD, (2000) Evolution of biological information. Nucleic Acids Res 28: 2794-2799.
    • (2000) Nucleic Acids Res , vol.28 , pp. 2794-2799
    • Schneider, T.D.1
  • 13
    • 70349961774 scopus 로고    scopus 로고
    • Different gene regulation strategies revealed by analysis of binding motifs
    • Wunderlich Z, Mirny L, (2009) Different gene regulation strategies revealed by analysis of binding motifs. Trends in genetics 25: 434-440.
    • (2009) Trends in Genetics , vol.25 , pp. 434-440
    • Wunderlich, Z.1    Mirny, L.2
  • 14
    • 43149085822 scopus 로고    scopus 로고
    • Determining physical constraints in transcriptional initiation complexes using DNA sequence analysis
    • doi:10.1371/journal.pone.0001199
    • Shultzaberger RK, Chiang DY, Moses AM, Eisen MB, (2007) Determining physical constraints in transcriptional initiation complexes using DNA sequence analysis. PLoS ONE 2: e1199 doi:10.1371/journal.pone.0001199.
    • (2007) PLoS ONE , vol.2
    • Shultzaberger, R.K.1    Chiang, D.Y.2    Moses, A.M.3    Eisen, M.B.4
  • 15
    • 0034667792 scopus 로고    scopus 로고
    • Orchestrated response: a symphony of transcription factors for gene control
    • Lemon B, Tjian R, (2000) Orchestrated response: a symphony of transcription factors for gene control. Genes & development 14: 2551-2569.
    • (2000) Genes & Development , vol.14 , pp. 2551-2569
    • Lemon, B.1    Tjian, R.2
  • 16
    • 0021891874 scopus 로고
    • Mechanism and control of transcription initiation in prokaryotes
    • McClure WR, (1985) Mechanism and control of transcription initiation in prokaryotes. Annu Rev Biochem 54: 171-204.
    • (1985) Annu Rev Biochem , vol.54 , pp. 171-204
    • McClure, W.R.1
  • 19
    • 77957357763 scopus 로고    scopus 로고
    • The Fitness Landscapes of cis-Acting Binding Sites in Different Promoter and Environmental Contexts
    • doi:10.1371/journal.pgen.1001042
    • Shultzaberger R, Malashock D, Kirsch J, Eisen M, (2010) The Fitness Landscapes of cis-Acting Binding Sites in Different Promoter and Environmental Contexts. PLoS Genet 6: e1001042 doi:10.1371/journal.pgen.1001042.
    • (2010) PLoS Genet , vol.6
    • Shultzaberger, R.1    Malashock, D.2    Kirsch, J.3    Eisen, M.4
  • 20
    • 50449102853 scopus 로고    scopus 로고
    • Energy-dependent fitness: A quantitative model for the evolution of yeast transcription factor binding sites
    • Mustonen V, Kinney J, Callan C, Lassig M, (2008) Energy-dependent fitness: A quantitative model for the evolution of yeast transcription factor binding sites. Proceedings of the National Academy of Sciences 105: 12376.
    • (2008) Proceedings of the National Academy of Sciences , vol.105 , pp. 12376
    • Mustonen, V.1    Kinney, J.2    Callan, C.3    Lassig, M.4
  • 21
    • 23144432213 scopus 로고    scopus 로고
    • Optimality and evolutionary tuning of the expression level of a protein
    • Dekel E, Alon U, (2005) Optimality and evolutionary tuning of the expression level of a protein. Nature 436: 588-592.
    • (2005) Nature , vol.436 , pp. 588-592
    • Dekel, E.1    Alon, U.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. Journal of molecular evolution 55: 386-400.
    • (2002) Journal of Molecular Evolution , vol.55 , pp. 386-400
    • Gerland, U.1    Hwa, T.2
  • 23
  • 24
    • 0032746803 scopus 로고    scopus 로고
    • Structural requirements for marbox function in transcriptional activation of mar/sox/rob regulon promoters in Escherichia coli: sequence, orientation and spatial relationship to the core promoter
    • Martin RG, Gillette WK, Rhee S, Rosner JL, (1999) Structural requirements for marbox function in transcriptional activation of mar/sox/rob regulon promoters in Escherichia coli: sequence, orientation and spatial relationship to the core promoter. Mol Microbiol 34: 431-441.
    • (1999) Mol Microbiol , vol.34 , pp. 431-441
    • Martin, R.G.1    Gillette, W.K.2    Rhee, S.3    Rosner, J.L.4
  • 25
    • 0036016825 scopus 로고    scopus 로고
    • Genomics of the marA/soxS/rob regulon of Escherichia coli: identification of directly activated promoters by application of molecular genetics and informatics to microarray data
    • Martin RG, Rosner JL, (2002) Genomics of the marA/soxS/rob regulon of Escherichia coli: identification of directly activated promoters by application of molecular genetics and informatics to microarray data. Mol Microbiol 44: 1611-1624.
    • (2002) Mol Microbiol , vol.44 , pp. 1611-1624
    • Martin, R.G.1    Rosner, J.L.2
  • 26
    • 1542335499 scopus 로고    scopus 로고
    • The Escherichia coli transcriptional regulator MarA directly represses transcription of purA and hdeA
    • Schneiders T, Barbosa TM, McMurry LM, Levy SB, (2004) The Escherichia coli transcriptional regulator MarA directly represses transcription of purA and hdeA. J Biol Chem 279: 9037-9042.
    • (2004) J Biol Chem , vol.279 , pp. 9037-9042
    • Schneiders, T.1    Barbosa, T.M.2    McMurry, L.M.3    Levy, S.B.4
  • 27
    • 0032844440 scopus 로고    scopus 로고
    • The mar regulon: multiple resistance to antibiotics and other toxic chemicals
    • Alekshun M, Levy S, (1999) The mar regulon: multiple resistance to antibiotics and other toxic chemicals. Trends in Microbiology 7: 410-413.
    • (1999) Trends in Microbiology , vol.7 , pp. 410-413
    • Alekshun, M.1    Levy, S.2
  • 28
    • 0032169864 scopus 로고    scopus 로고
    • A novel DNA-binding motif in MarA: the first structure for an AraC family transcriptional activator
    • Rhee S, Martin RG, Rosner JL, Davies DR, (1998) A novel DNA-binding motif in MarA: the first structure for an AraC family transcriptional activator. Proc Natl Acad Sci U S A 95: 10413-10418.
    • (1998) Proc Natl Acad Sci U S A , vol.95 , pp. 10413-10418
    • Rhee, S.1    Martin, R.G.2    Rosner, J.L.3    Davies, D.R.4
  • 29
    • 0035900538 scopus 로고    scopus 로고
    • Structure and dynamics of MarA-DNA complexes: an NMR investigation
    • Dangi B, Pelupessey P, Martin RG, Rosner JL, Louis JM, et al. (2001) Structure and dynamics of MarA-DNA complexes: an NMR investigation. J Mol Biol 314: 113-127.
    • (2001) J Mol Biol , vol.314 , pp. 113-127
    • Dangi, B.1    Pelupessey, P.2    Martin, R.G.3    Rosner, J.L.4    Louis, J.M.5
  • 30
    • 0036016825 scopus 로고    scopus 로고
    • Genomics of the marA/soxS/rob regulon of Escherichia coli: identification of directly activated promoters by application of molecular genetics and informatics to microarray data
    • Martin R, Rosner J, (2002) Genomics of the marA/soxS/rob regulon of Escherichia coli: identification of directly activated promoters by application of molecular genetics and informatics to microarray data. Molecular Microbiology 44: 1611-1624.
    • (2002) Molecular Microbiology , vol.44 , pp. 1611-1624
    • Martin, R.1    Rosner, J.2
  • 31
    • 0029806673 scopus 로고    scopus 로고
    • Reading of DNA sequence logos: Prediction of major groove binding by information theory
    • Schneider TD, (1996) Reading of DNA sequence logos: Prediction of major groove binding by information theory. Meth Enzym 274: 445-455.
    • (1996) Meth Enzym , vol.274 , pp. 445-455
    • Schneider, T.D.1
  • 32
    • 0035584142 scopus 로고    scopus 로고
    • Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation
    • Schneider TD, (2001) Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation. Nucleic Acids Res 29: 4881-4891.
    • (2001) Nucleic Acids Res , vol.29 , pp. 4881-4891
    • Schneider, T.D.1
  • 33
    • 0034705326 scopus 로고    scopus 로고
    • Probing the Escherichia coli transcriptional activator MarA using alanine-scanning mutagenesis: residues important for DNA binding and activation
    • Gillette WK, Martin RG, Rosner JL, (2000) Probing the Escherichia coli transcriptional activator MarA using alanine-scanning mutagenesis: residues important for DNA binding and activation. J Mol Biol 299: 1245-1255.
    • (2000) J Mol Biol , vol.299 , pp. 1245-1255
    • Gillette, W.K.1    Martin, R.G.2    Rosner, J.L.3
  • 34
    • 4744338150 scopus 로고    scopus 로고
    • Genetic evidence for pre-recruitment as the mechanism of transcription activation by SoxS of Escherichia coli: the dominance of DNA binding mutations of SoxS
    • Griffith KL, Wolf RE Jr, (2004) Genetic evidence for pre-recruitment as the mechanism of transcription activation by SoxS of Escherichia coli: the dominance of DNA binding mutations of SoxS. J Mol Biol 344: 1-10.
    • (2004) J Mol Biol , vol.344 , pp. 1-10
    • Griffith, K.L.1    Wolf Jr., R.E.2
  • 35
    • 0032529948 scopus 로고    scopus 로고
    • Overexpression of marA, soxS, or acrAB produces resistance to triclosan in laboratory and clinical strains of Escherichia coli
    • Mcmurry L, Oethinger M, Levy S, (1998) Overexpression of marA, soxS, or acrAB produces resistance to triclosan in laboratory and clinical strains of Escherichia coli. FEMS Microbiology Letters 166: 305-309.
    • (1998) FEMS Microbiology Letters , vol.166 , pp. 305-309
    • McMurry, L.1    Oethinger, M.2    Levy, S.3
  • 36
    • 0030029513 scopus 로고    scopus 로고
    • AcrAB efflux pump plays a major role in the antibiotic resistance phenotype of Escherichia coli multiple-antibiotic-resistance (Mar) mutants
    • Okusu H, Ma D, Nikaido H, (1996) AcrAB efflux pump plays a major role in the antibiotic resistance phenotype of Escherichia coli multiple-antibiotic-resistance (Mar) mutants. Journal of Bacteriology 178: 306-308.
    • (1996) Journal of Bacteriology , vol.178 , pp. 306-308
    • Okusu, H.1    Ma, D.2    Nikaido, H.3
  • 39
    • 0025008168 scopus 로고
    • Sequence logos: A new way to display consensus sequences
    • Schneider TD, Stephens RM, (1990) Sequence logos: A new way to display consensus sequences. Nucleic Acids Res 18: 6097-6100.
    • (1990) Nucleic Acids Res , vol.18 , pp. 6097-6100
    • Schneider, T.D.1    Stephens, R.M.2
  • 40
    • 3142736317 scopus 로고    scopus 로고
    • A phage display selection of engrailed homeodomain mutants and the importance of residue Q50
    • Simon MD, Sato K, Weiss GA, Shokat KM, (2004) A phage display selection of engrailed homeodomain mutants and the importance of residue Q50. Nucleic Acids Res 32: 3623-3631.
    • (2004) Nucleic Acids Res , vol.32 , pp. 3623-3631
    • Simon, M.D.1    Sato, K.2    Weiss, G.A.3    Shokat, K.M.4
  • 41
    • 84859239636 scopus 로고    scopus 로고
    • Cluster analysis and display of genome-wide expression patterns
    • Eisen M, Spellman P, Brown P, Botstein D, (1998) Cluster analysis and display of genome-wide expression patterns.
    • (1998)
    • Eisen, M.1    Spellman, P.2    Brown, P.3    Botstein, D.4
  • 43
    • 13844275301 scopus 로고    scopus 로고
    • Similarity of position frequency matrices for transcription factor binding sites
    • Schones D, Sumazin P, Zhang M, (2005) Similarity of position frequency matrices for transcription factor binding sites. Bioinformatics 21: 307-313.
    • (2005) Bioinformatics , vol.21 , pp. 307-313
    • Schones, D.1    Sumazin, P.2    Zhang, M.3
  • 44
    • 0031583033 scopus 로고    scopus 로고
    • Information content of individual genetic sequences
    • Schneider TD, (1997) Information content of individual genetic sequences. J Theor Biol 189: 427-441.
    • (1997) J Theor Biol , vol.189 , pp. 427-441
    • Schneider, T.D.1
  • 45
    • 0037109192 scopus 로고    scopus 로고
    • Additivity in protein-DNA interactions: how good an approximation is it?
    • Benos PV, Bulyk ML, Stormo GD, (2002) Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res 30: 4442-4451.
    • (2002) Nucleic Acids Res , vol.30 , pp. 4442-4451
    • Benos, P.V.1    Bulyk, M.L.2    Stormo, G.D.3
  • 46
    • 0016669094 scopus 로고
    • Evolution at two levels in humans and chimpanzees
    • King M, Wilson A, (1975) Evolution at two levels in humans and chimpanzees. Science 188: 107-116.
    • (1975) Science , vol.188 , pp. 107-116
    • King, M.1    Wilson, A.2
  • 47
    • 22744439568 scopus 로고    scopus 로고
    • Evolution at two levels: on genes and form
    • doi:10.1371/journal.pbio.0030245
    • Carroll S, (2005) Evolution at two levels: on genes and form. PLoS Biol 3: e245 doi:10.1371/journal.pbio.0030245.
    • (2005) PLoS Biol , vol.3
    • Carroll, S.1
  • 48
    • 33845442201 scopus 로고    scopus 로고
    • Engineering yeast transcription machinery for improved ethanol tolerance and production
    • Alper H, Moxley J, Nevoigt E, Fink G, Stephanopoulos G, (2006) Engineering yeast transcription machinery for improved ethanol tolerance and production. Science 314: 1565.
    • (2006) Science , vol.314 , pp. 1565
    • Alper, H.1    Moxley, J.2    Nevoigt, E.3    Fink, G.4    Stephanopoulos, G.5
  • 49
    • 2442537233 scopus 로고    scopus 로고
    • Gene regulatory network growth by duplication
    • Teichmann S, Babu M, (2004) Gene regulatory network growth by duplication. Nature Genetics 36: 492-496.
    • (2004) Nature Genetics , vol.36 , pp. 492-496
    • Teichmann, S.1    Babu, M.2
  • 50
    • 0037440734 scopus 로고    scopus 로고
    • Evolution of transcription factors and the gene regulatory network in Escherichia coli
    • Madan Babu M, Teichmann S, (2003) Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucleic Acids Research 31: 1234.
    • (2003) Nucleic Acids Research , vol.31 , pp. 1234
    • Madan Babu, M.1    Teichmann, S.2
  • 51
    • 10044223573 scopus 로고    scopus 로고
    • Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential
    • Slutsky M, Mirny L, (2004) Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential. Biophysical journal 87: 4021-4035.
    • (2004) Biophysical Journal , vol.87 , pp. 4021-4035
    • Slutsky, M.1    Mirny, L.2
  • 53
    • 33845503073 scopus 로고    scopus 로고
    • Adaptive evolution of transcription factor binding sites
    • Berg J, Willmann S, Lässig M, (2004) Adaptive evolution of transcription factor binding sites. BMC Evolutionary Biology 4: 42.
    • (2004) BMC Evolutionary Biology , vol.4 , pp. 42
    • Berg, J.1    Willmann, S.2    Lässig, M.3
  • 54
    • 3843146246 scopus 로고    scopus 로고
    • An efficient one-step site-directed and site-saturation mutagenesis protocol
    • Zheng L, Baumann U, Reymond J, (2004) An efficient one-step site-directed and site-saturation mutagenesis protocol. Nucleic acids research 32: e115.
    • (2004) Nucleic Acids Research , vol.32
    • Zheng, L.1    Baumann, U.2    Reymond, J.3


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