메뉴 건너뛰기




Volumn 1, Issue 2, 2010, Pages 103-111

Molecular basis of transcription initiation in Archaea

Author keywords

Archaea; Cryo electron microscopy; Initiation; Molecular fitting; RNAP; Transcription

Indexed keywords

MICROORGANISM PROTEIN; PROTEIN RPOD; PROTEIN RPOL; PROTEIN TBP; PROTEIN TFB; RNA POLYMERASE BETA SUBUNIT; RNA POLYMERASE II; UNCLASSIFIED DRUG;

EID: 79551676570     PISSN: 21541264     EISSN: 21541272     Source Type: Journal    
DOI: 10.4161/trns.1.2.13189     Document Type: Article
Times cited : (14)

References (47)
  • 1
    • 0034671288 scopus 로고    scopus 로고
    • RNA polymerase: Structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II
    • Ebright RH. RNA polymerase: structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II. J Mol Biol 2000; 304:687-98.
    • (2000) J Mol Biol , vol.304 , pp. 687-698
    • Ebright, R.H.1
  • 2
  • 3
    • 0037123602 scopus 로고    scopus 로고
    • Structural basis of transcription initiation: An RNA polymerase holoenzyme-DNA complex
    • Murakami KS, Masuda S, Campbell EA, Muzzin O, Darst SA. Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex. Science 2002; 296:1285-90.
    • (2002) Science , vol.296 , pp. 1285-1290
    • Murakami, K.S.1    Masuda, S.2    Campbell, E.A.3    Muzzin, O.4    Darst, S.A.5
  • 5
    • 0037495037 scopus 로고    scopus 로고
    • Architecture of initiation-competent 12-subunit RNA polymerase II
    • Armache KJ, Kettenberger H, Cramer P. Architecture of initiation-competent 12-subunit RNA polymerase II. PNAS 2003; 100:6964-8.
    • (2003) PNAS , vol.100 , pp. 6964-6968
    • Armache, K.J.1    Kettenberger, H.2    Cramer, P.3
  • 6
    • 1142274214 scopus 로고    scopus 로고
    • Structural basis of transcription: An RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms
    • Bushnell DA, Westover KD, Davis RE, Kornberg RD. Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms. Science 2004; 303:983-8.
    • (2004) Science , vol.303 , pp. 983-988
    • Bushnell, D.A.1    Westover, K.D.2    Davis, R.E.3    Kornberg, R.D.4
  • 7
    • 0035827346 scopus 로고    scopus 로고
    • Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution
    • Cramer P, Bushnell DA, Kornberg RD. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 2001; 292:1863-76.
    • (2001) Science , vol.292 , pp. 1863-1876
    • Cramer, P.1    Bushnell, D.A.2    Kornberg, R.D.3
  • 8
    • 33751235874 scopus 로고    scopus 로고
    • Structural basis of transcription: Role of the trigger loop in substrate specificity and catalysis
    • Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD. Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis. Cell 2006; 127:941-54.
    • (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
  • 10
    • 39149142997 scopus 로고    scopus 로고
    • The X-ray crystal structure of RNA polymerase from Archaea
    • Hirata A, Klein BJ, Murakami KS. The X-ray crystal structure of RNA polymerase from Archaea. Nature 2008; 451:851-4.
    • (2008) Nature , vol.451 , pp. 851-854
    • Hirata, A.1    Klein, B.J.2    Murakami, K.S.3
  • 12
    • 0031779081 scopus 로고    scopus 로고
    • RNA polymerase- promoter interactions: The comings and goings of RNA polymerase
    • deHaseth PL, Zupancic ML, Record MT Jr. RNA polymerase- promoter interactions: the comings and goings of RNA polymerase. J Bacteriol 1998; 180:3019-25.
    • (1998) J Bacteriol , vol.180 , pp. 3019-3025
    • deHaseth, P.L.1    Zupancic, M.L.2    Record Jr., M.T.3
  • 13
    • 2542428546 scopus 로고    scopus 로고
    • Structure and mechanism of the RNA polymerase II transcription machinery
    • Hahn S. Structure and mechanism of the RNA polymerase II transcription machinery. Nat Struct Mol Biol 2004; 11:394-403.
    • (2004) Nat Struct Mol Biol , vol.11 , pp. 394-403
    • Hahn, S.1
  • 14
    • 77954759030 scopus 로고    scopus 로고
    • The human Mediator complex: A versatile, genome-wide regulator of transcription
    • Taatjes DJ. The human Mediator complex: a versatile, genome-wide regulator of transcription. Trends Biochem Sci 2010; 35:315-22.
    • (2010) Trends Biochem Sci , vol.35 , pp. 315-322
    • Taatjes, D.J.1
  • 15
    • 33747881750 scopus 로고    scopus 로고
    • The general transcription machinery and general cofactors
    • Thomas MC, Chiang CM. The general transcription machinery and general cofactors. Crit Rev Biochem Mol 2006; 41:105-78.
    • (2006) Crit Rev Biochem Mol , vol.41 , pp. 105-178
    • Thomas, M.C.1    Chiang, C.M.2
  • 16
    • 20344386725 scopus 로고    scopus 로고
    • Archaeal transcription and its regulators
    • Geiduschek EP, Ouhammouch M. Archaeal transcription and its regulators. Mol Microbiol 2005; 56:1397-407.
    • (2005) Mol Microbiol , vol.56 , pp. 1397-1407
    • Geiduschek, E.P.1    Ouhammouch, M.2
  • 17
    • 27844564819 scopus 로고    scopus 로고
    • Determinants of transcription initiation by archaeal RNA polymerase
    • Bartlett MS. Determinants of transcription initiation by archaeal RNA polymerase. Curr Opin Microbiol 2005; 8:677-84.
    • (2005) Curr Opin Microbiol , vol.8 , pp. 677-684
    • Bartlett, M.S.1
  • 18
    • 20344396840 scopus 로고    scopus 로고
    • Archaeal transcriptional regulation-variation on a bacterial theme?
    • Bell SD. Archaeal transcriptional regulation-variation on a bacterial theme? Trends Microbiol 2005; 13:262-5.
    • (2005) Trends Microbiol , vol.13 , pp. 262-265
    • Bell, S.D.1
  • 20
    • 5444275331 scopus 로고    scopus 로고
    • Mapping the location of TFIIB within the RNA polymerase II transcription preinitiation complex: A model for the structure of the PIC
    • Chen HT, Hahn S. Mapping the location of TFIIB within the RNA polymerase II transcription preinitiation complex: a model for the structure of the PIC. Cell 2004; 119:169-80.
    • (2004) Cell , vol.119 , pp. 169-180
    • Chen, H.T.1    Hahn, S.2
  • 21
    • 34547683177 scopus 로고    scopus 로고
    • The positions of TFIIF and TFIIE in the RNA polymerase II transcription preinitiation complex
    • Chen HT, Warfield L, Hahn S. The positions of TFIIF and TFIIE in the RNA polymerase II transcription preinitiation complex. Nat Struct Mol Biol 2007; 14:696-703.
    • (2007) Nat Struct Mol Biol , vol.14 , pp. 696-703
    • Chen, H.T.1    Warfield, L.2    Hahn, S.3
  • 22
    • 70450171352 scopus 로고    scopus 로고
    • RNA-polymerase II-TFIIB structure and mechanism of transcription initiation
    • Kostrewa D, Zeller ME, Armache KJ, Seizl M, Leike K, Thomm M, et al. RNA-polymerase II-TFIIB structure and mechanism of transcription initiation. Nature 2009; 462:292-3.
    • (2009) Nature , vol.462 , pp. 292-293
    • Kostrewa, D.1    Zeller, M.E.2    Armache, K.J.3    Seizl, M.4    Leike, K.5    Thomm, M.6
  • 23
    • 74249102477 scopus 로고    scopus 로고
    • Structure of an RNA polymerase II-TFIIB complex and the transcription initiation mechanism
    • Liu X, Bushnell DA, Wang D, Calero G, Kornberg R. Structure of an RNA polymerase II-TFIIB complex and the transcription initiation mechanism. Science 2010; 327:206-9.
    • (2010) Science , vol.327 , pp. 206-209
    • Liu, X.1    Bushnell, D.A.2    Wang, D.3    Calero, G.4    Kornberg, R.5
  • 24
    • 53849145660 scopus 로고    scopus 로고
    • Archaeal RNA polymerase subunits E and F are not required for transcription in vitro, but a Thermococcus kodakarensis mutant lacking subunit F is temperature-sensitive
    • Hirata A, Kanai T, Santangelo TJ, Tajiri M, Reeve JN, Imanaka T, et al. Archaeal RNA polymerase subunits E and F are not required for transcription in vitro, but a Thermococcus kodakarensis mutant lacking subunit F is temperature-sensitive. Mol Microbiol 2008; 70: 623-33.
    • (2008) Mol Microbiol , vol.70 , pp. 623-633
    • Hirata, A.1    Kanai, T.2    Santangelo, T.J.3    Tajiri, M.4    Reeve, J.N.5    Imanaka, T.6
  • 26
  • 27
    • 0029975088 scopus 로고
    • SPIDER and WEB: Processing and visualization of images in 3-D electron microscopy and related fields
    • Frank J, Radermacher M, Penczek P, Zhu J, Li Y, Ladjadj M, et al. SPIDER and WEB: processing and visualization of images in 3-D electron microscopy and related fields. J Struct Biol 1995; 116:190-9.
    • (1995) J Struct Biol , vol.116 , pp. 190-199
    • Frank, J.1    Radermacher, M.2    Penczek, P.3    Zhu, J.4    Li, Y.5    Ladjadj, M.6
  • 28
    • 0028393194 scopus 로고
    • The ribosome at improved resolution: New techniques for merging and orientation refinement in 3D cryoelectron microscopy of biological particles
    • Penczek P, Grassucci RA, Frank J. The ribosome at improved resolution: New techniques for merging and orientation refinement in 3D cryoelectron microscopy of biological particles. Ultramicroscopy 1994; 53: 251-70.
    • (1994) Ultramicroscopy , vol.53 , pp. 251-270
    • Penczek, P.1    Grassucci, R.A.2    Frank, J.3
  • 29
    • 84985231782 scopus 로고
    • Three-dimensional reconstruction from a singleexposure, random conical tilt series applied to the 50S ribosomal subunit of Escherichia coli
    • Radermacher M, Wagenknecht T, Verschoor A, Frank J. Three-dimensional reconstruction from a singleexposure, random conical tilt series applied to the 50S ribosomal subunit of Escherichia coli. J Microsc 1987; 146:113-6.
    • (1987) J Microsc , vol.146 , pp. 113-116
    • Radermacher, M.1    Wagenknecht, T.2    Verschoor, A.3    Frank, J.4
  • 31
    • 33845291163 scopus 로고    scopus 로고
    • Ab initio resolution measurement for single particle structures
    • Sousa D, Grigorieff N. Ab initio resolution measurement for single particle structures. J Struct Biol 2007; 157:201-10.
    • (2007) J Struct Biol , vol.157 , pp. 201-210
    • Sousa, D.1    Grigorieff, N.2
  • 32
  • 33
    • 0036795476 scopus 로고    scopus 로고
    • On the fitting of model electron densities into EM reconstructions: A reciprocal-space formulation
    • Navaza J, Lepault J, Rey FA, Alvarez-Rua C, Borge J. On the fitting of model electron densities into EM reconstructions: a reciprocal-space formulation. Acta Cryst 2002; 58:1820-5.
    • (2002) Acta Cryst , vol.58 , pp. 1820-1825
    • Navaza, J.1    Lepault, J.2    Rey, F.A.3    Alvarez-Rua, C.4    Borge, J.5
  • 34
    • 0026852571 scopus 로고
    • Fast rigid-body refinement for molecular replacement techniques
    • Castellano E, Oliva G, Navaza J. Fast rigid-body refinement for molecular replacement techniques. J Appl Cryst 1992; 25:281-4.
    • (1992) J Appl Cryst , vol.25 , pp. 281-284
    • Castellano, E.1    Oliva, G.2    Navaza, J.3
  • 35
    • 0024342908 scopus 로고
    • Threedimensional structure of Escherichia coli RNA polymerase holoenzyme determined by electron crystallography
    • Darst SA, Kubalek EW, Kornberg RD. Threedimensional structure of Escherichia coli RNA polymerase holoenzyme determined by electron crystallography. Nature 1989; 340:730-2.
    • (1989) Nature , vol.340 , pp. 730-732
    • Darst, S.A.1    Kubalek, E.W.2    Kornberg, R.D.3
  • 36
    • 0037531306 scopus 로고    scopus 로고
    • Cryo-negative staining reveals conformational flexibility within yeast RNA polymerase I
    • De Carlo S, Carles C, Riva M, Schultz P. Cryo-negative staining reveals conformational flexibility within yeast RNA polymerase I. J Mol Biol 2003; 329:891-902.
    • (2003) J Mol Biol , vol.329 , pp. 891-902
    • de Carlo, S.1    Carles, C.2    Riva, M.3    Schultz, P.4
  • 37
    • 33947369108 scopus 로고    scopus 로고
    • Insights into transcription initiation and termination from the electron microscopy structure of yeast RNA polymerase III
    • Fernández-Tornero C, Bottcher B, Riva M, Carles C, Steuerwald U, Ruigrok RW, et al. Insights into transcription initiation and termination from the electron microscopy structure of yeast RNA polymerase III. Mol Cell 2007; 25:813-23.
    • (2007) Mol Cell , vol.25 , pp. 813-823
    • Fernández-Tornero, C.1    Bottcher, B.2    Riva, M.3    Carles, C.4    Steuerwald, U.5    Ruigrok, R.W.6
  • 38
    • 0031990302 scopus 로고    scopus 로고
    • Sequence-specific DNA binding by the S. shibatae TFIIB homolog, TFB and its effect on promoter strength
    • Qureshi SA, Jackson SP. Sequence-specific DNA binding by the S. shibatae TFIIB homolog, TFB and its effect on promoter strength. Mol Cell 1998; 1:389-400.
    • (1998) Mol Cell , vol.1 , pp. 389-400
    • Qureshi, S.A.1    Jackson, S.P.2
  • 39
    • 0030974754 scopus 로고    scopus 로고
    • Factor requirements for transcription in the Archaeon Sulfolobus shibatae
    • Qureshi SA, Bell SD, Jackson SP. Factor requirements for transcription in the Archaeon Sulfolobus shibatae. EMBO J 1997; 16:2927-36.
    • (1997) EMBO J , vol.16 , pp. 2927-2936
    • Qureshi, S.A.1    Bell, S.D.2    Jackson, S.P.3
  • 40
    • 0031562901 scopus 로고    scopus 로고
    • The 2.1 Å crystal structure of an archaeal pre-initiation complex: TATA-box binding protein/transcription factor (II) B core/TATA-box
    • Kosa PF, Ghosh G, DeDecker BS, Sigler PB. The 2.1 Å crystal structure of an archaeal pre-initiation complex: TATA-box binding protein/transcription factor (II) B core/TATA-box. PNAS 1997; 94:6042-7.
    • (1997) PNAS , vol.94 , pp. 6042-6047
    • Kosa, P.F.1    Ghosh, G.2    DeDecker, B.S.3    Sigler, P.B.4
  • 41
    • 34347236451 scopus 로고    scopus 로고
    • Visualizing flexibility at molecular resolution: Analysis of heterogeneity in single- particle electron microscopy reconstructions
    • Leschziner AE, Nogales E. Visualizing flexibility at molecular resolution: analysis of heterogeneity in single- particle electron microscopy reconstructions. Annu Rev Biophys Biomol Struct 2007; 36:43-62.
    • (2007) Annu Rev Biophys Biomol Struct , vol.36 , pp. 43-62
    • Leschziner, A.E.1    Nogales, E.2
  • 42
    • 14844290215 scopus 로고    scopus 로고
    • Structures of complete RNA polymerase II and its subcomplex, Rpb4/7
    • Armache KJ, Mitterweger S, Meinhart A, Cramer P. Structures of complete RNA polymerase II and its subcomplex, Rpb4/7. J Biol Chem 2005; 280:7131-4.
    • (2005) J Biol Chem , vol.280 , pp. 7131-7134
    • Armache, K.J.1    Mitterweger, S.2    Meinhart, A.3    Cramer, P.4
  • 43
    • 34548801789 scopus 로고    scopus 로고
    • The molecular basis of eukaryotic transcription
    • Kornberg RD. The molecular basis of eukaryotic transcription. PNAS 2007; 104:12955-61.
    • (2007) PNAS , vol.104 , pp. 12955-12961
    • Kornberg, R.D.1
  • 44
    • 0032417610 scopus 로고    scopus 로고
    • Temperature, template topology and factor requirements of archaeal transcription
    • Bell SD, Jaxel C, Nadal M, Kosa PF, Jackson SP. Temperature, template topology and factor requirements of archaeal transcription. PNAS 1998; 95: 15218-22.
    • (1998) PNAS , vol.95 , pp. 15218-15222
    • Bell, S.D.1    Jaxel, C.2    Nadal, M.3    Kosa, P.F.4    Jackson, S.P.5
  • 45
    • 33750043192 scopus 로고    scopus 로고
    • Protein-protein interactions in the Archaeal transcriptional machinery: Binding studies of isolated RNA polymerase subunits and transcription factors
    • Goede B, Naji S, von Kampen O, Ilg K, Thomm M. Protein-protein interactions in the Archaeal transcriptional machinery: binding studies of isolated RNA polymerase subunits and transcription factors. J Biol Chem 2006; 281:30581-92.
    • (2006) J Biol Chem , vol.281 , pp. 30581-30592
    • Goede, B.1    Naji, S.2    von Kampen, O.3    Ilg, K.4    Thomm, M.5
  • 46
    • 0035861674 scopus 로고    scopus 로고
    • Identification of a conserved Archaeal RNA polymerase subunit contacted by the basal transcription factor TFB
    • Magill CP, Jackson SP, Bell SD. Identification of a conserved Archaeal RNA polymerase subunit contacted by the basal transcription factor TFB. J Biol Chem 2001; 276:46693-6.
    • (2001) J Biol Chem , vol.276 , pp. 46693-46696
    • Magill, C.P.1    Jackson, S.P.2    Bell, S.D.3
  • 47
    • 33745842952 scopus 로고    scopus 로고
    • A DNA-tethered cleavage probe reveals the path for promoter DNA in the yeast preinitiation complex
    • Miller G, Hahn S. A DNA-tethered cleavage probe reveals the path for promoter DNA in the yeast preinitiation complex. Nat Struct Mol Biol 2006; 13: 603-10.
    • (2006) Nat Struct Mol Biol , vol.13 , pp. 603-610
    • Miller, G.1    Hahn, S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.