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Volumn 17, Issue 1, 2010, Pages 99-105

Role of the RNA polymerase trigger loop in catalysis and pausing

Author keywords

[No Author keywords available]

Indexed keywords

DNA DIRECTED RNA POLYMERASE; PRIMER DNA; PROTEIN SUBUNIT;

EID: 77449093660     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb.1732     Document Type: Article
Times cited : (119)

References (43)
  • 1
    • 2942576138 scopus 로고    scopus 로고
    • Evolution of bacterial RNA polymerase: Implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer
    • Iyer, L.M., Koonin, E.V. & Aravind, L. Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer. Gene 335, 73-88 (2004).
    • (2004) Gene , vol.335 , pp. 73-88
    • Iyer, L.M.1    Koonin, E.V.2    Aravind, L.3
  • 2
    • 1642417611 scopus 로고    scopus 로고
    • Active-site dynamics in RNA polymerases
    • Landick, R. Active-site dynamics in RNA polymerases. Cell 116, 351-353 (2004).
    • (2004) Cell , vol.116 , pp. 351-353
    • Landick, R.1
  • 3
    • 0016273095 scopus 로고
    • Ribonucleic acid chain elongation by Escherichia coli ribonucleic acid polymerase: Isolation of ternary complexes and the kinetics of elongation
    • Rhodes, G. & Chamberlin, M.J. Ribonucleic acid chain elongation by Escherichia coli ribonucleic acid polymerase: isolation of ternary complexes and the kinetics of elongation. J. Biol. Chem. 249, 6675-6683 (1974).
    • (1974) J. Biol. Chem. , vol.249 , pp. 6675-6683
    • Rhodes, G.1    Chamberlin, M.J.2
  • 4
    • 44449094019 scopus 로고    scopus 로고
    • Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation
    • Kireeva, M.L. et al. Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation. Mol. Cell 30, 557-566 (2008).
    • (2008) Mol. Cell , vol.30 , pp. 557-566
    • Kireeva, M.L.1
  • 5
    • 0041696782 scopus 로고    scopus 로고
    • Loading Rho to terminate transcription
    • Richardson, J.P. Loading Rho to terminate transcription. Cell 114, 157-159 (2003).
    • (2003) Cell , vol.114 , pp. 157-159
    • Richardson, J.P.1
  • 6
    • 34447513771 scopus 로고    scopus 로고
    • Structural basis for substrate loading in bacterial RNA polymerase
    • Vassylyev, D. et al. Structural basis for substrate loading in bacterial RNA polymerase. Nature 448, 157-162 (2007).
    • (2007) Nature , vol.448 , pp. 157-162
    • Vassylyev, D.1
  • 7
    • 0037071844 scopus 로고    scopus 로고
    • Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution
    • Vassylyev, D.G. et al. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution. Nature 417, 712-719 (2002).
    • (2002) Nature , vol.417 , pp. 712-719
    • Vassylyev, D.G.1
  • 8
    • 33751235874 scopus 로고    scopus 로고
    • Structural basis of transcription: Role of the trigger loop in substrate specificity and catalysis
    • Wang, D., Bushnell, D.A., Westover, K.D., Kaplan, C.D. & Kornberg, R.D. Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis. Cell 127, 941-954 (2006).
    • (2006) Cell , vol.127 , pp. 941-954
    • Wang, D.1    Bushnell, D.A.2    Westover, K.D.3    Kaplan, C.D.4    Kornberg, R.D.5
  • 9
    • 0033597435 scopus 로고    scopus 로고
    • Mechanism of instrinsic termination and antitermination
    • Yarnell, W.S. & Roberts, J.W. Mechanism of instrinsic termination and antitermination. Science 284, 611-615 (1999).
    • (1999) Science , vol.284 , pp. 611-615
    • Yarnell, W.S.1    Roberts, J.W.2
  • 10
    • 33746634704 scopus 로고    scopus 로고
    • Transcript-assisted transcriptional proofreading
    • Zenkin, N., Yuzenkova, Y. & Severinov, K. Transcript-assisted transcriptional proofreading. Science 313, 518-520 (2006).
    • (2006) Science , vol.313 , pp. 518-520
    • Zenkin, N.1    Yuzenkova, Y.2    Severinov, K.3
  • 11
    • 0037543997 scopus 로고    scopus 로고
    • Unified two-metal mechanism of RNA synthesis and degradation by RNA polymerase
    • Sosunov, V. et al. Unified two-metal mechanism of RNA synthesis and degradation by RNA polymerase. EMBO J. 22, 2234-2244 (2003).
    • (2003) EMBO J , vol.22 , pp. 2234-2244
    • Sosunov, V.1
  • 12
    • 10944232674 scopus 로고    scopus 로고
    • Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS
    • Kettenberger, H., Armache, K.J. & Cramer, P. Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol. Cell 16, 955-965 (2004).
    • (2004) Mol. Cell , vol.16 , pp. 955-965
    • Kettenberger, H.1    Armache, K.J.2    Cramer, P.3
  • 13
    • 0043244877 scopus 로고    scopus 로고
    • Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase
    • Opalka, N. et al. Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase. Cell 114, 335-345 (2003).
    • (2003) Cell , vol.114 , pp. 335-345
    • Opalka, N.1
  • 15
    • 0347994909 scopus 로고    scopus 로고
    • Donation of catalytic residues to RNA polymerase active center by transcription factor Gre
    • Sosunova, E. et al. Donation of catalytic residues to RNA polymerase active center by transcription factor Gre. Proc. Natl. Acad. Sci. USA 100, 15469-15474 (2003).
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 15469-15474
    • Sosunova, E.1
  • 16
    • 66349138227 scopus 로고    scopus 로고
    • Structural basis of transcription: Backtracked RNA polymerase II at 3.4 angstrom resolution
    • Wang, D. et al. Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution. Science 324, 1203-1206 (2009).
    • (2009) Science , vol.324 , pp. 1203-1206
    • Wang, D.1
  • 17
    • 0032518374 scopus 로고    scopus 로고
    • A mechanism for all polymerases
    • Steitz, T.A. A mechanism for all polymerases. Nature 391, 231-232 (1998).
    • (1998) Nature , vol.391 , pp. 231-232
    • Steitz, T.A.1
  • 18
    • 0030917007 scopus 로고    scopus 로고
    • Modular organization of the catalytic center of RNA polymerase
    • Mustaev, A. et al. Modular organization of the catalytic center of RNA polymerase. Proc. Natl. Acad. Sci. USA 94, 6641-6645 (1997).
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 6641-6645
    • Mustaev, A.1
  • 19
    • 34248349170 scopus 로고    scopus 로고
    • Two proton transfers in the transition state for nucleotidyl transfer catalyzed by RNA- and DNA-dependent RNA and DNA polymerases
    • Castro, C. et al. Two proton transfers in the transition state for nucleotidyl transfer catalyzed by RNA- and DNA-dependent RNA and DNA polymerases. Proc. Natl. Acad. Sci. USA 104, 4267-4272 (2007).
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 4267-4272
    • Castro, C.1
  • 20
    • 59649110607 scopus 로고    scopus 로고
    • Nucleic acid polymerases use a general acid for nucleotidyl transfer
    • Castro, C. et al. Nucleic acid polymerases use a general acid for nucleotidyl transfer. Nat. Struct. Mol. Biol. 16, 212-218 (2009).
    • (2009) Nat. Struct. Mol. Biol. , vol.16 , pp. 212-218
    • Castro, C.1
  • 21
    • 57249108333 scopus 로고    scopus 로고
    • Bridge helix and trigger loop perturbations generate superactive RNA polymerases
    • Tan, L., Wiesler, S., Trzaska, D., Carney, H.C. & Weinzierl, R.O. Bridge helix and trigger loop perturbations generate superactive RNA polymerases. J. Biol. 7, 40-54 (2008).
    • (2008) J. Biol. , vol.7 , pp. 40-54
    • Tan, L.1    Wiesler, S.2    Trzaska, D.3    Carney, H.C.4    Weinzierl, R.O.5
  • 22
    • 34547204502 scopus 로고    scopus 로고
    • A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing
    • Toulokhonov, I., Zhang, J., Palangat, M. & Landick, R. A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing. Mol. Cell 27, 406-419 (2007).
    • (2007) Mol. Cell , vol.27 , pp. 406-419
    • Toulokhonov, I.1    Zhang, J.2    Palangat, M.3    Landick, R.4
  • 23
    • 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. & 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, 12344-12355 (2003).
    • (2003) J. Biol. Chem. , vol.278 , pp. 12344-12355
    • Artsimovitch, I.1    Svetlov, V.2    Murakami, K.3    Landick, R.4
  • 24
    • 25144510935 scopus 로고    scopus 로고
    • Structure and function of lineage-specific sequence insertions in the bacterial RNA polymerase p' subunit
    • Chlenov, M. et al. Structure and function of lineage-specific sequence insertions in the bacterial RNA polymerase p' subunit. J. Mol. Biol. 353, 138-154 (2005).
    • (2005) J. Mol. Biol. , vol.353 , pp. 138-154
    • Chlenov, M.1
  • 25
    • 49449102926 scopus 로고    scopus 로고
    • Structural basis of transcription inhibition by alpha- amanitin and implications for RNA polymerase II translocation
    • Brueckner, F. & Cramer, P. Structural basis of transcription inhibition by alpha- amanitin and implications for RNA polymerase II translocation. Nat. Struct. Mol. Biol. 15, 811-818 (2008).
    • (2008) Nat. Struct. Mol. Biol. , vol.15 , pp. 811-818
    • Brueckner, F.1    Cramer, P.2
  • 26
    • 44449103640 scopus 로고    scopus 로고
    • The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitin
    • Kaplan, C.D., Larsson, K.M. & Kornberg, R.D. The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitin. Mol. Cell 30, 547-556 (2008).
    • (2008) Mol. Cell , vol.30 , pp. 547-556
    • Kaplan, C.D.1    Larsson, K.M.2    Kornberg, R.D.3
  • 27
    • 24044497229 scopus 로고    scopus 로고
    • Structural basis of transcription inhibition by antibiotic streptolydigin
    • Temiakov, D. et al. Structural basis of transcription inhibition by antibiotic streptolydigin. Mol. Cell 19, 655-666 (2005).
    • (2005) Mol. Cell , vol.19 , pp. 655-666
    • Temiakov, D.1
  • 28
    • 23944521364 scopus 로고    scopus 로고
    • Inhibition of bacterial RNA polymerase by streptolydigin: Stabilization of a straight-bridge-helix active-center conformation
    • Tuske, S. et al. Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation. Cell 122, 541-552 (2005).
    • (2005) Cell , vol.122 , pp. 541-552
    • Tuske, S.1
  • 29
    • 33744981369 scopus 로고    scopus 로고
    • Sequence-resolved detection of pausing by single RNA polymerase molecules
    • Herbert, K.M. et al. Sequence-resolved detection of pausing by single RNA polymerase molecules. Cell 125, 1083-1094 (2006).
    • (2006) Cell , vol.125 , pp. 1083-1094
    • Herbert, K.M.1
  • 30
    • 0345047725 scopus 로고    scopus 로고
    • Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking
    • Neuman, K.C., Abbondanzieri, E.A., Landick, R., Gelles, J. & Block, S.M. Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking. Cell 115, 437-447 (2003).
    • (2003) Cell , vol.115 , pp. 437-447
    • Neuman, K.C.1    Abbondanzieri, E.A.2    Landick, R.3    Gelles, J.4    Block, S.M.5
  • 31
    • 4644265121 scopus 로고    scopus 로고
    • Discrimination against deoxyribonucleotide substrates by bacterial RNA polymerase
    • Svetlov, V., Vassylyev, D.G. & Artsimovitch, I. Discrimination against deoxyribonucleotide substrates by bacterial RNA polymerase. J. Biol. Chem. 279, 38087-38090 (2004).
    • (2004) J. Biol. Chem. , vol.279 , pp. 38087-38090
    • Svetlov, V.1    Vassylyev, D.G.2    Artsimovitch, I.3
  • 32
    • 33646188087 scopus 로고    scopus 로고
    • Mutations in the Saccharomyces cerevisiae RPB1 gene conferring hypersensitivity to 6-azauracil
    • Malagon, F. et al. Mutations in the Saccharomyces cerevisiae RPB1 gene conferring hypersensitivity to 6-azauracil. Genetics 172, 2201-2209 (2006).
    • (2006) Genetics , vol.172 , pp. 2201-2209
    • Malagon, F.1
  • 33
    • 12944324227 scopus 로고    scopus 로고
    • A ratchet mechanism of transcription elongation and its control
    • Bar-Nahum, G. et al. A ratchet mechanism of transcription elongation and its control. Cell 120, 183-193 (2005).
    • (2005) Cell , vol.120 , pp. 183-193
    • Bar-Nahum, G.1
  • 34
    • 67049100283 scopus 로고    scopus 로고
    • Mechanism of sequence-specific pausing of bacterial RNA polymerase
    • Kireeva, M.L. & Kashlev, M. Mechanism of sequence-specific pausing of bacterial RNA polymerase. Proc. Natl. Acad. Sci. USA 106, 8900-8905 (2009).
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 8900-8905
    • Kireeva, M.L.1    Kashlev, M.2
  • 35
    • 67049154068 scopus 로고    scopus 로고
    • Transcriptional pausing without backtracking
    • Landick, R. Transcriptional pausing without backtracking. Proc. Natl. Acad. Sci. USA 106, 8797-8798 (2009).
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 8797-8798
    • Landick, R.1
  • 36
    • 0034719142 scopus 로고    scopus 로고
    • DNA polymerase p: Contributions of template-positioning and dNTP triphosphate-binding residues to catalysis and fidelity
    • Kraynov, V.S., Showalter, A.K., Liu, J., Zhong, X. & Tsai, M.D. DNA polymerase p: contributions of template-positioning and dNTP triphosphate-binding residues to catalysis and fidelity. Biochemistry 39, 16008-16015 (2000).
    • (2000) Biochemistry , vol.39 , pp. 16008-16015
    • Kraynov, V.S.1    Showalter, A.K.2    Liu, J.3    Zhong, X.4    Tsai, M.D.5
  • 37
    • 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. & 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, 1125-1136 (2003).
    • (2003) Mol. Cell , vol.12 , pp. 1125-1136
    • Toulokhonov, I.1    Landick, R.2
  • 38
    • 0031585994 scopus 로고    scopus 로고
    • Multiple interactions stabilize a single paused transcription intermediate in which hairpin to 3' end spacing distinguishes pause and termination pathways
    • Chan, C.L., Wang, D. & Landick, R. Multiple interactions stabilize a single paused transcription intermediate in which hairpin to 3' end spacing distinguishes pause and termination pathways. J. Mol. Biol. 268, 54-68 (1997).
    • (1997) J. Mol. Biol. , vol.268 , pp. 54-68
    • Chan, C.L.1    Wang, D.2    Landick, R.3
  • 39
    • 67449116330 scopus 로고    scopus 로고
    • Structural basis of transcription: Mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA
    • Sydow, J.F. et al. Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA. Mol. Cell 34, 710-721 (2009).
    • (2009) Mol. Cell , vol.34 , pp. 710-721
    • Sydow, J.F.1
  • 41
    • 0029029468 scopus 로고
    • Discontinuous movements of DNA and RNA in RNA polymerase accompany formation of a paused transcription complex
    • Wang, D. et al. Discontinuous movements of DNA and RNA in RNA polymerase accompany formation of a paused transcription complex. Cell 81, 341-350 (1995).
    • (1995) Cell , vol.81 , pp. 341-350
    • Wang, D.1
  • 42
    • 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. & Palangat, M. Direct versus limited-step reconstitution reveals key features of an RNA hairpin-stabilized paused transcription complex. J. Biol. Chem. 282, 19020-19028 (2007).
    • (2007) J. Biol. Chem. , vol.282 , pp. 19020-19028
    • Kyzer, S.1    Ha, K.S.2    Landick, R.3    Palangat, M.4
  • 43
    • 0032113494 scopus 로고    scopus 로고
    • Crucial role of the RNA:DNA hybrid in the processivity of transcription
    • Sidorenkov, I., Komissarova, N. & Kashlev, M. Crucial role of the RNA:DNA hybrid in the processivity of transcription. Mol. Cell 2, 55-64 (1998).
    • (1998) Mol. Cell , vol.2 , pp. 55-64
    • Sidorenkov, I.1    Komissarova, N.2    Kashlev, M.3


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