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Volumn 84, Issue , 2008, Pages 25-52

Linked Equilibria in Regulation of Transcription Initiation

Author keywords

[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETIC TRANSCRIPTION; GENETICS; PROTEIN BINDING; REVIEW;

EID: 35448947788     PISSN: 0091679X     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0091-679X(07)84002-7     Document Type: Review
Times cited : (2)

References (44)
  • 1
    • 0030790119 scopus 로고    scopus 로고
    • Allosteric mechanism of induction of CytR-regulated gene expression. Cytr repressor-cytidine interaction
    • Barbier C.S., Short S.A., and Senear D.F. Allosteric mechanism of induction of CytR-regulated gene expression. Cytr repressor-cytidine interaction. J. Biol. Chem. 272 27 (1997) 16962-16971
    • (1997) J. Biol. Chem. , vol.272 , Issue.27 , pp. 16962-16971
    • Barbier, C.S.1    Short, S.A.2    Senear, D.F.3
  • 2
    • 0022437260 scopus 로고
    • Quantitative DNase footprint titration: A method for studying protein-DNA interactions
    • Brenowitz M., Senear D.F., Shea M.A., and Ackers G.K. Quantitative DNase footprint titration: A method for studying protein-DNA interactions. Methods Enzymol. 130 (1986) 132-181
    • (1986) Methods Enzymol. , vol.130 , pp. 132-181
    • Brenowitz, M.1    Senear, D.F.2    Shea, M.A.3    Ackers, G.K.4
  • 3
    • 0023229226 scopus 로고
    • A general method of analysis of ligand-macromolecule equilibria using a spectroscopic signal from the ligand to monitor binding. Application to Escherichia coli single-strand binding protein-nucleic acid interactions
    • Bujalowski W., and Lohman T.M. A general method of analysis of ligand-macromolecule equilibria using a spectroscopic signal from the ligand to monitor binding. Application to Escherichia coli single-strand binding protein-nucleic acid interactions. Biochemistry 26 11 (1987) 3099-3106
    • (1987) Biochemistry , vol.26 , Issue.11 , pp. 3099-3106
    • Bujalowski, W.1    Lohman, T.M.2
  • 4
    • 0026346185 scopus 로고
    • Gel retardation
    • Carey J. Gel retardation. Methods Enzymol. 208 (1991) 103-117
    • (1991) Methods Enzymol. , vol.208 , pp. 103-117
    • Carey, J.1
  • 5
    • 0344838625 scopus 로고    scopus 로고
    • Role of protein-protein bridging interactions on cooperative assembly of DNA-bound CRP-CytR-CRP complex and regulation of the Escherichia coli CytR regulon
    • Chahla M., Wooll J., Laue T.M., Nguyen N., and Senear D.F. Role of protein-protein bridging interactions on cooperative assembly of DNA-bound CRP-CytR-CRP complex and regulation of the Escherichia coli CytR regulon. Biochemistry 42 13 (2003) 3812-3825
    • (2003) Biochemistry , vol.42 , Issue.13 , pp. 3812-3825
    • Chahla, M.1    Wooll, J.2    Laue, T.M.3    Nguyen, N.4    Senear, D.F.5
  • 6
    • 1842481270 scopus 로고    scopus 로고
    • Analysis of heterogeneous interactions
    • Cole J.L. Analysis of heterogeneous interactions. Methods Enzymol. 384 (2004) 212-232
    • (2004) Methods Enzymol. , vol.384 , pp. 212-232
    • Cole, J.L.1
  • 7
    • 0035814804 scopus 로고    scopus 로고
    • Sedimentation studies reveal a direct role of phosphorylation in Smad3:Smad4 homo- and hetero-trimerization
    • Correia J.J., Chacko B.M., Lam S.S., and Lin K. Sedimentation studies reveal a direct role of phosphorylation in Smad3:Smad4 homo- and hetero-trimerization. Biochemistry 40 5 (2001) 1473-1482
    • (2001) Biochemistry , vol.40 , Issue.5 , pp. 1473-1482
    • Correia, J.J.1    Chacko, B.M.2    Lam, S.S.3    Lin, K.4
  • 8
    • 23244445215 scopus 로고    scopus 로고
    • Sedimentation velocity analysis of heterogeneous protein-protein interactions: Sedimentation coefficient distributions c(s) and asymptotic boundary profiles from Gilbert-Jenkins theory
    • Dam J., and Schuck P. Sedimentation velocity analysis of heterogeneous protein-protein interactions: Sedimentation coefficient distributions c(s) and asymptotic boundary profiles from Gilbert-Jenkins theory. Biophys. J. 89 1 (2005) 651-666
    • (2005) Biophys. J. , vol.89 , Issue.1 , pp. 651-666
    • Dam, J.1    Schuck, P.2
  • 9
    • 20444380585 scopus 로고    scopus 로고
    • Sedimentation velocity analysis of heterogeneous protein-protein interactions: Lamm equation modeling and sedimentation coefficient distributions c(s)
    • Dam J., Velikovsky C.A., Mariuzza R.A., Urbanke C., and Schuck P. Sedimentation velocity analysis of heterogeneous protein-protein interactions: Lamm equation modeling and sedimentation coefficient distributions c(s). Biophys. J. 89 1 (2005) 619-634
    • (2005) Biophys. J. , vol.89 , Issue.1 , pp. 619-634
    • Dam, J.1    Velikovsky, C.A.2    Mariuzza, R.A.3    Urbanke, C.4    Schuck, P.5
  • 10
    • 0030956737 scopus 로고    scopus 로고
    • Fluorescence methods for studying equilibrium macromolecule-ligand interactions
    • Eftink M.R. Fluorescence methods for studying equilibrium macromolecule-ligand interactions. Methods Enzymol. 278 (1997) 221-257
    • (1997) Methods Enzymol. , vol.278 , pp. 221-257
    • Eftink, M.R.1
  • 11
    • 0032830564 scopus 로고    scopus 로고
    • Dimerization of the Escherichia coli biotin repressor: Corepressor function in protein assembly
    • Eisenstein E., and Beckett D. Dimerization of the Escherichia coli biotin repressor: Corepressor function in protein assembly. Biochemistry 38 40 (1999) 13077-13084
    • (1999) Biochemistry , vol.38 , Issue.40 , pp. 13077-13084
    • Eisenstein, E.1    Beckett, D.2
  • 12
    • 0018199224 scopus 로고
    • DNAse footprinting: A simple method for the detection of protein-DNA binding specificity
    • Galas D.J., and Schmitz A. DNAse footprinting: A simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res. 5 9 (1978) 3157-3170
    • (1978) Nucleic Acids Res. , vol.5 , Issue.9 , pp. 3157-3170
    • Galas, D.J.1    Schmitz, A.2
  • 13
    • 0019877067 scopus 로고
    • A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: Application to components of the Escherichia coli lactose operon regulatory system
    • Garner M.M., and Revzin A. A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: Application to components of the Escherichia coli lactose operon regulatory system. Nucleic Acids Res. 9 13 (1981) 3047-3060
    • (1981) Nucleic Acids Res. , vol.9 , Issue.13 , pp. 3047-3060
    • Garner, M.M.1    Revzin, A.2
  • 14
    • 21844477014 scopus 로고    scopus 로고
    • Self-association energetics of an intact, full-length nuclear receptor: The B-isoform of human progesterone receptor dimerizes in the micromolar range
    • Heneghan A.F., Berton N., Miura M.T., and Bain D.L. Self-association energetics of an intact, full-length nuclear receptor: The B-isoform of human progesterone receptor dimerizes in the micromolar range. Biochemistry 44 27 (2005) 9528-9537
    • (2005) Biochemistry , vol.44 , Issue.27 , pp. 9528-9537
    • Heneghan, A.F.1    Berton, N.2    Miura, M.T.3    Bain, D.L.4
  • 15
    • 33644855967 scopus 로고    scopus 로고
    • Cooperative DNA binding by the B-isoform of human progesterone receptor: Thermodynamic analysis reveals strongly favorable and unfavorable contributions to assembly
    • Heneghan A.F., Connaghan-Jones K.D., Miura M.T., and Bain D.L. Cooperative DNA binding by the B-isoform of human progesterone receptor: Thermodynamic analysis reveals strongly favorable and unfavorable contributions to assembly. Biochemistry 45 10 (2006) 3285-3296
    • (2006) Biochemistry , vol.45 , Issue.10 , pp. 3285-3296
    • Heneghan, A.F.1    Connaghan-Jones, K.D.2    Miura, M.T.3    Bain, D.L.4
  • 16
    • 0030919292 scopus 로고    scopus 로고
    • Fluorescence approaches to study of protein-nucleic acid complexation
    • Hill J.J., and Royer C.A. Fluorescence approaches to study of protein-nucleic acid complexation. Methods Enzymol. 278 (1997) 390-416
    • (1997) Methods Enzymol. , vol.278 , pp. 390-416
    • Hill, J.J.1    Royer, C.A.2
  • 17
    • 0019756004 scopus 로고
    • Analysis of data from the analytical ultracentrifuge by nonlinear least-squares techniques
    • Johnson M.L., Correia J.J., Yphantis D.A., and Halvorson H.R. Analysis of data from the analytical ultracentrifuge by nonlinear least-squares techniques. Biophys. J. 36 3 (1981) 575-588
    • (1981) Biophys. J. , vol.36 , Issue.3 , pp. 575-588
    • Johnson, M.L.1    Correia, J.J.2    Yphantis, D.A.3    Halvorson, H.R.4
  • 18
    • 0026718393 scopus 로고
    • Parameter estimation by least-squares methods
    • Johnson M.L., and Faunt L.M. Parameter estimation by least-squares methods. Methods Enzymol. 210 (1992) 1-37
    • (1992) Methods Enzymol. , vol.210 , pp. 1-37
    • Johnson, M.L.1    Faunt, L.M.2
  • 20
    • 10044226082 scopus 로고    scopus 로고
    • Application of isothermal titration calorimetry in the biological sciences: Things are heating up!
    • Ladbury J.E. Application of isothermal titration calorimetry in the biological sciences: Things are heating up!. Biotechniques 37 6 (2004) 885-887
    • (2004) Biotechniques , vol.37 , Issue.6 , pp. 885-887
    • Ladbury, J.E.1
  • 21
    • 0029118618 scopus 로고
    • Sedimentation equilibrium as thermodynamic tool
    • Laue T.M. Sedimentation equilibrium as thermodynamic tool. Methods Enzymol. 259 (1995) 427-452
    • (1995) Methods Enzymol. , vol.259 , pp. 427-452
    • Laue, T.M.1
  • 22
    • 0347627644 scopus 로고    scopus 로고
    • Progesterone receptor transcription and non-transcription signaling mechanisms
    • Leonhardt S.A., Boonyaratanakornkit V., and Edwards D.P. Progesterone receptor transcription and non-transcription signaling mechanisms. Steroids 68 10-13 (2003) 761-770
    • (2003) Steroids , vol.68 , Issue.10-13 , pp. 761-770
    • Leonhardt, S.A.1    Boonyaratanakornkit, V.2    Edwards, D.P.3
  • 23
    • 0141891343 scopus 로고    scopus 로고
    • Unfolding the action of progesterone receptors
    • Li X., and O'Malley B.W. Unfolding the action of progesterone receptors. J. Biol. Chem. 278 41 (2003) 39261-39264
    • (2003) J. Biol. Chem. , vol.278 , Issue.41 , pp. 39261-39264
    • Li, X.1    O'Malley, B.W.2
  • 25
    • 33744821893 scopus 로고    scopus 로고
    • Coactivator cross-talk specifies transcriptional output
    • Marr II M.T., Isogai Y., Wright K.J., and Tjian R. Coactivator cross-talk specifies transcriptional output. Genes Dev. 20 11 (2006) 1458-1469
    • (2006) Genes Dev. , vol.20 , Issue.11 , pp. 1458-1469
    • Marr II, M.T.1    Isogai, Y.2    Wright, K.J.3    Tjian, R.4
  • 27
    • 0025990732 scopus 로고
    • Heterologous cooperativity in Escherichia coli. The CytR repressor both contacts DNA and the cAMP receptor protein when binding to the deoP2 promoter
    • Pedersen H., Sogaard-Andersen L., Holst B., and Valentin-Hansen P. Heterologous cooperativity in Escherichia coli. The CytR repressor both contacts DNA and the cAMP receptor protein when binding to the deoP2 promoter. J. Biol. Chem. 266 27 (1991) 17804-17808
    • (1991) J. Biol. Chem. , vol.266 , Issue.27 , pp. 17804-17808
    • Pedersen, H.1    Sogaard-Andersen, L.2    Holst, B.3    Valentin-Hansen, P.4
  • 28
    • 0030448103 scopus 로고    scopus 로고
    • Multiple specific CytR binding sites at the Escherichia coli deoP2 promoter mediate both cooperative and competitive interactions between CytR and cAMP receptor protein
    • Perini L.T., Doherty E.A., Werner E., and Senear D.F. Multiple specific CytR binding sites at the Escherichia coli deoP2 promoter mediate both cooperative and competitive interactions between CytR and cAMP receptor protein. J. Biol. Chem. 271 52 (1996) 33242-33255
    • (1996) J. Biol. Chem. , vol.271 , Issue.52 , pp. 33242-33255
    • Perini, L.T.1    Doherty, E.A.2    Werner, E.3    Senear, D.F.4
  • 29
    • 0035223267 scopus 로고    scopus 로고
    • Calorimetry of protein-DNA complexes and their components
    • Read C.M., and Jelesarov I. Calorimetry of protein-DNA complexes and their components. Methods Mol. Biol. 148 (2001) 511-533
    • (2001) Methods Mol. Biol. , vol.148 , pp. 511-533
    • Read, C.M.1    Jelesarov, I.2
  • 31
    • 0017107966 scopus 로고
    • Sedimentation equilibrium techniques: Multiple speed analyses and an overspeed procedure
    • Roark D.E. Sedimentation equilibrium techniques: Multiple speed analyses and an overspeed procedure. Biophys. Chem. 5 1-2 (1976) 185-196
    • (1976) Biophys. Chem. , vol.5 , Issue.1-2 , pp. 185-196
    • Roark, D.E.1
  • 32
    • 0031688168 scopus 로고    scopus 로고
    • Sedimentation analysis of noninteracting and self-associating solutes using numerical solutions to the Lamm equation
    • Schuck P. Sedimentation analysis of noninteracting and self-associating solutes using numerical solutions to the Lamm equation. Biophys. J. 75 3 (1998) 1503-1512
    • (1998) Biophys. J. , vol.75 , Issue.3 , pp. 1503-1512
    • Schuck, P.1
  • 33
    • 33646079413 scopus 로고    scopus 로고
    • Three-stage regulation of the amphibolic gal operon: From repressosome to GalR-free DNA
    • Semsey S., Virnik K., and Adhya S. Three-stage regulation of the amphibolic gal operon: From repressosome to GalR-free DNA. J. Mol. Biol. 358 2 (2006) 355-363
    • (2006) J. Mol. Biol. , vol.358 , Issue.2 , pp. 355-363
    • Semsey, S.1    Virnik, K.2    Adhya, S.3
  • 34
    • 0025768548 scopus 로고
    • Determination of binding constants for cooperative site-specific protein-DNA interactions using the gel mobility-shift assay
    • Senear D.F., and Brenowitz M. Determination of binding constants for cooperative site-specific protein-DNA interactions using the gel mobility-shift assay. J. Biol. Chem. 266 21 (1991) 13661-13671
    • (1991) J. Biol. Chem. , vol.266 , Issue.21 , pp. 13661-13671
    • Senear, D.F.1    Brenowitz, M.2
  • 35
    • 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.J., Fujita N., Ishihama A., Valentin-Hansen P., and Choy H.E. Repression of deoP2 in Escherichia coli by CytR: Conversion of a transcription activator into a repressor. EMBO J. 20 19 (2001) 5392-5399
    • (2001) EMBO J. , vol.20 , Issue.19 , pp. 5392-5399
    • Shin, M.1    Kang, S.2    Hyun, S.J.3    Fujita, N.4    Ishihama, A.5    Valentin-Hansen, P.6    Choy, H.E.7
  • 36
    • 0027489919 scopus 로고
    • Protein-protein interactions in gene regulation: The cAMP-CRP complex sets the specificity of a second DNA-binding protein, the CytR repressor
    • Sogaard-Andersen L., and Valentin-Hansen P. Protein-protein interactions in gene regulation: The cAMP-CRP complex sets the specificity of a second DNA-binding protein, the CytR repressor. Cell 75 3 (1993) 557-566
    • (1993) Cell , vol.75 , Issue.3 , pp. 557-566
    • Sogaard-Andersen, L.1    Valentin-Hansen, P.2
  • 37
    • 0034581366 scopus 로고    scopus 로고
    • Analysis of reversibly interacting macromolecular systems by time derivative sedimentation velocity
    • Stafford W.F. Analysis of reversibly interacting macromolecular systems by time derivative sedimentation velocity. Methods Enzymol. 323 (2000) 302-325
    • (2000) Methods Enzymol. , vol.323 , pp. 302-325
    • Stafford, W.F.1
  • 38
    • 1642368109 scopus 로고    scopus 로고
    • Analysis of heterologous interacting systems by sedimentation velocity: Curve fitting algorithms for estimation of sedimentation coefficients, equilibrium and kinetic constants
    • Stafford W.F., and Sherwood P.J. Analysis of heterologous interacting systems by sedimentation velocity: Curve fitting algorithms for estimation of sedimentation coefficients, equilibrium and kinetic constants. Biophys. Chem. 108 1-3 (2004) 231-243
    • (2004) Biophys. Chem. , vol.108 , Issue.1-3 , pp. 231-243
    • Stafford, W.F.1    Sherwood, P.J.2
  • 39
    • 0030955767 scopus 로고    scopus 로고
    • Hinge and amino-terminal sequences contribute to solution dimerization of human progesterone receptor
    • Tetel M.J., Jung S., Carbajo P., Ladtkow T., Skafar D.F., and Edwards D.P. Hinge and amino-terminal sequences contribute to solution dimerization of human progesterone receptor. Mol. Endocrinol. 11 8 (1997) 1114-1128
    • (1997) Mol. Endocrinol. , vol.11 , Issue.8 , pp. 1114-1128
    • Tetel, M.J.1    Jung, S.2    Carbajo, P.3    Ladtkow, T.4    Skafar, D.F.5    Edwards, D.P.6
  • 40
    • 33747767961 scopus 로고    scopus 로고
    • Flexibility and adaptability in binding of E. coli cytidine repressor to different operators suggests a role in differential gene regulation
    • Tretyachenko-Ladokhina V., Cocco M.J., and Senear D.F. Flexibility and adaptability in binding of E. coli cytidine repressor to different operators suggests a role in differential gene regulation. J. Mol. Biol. 362 2 (2006) 271-286
    • (2006) J. Mol. Biol. , vol.362 , Issue.2 , pp. 271-286
    • Tretyachenko-Ladokhina, V.1    Cocco, M.J.2    Senear, D.F.3
  • 41
    • 3242726206 scopus 로고    scopus 로고
    • Characterization of protein-protein interactions by isothermal titration calorimetry
    • Velazquez-Campoy A., Leavitt S.A., and Freire E. Characterization of protein-protein interactions by isothermal titration calorimetry. Methods Mol. Biol. 261 (2004) 35-54
    • (2004) Methods Mol. Biol. , vol.261 , pp. 35-54
    • Velazquez-Campoy, A.1    Leavitt, S.A.2    Freire, E.3
  • 42
    • 0026724966 scopus 로고
    • A family of bacterial regulators homologous to Gal and Lac repressors
    • Weickert M.J., and Adhya S. A family of bacterial regulators homologous to Gal and Lac repressors. J. Biol. Chem. 267 22 (1992) 15869-15874
    • (1992) J. Biol. Chem. , vol.267 , Issue.22 , pp. 15869-15874
    • Weickert, M.J.1    Adhya, S.2
  • 43
    • 0037756781 scopus 로고    scopus 로고
    • Analytical exclusion chromatography
    • Winzor D.J. Analytical exclusion chromatography. J. Biochem. Biophys. Methods 56 1-3 (2003) 15-52
    • (2003) J. Biochem. Biophys. Methods , vol.56 , Issue.1-3 , pp. 15-52
    • Winzor, D.J.1
  • 44
    • 0142138241 scopus 로고    scopus 로고
    • Analysis of protein interactions using fluorescence technologies
    • Yan Y., and Marriott G. Analysis of protein interactions using fluorescence technologies. Curr. Opin. Chem. Biol. 7 5 (2003) 635-640
    • (2003) Curr. Opin. Chem. Biol. , vol.7 , Issue.5 , pp. 635-640
    • Yan, Y.1    Marriott, G.2


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