메뉴 건너뛰기




Volumn 47, Issue 27, 2008, Pages 7264-7273

TATA-binding protein recognition and bending of a consensus promoter are protein species dependent

Author keywords

[No Author keywords available]

Indexed keywords

ORGANIC ACIDS;

EID: 46849083475     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi800139w     Document Type: Article
Times cited : (21)

References (48)
  • 1
    • 0027268306 scopus 로고
    • TBP, a universal eukaryotic transcription factor?
    • Hernandez, N. (1993) TBP, a universal eukaryotic transcription factor? Genes Dev. 7, 1291-1308.
    • (1993) Genes Dev , vol.7 , pp. 1291-1308
    • Hernandez, N.1
  • 2
    • 0030013203 scopus 로고    scopus 로고
    • Biochemistry and structural biology of transcription factor IID (TFIID)
    • Burley, S. K., and Roeder, R. G. (1996) Biochemistry and structural biology of transcription factor IID (TFIID). Annu. Rev. Biochem. 65, 769-799.
    • (1996) Annu. Rev. Biochem , vol.65 , pp. 769-799
    • Burley, S.K.1    Roeder, R.G.2
  • 3
    • 0029965491 scopus 로고    scopus 로고
    • Transcription revisited: A commentary on the 1995 Cold Spring Harbor Laboratory meeting, Mechanisms of Eukaryotic Transcription
    • McKnight, S. L. (1996) Transcription revisited: a commentary on the 1995 Cold Spring Harbor Laboratory meeting, Mechanisms of Eukaryotic Transcription. Genes Dev. 10, 367-381.
    • (1996) Genes Dev , vol.10 , pp. 367-381
    • McKnight, S.L.1
  • 4
    • 0029899068 scopus 로고    scopus 로고
    • A new class of activation-defective TATA-binding protein mutants: Evidence for two steps of transcriptional activation in vivo
    • Stargell, L. A., and Struhl, K. (1996) A new class of activation-defective TATA-binding protein mutants: evidence for two steps of transcriptional activation in vivo. Mol. Cell. Biol. 16, 4456-4464.
    • (1996) Mol. Cell. Biol , vol.16 , pp. 4456-4464
    • Stargell, L.A.1    Struhl, K.2
  • 5
    • 0035805499 scopus 로고    scopus 로고
    • DNA bends in TATA-binding protein-TATA complexes in solution are DNA sequence-dependent
    • Wu, J., Parkhurst, K. M., Powell, R. M., Brenowitz, M., and Parkhurst, L. J. (2001) DNA bends in TATA-binding protein-TATA complexes in solution are DNA sequence-dependent. J. Biol. Chem. 276, 14614-14622.
    • (2001) J. Biol. Chem , vol.276 , pp. 14614-14622
    • Wu, J.1    Parkhurst, K.M.2    Powell, R.M.3    Brenowitz, M.4    Parkhurst, L.J.5
  • 6
    • 0027504913 scopus 로고
    • Crystal structure of a yeast TBP/TATA-box complex
    • Kim, Y., Geiger, J. H., Hahn, S., and Sigler, P. B. (1993) Crystal structure of a yeast TBP/TATA-box complex. Nature 365, 512-520.
    • (1993) Nature , vol.365 , pp. 512-520
    • Kim, Y.1    Geiger, J.H.2    Hahn, S.3    Sigler, P.B.4
  • 9
    • 0027483012 scopus 로고
    • Co-crystal structure of TBP recognizing the minor groove of a TATA element
    • Kim, J. L., Nikolov, D. B., and Burley, S. K. (1993) Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature 365, 520-527.
    • (1993) Nature , vol.365 , pp. 520-527
    • Kim, J.L.1    Nikolov, D.B.2    Burley, S.K.3
  • 10
    • 0033573008 scopus 로고    scopus 로고
    • TATA element recognition by the TATA box-binding protein has been conserved throughout evolution
    • Patikoglou, G. A., Kim, J. L., Sun, L., Yang, S. H., Kodadek, T., and Burley, S. K. (1999) TATA element recognition by the TATA box-binding protein has been conserved throughout evolution. Genes Dev. 13, 3217-3230.
    • (1999) Genes Dev , vol.13 , pp. 3217-3230
    • Patikoglou, G.A.1    Kim, J.L.2    Sun, L.3    Yang, S.H.4    Kodadek, T.5    Burley, S.K.6
  • 11
    • 0041825432 scopus 로고    scopus 로고
    • Novel interactions between the components of human and yeast TFIIA/TBP/DNA complexes
    • Bleichenbacher, M., Tan, S., and Richmond, T. J. (2003) Novel interactions between the components of human and yeast TFIIA/TBP/DNA complexes. J. Mol. Biol. 332, 783-793.
    • (2003) J. Mol. Biol , vol.332 , pp. 783-793
    • Bleichenbacher, M.1    Tan, S.2    Richmond, T.J.3
  • 12
    • 0029127570 scopus 로고
    • DNA bending is an important component of site-specific recognition by the TATA binding protein
    • Starr, D. B., Hoopes, B. C., and Hawley, D. K. (1995) DNA bending is an important component of site-specific recognition by the TATA binding protein. J. Mol. Biol. 250, 434-446.
    • (1995) J. Mol. Biol , vol.250 , pp. 434-446
    • Starr, D.B.1    Hoopes, B.C.2    Hawley, D.K.3
  • 13
    • 0030055654 scopus 로고    scopus 로고
    • TBP binds the transcriptionally inactive TA5 sequence but the resulting complex is not efficiently recognised by TFIIB and TFIIA
    • Bernues, J., Carrera, P., and Azorin, F. (1996) TBP binds the transcriptionally inactive TA5 sequence but the resulting complex is not efficiently recognised by TFIIB and TFIIA. Nucleic Acids Res. 24, 2950-2958.
    • (1996) Nucleic Acids Res , vol.24 , pp. 2950-2958
    • Bernues, J.1    Carrera, P.2    Azorin, F.3
  • 14
    • 0035805572 scopus 로고    scopus 로고
    • DNA sequence-dependent differences in TATA-binding protein-induced DNA bending in solution are highly sensitive to osmolytes
    • Wu, J., Parkhurst, K. M., Powell, R. M., and Parkhurst, L. J. (2001) DNA sequence-dependent differences in TATA-binding protein-induced DNA bending in solution are highly sensitive to osmolytes. J. Biol. Chem. 276, 14623-14627.
    • (2001) J. Biol. Chem , vol.276 , pp. 14623-14627
    • Wu, J.1    Parkhurst, K.M.2    Powell, R.M.3    Parkhurst, L.J.4
  • 15
    • 0035839638 scopus 로고    scopus 로고
    • Marked stepwise differences within a common kinetic mechanism characterize TATA-binding protein interactions with two consensus promoters
    • Powell, R. M., Parkhurst, K. M., Brenowitz, M., and Parkhurst, L. J. (2001) Marked stepwise differences within a common kinetic mechanism characterize TATA-binding protein interactions with two consensus promoters. J. Biol. Chem. 276, 29782-29791.
    • (2001) J. Biol. Chem , vol.276 , pp. 29782-29791
    • Powell, R.M.1    Parkhurst, K.M.2    Brenowitz, M.3    Parkhurst, L.J.4
  • 16
    • 0037040899 scopus 로고    scopus 로고
    • Comparison of TATA-binding protein recognition of a variant and consensus DNA promoters
    • Powell, R. M., Parkhurst, K. M., and Parkhurst, L. J. (2002) Comparison of TATA-binding protein recognition of a variant and consensus DNA promoters. J. Biol. Chem. 277, 7776-7784.
    • (2002) J. Biol. Chem , vol.277 , pp. 7776-7784
    • Powell, R.M.1    Parkhurst, K.M.2    Parkhurst, L.J.3
  • 17
    • 0037642518 scopus 로고    scopus 로고
    • Sequence-dependent solution structure and motions of 13 TATA/TBP (TATA-box binding protein) complexes
    • Strahs, D., Barash, D., Qian, X., and Schlick, T. (2003) Sequence-dependent solution structure and motions of 13 TATA/TBP (TATA-box binding protein) complexes. Biopolymers 69, 216-243.
    • (2003) Biopolymers , vol.69 , pp. 216-243
    • Strahs, D.1    Barash, D.2    Qian, X.3    Schlick, T.4
  • 18
    • 0033603388 scopus 로고    scopus 로고
    • Intermediate species possessing bent DNA are present along the pathway to formation of a final TBP-TATA complex
    • Parkhurst, K. M., Richards, R. M., Brenowitz, M., and Parkhurst, L. J. (1999) Intermediate species possessing bent DNA are present along the pathway to formation of a final TBP-TATA complex. J. Mol. Biol. 289, 1327-1341.
    • (1999) J. Mol. Biol , vol.289 , pp. 1327-1341
    • Parkhurst, K.M.1    Richards, R.M.2    Brenowitz, M.3    Parkhurst, L.J.4
  • 19
    • 0029080688 scopus 로고
    • Thermodynamic and kinetic characterization of the binding of the TATA binding protein to the adenovirus E4 promoter
    • Petri, V., Hsieh, M., and Brenowitz, M. (1995) Thermodynamic and kinetic characterization of the binding of the TATA binding protein to the adenovirus E4 promoter. Biochemistry 34, 9977-9984.
    • (1995) Biochemistry , vol.34 , pp. 9977-9984
    • Petri, V.1    Hsieh, M.2    Brenowitz, M.3
  • 20
    • 0029943025 scopus 로고    scopus 로고
    • Simultaneous binding and bending of promoter DNA by the TATA binding protein: Real time kinetic measurements
    • Parkhurst, K. M., Brenowitz, M., and Parkhurst, L. J. (1996) Simultaneous binding and bending of promoter DNA by the TATA binding protein: real time kinetic measurements. Biochemistry 35, 7459-7465.
    • (1996) Biochemistry , vol.35 , pp. 7459-7465
    • Parkhurst, K.M.1    Brenowitz, M.2    Parkhurst, L.J.3
  • 21
    • 0037040419 scopus 로고    scopus 로고
    • A regulated two-step mechanism of TBP binding to DNA: A solvent-exposed surface of TBP inhibits TATA box recognition
    • Zhao, X., and Herr, W. (2002) A regulated two-step mechanism of TBP binding to DNA: a solvent-exposed surface of TBP inhibits TATA box recognition. Cell 108, 615-627.
    • (2002) Cell , vol.108 , pp. 615-627
    • Zhao, X.1    Herr, W.2
  • 22
    • 0041856190 scopus 로고    scopus 로고
    • Native human TATA-binding protein simultaneously binds and bends promoter DNA without a slow isomerization step or TFIIB requirement
    • Masters, K. M., Parkhurst, K. M., Daugherty, M. A., and Parkhurst, L. J. (2003) Native human TATA-binding protein simultaneously binds and bends promoter DNA without a slow isomerization step or TFIIB requirement. J. Biol. Chem. 278, 31685-31690.
    • (2003) J. Biol. Chem , vol.278 , pp. 31685-31690
    • Masters, K.M.1    Parkhurst, K.M.2    Daugherty, M.A.3    Parkhurst, L.J.4
  • 23
    • 14244270749 scopus 로고    scopus 로고
    • Time-resolved fluorescence resonance energy transfer studies of DNA bending in double-stranded oligonucleotides and in DNA-protein complexes
    • Parkhurst, L. J., Parkhurst, K. M., Powell, R., Wu, J., and Williams, S. (2001) Time-resolved fluorescence resonance energy transfer studies of DNA bending in double-stranded oligonucleotides and in DNA-protein complexes. Biopolymers 61, 180-200.
    • (2001) Biopolymers , vol.61 , pp. 180-200
    • Parkhurst, L.J.1    Parkhurst, K.M.2    Powell, R.3    Wu, J.4    Williams, S.5
  • 24
    • 1542358918 scopus 로고    scopus 로고
    • Distance parameters derived from time-resolved Forster resonance energy transfer measurements and their use in structural interpretations of thermodynamic quantities associated with protein-DNA interactions
    • Parkhurst, L. J. (2004) Distance parameters derived from time-resolved Forster resonance energy transfer measurements and their use in structural interpretations of thermodynamic quantities associated with protein-DNA interactions. Methods Enzymol. 379, 235-262.
    • (2004) Methods Enzymol , vol.379 , pp. 235-262
    • Parkhurst, L.J.1
  • 25
    • 33644855950 scopus 로고    scopus 로고
    • Changes in DNA bending and flexing due to tethered cations detected by fluorescence resonance energy transfer
    • Williams, S. L., Parkhurst, L. K., and Parkhurst, L. J. (2006) Changes in DNA bending and flexing due to tethered cations detected by fluorescence resonance energy transfer. Nucleic Acids Res. 34, 1028-1035.
    • (2006) Nucleic Acids Res , vol.34 , pp. 1028-1035
    • Williams, S.L.1    Parkhurst, L.K.2    Parkhurst, L.J.3
  • 26
    • 0032401007 scopus 로고    scopus 로고
    • Biopolymers 46
    • 445-4-53
    • Sjöback, R., Nygren, J., and Kubista, M. (1998) Characterization of fluorescein-oligonucleotide conjugates and measurement of local electrostatic potential. Biopolymers 46, 445-4-53.
    • (1998)
    • Sjöback, R.1    Nygren, J.2    Kubista, M.3
  • 27
    • 0024915465 scopus 로고
    • A matrix series method for the integration of rate equations in a reaction network. An alternative to Runge-Kutta methods
    • Zamis, T. M., Parkhurst, L. J., and Gallup, G. A. (1989) A matrix series method for the integration of rate equations in a reaction network. An alternative to Runge-Kutta methods. Comput. Chem. 13, 165-171.
    • (1989) Comput. Chem , vol.13 , pp. 165-171
    • Zamis, T.M.1    Parkhurst, L.J.2    Gallup, G.A.3
  • 28
    • 0037129935 scopus 로고    scopus 로고
    • DNA bending by bZIP charge variants: A unified study using electrophoretic phasing and fluorescence resonance energy transfer
    • Hardwidge, P. R., Wu, J., Williams, S. L., Parkhurst, K. M., Parkhurst, L. J., and Maher, L. J. (2002) DNA bending by bZIP charge variants: a unified study using electrophoretic phasing and fluorescence resonance energy transfer. Biochemistry 41, 7732-7742.
    • (2002) Biochemistry , vol.41 , pp. 7732-7742
    • Hardwidge, P.R.1    Wu, J.2    Williams, S.L.3    Parkhurst, K.M.4    Parkhurst, L.J.5    Maher, L.J.6
  • 29
    • 0032213753 scopus 로고    scopus 로고
    • Inherent DNA curvature and flexibility correlate with TATA box functionality
    • de Souza, O. N., and Ornstein, R. L. (1998) Inherent DNA curvature and flexibility correlate with TATA box functionality. Biopolymers 46, 403-415.
    • (1998) Biopolymers , vol.46 , pp. 403-415
    • de Souza, O.N.1    Ornstein, R.L.2
  • 30
    • 0029916115 scopus 로고    scopus 로고
    • DNA binding by TATA-box binding protein (TBP): A molecular dynamics computational study
    • Miaskiewicz, K., and Ornstein, R. L. (1996) DNA binding by TATA-box binding protein (TBP): a molecular dynamics computational study. J. Biomol. Struct. Dyn. 13, 593-600.
    • (1996) J. Biomol. Struct. Dyn , vol.13 , pp. 593-600
    • Miaskiewicz, K.1    Ornstein, R.L.2
  • 32
    • 0029008807 scopus 로고
    • Yeast TATA binding protein interaction with DNA: Fluorescence determination of oligomeric state, equilibrium binding, on-rate, and dissociation kinetics
    • Perez-Howard, G. M., Weil, P. A., and Beechem, J. M. (1995) Yeast TATA binding protein interaction with DNA: fluorescence determination of oligomeric state, equilibrium binding, on-rate, and dissociation kinetics. Biochemistry 34, 8005-8017.
    • (1995) Biochemistry , vol.34 , pp. 8005-8017
    • Perez-Howard, G.M.1    Weil, P.A.2    Beechem, J.M.3
  • 33
    • 0037199428 scopus 로고    scopus 로고
    • Solution structural studies of the Saccharomyces cerevisiae TATA binding protein (TBP)
    • Khrapunov, S., Pastor, N., and Brenowitz, M. (2002) Solution structural studies of the Saccharomyces cerevisiae TATA binding protein (TBP). Biochemistry 41, 9559-9571.
    • (2002) Biochemistry , vol.41 , pp. 9559-9571
    • Khrapunov, S.1    Pastor, N.2    Brenowitz, M.3
  • 34
    • 0345269999 scopus 로고    scopus 로고
    • Solution structure and interdomain interactions of the Saccharomyces cerevisiae "TATA binding protein" (TBP) probed by radiolytic protein footprinting
    • Rashidzadeh, H., Khrapunov, S., Chance, M. R., and Brenowitz, M. (2003) Solution structure and interdomain interactions of the Saccharomyces cerevisiae "TATA binding protein" (TBP) probed by radiolytic protein footprinting. Biochemistry 42, 3655-3665.
    • (2003) Biochemistry , vol.42 , pp. 3655-3665
    • Rashidzadeh, H.1    Khrapunov, S.2    Chance, M.R.3    Brenowitz, M.4
  • 35
    • 34548499082 scopus 로고    scopus 로고
    • DNA and protein footprinting analysis of the modulation of DNA binding by the N-terminal domain of the Saccharomyces cerevisiae TATA binding protein
    • Gupta, S., Cheng, H., Mollah, A. K., Jamison, E., Morris, S., Chance, M. R., Khrapunov, S., and Brenowitz, M. (2007) DNA and protein footprinting analysis of the modulation of DNA binding by the N-terminal domain of the Saccharomyces cerevisiae TATA binding protein. Biochemistry 46, 9886-9898.
    • (2007) Biochemistry , vol.46 , pp. 9886-9898
    • Gupta, S.1    Cheng, H.2    Mollah, A.K.3    Jamison, E.4    Morris, S.5    Chance, M.R.6    Khrapunov, S.7    Brenowitz, M.8
  • 36
    • 34247523727 scopus 로고    scopus 로고
    • Influence of the N-terminal domain and divalent cations on self-association and DNA binding by the Saccharomyces cerevisiae TATA binding protein
    • Khrapunov, S., and Brenowitz, M. (2007) Influence of the N-terminal domain and divalent cations on self-association and DNA binding by the Saccharomyces cerevisiae TATA binding protein. Biochemistry 46, 4876-4887.
    • (2007) Biochemistry , vol.46 , pp. 4876-4887
    • Khrapunov, S.1    Brenowitz, M.2
  • 38
    • 0025309524 scopus 로고
    • Yeast and human TATA-binding proteins have nearly identical DNA sequence requirements for transcription in vitro
    • Wobbe, C. R., and Struhl, K. (1990) Yeast and human TATA-binding proteins have nearly identical DNA sequence requirements for transcription in vitro. Mol. Cell. Biol. 10, 3859-3867.
    • (1990) Mol. Cell. Biol , vol.10 , pp. 3859-3867
    • Wobbe, C.R.1    Struhl, K.2
  • 39
    • 0029907837 scopus 로고    scopus 로고
    • Goppelt, A., and Meisterernst, M. (1996) Characterization of the basal inhibitor of class II transcription NC2 from Saccharomyces cerevisiae. Nucleic Acids Res. 24, 4450-4-455.
    • Goppelt, A., and Meisterernst, M. (1996) Characterization of the basal inhibitor of class II transcription NC2 from Saccharomyces cerevisiae. Nucleic Acids Res. 24, 4450-4-455.
  • 40
    • 0025286259 scopus 로고
    • Analysis of structure-function relationships of yeast TATA box binding factor TFIID
    • Horikoshi, M., Yamamoto, T., Ohkuma, Y., Weil, P. A., and Roeder, R. G. (1990) Analysis of structure-function relationships of yeast TATA box binding factor TFIID. Cell 61, 1171-1178.
    • (1990) Cell , vol.61 , pp. 1171-1178
    • Horikoshi, M.1    Yamamoto, T.2    Ohkuma, Y.3    Weil, P.A.4    Roeder, R.G.5
  • 41
    • 0027298879 scopus 로고
    • Effect of the non-conserved N-terminus on the DNA binding activity of the yeast TATA binding protein
    • Kuddus, R., and Schmidt, M. C. (1993) Effect of the non-conserved N-terminus on the DNA binding activity of the yeast TATA binding protein. Nucleic Acids Res. 21, 1789-1796.
    • (1993) Nucleic Acids Res , vol.21 , pp. 1789-1796
    • Kuddus, R.1    Schmidt, M.C.2
  • 42
    • 0035024076 scopus 로고    scopus 로고
    • Multiple functions of the nonconserved N-terminal domain of yeast TATA-binding protein
    • Lee, M., and Struhl, K. (2001) Multiple functions of the nonconserved N-terminal domain of yeast TATA-binding protein. Genetics 158, 87-93.
    • (2001) Genetics , vol.158 , pp. 87-93
    • Lee, M.1    Struhl, K.2
  • 43
    • 0029926760 scopus 로고    scopus 로고
    • Monoclonal antibodies directed against the amino-terminal domain of human TBP cross-react with TBP from other species
    • Ruppert, S. M., McCulloch, V., Meyer, M., Bautista, C., Falkowski, M., Stunnenberg, H. G., and Hernandez, N. (1996) Monoclonal antibodies directed against the amino-terminal domain of human TBP cross-react with TBP from other species. Hybridoma 15, 55-68.
    • (1996) Hybridoma , vol.15 , pp. 55-68
    • Ruppert, S.M.1    McCulloch, V.2    Meyer, M.3    Bautista, C.4    Falkowski, M.5    Stunnenberg, H.G.6    Hernandez, N.7
  • 44
    • 46849107995 scopus 로고    scopus 로고
    • Bard, Y. (1974) Nonlinear parameter estimation, pp 97, 178 (eqs 5-9-3, 7-15-14, 7-15-15), Academic Press, New York.
    • Bard, Y. (1974) Nonlinear parameter estimation, pp 97, 178 (eqs 5-9-3, 7-15-14, 7-15-15), Academic Press, New York.
  • 48
    • 0003921047 scopus 로고
    • Wiley-Interscience, New York
    • Hague, D. N. (1971) Fast reactions, pp 33-37, Wiley-Interscience, New York.
    • (1971) Fast reactions , pp. 33-37
    • Hague, D.N.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.