Insights into Transcription Initiation and Termination from the Electron Microscopy Structure of Yeast RNA Polymerase III

Fernández‐Tornero, Carlos; Böttcher, Bettina; Riva, Michel; Carles, Christophe; Steuerwald, Ulrich; Ruigrok, Rob W.H.; Sentenac, André; Müller, Christoph W.; Schoehn, Guy

doi:10.1016/j.molcel.2007.02.016

Cited by 76 publications

(91 citation statements)

References 36 publications

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“…These experiments strongly suggest that termination and cleavage of the RNA precursor are not coupled in the RNAPIII transcription process. Consistent with its role in termination, structural analysis of RNA-PIII showed that the C37/C53 heterodimer is positioned at the outer end of the DNA-binding cleft, toward the front of the EC, allowing the complex to sense the incoming DNA (Fernandez-Tornero et al 2007).…”

Section: Rnapiii: a Terminator On Its Own?mentioning

confidence: 84%

Transcription termination by nuclear RNA polymerases

Richard

Manley²

2009

Genes Dev.

289

326

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Gene transcription in the cell nucleus is a complex and highly regulated process. Transcription in eukaryotes requires three distinct RNA polymerases, each of which employs its own mechanisms for initiation, elongation, and termination. Termination mechanisms vary considerably, ranging from relatively simple to exceptionally complex. In this review, we describe the present state of knowledge on how each of the three RNA polymerases terminates and how mechanisms are conserved, or vary, from yeast to human.

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Section: Rnapiii: a Terminator On Its Own?mentioning

confidence: 84%

Transcription termination by nuclear RNA polymerases

Richard

Manley²

2009

Genes Dev.

289

326

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“…5), and TFIIF exerts a comparable effect in stabilizing the incorporation of a 5-nt RNA into a pol II heteroduplex DNA complex containing a 10-bp bubble (55). In addition to these functional similarities, TFIIF and the C53/C37 subcomplex appear to attach to similar sites on the second largest subunits of their respective RNA polymerases, the Rpb2/C128 lobe domains above the DNA binding cleft (11,48), and the stability of these interactions is also dependent on attachment of the respective paralogue Rpb9/C11 subunits to the lobe domain (7,8,56).…”

Section: Discussionmentioning

confidence: 97%

“…The ␤-hairpin and the two acidic residues at its tip are conserved in C11, and the acidic residues are essential for the intrinsic cleavage activity of pol III (8). Cryoelectron microscopy structural analysis of pol III (11) shows mass density compatible with the N-terminal zinc binding domain of C11, occupying a position on the C128 lobe domain of pol III that resembles the location of the N-terminal zinc binding domain of Rpb9 on Rpb2 in the structure of pol II (12). A mass corresponding to the C-terminal zinc binding domain of C11 was not observed in the pol III electron microscopic structure, but it has been suggested that this domain may bind to the pol III pore 1 (10).…”

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confidence: 99%

The C53/C37 Subcomplex of RNA Polymerase III Lies Near the Active Site and Participates in Promoter Opening

Kassavetis

Prakash²,

Shim

2010

Journal of Biological Chemistry

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The C53 and C37 subunits of RNA polymerase III (pol III) form a subassembly that is required for efficient termination; pol III lacking this subcomplex displays increased processivity of RNA chain elongation. We show that the C53/C37 subcomplex additionally plays a role in formation of the initiation-ready open promoter complex similar to that of the Brf1 N-terminal zinc ribbon domain. In the absence of C53 and C37, the transcription bubble fails to stably propagate to and beyond the transcriptional start site even when the DNA template is supercoiled. The C53/C37 subcomplex also stimulates the formation of an artificially assembled elongation complex from its component DNA and RNA strands. Protein-RNA and protein-DNA photochemical cross-linking analysis places a segment of C53 close to the RNA 3 end and transcribed DNA strand at the catalytic center of the pol III elongation complex. We discuss the implications of these findings for the mechanism of transcriptional termination by pol III and propose a structural as well as functional correspondence between the C53/C37 subcomplex and the RNA polymerase II initiation factor TFIIF. RNA polymerase III (pol III)3 transcribes genes encoding short RNA products that are essential for protein synthesis (e.g. tRNAs, 5 S rRNA), RNA processing (e.g. U6 small nuclear RNA, the RNA subunit of RNase P), protein transport (7SL RNA of the signal recognition particle), and diverse other functions, particularly in higher eukaryotes (1). Pol III is brought to the transcriptional start sites of its genes through interactions with its central 3-subunit initiation factor, TFIIIB (subunits Brf1, TBP, and Bdp1). TFIIIB, in turn, is assembled on DNA upstream of the transcriptional start site in a largely sequenceindependent process by its six-subunit assembly factor, TFIIIC, which binds to two promoter elements (boxA and boxB) located downstream of the transcriptional start site. An additional initiation factor, TFIIIA, serves solely as the adaptor for assembling TFIIIC on 5 S rRNA genes. Vertebrates contain an additional form of TFIIIB in which its paralogue Brf2 replaces Brf1 for transcription of a class of genes that use the SNAP c complex in place of TFIIIC as their TFIIIB-assembly factor (2, 3). Once it has been assembled onto DNA, Saccharomyces cerevisiae TFIIIB suffices for recruiting pol III for robust and accurately initiating transcription in vitro (4); at least in yeast, this also appears to be the case in vivo (5). The complexity of pol III contrasts with the apparent simplicity of its core transcription apparatus (the TFIIIB⅐DNA complex and diverse assembly factors). Five pol III subunits have no counterparts in the considerably less complex pol II (with its merely 12 subunits). Three of these pol III subunits (C82, C34, and C31) form a subassembly that interacts with the TFIIIB⅐DNA complex and is required for specifically initiating transcription (6). Two subunits, C53 and C37, form a subassembly that limits the processivity of pol III elongation and contributes to the abil...

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“…Discrepancies in the location of A49/34.5 and TFIIF may be explained by different locations of a related dimerization module on the two polymerases, or by the presence of additional, unrelated domains in both factors. Sequence analysis showed that A49/34.5 and TFIIF possibly have a counterpart in Pol III, the C37/53 heterodimer (not shown), which may occupy a similar location on the Pol III surface near the lobe and funnel (Fernandez-Tornero et al, 2007).…”

Section: A49 and A345 Form A Tfiif-like Heterodimer Near The Funnelmentioning

confidence: 99%

“…For Pol III, a 17 Å electron microscopy (EM) structure (Fernandez-Tornero et al, 2007) and a homology model for the core enzyme and the crystal structure of the C17/25 subcomplex are available (Jasiak et al, 2006) (for comparability, EM resolutions throughout this paper generally refer to a Fourier shell correlation (FSC) of 0.5). For Pol I, the overall shape and dimensions were first revealed by EM analysis of two-dimensional crystals (Schultz et al, 1993).…”

Section: Introductionmentioning

confidence: 99%

Functional architecture of RNA polymerase I

Geiger¹,

Kuhn²,

Baumli³

et al. 2009

Acta Cryst Sect A

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SUMMARYSynthesis of ribosomal RNA (rRNA) by RNA polymerase (Pol) I is the first step in ribosome biogenesis and a regulatory switch in eukaryotic cell growth. Here we report the 12 Å cryoelectron microscopic structure for the complete 14-subunit yeast Pol I, a homology model for the core enzyme, and the crystal structure of the subcomplex A14/43. In the resulting hybrid structure of Pol I, A14/43, the clamp, and the dock domain contribute to a unique surface interacting with promoter-specific initiation factors. The Pol I-specific subunits A49 and A34.5 form a heterodimer near the enzyme funnel that acts as a built-in elongation factor and is related to the Pol II-associated factor TFIIF. In contrast to Pol II, Pol I has a strong intrinsic 3 0 -RNA cleavage activity, which requires the C-terminal domain of subunit A12.2 and, apparently, enables ribosomal RNA proofreading and 3 0 -end trimming.

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Insights into Transcription Initiation and Termination from the Electron Microscopy Structure of Yeast RNA Polymerase III

Cited by 76 publications

References 36 publications

Transcription termination by nuclear RNA polymerases

Transcription termination by nuclear RNA polymerases

The C53/C37 Subcomplex of RNA Polymerase III Lies Near the Active Site and Participates in Promoter Opening

Functional architecture of RNA polymerase I

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