메뉴 건너뛰기




Volumn 342, Issue 4, 2004, Pages 1085-1099

Transcription factors IIF and IIS and nucleoside triphosphate substrates as dynamic probes of the human RNA polymerase II mechanism

Author keywords

NTP driven translocation; RNA polymerase II; transcription factor IIF; transcription factor IIS; transient state kinetics

Indexed keywords

NUCLEOSIDE TRIPHOSPHATE; PHOSPHODIESTERASE; RNA POLYMERASE II; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR 2F; TRANSCRIPTION FACTOR 2S; UNCLASSIFIED DRUG;

EID: 4444228491     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.07.070     Document Type: Article
Times cited : (43)

References (50)
  • 1
    • 0028916224 scopus 로고
    • Rapid quench kinetic analysis of polymerases, adenosinetriphosphatases, and enzyme intermediates
    • K.A. Johnson Rapid quench kinetic analysis of polymerases, adenosinetriphosphatases, and enzyme intermediates Methods Enzymol. 249 1995 38 61
    • (1995) Methods Enzymol. , vol.249 , pp. 38-61
    • Johnson, K.A.1
  • 2
    • 0642315208 scopus 로고
    • Transient-state kinetic analysis of enzyme reaction pathways
    • K.A. Johnson Transient-state kinetic analysis of enzyme reaction pathways Enzymes 20 1992 1 61
    • (1992) Enzymes , vol.20 , pp. 1-61
    • Johnson, K.A.1
  • 3
    • 0346749472 scopus 로고    scopus 로고
    • Combinatorial control of human RNA polymerase II (RNAP II) pausing and transcript cleavage by transcription factor IIF. Hepatitis {delta} antigen, and stimulatory factor II
    • C. Zhang, H. Yan, and Z.F. Burton Combinatorial control of human RNA polymerase II (RNAP II) pausing and transcript cleavage by transcription factor IIF. Hepatitis {delta} antigen, and stimulatory factor II J. Biol. Chem. 278 2003 50101 50111
    • (2003) J. Biol. Chem. , vol.278 , pp. 50101-50111
    • Zhang, C.1    Yan, H.2    Burton, Z.F.3
  • 8
    • 0026065031 scopus 로고
    • Role of the mammalian transcription factors IIF, IIS, and IIX during elongation by RNA polymerase II
    • E. Bengal, O. Flores, A. Krauskopf, D. Reinberg, and Y. Aloni Role of the mammalian transcription factors IIF, IIS, and IIX during elongation by RNA polymerase II Mol. Cell. Biol. 11 1991 1195 1206
    • (1991) Mol. Cell. Biol. , vol.11 , pp. 1195-1206
    • Bengal, E.1    Flores, O.2    Krauskopf, A.3    Reinberg, D.4    Aloni, Y.5
  • 9
    • 0026629273 scopus 로고
    • Factor-stimulated RNA polymerase II transcribes at physiological elongation rates on naked DNA but very poorly on chromatin templates
    • M.G. Izban, and D.S. Luse Factor-stimulated RNA polymerase II transcribes at physiological elongation rates on naked DNA but very poorly on chromatin templates J. Biol. Chem. 267 1992 13647 13655
    • (1992) J. Biol. Chem. , vol.267 , pp. 13647-13655
    • Izban, M.G.1    Luse, D.S.2
  • 10
    • 0033513098 scopus 로고    scopus 로고
    • The RAP74 subunit of human transcription factor IIF has similar roles in initiation and elongation
    • L. Lei, D. Ren, and Z.F. Burton The RAP74 subunit of human transcription factor IIF has similar roles in initiation and elongation Mol. Cell. Biol. 19 1999 8372 8382
    • (1999) Mol. Cell. Biol. , vol.19 , pp. 8372-8382
    • Lei, L.1    Ren, D.2    Burton, Z.F.3
  • 11
    • 0035834647 scopus 로고    scopus 로고
    • A highly purified RNA polymerase II elongation control system
    • D.B. Renner, Y. Yamaguchi, T. Wada, H. Handa, and D.H. Price A highly purified RNA polymerase II elongation control system J. Biol. Chem. 276 2001 42601 42609
    • (2001) J. Biol. Chem. , vol.276 , pp. 42601-42609
    • Renner, D.B.1    Yamaguchi, Y.2    Wada, T.3    Handa, H.4    Price, D.H.5
  • 12
    • 0027943675 scopus 로고
    • Roles for both the RAP30 and RAP74 subunits of transcription factor IIF in transcription initiation and elongation by RNA polymerase II
    • S. Tan, T. Aso, R.C. Conaway, and J.W. Conaway Roles for both the RAP30 and RAP74 subunits of transcription factor IIF in transcription initiation and elongation by RNA polymerase II J. Biol. Chem. 269 1994 25684 25691
    • (1994) J. Biol. Chem. , vol.269 , pp. 25684-25691
    • Tan, S.1    Aso, T.2    Conaway, R.C.3    Conaway, J.W.4
  • 13
    • 0037033094 scopus 로고    scopus 로고
    • A key role for the alpha 1 helix of human RAP74 in the initiation and elongation of RNA chains
    • J.D. Funk, Y.A. Nedialkov, D. Xu, and Z.F. Burton A key role for the alpha 1 helix of human RAP74 in the initiation and elongation of RNA chains J. Biol. Chem. 277 2002 46998 47003
    • (2002) J. Biol. Chem. , vol.277 , pp. 46998-47003
    • Funk, J.D.1    Nedialkov, Y.A.2    Xu, D.3    Burton, Z.F.4
  • 14
    • 0027178662 scopus 로고
    • Mechanism of DmS-II-mediated pause suppression by Drosophila RNA polymerase II
    • H. Guo, and D.H. Price Mechanism of DmS-II-mediated pause suppression by Drosophila RNA polymerase II J. Biol. Chem. 268 1993 18762 18770
    • (1993) J. Biol. Chem. , vol.268 , pp. 18762-18770
    • Guo, H.1    Price, D.H.2
  • 15
    • 0026648570 scopus 로고
    • The polymerase RNA II ternary complex cleaves the nascent transcript in a 3′-5′ direction in the presence of elongation factor SII
    • M.G. Izban, and D.S. Luse The polymerase RNA II ternary complex cleaves the nascent transcript in a 3′-5′ direction in the presence of elongation factor SII Genes Dev. 6 1992 1342 1356
    • (1992) Genes Dev. , vol.6 , pp. 1342-1356
    • Izban, M.G.1    Luse, D.S.2
  • 16
    • 0027163013 scopus 로고
    • The increment of SII-facilitated transcript cleavage varies dramatically between elongation competent and incompetent RNA polymerase II ternary complexes
    • M.G. Izban, and D.S. Luse The increment of SII-facilitated transcript cleavage varies dramatically between elongation competent and incompetent RNA polymerase II ternary complexes J. Biol. Chem. 268 1993 12874 12885
    • (1993) J. Biol. Chem. , vol.268 , pp. 12874-12885
    • Izban, M.G.1    Luse, D.S.2
  • 17
    • 0029559444 scopus 로고
    • Variation in the size of nascent RNA cleavage products as a function of transcript length and elongation competence
    • W. Gu, and D. Reines Variation in the size of nascent RNA cleavage products as a function of transcript length and elongation competence J. Biol. Chem. 270 1995 30441 30447
    • (1995) J. Biol. Chem. , vol.270 , pp. 30441-30447
    • Gu, W.1    Reines, D.2
  • 18
    • 0043244876 scopus 로고    scopus 로고
    • Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage
    • H. Kettenberger, K.J. Armache, and P. Cramer 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
  • 19
    • 0035827332 scopus 로고    scopus 로고
    • Structural basis of transcription: An RNA polymerase II elongation complex at 3.3 Å resolution
    • A.L. Gnatt, P. Cramer, J. Fu, D.A. Bushnell, and R.D. Kornberg 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.L.1    Cramer, P.2    Fu, J.3    Bushnell, D.A.4    Kornberg, R.D.5
  • 20
    • 1142310578 scopus 로고    scopus 로고
    • Structural basis of transcription: Separation of RNA from DNA by RNA polymerase II
    • K.D. Westover, D.A. Bushnell, and R.D. Kornberg Structural basis of transcription: separation of RNA from DNA by RNA polymerase II Science 303 2004 1014 1016
    • (2004) Science , vol.303 , pp. 1014-1016
    • Westover, K.D.1    Bushnell, D.A.2    Kornberg, R.D.3
  • 21
    • 0035827346 scopus 로고    scopus 로고
    • Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution
    • P. Cramer, D.A. Bushnell, and R.D. Kornberg Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution Science 292 2001 1863 1876
    • (2001) Science , vol.292 , pp. 1863-1876
    • Cramer, P.1    Bushnell, D.A.2    Kornberg, R.D.3
  • 22
    • 0032518374 scopus 로고    scopus 로고
    • A mechanism for all polymerases
    • T.A. Steitz A mechanism for all polymerases Nature 391 1998 231 232
    • (1998) Nature , vol.391 , pp. 231-232
    • Steitz, T.A.1
  • 23
    • 0028606031 scopus 로고
    • A unified polymerase mechanism for nonhomologous DNA and RNA polymerases
    • T.A. Steitz, S.J. Smerdon, J. Jager, and C.M. Joyce A unified polymerase mechanism for nonhomologous DNA and RNA polymerases Science 266 1994 2022 2025
    • (1994) Science , vol.266 , pp. 2022-2025
    • Steitz, T.A.1    Smerdon, S.J.2    Jager, J.3    Joyce, C.M.4
  • 25
    • 0037543997 scopus 로고    scopus 로고
    • Unified two-metal mechanism of RNA synthesis and degradation by RNA polymerase
    • V. Sosunov, E. Sosunova, A. Mustaev, I. Bass, V. Nikiforov, and A. Goldfarb 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
  • 26
    • 0041315524 scopus 로고    scopus 로고
    • Downstream DNA sequence effects on transcription elongation. Allosteric binding of nucleoside triphosphates facilitates translocation via a ratchet motion
    • S.F. Holmes, and D.A. Erie Downstream DNA sequence effects on transcription elongation. Allosteric binding of nucleoside triphosphates facilitates translocation via a ratchet motion J. Biol. Chem. 278 2003 35597 35608
    • (2003) J. Biol. Chem. , vol.278 , pp. 35597-35608
    • Holmes, S.F.1    Erie, D.A.2
  • 27
    • 0033578701 scopus 로고    scopus 로고
    • Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution
    • G. Zhang, E.A. Campbell, L. Minakhin, C. Richter, K. Severinov, and S.A. Darst 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
  • 28
    • 0035958552 scopus 로고    scopus 로고
    • Allosteric binding of nucleoside triphosphates to RNA polymerase regulates transcription elongation
    • J.E. Foster, S.F. Holmes, and D.A. Erie 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
  • 29
    • 3042595545 scopus 로고    scopus 로고
    • Alpha-amanitin blocks translocation by human RNA polymerase II
    • X.Q. Gong, Y.A. Nedialkov, and Z.F. Burton Alpha-amanitin blocks translocation by human RNA polymerase II J. Biol. Chem. 279 2004 27422 27427
    • (2004) J. Biol. Chem. , vol.279 , pp. 27422-27427
    • Gong, X.Q.1    Nedialkov, Y.A.2    Burton, Z.F.3
  • 30
    • 0037022279 scopus 로고    scopus 로고
    • Structural basis of transcription: Alpha-amanitin-RNA polymerase II cocrystal at 2.8 Å resolution
    • D.A. Bushnell, P. Cramer, and R.D. Kornberg Structural basis of transcription: alpha-amanitin-RNA polymerase II cocrystal at 2.8 Å 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
  • 31
    • 0035838977 scopus 로고    scopus 로고
    • Roles of RNA:DNA hybrid stability, RNA structure, and active site conformation in pausing by human RNA polymerase II
    • M. Palangat, and R. Landick Roles of RNA:DNA hybrid stability, RNA structure, and active site conformation in pausing by human RNA polymerase II J. Mol. Biol. 311 2001 265 282
    • (2001) J. Mol. Biol. , vol.311 , pp. 265-282
    • Palangat, M.1    Landick, R.2
  • 32
    • 0345047725 scopus 로고    scopus 로고
    • Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking
    • K.C. Neuman, E.A. Abbondanzieri, R. Landick, J. Gelles, and S.M. Block Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking Cell 115 2003 437 447
    • (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
  • 33
    • 0346258014 scopus 로고    scopus 로고
    • Backtracking by single RNA polymerase molecules observed at near-base-pair resolution
    • J.W. Shaevitz, E.A. Abbondanzieri, R. Landick, and S.M. Block Backtracking by single RNA polymerase molecules observed at near-base-pair resolution Nature 426 2003 684 687
    • (2003) Nature , vol.426 , pp. 684-687
    • Shaevitz, J.W.1    Abbondanzieri, E.A.2    Landick, R.3    Block, S.M.4
  • 34
    • 0028143584 scopus 로고
    • Physiological concentrations of purines and pyrimidines
    • T.W. Traut Physiological concentrations of purines and pyrimidines Mol. Cell. Biochem. 140 1994 1 22
    • (1994) Mol. Cell. Biochem. , vol.140 , pp. 1-22
    • Traut, T.W.1
  • 35
    • 0027289722 scopus 로고
    • SII-facilitated transcript cleavage in RNA polymerase II complexes stalled early after initiation occurs in primarily dinucleotide increments
    • M.G. Izban, and D.S. Luse SII-facilitated transcript cleavage in RNA polymerase II complexes stalled early after initiation occurs in primarily dinucleotide increments J. Biol. Chem. 268 1993 12864 12873
    • (1993) J. Biol. Chem. , vol.268 , pp. 12864-12873
    • Izban, M.G.1    Luse, D.S.2
  • 36
    • 0037125947 scopus 로고    scopus 로고
    • Use of 2-aminopurine and tryptophan fluorescence as probes in kinetic analyses of DNA polymerase Beta
    • C.A. Dunlap, and M.D. Tsai Use of 2-aminopurine and tryptophan fluorescence as probes in kinetic analyses of DNA polymerase Beta Biochemistry 41 2002 11226 11235
    • (2002) Biochemistry , vol.41 , pp. 11226-11235
    • Dunlap, C.A.1    Tsai, M.D.2
  • 37
    • 0029902679 scopus 로고    scopus 로고
    • Program DYNAFIT for the analysis of enzyme kinetic data: Application to HIV proteinase
    • P. Kuzmic Program DYNAFIT for the analysis of enzyme kinetic data: application to HIV proteinase Anal. Biochem. 237 1996 260 273
    • (1996) Anal. Biochem. , vol.237 , pp. 260-273
    • Kuzmic, P.1
  • 38
    • 0022360597 scopus 로고
    • Isolation of three proteins that bind to mammalian RNA polymerase II
    • M. Sopta, R.W. Carthew, and J. Greenblatt Isolation of three proteins that bind to mammalian RNA polymerase II J. Biol. Chem. 260 1985 10353 10360
    • (1985) J. Biol. Chem. , vol.260 , pp. 10353-10360
    • Sopta, M.1    Carthew, R.W.2    Greenblatt, J.3
  • 39
    • 1642417611 scopus 로고    scopus 로고
    • Active-site dynamics in RNA polymerases
    • R. Landick Active-site dynamics in RNA polymerases Cell 116 2004 351 353
    • (2004) Cell , vol.116 , pp. 351-353
    • Landick, R.1
  • 40
    • 0036681047 scopus 로고    scopus 로고
    • Ratchets, power strokes, and molecular motors
    • H. Wang, and G. Oster Ratchets, power strokes, and molecular motors Appl. Phys. A 75 2002 315 323
    • (2002) Appl. Phys. a , vol.75 , pp. 315-323
    • Wang, H.1    Oster, G.2
  • 41
    • 1342313235 scopus 로고    scopus 로고
    • The structural mechanism of translocation and helicase activity in T7 RNA polymerase
    • Y.W. Yin, and T.A. Steitz The structural mechanism of translocation and helicase activity in T7 RNA polymerase Cell 116 2004 393 404
    • (2004) Cell , vol.116 , pp. 393-404
    • Yin, Y.W.1    Steitz, T.A.2
  • 43
    • 0037388383 scopus 로고    scopus 로고
    • Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations
    • S.J. Johnson, J.S. Taylor, and L.S. Beese Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations Proc. Natl Acad. Sci. USA 100 2003 3895 3900
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 3895-3900
    • Johnson, S.J.1    Taylor, J.S.2    Beese, L.S.3
  • 44
    • 0032518398 scopus 로고    scopus 로고
    • Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution
    • S. Doublie, S. Tabor, A.M. Long, C.C. Richardson, and T. Ellenberger Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution Nature 391 1998 251 258
    • (1998) Nature , vol.391 , pp. 251-258
    • Doublie, S.1    Tabor, S.2    Long, A.M.3    Richardson, C.C.4    Ellenberger, T.5
  • 45
    • 0037183526 scopus 로고    scopus 로고
    • A reexamination of the nucleotide incorporation fidelity of DNA polymerases
    • A.K. Showalter, and M.D. Tsai A reexamination of the nucleotide incorporation fidelity of DNA polymerases Biochemistry 41 2002 10571 10576
    • (2002) Biochemistry , vol.41 , pp. 10571-10576
    • Showalter, A.K.1    Tsai, M.D.2
  • 46
    • 0035933769 scopus 로고    scopus 로고
    • Transcription factors TFIIF, ELL, and Elongin negatively regulate SII- induced nascent transcript cleavage by non-arrested RNA polymerase II elongation intermediates
    • B.J. Elmendorf, A. Shilatifard, Q. Yan, J.W. Conaway, and R.C. Conaway Transcription factors TFIIF, ELL, and Elongin negatively regulate SII- induced nascent transcript cleavage by non-arrested RNA polymerase II elongation intermediates J. Biol. Chem. 276 2001 23109 23114
    • (2001) J. Biol. Chem. , vol.276 , pp. 23109-23114
    • Elmendorf, B.J.1    Shilatifard, A.2    Yan, Q.3    Conaway, J.W.4    Conaway, R.C.5
  • 47
    • 0037073076 scopus 로고    scopus 로고
    • Elongation by RNA polymerase II: Structure-function relationship
    • A. Gnatt Elongation by RNA polymerase II: structure-function relationship Biochim. Biophys. Acta 1577 2002 175 190
    • (2002) Biochim. Biophys. Acta , vol.1577 , pp. 175-190
    • Gnatt, A.1
  • 48
    • 0023835505 scopus 로고
    • A high-efficiency HeLa cell nuclear transcription extract
    • D.J. Shapiro, P.A. Sharp, W.W. Wahli, and M.J. Keller A high-efficiency HeLa cell nuclear transcription extract DNA 7 1988 47 55
    • (1988) DNA , vol.7 , pp. 47-55
    • Shapiro, D.J.1    Sharp, P.A.2    Wahli, W.W.3    Keller, M.J.4
  • 50
    • 0028518550 scopus 로고
    • Importance of codon preference for production of human RAP74 and reconstitution of the RAP30/74 complex
    • B.Q. Wang, L. Lei, and Z.F. Burton Importance of codon preference for production of human RAP74 and reconstitution of the RAP30/74 complex Protein Expt. Purif. 5 1994 476 485
    • (1994) Protein Expt. Purif. , vol.5 , pp. 476-485
    • Wang, B.Q.1    Lei, L.2    Burton, Z.F.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.