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Volumn 3, Issue 2, 2000, Pages 118-125

RNA polymerase structure-function: Insights into points of transcriptional regulation

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; RNA POLYMERASE; SINGLE STRANDED DNA; TRANSCRIPTION FACTOR;

EID: 0034026376     PISSN: 13695274     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1369-5274(00)00062-X     Document Type: Review
Times cited : (46)

References (51)
  • 2
    • 0032035316 scopus 로고    scopus 로고
    • Subunits of yeast RNA polymerases: Structure and function
    • Ishihama A., Kimura M., Mitsuzawa H. Subunits of yeast RNA polymerases: structure and function. Curr Opin Microbiol. 1:1998;190-196.
    • (1998) Curr Opin Microbiol , vol.1 , pp. 190-196
    • Ishihama, A.1    Kimura, M.2    Mitsuzawa, H.3
  • 3
    • 0022132080 scopus 로고
    • Extensive homology among the largest subunits of eukaryotic and prokaryotic RNA polymerases
    • Allison L.A., Moyle M., Shales M., Ingles C.J. Extensive homology among the largest subunits of eukaryotic and prokaryotic RNA polymerases. Cell. 42:1985;599-610.
    • (1985) Cell , vol.42 , pp. 599-610
    • Allison, L.A.1    Moyle, M.2    Shales, M.3    Ingles, C.J.4
  • 4
    • 0344271983 scopus 로고
    • Prokaryotic and eukaryotic RNA polymerases have homologous core subunits
    • Sweetser D., Nonet M., Young R.A. Prokaryotic and eukaryotic RNA polymerases have homologous core subunits. Proc Natl Acad Sci USA. 84:1987;1192-1196.
    • (1987) Proc Natl Acad Sci USA , vol.84 , pp. 1192-1196
    • Sweetser, D.1    Nonet, M.2    Young, R.A.3
  • 6
    • 0026690373 scopus 로고
    • Dissection of the β subunit in the E. coli RNA polymerase into domains by proteolitic cleavage
    • Severinov K., Mustaev A., Kashlev M., Borukhov S., Nikiforov V., Goldfarb A. Dissection of the β subunit in the E. coli RNA polymerase into domains by proteolitic cleavage. J Biol Chem. 267:1992;12813-12819.
    • (1992) J Biol Chem , vol.267 , pp. 12813-12819
    • Severinov, K.1    Mustaev, A.2    Kashlev, M.3    Borukhov, S.4    Nikiforov, V.5    Goldfarb, A.6
  • 8
    • 0032544695 scopus 로고    scopus 로고
    • Mutations in and monoclonal antibody binding to evolutionary hypervariable region of E. coli RNA polymerase β′ subunit inhibit transcript cleavage and transcript elongation
    • Zakharova N., Bass A., Arsenieva E., Nikiforov V., Severinov K. Mutations in and monoclonal antibody binding to evolutionary hypervariable region of E. coli RNA polymerase β′ subunit inhibit transcript cleavage and transcript elongation. J Biol Chem. 273:1998;24912-24920.
    • (1998) J Biol Chem , vol.273 , pp. 24912-24920
    • Zakharova, N.1    Bass, A.2    Arsenieva, E.3    Nikiforov, V.4    Severinov, K.5
  • 9
    • 0033578701 scopus 로고    scopus 로고
    • Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution
    • A must. This extremely important paper describes the 3.3 Å resolution structure of T. aquaticus RNAP and provides, for the first time, the atomic view of multisubunit RNA polymerase. The structure reveals an extensive network of inter- and intra-subunit contacts that hold the RNAP molecule together. Superposition of functional data from E. coli and structural data from T. aquaticus allows the authors to put forward a structural model of the transcription complex
    • Zhang G., Campbell L., Minakhin L., Richter C., Severinov K., Darst S.A. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution. Cell. 98:1999;811-824. A must. This extremely important paper describes the 3.3 Å resolution structure of T. aquaticus RNAP and provides, for the first time, the atomic view of multisubunit RNA polymerase. The structure reveals an extensive network of inter- and intra-subunit contacts that hold the RNAP molecule together. Superposition of functional data from E. coli and structural data from T. aquaticus allows the authors to put forward a structural model of the transcription complex.
    • (1999) Cell , vol.98 , pp. 811-824
    • Zhang, G.1    Campbell, L.2    Minakhin, L.3    Richter, C.4    Severinov, K.5    Darst, S.A.6
  • 10
    • 0028875725 scopus 로고
    • Three-dimensional structure of E. coli core RNA polymerase: Promoter binding and elongation conformations of the enzyme
    • Polyakov A., Severinova E., Darst S.A. Three-dimensional structure of E. coli core RNA polymerase: promoter binding and elongation conformations of the enzyme. Cell. 83:1995;365-373.
    • (1995) Cell , vol.83 , pp. 365-373
    • Polyakov, A.1    Severinova, E.2    Darst, S.A.3
  • 11
    • 0033578860 scopus 로고    scopus 로고
    • RNA polymerase unveiled
    • ••] and present a structure-functional model of transcription initiation complex
    • ••] and present a structure-functional model of transcription initiation complex.
    • (1999) Cell , vol.98 , pp. 687-690
    • Mooney, R.A.1    Landick, R.2
  • 12
    • 0030738525 scopus 로고    scopus 로고
    • Preferential interaction of the his pause RNA hairpin with RNA polymerase beta subunit residues 904-950 correlates with strong transcriptional pausing
    • Wang D., Severinov K., Landick R. Preferential interaction of the his pause RNA hairpin with RNA polymerase beta subunit residues 904-950 correlates with strong transcriptional pausing. Proc Natl Acad Sci USA. 94:1997;8433-8438.
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 8433-8438
    • Wang, D.1    Severinov, K.2    Landick, R.3
  • 13
    • 0028061282 scopus 로고
    • Promoter structure, promoter recognition, and transcription activation in prokaryotes
    • Busby S., Ebright R.H. Promoter structure, promoter recognition, and transcription activation in prokaryotes. Cell. 79:1994;743-746.
    • (1994) Cell , vol.79 , pp. 743-746
    • Busby, S.1    Ebright, R.H.2
  • 14
    • 0028933852 scopus 로고
    • The Escherichia coli RNA polymerase alpha subunit: Structure and function
    • Ebright R.H., Busby S. The Escherichia coli RNA polymerase alpha subunit: structure and function. Curr Opin Genet Dev. 5:1995;197-203.
    • (1995) Curr Opin Genet Dev , vol.5 , pp. 197-203
    • Ebright, R.H.1    Busby, S.2
  • 15
    • 0031026786 scopus 로고    scopus 로고
    • Transcription activation at class II CAP-dependent promoters
    • Busby S., Ebright R.H. Transcription activation at class II CAP-dependent promoters. Mol Microbiol. 23:1997;853-859.
    • (1997) Mol Microbiol , vol.23 , pp. 853-859
    • Busby, S.1    Ebright, R.H.2
  • 16
    • 0030582675 scopus 로고    scopus 로고
    • Transcription activation at class II CAP-dependent promoters: Two interactions between CAP and RNA polymerase
    • Niu W., Kim Y., Tau G., Heyduk T., Ebright R.H. Transcription activation at class II CAP-dependent promoters: two interactions between CAP and RNA polymerase. Cell. 87:1996;1123-1134.
    • (1996) Cell , vol.87 , pp. 1123-1134
    • Niu, W.1    Kim, Y.2    Tau, G.3    Heyduk, T.4    Ebright, R.H.5
  • 17
    • 0032504132 scopus 로고    scopus 로고
    • Structure of the Escherichia coli RNA polymerase alpha subunit amino-terminal domain
    • ••]
    • ••].
    • (1998) Science , vol.281 , pp. 262-266
    • Zhang, G.1    Darst, S.A.2
  • 18
    • 0028094718 scopus 로고
    • Transcription activation by the Escherichia coli cyclic AMP receptor protein. Receptors bound in tandem at promoters can interact synergistically
    • Busby S., West D., Lawes M., Webster C., Ishihama A., Kolb A. Transcription activation by the Escherichia coli cyclic AMP receptor protein. Receptors bound in tandem at promoters can interact synergistically. J Mol Biol. 241:1994;341-352.
    • (1994) J Mol Biol , vol.241 , pp. 341-352
    • Busby, S.1    West, D.2    Lawes, M.3    Webster, C.4    Ishihama, A.5    Kolb, A.6
  • 19
    • 0023665959 scopus 로고
    • Competition between sigma factors for core RNA polymerase
    • Malik S., Zalenskaya K., Goldfarb A. Competition between sigma factors for core RNA polymerase. Nucleic Acids Res. 15:1987;8521-8530.
    • (1987) Nucleic Acids Res , vol.15 , pp. 8521-8530
    • Malik, S.1    Zalenskaya, K.2    Goldfarb, A.3
  • 20
    • 0031844376 scopus 로고    scopus 로고
    • Negative regulation by RpoS: A case of sigma factor competition
    • Farewell A., Kvint K., Nystrom T. Negative regulation by RpoS: a case of sigma factor competition. Mol Microbiol. 29:1998;1039-1051.
    • (1998) Mol Microbiol , vol.29 , pp. 1039-1051
    • Farewell, A.1    Kvint, K.2    Nystrom, T.3
  • 21
    • 0032553125 scopus 로고    scopus 로고
    • Localization of a sigma70 binding site on the N terminus of the Escherichia coli RNA polymerase beta′ subunit
    • 70 binding to within 46 amino acids of E. coli RNAP β′ subunit
    • 70 binding to within 46 amino acids of E. coli RNAP β′ subunit.
    • (1998) J Biol Chem , vol.273 , pp. 31381-31387
    • Arthur, T.M.1    Burgess, R.R.2
  • 23
    • 0030227080 scopus 로고    scopus 로고
    • Molecular anatomy of the beta′ subunit of the E. coli RNA polymerase: Identification of regions involved in polymerase assembly
    • Luo J., Sharif K.A., Jin R., Fujita N., Ishihama A., Krakow J.S. Molecular anatomy of the beta′ subunit of the E. coli RNA polymerase: identification of regions involved in polymerase assembly. Genes Cells. 1:1996;819-827.
    • (1996) Genes Cells , vol.1 , pp. 819-827
    • Luo, J.1    Sharif, K.A.2    Jin, R.3    Fujita, N.4    Ishihama, A.5    Krakow, J.S.6
  • 25
    • 0032568456 scopus 로고    scopus 로고
    • Mapping the sigma70 subunit contact sites on Escherichia coli RNA polymerase with a sigma70-conjugated chemical protease
    • 70 and the RNAP core the authors covalently tethered FeEDTA probes at seven strategic positions of σ, formed RNAP holoenzymes and induced hydroxyl radical formation. The cut sites from different probe-modified σ proteins were clustered in distinct regions of the largest subunits of RNAP. Cleavages in conserved segments C, D and G of subunit β, and segments C and D of β′ were observed, indicating that the RNAP core-σ interface is extensive
    • 70 and the RNAP core the authors covalently tethered FeEDTA probes at seven strategic positions of σ, formed RNAP holoenzymes and induced hydroxyl radical formation. The cut sites from different probe-modified σ proteins were clustered in distinct regions of the largest subunits of RNAP. Cleavages in conserved segments C, D and G of subunit β, and segments C and D of β′ were observed, indicating that the RNAP core-σ interface is extensive.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 6021-6026
    • Owens, J.T.1    Miyake, R.2    Murakami, K.3    Chmura, A.J.4    Fujita, N.5    Ishihama, A.6    Meares, C.F.7
  • 26
    • 0033528675 scopus 로고    scopus 로고
    • Mapping protein-protein interactions with a library of tethered cutting reagents: The binding site of sigma 70 on Escherichia coli RNA polymerase
    • ••], σ-induced cleavage was detected in β subunit conserved segments B, E and H, and β′ conserved segments A and G
    • ••], σ-induced cleavage was detected in β subunit conserved segments B, E and H, and β′ conserved segments A and G.
    • (1999) Biochemistry , vol.38 , pp. 4259-4265
    • Traviglia, S.L.1    Datwyler, S.A.2    Meares, C.F.3
  • 28
    • 0024974082 scopus 로고
    • Characterization of the Escherichia coli transcription factor sigma 70: Localization of a region involved in the interaction with core RNA polymerase
    • Lesley S.A., Burgess R.R. Characterization of the Escherichia coli transcription factor sigma 70: localization of a region involved in the interaction with core RNA polymerase. Biochemistry. 28:1989;7728-7734.
    • (1989) Biochemistry , vol.28 , pp. 7728-7734
    • Lesley, S.A.1    Burgess, R.R.2
  • 29
    • 0030271890 scopus 로고    scopus 로고
    • Crystal structure of a sigma 70 subunit fragment from E. coli RNA polymerase
    • Malhotra A., Severinova E., Darst S.A. Crystal structure of a sigma 70 subunit fragment from E. coli RNA polymerase. Cell. 87:1996;127-136.
    • (1996) Cell , vol.87 , pp. 127-136
    • Malhotra, A.1    Severinova, E.2    Darst, S.A.3
  • 30
    • 0030576519 scopus 로고    scopus 로고
    • Base-specific recognition of the nontemplate strand of promoter DNA by E. coli RNA polymerase
    • Roberts C.W., Roberts J.W. Base-specific recognition of the nontemplate strand of promoter DNA by E. coli RNA polymerase. Cell. 86:1996;495-501.
    • (1996) Cell , vol.86 , pp. 495-501
    • Roberts, C.W.1    Roberts, J.W.2
  • 31
    • 0024593347 scopus 로고
    • RpoZ, encoding the omega subunit of Escherichia coli RNA polymerase, is in the same operon as spoT
    • Gentry D.R., Burgess R.R. rpoZ, encoding the omega subunit of Escherichia coli RNA polymerase, is in the same operon as spoT. J Bacteriol. 171:1989;1271-1277.
    • (1989) J Bacteriol , vol.171 , pp. 1271-1277
    • Gentry, D.R.1    Burgess, R.R.2
  • 33
    • 0032907144 scopus 로고    scopus 로고
    • Localization of E. coli rpoC mutations that affect RNA polymerase assembly and activity at high temperature
    • Nedea E.C., Markov D., Naryshkina T., Severinov K. Localization of E. coli rpoC mutations that affect RNA polymerase assembly and activity at high temperature. J Bacteriol. 181:1999;2663-2665.
    • (1999) J Bacteriol , vol.181 , pp. 2663-2665
    • Nedea, E.C.1    Markov, D.2    Naryshkina, T.3    Severinov, K.4
  • 34
    • 0029830434 scopus 로고    scopus 로고
    • Escherichia coli rpoC397 encodes a temperature-sensitive C-terminal frameshift in the beta′ subunit of RNA polymerase that blocks growth of bacteriophage P2
    • Christie G.E., Cale S.B., Isaksson L.A., Jin D.J., Xu M., Sauer B., Calendar R. Escherichia coli rpoC397 encodes a temperature-sensitive C-terminal frameshift in the beta′ subunit of RNA polymerase that blocks growth of bacteriophage P2. J Bacteriol. 178:1996;6991-6993.
    • (1996) J Bacteriol , vol.178 , pp. 6991-6993
    • Christie, G.E.1    Cale, S.B.2    Isaksson, L.A.3    Jin, D.J.4    Xu, M.5    Sauer, B.6    Calendar, R.7
  • 35
    • 0033571313 scopus 로고    scopus 로고
    • GroEL is involved in activation of Escherichia coli RNA polymerase devoid of the omega subunit in vivo
    • Mukherjee K., Nagai H., Shimamoto N., Chatterji D. GroEL is involved in activation of Escherichia coli RNA polymerase devoid of the omega subunit in vivo. Eur J Biochem. 266:1999;228-235.
    • (1999) Eur J Biochem , vol.266 , pp. 228-235
    • Mukherjee, K.1    Nagai, H.2    Shimamoto, N.3    Chatterji, D.4
  • 36
    • 0030832404 scopus 로고    scopus 로고
    • Studies on the omega subunit of Escherichia coli RNA polymerase - its role in the recovery of denatured enzyme activity
    • Mukherjee K., Chatterji D. Studies on the omega subunit of Escherichia coli RNA polymerase - its role in the recovery of denatured enzyme activity. Eur J Biochem. 247:1997;884-889.
    • (1997) Eur J Biochem , vol.247 , pp. 884-889
    • Mukherjee, K.1    Chatterji, D.2
  • 37
    • 0032032533 scopus 로고    scopus 로고
    • Conversion of the omega subunit of Escherichia coli RNA polymerase into a transcriptional activator or an activation target
    • Dove S.L., Hochschild A. Conversion of the omega subunit of Escherichia coli RNA polymerase into a transcriptional activator or an activation target. Genes Dev. 12:1998;745-754.
    • (1998) Genes Dev , vol.12 , pp. 745-754
    • Dove, S.L.1    Hochschild, A.2
  • 38
    • 0033022148 scopus 로고    scopus 로고
    • Inhibition of E. coli RNA polymerase by bacteriophage T7 gene 2 protein
    • 70, either directly or indirectly
    • 70, either directly or indirectly.
    • (1999) J Mol Biol , vol.289 , pp. 815-826
    • Nechaev, S.1    Severinov, K.2
  • 39
    • 0030896970 scopus 로고    scopus 로고
    • RNA polymerase beta′ subunit: A target of DNA binding-independent activation
    • Miller A., Wood D., Ebright R.H., Rothman-Denes L.B. RNA polymerase beta′ subunit: a target of DNA binding-independent activation. Science. 275:1997;1655-1657.
    • (1997) Science , vol.275 , pp. 1655-1657
    • Miller, A.1    Wood, D.2    Ebright, R.H.3    Rothman-Denes, L.B.4
  • 40
    • 0030893452 scopus 로고    scopus 로고
    • Paths to activation of transcription
    • Geiduschek E.P. Paths to activation of transcription. Science. 275:1997;1614-1616.
    • (1997) Science , vol.275 , pp. 1614-1616
    • Geiduschek, E.P.1
  • 41
    • 0027536870 scopus 로고
    • Transcript cleavage factors from E. coli
    • Borukhov S., Sagitov V., Goldfarb A. Transcript cleavage factors from E. coli. Cell. 72:1993;459-466.
    • (1993) Cell , vol.72 , pp. 459-466
    • Borukhov, S.1    Sagitov, V.2    Goldfarb, A.3
  • 43
    • 0031059249 scopus 로고    scopus 로고
    • Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3′ end of the RNA intact and extruded
    • Komissarova N., Kashlev M. Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3′ end of the RNA intact and extruded. Proc Natl Acad Sci USA. 94:1997;1755-1760.
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 1755-1760
    • Komissarova, N.1    Kashlev, M.2
  • 44
    • 0030950638 scopus 로고    scopus 로고
    • RNA polymerase switches between inactivated and activated states By translocating back and forth along the DNA and the RNA
    • Komissarova N., Kashlev M. RNA polymerase switches between inactivated and activated states By translocating back and forth along the DNA and the RNA. J Biol Chem. 272:1997;15329-15338.
    • (1997) J Biol Chem , vol.272 , pp. 15329-15338
    • Komissarova, N.1    Kashlev, M.2
  • 45
    • 0025049862 scopus 로고
    • The nucleotide sequence of greA, a suppressor gene that restores growth of an Escherichia coli RNA polymerase mutant at high temperature
    • Sparkowski J., Das A. The nucleotide sequence of greA, a suppressor gene that restores growth of an Escherichia coli RNA polymerase mutant at high temperature. Nucleic Acids Res. 18:1990;6443.
    • (1990) Nucleic Acids Res , vol.18 , pp. 6443
    • Sparkowski, J.1    Das, A.2
  • 46
    • 0030972676 scopus 로고    scopus 로고
    • Domain organization of Escherichia coli transcript cleavage factors GreA and GreB
    • Koulich D., Orlova M., Malhotra A., Sali A., Darst S.A., Borukhov S. Domain organization of Escherichia coli transcript cleavage factors GreA and GreB. J Biol Chem. 272:1997;7201-7210.
    • (1997) J Biol Chem , vol.272 , pp. 7201-7210
    • Koulich, D.1    Orlova, M.2    Malhotra, A.3    Sali, A.4    Darst, S.A.5    Borukhov, S.6
  • 47
  • 48
    • 0032555712 scopus 로고    scopus 로고
    • Visualization of the binding site for the transcript cleavage factor GreB on Escherichia coli RNA polymerase
    • GreB is a small protein that binds to RNAP and activates the endonucleolytic RNA cleaving activity of the RNAP catalytic center. The GreB-binding site on the E. coli RNAP core enzyme is localized using electron crystallography. The low-resolution results position bound GreB on the surface of RNAP, away from the DNA-binding channel and the catalytic center of the enzyme. Thus, GreB effects on the catalytic center activities are probably not direct, but conformational
    • Polyakov A., Richter C., Malhotra A., Koulich D., Borukhov S., Darst S.A. Visualization of the binding site for the transcript cleavage factor GreB on Escherichia coli RNA polymerase. J Mol Biol. 281:1998;465-473. GreB is a small protein that binds to RNAP and activates the endonucleolytic RNA cleaving activity of the RNAP catalytic center. The GreB-binding site on the E. coli RNAP core enzyme is localized using electron crystallography. The low-resolution results position bound GreB on the surface of RNAP, away from the DNA-binding channel and the catalytic center of the enzyme. Thus, GreB effects on the catalytic center activities are probably not direct, but conformational.
    • (1998) J Mol Biol , vol.281 , pp. 465-473
    • Polyakov, A.1    Richter, C.2    Malhotra, A.3    Koulich, D.4    Borukhov, S.5    Darst, S.A.6
  • 49
    • 0027517721 scopus 로고
    • Bacteriophage T4 Alc protein: A transcription termination factor sensing local modification of DNA
    • Kashlev M., Nudler E., Goldfarb A., White T., Kutter E. Bacteriophage T4 Alc protein: a transcription termination factor sensing local modification of DNA. Cell. 75:1993;147-154.
    • (1993) Cell , vol.75 , pp. 147-154
    • Kashlev, M.1    Nudler, E.2    Goldfarb, A.3    White, T.4    Kutter, E.5
  • 50
    • 0029818631 scopus 로고    scopus 로고
    • Transcription processivity: Protein-DNA interactions holding together the elongation complex
    • Nudler E., Avetissova E., Markovtsov V., Goldfarb A. Transcription processivity: protein-DNA interactions holding together the elongation complex. Science. 273:1996;211-217.
    • (1996) Science , vol.273 , pp. 211-217
    • Nudler, E.1    Avetissova, E.2    Markovtsov, V.3    Goldfarb, A.4
  • 51
    • 0031456021 scopus 로고    scopus 로고
    • A mutant RNA polymerase that forms unusual open promoter complexes
    • Severinov K., Darst S.A. A mutant RNA polymerase that forms unusual open promoter complexes. Proc Natl Acad Sci USA. 94:1997;13481-13486.
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 13481-13486
    • Severinov, K.1    Darst, S.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.