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The authors determine the crystal structure of the complete archaeal RNA polymerase from Sulfolobus shibatae at 3.35 Å resolution including Rpo8/G subunit and a newly identified component of the Sulfolobales order enzyme, Rpo13.
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The yeast Pol III envelope, determined at 17 Å resolution by cryo-electron microscopy and single-particle analysis, shows a hand-like shape typical of RNA polymerases and, compared with Pol II structure, prominent features attributed to Pol-III-specific subunits and a bulkier stalk.
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Fernandez-Tornero C., Bottcher B., Riva M., Carles C., Steuerwald U., Ruigrok R.W., Sentenac A., Muller C.W., and Schoehn G. Insights into transcription initiation and termination from the electron microscopy structure of yeast RNA polymerase III. Mol Cell 25 (2007) 813-823. The yeast Pol III envelope, determined at 17 Å resolution by cryo-electron microscopy and single-particle analysis, shows a hand-like shape typical of RNA polymerases and, compared with Pol II structure, prominent features attributed to Pol-III-specific subunits and a bulkier stalk.
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This paper provides an 11 subunit model of yeast Pol III by combining a homology model of the 9 subunit core enzyme with a X-ray structure at 3.2 Å resolution of the stalk subcomplex Rpc17/25 revealing specific features of Pol III that can account for functional differences between nuclear RNA polymerases.
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Jasiak A.J., Armache K.J., Martens B., Jansen R.P., and Cramer P. Structural biology of RNA polymerase III: subcomplex C17/25 X-ray structure and 11 subunit enzyme model. Mol Cell 23 (2006) 71-81. This paper provides an 11 subunit model of yeast Pol III by combining a homology model of the 9 subunit core enzyme with a X-ray structure at 3.2 Å resolution of the stalk subcomplex Rpc17/25 revealing specific features of Pol III that can account for functional differences between nuclear RNA polymerases.
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Identification of an autonomously initiating RNA polymerase III holoenzyme containing a novel factor that is selectively inactivated during protein synthesis inhibition
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Chen H.T., and Hahn S. Mapping the location of TFIIB within the RNA polymerase II transcription preinitiation complex: a model for the structure of the PIC. Cell 119 (2004) 169-180
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0037495037
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Architecture of initiation-competent 12-subunit RNA polymerase II
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The authors report a model of the complete Pol II by fitting structures of the core and Rpb4/7 to a 4.2 Å crystallographic electron density map.
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Armache K.J., Kettenberger H., and Cramer P. Architecture of initiation-competent 12-subunit RNA polymerase II. Proc Natl Acad Sci USA 100 (2003) 6964-6968. The authors report a model of the complete Pol II by fitting structures of the core and Rpb4/7 to a 4.2 Å crystallographic electron density map.
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The X-ray structure of complete Pol II from S. cerevisiae at 4.1 Å resolution including the Rpb4/7 heterodimer is described.
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Bushnell D.A., and Kornberg R.D. Complete, 12-subunit RNA polymerase II at 4.1-A resolution: implications for the initiation of transcription. Proc Natl Acad Sci U S A 100 (2003) 6969-6973. The X-ray structure of complete Pol II from S. cerevisiae at 4.1 Å resolution including the Rpb4/7 heterodimer is described.
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Bushnell, D.A.1
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Zaros C., and Thuriaux P. Rpc25, a conserved RNA polymerase III subunit, is critical for transcription initiation. Mol Microbiol 55 (2005) 104-114
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An Rpb4/Rpb7-like complex in yeast RNA polymerase III contains the orthologue of mammalian CGRP-RCP
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Siaut M., Zaros C., Levivier E., Ferri M.L., Court M., Werner M., Callebaut I., Thuriaux P., Sentenac A., and Conesa C. An Rpb4/Rpb7-like complex in yeast RNA polymerase III contains the orthologue of mammalian CGRP-RCP. Mol Cell Biol 23 (2003) 195-205
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30444450804
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A subcomplex of RNA polymerase III subunits is required for transcription termination and reinitiation
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This paper shows the specific requirement for the Rpc37/53 subcomplex in Pol III termination and the role of Rpc11 subunit in recycling, independent of its role in RNA cleavage.
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Landrieux E., Nazif A., Ducrot C., Acker J., Riva M., and Carles C. A subcomplex of RNA polymerase III subunits is required for transcription termination and reinitiation. EMBO J 25 (2005) 118-128. This paper shows the specific requirement for the Rpc37/53 subcomplex in Pol III termination and the role of Rpc11 subunit in recycling, independent of its role in RNA cleavage.
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24
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Diversification of function by different isoforms of conventionally shared RNA polymerase subunits
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Devaux S., Kelly S., Lecordier L., Wickstead B., Perez-Morga D., Pays E., Vanhamme L., and Gull K. Diversification of function by different isoforms of conventionally shared RNA polymerase subunits. Mol Biol Cell 18 (2007) 1293-1301
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37349041027
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This paper substantially improves the structural data available so far for yeast Pol I, combining a 12 Å EM envelope structure with an atomic crystal structure of the Rpa14/Rpa43 stalk. It also documents the contribution of Rpa12 to the intrinsic transcript cleavage activity of Pol I and suggests that the Pol-I-specific subunits Rpa34 and Rpa49 may be functionally and structurally equivalent to the two main subunits of TFIIF, thus acting as a built-in elongation factor.
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Kuhn C.D., Geiger S.R., Baumli S., Gartmann M., Gerber J., Jennebach S., Mielke T., Tschochner H., Beckmann R., and Cramer P. Functional architecture of RNA polymerase I. Cell 131 (2007) 1260-1272. This paper substantially improves the structural data available so far for yeast Pol I, combining a 12 Å EM envelope structure with an atomic crystal structure of the Rpa14/Rpa43 stalk. It also documents the contribution of Rpa12 to the intrinsic transcript cleavage activity of Pol I and suggests that the Pol-I-specific subunits Rpa34 and Rpa49 may be functionally and structurally equivalent to the two main subunits of TFIIF, thus acting as a built-in elongation factor.
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Jennebach, S.6
Mielke, T.7
Tschochner, H.8
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Cramer, P.10
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26
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A34.5, a nonessential component of yeast RNA polymerase I, cooperates with subunit A14 and DNA topoisomerase I to produce a functional rRNA synthesis machine
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Gadal O., Mariotte-Labarre S., Chedin S., Quemeneur E., Carles C., Sentenac A., and Thuriaux P. A34.5, a nonessential component of yeast RNA polymerase I, cooperates with subunit A14 and DNA topoisomerase I to produce a functional rRNA synthesis machine. Mol Cell Biol 17 (1997) 1787-1795
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This paper presents genetic evidence showing that the Rpa49 subunit (and its Rpa34 partner) contributes to the early phase of elongation by favouring the release of the Rrn3 initiation factor during promoter escape, but also suggests that Rpa49 may directly affect the efficiency of Pol I recruitment at the rDNA promoter.
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Beckouet F., Labarre-Mariotte S., Albert B., Imazawa Y., Werner M., Gadal O., Nogi Y., and Thuriaux P. Two RNA polymerase I subunits control the binding and release of Rrn3 during transcription. Mol Cell Biol 28 (2008) 1596-1605. This paper presents genetic evidence showing that the Rpa49 subunit (and its Rpa34 partner) contributes to the early phase of elongation by favouring the release of the Rrn3 initiation factor during promoter escape, but also suggests that Rpa49 may directly affect the efficiency of Pol I recruitment at the rDNA promoter.
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RNA polymerase I-specific subunit CAST/hPAF49 has a role in the activation of transcription by upstream binding factor
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Panov K.I., Panova T.B., Gadal O., Nishiyama K., Saito T., Russell J., and Zomerdijk J.C. RNA polymerase I-specific subunit CAST/hPAF49 has a role in the activation of transcription by upstream binding factor. Mol Cell Biol 26 (2006) 5436-5448
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First direct evidence that Pol I needs to form a Pol I-Rrn3 complex in order to be recruited at the rDNA promoter, due to a direct contact between Rrn3 and Rpa43 that is the main component of the Pol I 'stalk'.
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Peyroche G., Milkereit P., Bischler N., Tschochner H., Schultz P., Sentenac A., Carles C., and Riva M. The recruitment of RNA polymerase I on rDNA is mediated by the interaction of the A43 subunit with Rrn3. EMBO J 19 (2000) 5473-5482. First direct evidence that Pol I needs to form a Pol I-Rrn3 complex in order to be recruited at the rDNA promoter, due to a direct contact between Rrn3 and Rpa43 that is the main component of the Pol I 'stalk'.
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Using a yeast strain constitutively competent for Pol I recruitment at the rDNA promoter, the authors demonstrate that constitutive rDNA transcription correlates with an activation of the Pol II-dependent transcription of ribosomal protein genes. They also observe a de-regulation of Pol III, possibly limited to the synthesis of the 5S rRNA.
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Laferté A., Favry E., Sentenac A., Riva M., Carles C., and Chédin S. The transcriptional activity of RNA polymerase I is a key determinant for the level of all ribosome components. Genes Dev 20 (2006) 2030-2040. Using a yeast strain constitutively competent for Pol I recruitment at the rDNA promoter, the authors demonstrate that constitutive rDNA transcription correlates with an activation of the Pol II-dependent transcription of ribosomal protein genes. They also observe a de-regulation of Pol III, possibly limited to the synthesis of the 5S rRNA.
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RNA pol II subunit RPB7 is required for RNA pol I-mediated transcription in Trypanosoma brucei
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In trypanosomes and other kinetoplastids, Pol I transcribes several strongly expressed protein-encoding genes, in addition to its canonical rDNA template. This paper provides an interesting clue by suggesting that the Rpb7 component of the Pol II stalk is associated to the trypanosomal Pol I.
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Penate X., Lopez-Farfan D., Landeira D., Wentland A., Vidal I., and Navarro M. RNA pol II subunit RPB7 is required for RNA pol I-mediated transcription in Trypanosoma brucei. EMBO Rep 10 (2009) 252-257. In trypanosomes and other kinetoplastids, Pol I transcribes several strongly expressed protein-encoding genes, in addition to its canonical rDNA template. This paper provides an interesting clue by suggesting that the Rpb7 component of the Pol II stalk is associated to the trypanosomal Pol I.
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Penate, X.1
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Fish R.N., and Kane C.M. Promoting elongation with transcript cleavage stimulatory factors. Biochim Biophys Acta 1577 (2002) 287-307
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Members of the SAGA and Mediator complexes are partners of the transcription elongation factor TFIIS
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Wery M., Shematorova E., Van Driessche B., Vandenhaute J., Thuriaux P., and Van Mullem V. Members of the SAGA and Mediator complexes are partners of the transcription elongation factor TFIIS. EMBO J 23 (2004) 4232-4242
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Genetic interactions of DST1 in Saccharomyces cerevisiae suggest a role of TFIIS in the initiation-elongation transition
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Malagon F., Tong A.H., Shafer B.K., and Strathern J.N. Genetic interactions of DST1 in Saccharomyces cerevisiae suggest a role of TFIIS in the initiation-elongation transition. Genetics 166 (2004) 1215-1227
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Prather D.M., Larschan E., and Winston F. Evidence that the elongation factor TFIIS plays a role in transcription initiation at GAL1 in Saccharomyces cerevisiae. Mol Cell Biol 25 (2005) 2650-2659
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The transcription elongation factor TFIIS is a component of RNA polymerase II preinitiation complexes
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Kim B., Nesvizhskii A.I., Rani P.G., Hahn S., Aebersold R., and Ranish J.A. The transcription elongation factor TFIIS is a component of RNA polymerase II preinitiation complexes. Proc Natl Acad Sci U S A 104 (2007) 16068-16073
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TFIIS elongation factor and Mediator act in conjunction during transcription initiation in vivo
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Guglielmi B., Soutourina J., Esnault C., and Werner M. TFIIS elongation factor and Mediator act in conjunction during transcription initiation in vivo. Proc Natl Acad Sci U S A 104 (2007) 16062-16067
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Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage
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A crystal structure model of the Pol II-TFIIS complex at 3.8 Å resolution shows that TFIIS central domain extends from the polymerase surface via a pore and brings the C-terminal conserved SADE motif very close to the Pol II active site to stimulate the intrinsic transcript cleavage activity of the enzyme.
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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. A crystal structure model of the Pol II-TFIIS complex at 3.8 Å resolution shows that TFIIS central domain extends from the polymerase surface via a pore and brings the C-terminal conserved SADE motif very close to the Pol II active site to stimulate the intrinsic transcript cleavage activity of the enzyme.
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Genome-wide location analysis reveals a role for TFIIS in RNA polymerase III transcription
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On the basis of genome-wide location analysis, this paper reveals a previously unsuspected role of TFIIS, one of the well-characterized Pol II transcription elongation factor, in Pol III transcription and provides strong in vivo and in vitro evidence in favour of a role for TFIIS as a general Pol III transcription factor.
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Ghavi-Helm Y., Michaut M., Acker J., Aude J., Thuriaux P., Werner M., and Soutourina J. Genome-wide location analysis reveals a role for TFIIS in RNA polymerase III transcription. Genes Dev 22 (2008) 1934-1947. On the basis of genome-wide location analysis, this paper reveals a previously unsuspected role of TFIIS, one of the well-characterized Pol II transcription elongation factor, in Pol III transcription and provides strong in vivo and in vitro evidence in favour of a role for TFIIS as a general Pol III transcription factor.
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The RNA cleavage activity of RNA polymerase III is mediated by an essential TFIIS-like subunit and is important for transcription termination
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Chedin S., Riva M., Schultz P., Sentenac A., and Carles C. The RNA cleavage activity of RNA polymerase III is mediated by an essential TFIIS-like subunit and is important for transcription termination. Genes Dev 12 (1998) 3857-3871
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Transcriptional termination by RNA polymerase I requires the small subunit Rpa12p
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Prescott E.M., Osheim Y.N., Jones H.S., Alen C.M., Roan J.G., Reeder R.H., Beyer A.L., and Proudfoot N.J. Transcriptional termination by RNA polymerase I requires the small subunit Rpa12p. Proc Natl Acad Sci U S A 101 (2004) 6068-6073
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Transcription elongation through DNA arrest sites. A multistep process involving both RNA polymerase II subunit RPB9 and TFIIS
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Hausner W., Lange U., and Musfeldt M. Transcription factor S, a cleavage induction factor of the archaeal RNA polymerase. J Biol Chem 275 (2000) 12393-12399
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RNA polymerase II elongation factors Spt4p and Spt5p play roles in transcription elongation by RNA polymerase I and rRNA processing
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This paper establishes that rDNA transcription depends on Spt4 and Spt5, two elongation factors initially identified by their association with Pol II. Intriguingly, Spt4 and Spt5 are also homologous to archaeal proteins and was thus probably inherited from the last ancestor shared by Archaea and Eukaryotes.
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Schneider D.A., French S.L., Osheim Y.N., Bailey A.O., Vu L., Dodd J., Yates J.R., Beyer A.L., and Nomura M. RNA polymerase II elongation factors Spt4p and Spt5p play roles in transcription elongation by RNA polymerase I and rRNA processing. Proc Natl Acad Sci USA (2006). This paper establishes that rDNA transcription depends on Spt4 and Spt5, two elongation factors initially identified by their association with Pol II. Intriguingly, Spt4 and Spt5 are also homologous to archaeal proteins and was thus probably inherited from the last ancestor shared by Archaea and Eukaryotes.
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(2006)
Proc Natl Acad Sci USA
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Schneider, D.A.1
French, S.L.2
Osheim, Y.N.3
Bailey, A.O.4
Vu, L.5
Dodd, J.6
Yates, J.R.7
Beyer, A.L.8
Nomura, M.9
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