메뉴 건너뛰기




Volumn 27, Issue 3, 2007, Pages 406-419

A Central Role of the RNA Polymerase Trigger Loop in Active-Site Rearrangement during Transcriptional Pausing

Author keywords

DNA

Indexed keywords

NUCLEOTIDE; RNA POLYMERASE;

EID: 34547204502     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molcel.2007.06.008     Document Type: Article
Times cited : (173)

References (57)
  • 2
    • 0141785208 scopus 로고    scopus 로고
    • Running with RNA polymerase: eukaryotic transcript elongation
    • Arndt K.M., and Kane C.M. Running with RNA polymerase: eukaryotic transcript elongation. Trends Genet. 19 (2003) 543-550
    • (2003) Trends Genet. , vol.19 , pp. 543-550
    • Arndt, K.M.1    Kane, C.M.2
  • 3
    • 0034691146 scopus 로고    scopus 로고
    • Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals
    • Artsimovitch I., and Landick R. Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals. Proc. Natl. Acad. Sci. USA 97 (2000) 7090-7095
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 7090-7095
    • Artsimovitch, I.1    Landick, R.2
  • 4
    • 0038823636 scopus 로고    scopus 로고
    • Co-overexpression of E. coli RNA polymerase subunits allows isolation and analysis of mutant enzymes lacking lineage-specific sequence insertions
    • Artsimovitch I., Svetlov V., Murakami K., and Landick R. Co-overexpression of E. coli RNA polymerase subunits allows isolation and analysis of mutant enzymes lacking lineage-specific sequence insertions. J. Biol. Chem. 278 (2003) 12344-12355
    • (2003) J. Biol. Chem. , vol.278 , pp. 12344-12355
    • Artsimovitch, I.1    Svetlov, V.2    Murakami, K.3    Landick, R.4
  • 5
    • 7444253928 scopus 로고    scopus 로고
    • Sequence-dependent kinetic model for transcription elongation by RNA polymerase
    • Bai L., Shundrovsky A., and Wang M.D. Sequence-dependent kinetic model for transcription elongation by RNA polymerase. J. Mol. Biol. 344 (2004) 335-349
    • (2004) J. Mol. Biol. , vol.344 , pp. 335-349
    • Bai, L.1    Shundrovsky, A.2    Wang, M.D.3
  • 7
    • 0026317447 scopus 로고
    • Mapping of a contact for the RNA 3′ terminus in the largest subunit of RNA polymerase
    • Borukhov S., Lee J., and Goldfarb A. Mapping of a contact for the RNA 3′ terminus in the largest subunit of RNA polymerase. J. Biol. Chem. 266 (1991) 23932-23935
    • (1991) J. Biol. Chem. , vol.266 , pp. 23932-23935
    • Borukhov, S.1    Lee, J.2    Goldfarb, A.3
  • 8
    • 0037022279 scopus 로고    scopus 로고
    • Structural basis of transcription: alpha-amanitin-RNA polymerase II cocrystal at 2.8 A resolution
    • Bushnell D.A., Cramer P., and Kornberg R.D. Structural basis of transcription: alpha-amanitin-RNA polymerase II cocrystal at 2.8 A resolution. Proc. Natl. Acad. Sci. USA 99 (2002) 1218-1222
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 1218-1222
    • Bushnell, D.A.1    Cramer, P.2    Kornberg, R.D.3
  • 9
    • 0028222235 scopus 로고
    • Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions
    • Chakrabartty A., Kortemme T., and Baldwin R.L. Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci. 3 (1994) 843-852
    • (1994) Protein Sci. , vol.3 , pp. 843-852
    • Chakrabartty, A.1    Kortemme, T.2    Baldwin, R.L.3
  • 10
    • 0031585994 scopus 로고    scopus 로고
    • Spacing from the transcript 3′ end determines whether a nascent RNA hairpin interacts with RNA polymerase to prolong pausing or triggers termination
    • Chan C., Wang D., and Landick R. Spacing from the transcript 3′ end determines whether a nascent RNA hairpin interacts with RNA polymerase to prolong pausing or triggers termination. J. Mol. Biol. 268 (1997) 54-68
    • (1997) J. Mol. Biol. , vol.268 , pp. 54-68
    • Chan, C.1    Wang, D.2    Landick, R.3
  • 11
    • 25144510935 scopus 로고    scopus 로고
    • Structure and function of lineage-specific sequence insertions in the bacteria RNA polymerase β′ subunit
    • Chlenov M., Masuda S., Murakami K., Nikiforov V., Darst S., and Mustaev A. Structure and function of lineage-specific sequence insertions in the bacteria RNA polymerase β′ subunit. J. Mol. Biol. 353 (2005) 38-54
    • (2005) J. Mol. Biol. , vol.353 , pp. 38-54
    • Chlenov, M.1    Masuda, S.2    Murakami, K.3    Nikiforov, V.4    Darst, S.5    Mustaev, A.6
  • 12
    • 0035827346 scopus 로고    scopus 로고
    • Structural basis of transcription: RNA polymerase II at 2.8 Å resolution
    • Cramer P., Bushnell D., and Kornberg R. Structural basis of transcription: RNA polymerase II at 2.8 Å resolution. Science 292 (2001) 1863-1876
    • (2001) Science , vol.292 , pp. 1863-1876
    • Cramer, P.1    Bushnell, D.2    Kornberg, R.3
  • 14
    • 32044451311 scopus 로고    scopus 로고
    • Functional interplay between the downstream DNA-Jaw domain of bacterial RNA polymerase and allele-specific residues in the product RNA-binding pocket
    • Ederth J., Mooney R., Isaksson L., and Landick R. Functional interplay between the downstream DNA-Jaw domain of bacterial RNA polymerase and allele-specific residues in the product RNA-binding pocket. J. Mol. Biol. 356 (2006) 1163-1179
    • (2006) J. Mol. Biol. , vol.356 , pp. 1163-1179
    • Ederth, J.1    Mooney, R.2    Isaksson, L.3    Landick, R.4
  • 16
    • 0037073062 scopus 로고    scopus 로고
    • The many conformational states of RNA polymerase elongation complexes and their roles in the regulation of transcription
    • Erie D.A. The many conformational states of RNA polymerase elongation complexes and their roles in the regulation of transcription. Biochim. Biophys. Acta 1577 (2002) 224-239
    • (2002) Biochim. Biophys. Acta , vol.1577 , pp. 224-239
    • Erie, D.A.1
  • 17
    • 0027761137 scopus 로고
    • Multiple RNA polymerase conformations and GreA: control of fidelity of transcription
    • Erie D.A., Hajiseyedjavadi O., Young M.C., and von Hippel P.H. Multiple RNA polymerase conformations and GreA: control of fidelity of transcription. Science 262 (1993) 867-873
    • (1993) Science , vol.262 , pp. 867-873
    • Erie, D.A.1    Hajiseyedjavadi, O.2    Young, M.C.3    von Hippel, P.H.4
  • 18
    • 0035958552 scopus 로고    scopus 로고
    • Allosteric binding of nucleoside triphosphates to RNA polymerase regulates transcription elongation
    • Foster J.E., Holmes S.F., and Erie D.A. Allosteric binding of nucleoside triphosphates to RNA polymerase regulates transcription elongation. Cell 106 (2001) 243-252
    • (2001) Cell , vol.106 , pp. 243-252
    • Foster, J.E.1    Holmes, S.F.2    Erie, D.A.3
  • 19
    • 0035827332 scopus 로고    scopus 로고
    • Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 Å resolution
    • Gnatt A., Cramer P., Fu J., Bushnell D., and Kornberg R.D. Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 Å resolution. Science 292 (2001) 1876-1882
    • (2001) Science , vol.292 , pp. 1876-1882
    • Gnatt, A.1    Cramer, P.2    Fu, J.3    Bushnell, D.4    Kornberg, R.D.5
  • 20
    • 0033120034 scopus 로고    scopus 로고
    • The mechanism of intrinsic transcription termination
    • Gusarov I., and Nudler E. The mechanism of intrinsic transcription termination. Mol. Cell 3 (1999) 495-504
    • (1999) Mol. Cell , vol.3 , pp. 495-504
    • Gusarov, I.1    Nudler, E.2
  • 21
    • 33744981369 scopus 로고    scopus 로고
    • Sequence-resolved detection of pausing by single RNA polymerase molecules
    • Herbert R., La Porta A., Wong B., Mooney R., Neuman K., Landick R., and Block S. Sequence-resolved detection of pausing by single RNA polymerase molecules. Cell 125 (2006) 1083-1094
    • (2006) Cell , vol.125 , pp. 1083-1094
    • Herbert, R.1    La Porta, A.2    Wong, B.3    Mooney, R.4    Neuman, K.5    Landick, R.6    Block, S.7
  • 22
    • 0043244876 scopus 로고    scopus 로고
    • Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage
    • Kettenberger H., Armache K.J., and Cramer P. Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage. Cell 114 (2003) 347-357
    • (2003) Cell , vol.114 , pp. 347-357
    • Kettenberger, H.1    Armache, K.J.2    Cramer, P.3
  • 23
    • 10944232674 scopus 로고    scopus 로고
    • Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS
    • Kettenberger H., Armache K.J., and Cramer P. Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol. Cell 16 (2004) 955-965
    • (2004) Mol. Cell , vol.16 , pp. 955-965
    • Kettenberger, H.1    Armache, K.J.2    Cramer, P.3
  • 26
    • 34547097808 scopus 로고    scopus 로고
    • Direct versus limited-step reconstitution reveals key features of an RNA hairpin-stabilized paused transcription complex
    • Kyzer S., Ha K.S., Landick R., and Palangat M. Direct versus limited-step reconstitution reveals key features of an RNA hairpin-stabilized paused transcription complex. J. Biol. Chem. 282 (2007) 19020-19028
    • (2007) J. Biol. Chem. , vol.282 , pp. 19020-19028
    • Kyzer, S.1    Ha, K.S.2    Landick, R.3    Palangat, M.4
  • 27
    • 0035368724 scopus 로고    scopus 로고
    • RNA polymerase clamps down
    • Landick R. RNA polymerase clamps down. Cell 105 (2001) 567-570
    • (2001) Cell , vol.105 , pp. 567-570
    • Landick, R.1
  • 28
    • 1642417611 scopus 로고    scopus 로고
    • Active-site dynamics in RNA polymerases
    • Landick R. Active-site dynamics in RNA polymerases. Cell 116 (2004) 351-353
    • (2004) Cell , vol.116 , pp. 351-353
    • Landick, R.1
  • 29
    • 33846914726 scopus 로고    scopus 로고
    • The regulatory roles and mechanism of transcriptional pausing
    • Landick R. The regulatory roles and mechanism of transcriptional pausing. Biochem. Soc. Trans. 34 (2006) 1062-1066
    • (2006) Biochem. Soc. Trans. , vol.34 , pp. 1062-1066
    • Landick, R.1
  • 30
    • 0023660755 scopus 로고
    • Isolation and structural analysis of the Escherichia coli trp leader paused transcription complex
    • Landick R., and Yanofsky C. Isolation and structural analysis of the Escherichia coli trp leader paused transcription complex. J. Mol. Biol. 196 (1987) 363-377
    • (1987) J. Mol. Biol. , vol.196 , pp. 363-377
    • Landick, R.1    Yanofsky, C.2
  • 31
    • 0025062984 scopus 로고
    • Amino acid changes in conserved regions of the β-subunit of Escherichia coli RNA polymerase alter transcription pausing and termination
    • Landick R., Stewart J., and Lee D.N. Amino acid changes in conserved regions of the β-subunit of Escherichia coli RNA polymerase alter transcription pausing and termination. Genes Dev. 4 (1990) 1623-1636
    • (1990) Genes Dev. , vol.4 , pp. 1623-1636
    • Landick, R.1    Stewart, J.2    Lee, D.N.3
  • 32
    • 0029983157 scopus 로고    scopus 로고
    • Protein-RNA interactions in the active center of the transcription elongation complex
    • Markovtsov V., Mustaev A., and Goldfarb A. Protein-RNA interactions in the active center of the transcription elongation complex. Proc. Natl. Acad. Sci. USA 93 (1996) 3221-3226
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 3221-3226
    • Markovtsov, V.1    Mustaev, A.2    Goldfarb, A.3
  • 33
    • 0034646194 scopus 로고    scopus 로고
    • Importance of terminal base pair hydrogen-bonding in 3′-end proofreading by the Klenow fragment of DNA polymerase I
    • Morales J.C., and Kool E.T. Importance of terminal base pair hydrogen-bonding in 3′-end proofreading by the Klenow fragment of DNA polymerase I. Biochemistry 39 (2000) 2626-2632
    • (2000) Biochemistry , vol.39 , pp. 2626-2632
    • Morales, J.C.1    Kool, E.T.2
  • 35
    • 0345047725 scopus 로고    scopus 로고
    • Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking
    • Neuman K., Abbondanzieri E., Landick R., Gelles J., and Block S.M. Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking. Cell 115 (2003) 437-447
    • (2003) Cell , vol.115 , pp. 437-447
    • Neuman, K.1    Abbondanzieri, E.2    Landick, R.3    Gelles, J.4    Block, S.M.5
  • 36
    • 0028066790 scopus 로고
    • Discontinuous mechanism of transcription elongation
    • Nudler E., Goldfarb A., and Kashlev M. Discontinuous mechanism of transcription elongation. Science 265 (1994) 793-796
    • (1994) Science , vol.265 , pp. 793-796
    • Nudler, E.1    Goldfarb, A.2    Kashlev, M.3
  • 37
    • 0029818631 scopus 로고    scopus 로고
    • Transcription processivity: RNA polymerase-DNA interactions holding together the elongation complex
    • Nudler E., Avetissova E., Markovstov V., and Goldfarb A. Transcription processivity: RNA polymerase-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    Markovstov, V.3    Goldfarb, A.4
  • 38
    • 1842715585 scopus 로고    scopus 로고
    • Forward translocation is the natural pathway of RNA release at an intrinsic terminator
    • Santangelo T.J., and Roberts J.W. Forward translocation is the natural pathway of RNA release at an intrinsic terminator. Mol. Cell 14 (2004) 117-126
    • (2004) Mol. Cell , vol.14 , pp. 117-126
    • Santangelo, T.J.1    Roberts, J.W.2
  • 39
    • 0032113494 scopus 로고    scopus 로고
    • Crucial role of the RNA:DNA hybrid in the processivity of transcription
    • Sidorenkov I., Komissarova N., and Kashlev M. Crucial role of the RNA:DNA hybrid in the processivity of transcription. Mol. Cell 2 (1998) 55-64
    • (1998) Mol. Cell , vol.2 , pp. 55-64
    • Sidorenkov, I.1    Komissarova, N.2    Kashlev, M.3
  • 40
    • 0037543997 scopus 로고    scopus 로고
    • Unified two-metal mechanism of RNA synthesis and degradation by RNA polymerase
    • Sosunov V., Sosunova E., Mustaev A., Bass I., Nikiforov V., and Goldfarb A. Unified two-metal mechanism of RNA synthesis and degradation by RNA polymerase. EMBO J. 22 (2003) 2234-2244
    • (2003) EMBO J. , vol.22 , pp. 2234-2244
    • Sosunov, V.1    Sosunova, E.2    Mustaev, A.3    Bass, I.4    Nikiforov, V.5    Goldfarb, A.6
  • 41
    • 0032518374 scopus 로고    scopus 로고
    • A mechanism for all polymerases
    • Steitz T.A. A mechanism for all polymerases. Nature 391 (1998) 231-232
    • (1998) Nature , vol.391 , pp. 231-232
    • Steitz, T.A.1
  • 43
    • 0032524661 scopus 로고    scopus 로고
    • Transcriptional fidelity and proofreading by RNA polymerase II
    • Thomas M.J., Platas A.A., and Hawley D.K. Transcriptional fidelity and proofreading by RNA polymerase II. Cell 93 (1998) 627-637
    • (1998) Cell , vol.93 , pp. 627-637
    • Thomas, M.J.1    Platas, A.A.2    Hawley, D.K.3
  • 44
    • 0344413496 scopus 로고    scopus 로고
    • The flap domain is required for pause RNA hairpin inhibition of catalysis by RNA polymerase and can modulate intrinsic termination
    • Toulokhonov I., and Landick R. The flap domain is required for pause RNA hairpin inhibition of catalysis by RNA polymerase and can modulate intrinsic termination. Mol. Cell 12 (2003) 1125-1136
    • (2003) Mol. Cell , vol.12 , pp. 1125-1136
    • Toulokhonov, I.1    Landick, R.2
  • 45
    • 0035957687 scopus 로고    scopus 로고
    • Allosteric control of RNA polymerase by a site that contacts nascent RNA hairpins
    • Toulokhonov I., Artsimovitch I., and Landick R. Allosteric control of RNA polymerase by a site that contacts nascent RNA hairpins. Science 292 (2001) 730-733
    • (2001) Science , vol.292 , pp. 730-733
    • Toulokhonov, I.1    Artsimovitch, I.2    Landick, R.3
  • 50
    • 0037058904 scopus 로고    scopus 로고
    • Reaction pathways in transcript elongation
    • von Hippel P.H., and Pasman Z. Reaction pathways in transcript elongation. Biophys. Chem. 101-102 (2002) 401-423
    • (2002) Biophys. Chem. , vol.101-102 , pp. 401-423
    • von Hippel, P.H.1    Pasman, Z.2
  • 51
    • 0029029468 scopus 로고
    • Discontinuous movements of DNA and RNA in E. coli RNA polymerase accompany formation of a paused transcription complex
    • Wang D., Meier T., Chan C., Feng G., Lee D., and Landick R. Discontinuous movements of DNA and RNA in E. coli RNA polymerase accompany formation of a paused transcription complex. Cell 81 (1995) 341-350
    • (1995) Cell , vol.81 , pp. 341-350
    • Wang, D.1    Meier, T.2    Chan, C.3    Feng, G.4    Lee, D.5    Landick, R.6
  • 52
    • 33751235874 scopus 로고    scopus 로고
    • Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis
    • Wang D., Bushnell D., Westover K., Kaplan C., and Kornberg R. Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis. Cell 127 (2006) 941-954
    • (2006) Cell , vol.127 , pp. 941-954
    • Wang, D.1    Bushnell, D.2    Westover, K.3    Kaplan, C.4    Kornberg, R.5
  • 53
    • 0028104343 scopus 로고
    • Termination-altering amino acid substitutions in the β′ subunit of Escherichia coli RNA polymerase identify regions involved in RNA chain elongation
    • Weilbaecher R., Hebron C., Feng G., and Landick R. Termination-altering amino acid substitutions in the β′ subunit of Escherichia coli RNA polymerase identify regions involved in RNA chain elongation. Genes Dev. 8 (1994) 2913-2917
    • (1994) Genes Dev. , vol.8 , pp. 2913-2917
    • Weilbaecher, R.1    Hebron, C.2    Feng, G.3    Landick, R.4
  • 54
    • 8344234112 scopus 로고    scopus 로고
    • Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center
    • Westover K.D., Bushnell D.A., and Kornberg R.D. Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center. Cell 119 (2004) 481-489
    • (2004) Cell , vol.119 , pp. 481-489
    • Westover, K.D.1    Bushnell, D.A.2    Kornberg, R.D.3
  • 55
    • 33750972017 scopus 로고    scopus 로고
    • RNA polymerase pausing regulates translation initiation by providing additional time for TRAP-RNA interaction
    • Yakhnin A.V., Yakhnin H., and Babitzke P. RNA polymerase pausing regulates translation initiation by providing additional time for TRAP-RNA interaction. Mol. Cell 24 (2006) 547-557
    • (2006) Mol. Cell , vol.24 , pp. 547-557
    • Yakhnin, A.V.1    Yakhnin, H.2    Babitzke, P.3
  • 56
    • 33746634704 scopus 로고    scopus 로고
    • Transcript-assisted transcriptional proofreading
    • Zenkin N., Yuzenkova Y., and Severinov K. Transcript-assisted transcriptional proofreading. Science 313 (2006) 518-520
    • (2006) Science , vol.313 , pp. 518-520
    • Zenkin, N.1    Yuzenkova, Y.2    Severinov, K.3
  • 57
    • 0033578701 scopus 로고    scopus 로고
    • Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution
    • Zhang G., Campbell E.A., Minakhin L., Richter C., Severinov K., and Darst S.A. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution. Cell 98 (1999) 811-824
    • (1999) Cell , vol.98 , pp. 811-824
    • Zhang, G.1    Campbell, E.A.2    Minakhin, L.3    Richter, C.4    Severinov, K.5    Darst, S.A.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.