Architecture of the RNA polymerase II–TFIIF complex revealed by cross-linking and mass spectrometry

Chen, Zhuo A.; Jawhari, Anass; Fischer, Lutz; Buchen, Claudia; Tahir, Salman; Kamenski, Tomislav; Rasmussen, Morten; Larivière, L.; Wills, Jimi; Nilges, Michaël; Cramer, Patrick; Rappsilber, Juri

doi:10.1038/emboj.2009.401

Cited by 365 publications

(487 citation statements)

References 69 publications

Supporting

Mentioning

455

Contrasting

Order By: Relevance

“…Another 33 crosslinks were observed between TFIIF subunits Tfg1 and Tfg2, and could be explained with the TFIIF dimerization module structure 16 . Only 18 crosslinks showed Ca distances above the maximum expected distance of 27±3 Å 12 (Fig. 1c).…”

Section: Resultsmentioning

confidence: 99%

“…We have previously modelled the architecture of the core Pol II initiation complex 9 by structural superposition of our Pol II-TFIIB crystal structures 10,11 with a Pol II-TFIIF complex model obtained by XL-MS 12 . However, the model awaited experimental confirmation because both TFIIF and TFIIB are modular factors with flexible domains that may be repositioned on complex assembly.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Conserved architecture of the core RNA polymerase II initiation complex

et al. 2014

Self Cite

View full text Add to dashboard Cite

During transcription initiation at promoters of protein-coding genes, RNA polymerase (Pol) II assembles with TBP, TFIIB and TFIIF into a conserved core initiation complex that recruits additional factors. The core complex stabilizes open DNA and initiates RNA synthesis, and it is conserved in the Pol I and Pol III transcription systems. Here, we derive the domain architecture of the yeast core pol II initiation complex during transcription initiation. The yeast complex resembles the human initiation complex and reveals that the TFIIF Tfg2 winged helix domain swings over promoter DNA. An 'arm' and a 'charged helix' in TFIIF function in transcription start site selection and initial RNA synthesis, respectively, and apparently extend into the active centre cleft. Our model provides the basis for further structure-function analysis of the entire transcription initiation complex.

show abstract

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

Conserved architecture of the core RNA polymerase II initiation complex

et al. 2014

Self Cite

View full text Add to dashboard Cite

show abstract

“…1b) may close over nucleic acids in the cleft 11 to increase transcription processivity 9,21 . The A49-A34.5 subcomplex is related to the Pol II initiation factor TFIIF and to the Pol III subcomplex C37-C53, which contain similar dimerization domains located at corresponding positions [22][23][24] .…”

Section: Composite Active Centrementioning

confidence: 99%

RNA polymerase I structure and transcription regulation

Engel

Sainsbury

Cheung

et al. 2013

Nature

Self Cite

200

305

View full text Add to dashboard Cite

Transcription of ribosomal RNA by RNA polymerase (Pol) I initiates ribosome biogenesis and regulates eukaryotic cell growth. The crystal structure of Pol I fromthe yeast Saccharomyces cerevisiae at 2.8A˚ resolution reveals all 14 subunits of the 590-kilodalton enzyme, and shows differences to Pol II. An ‘expander’ element occupies the DNA template site and stabilizes an expanded active centre cleft with an unwound bridge helix. A ‘connector’ element invades the cleft of an adjacent polymerase and stabilizes an inactive polymerase dimer. The connector and expander must detach during Pol I activation to enable transcription initiation and cleft contraction by convergent movement of the polymerase ‘core’ and ‘shelf’ modules. Conversion between an inactive expanded and an active contracted polymerase state may generally underlie transcription. Regulatory factors can modulate the core–shelf interface that includes a ‘composite’ active site for RNA chain initiation, elongation, proofreading and termination

show abstract

“…To induce these changes, the B-ribbon may bind the dock, causing the wall to rotate, which then enables the B-core to bind the wall and protrusion (Figs 1d and 2a). TFIIF also binds the lobe and protrusion 12,13 , and stabilizes TFIIB on Pol II 14 , in particular binding of the B-core to the wall 15 . These changes contribute to TFIIB function, because mutations in the lobe and protrusion (Supplementary Fig.…”

mentioning

confidence: 99%

Structure and function of the initially transcribing RNA polymerase II–TFIIB complex

Sainsbury

Niesser

Cramer

2012

Nature

Self Cite

179

195

View full text Add to dashboard Cite

The general transcription factor (TF) IIB is required for RNA polymerase (Pol) II initiation and extends with its B-reader element into the Pol II active centre cleft. Low-resolution structures of the Pol II-TFIIB complex 1,2 indicated how TFIIB functions in DNA recruitment, but they lacked nucleic acids and half of the B-reader, leaving other TFIIB functions 3,4 enigmatic. Here we report crystal structures of the Pol II-TFIIB complex from the yeast Saccharomyces cerevisiae at 3.4 Å resolution and of an initially transcribing complex that additionally contains the DNA template and a 6-nucleotide RNA product. The structures reveal the entire B-reader and proteinnucleic acid interactions, and together with functional data lead to a more complete understanding of transcription initiation. TFIIB partially closes the polymerase cleft to position DNA and assist in its opening. The B-reader does not reach the active site but binds the DNA template strand upstream to assist in the recognition of the initiator sequence and in positioning the transcription start site. TFIIB rearranges active-site residues, induces binding of the catalytic metal ion B, and stimulates initial RNA synthesis allosterically. TFIIB then prevents the emerging DNA-RNA hybrid duplex from tilting, which would impair RNA synthesis. When the RNA grows beyond 6 nucleotides, it is separated from DNA and is directed to its exit tunnel by the B-reader loop. Once the RNA grows to 12-13 nucleotides, it clashes with TFIIB, triggering TFIIB displacement and elongation complex formation. Similar mechanisms may underlie all cellular transcription because all eukaryotic and archaeal RNA polymerases use TFIIB-like factors 5 , and the bacterial initiation factor sigma has TFIIB-like topology 1,2 and contains the loop region 3.2 that resembles the B-reader loop in location, charge and function [6][7][8] . TFIIB and its counterparts may thus account for the two fundamental properties that distinguish RNA from DNA polymerases: primer-independent chain initiation and product separation from the template.Our previous X-ray analysis of the Pol II-TFIIB complex at 4.3 Å resolution provided a partial backbone model of TFIIB 1 . To obtain a complete and atomic structure, we co-crystallized Pol II with a TFIIB variant lacking the mobile amino-terminal tail and carboxy-terminal cyclin fold (Methods, Supplementary Table and Supplementary Fig. 1). The resulting Pol II-TFIIB structure at 3.4 Å resolution provides details of the interactions of the four TFIIB domains with Pol II: the B-ribbon with the dock, the B-core N-terminal cyclin fold with the wall, the B-reader helix with the RNA exit tunnel, and the B-linker helix with the coiled-coil of the clamp (Fig. 1).The structure reveals the entire course of the TFIIB polypeptide chain through the Pol II cleft, including the previously lacking 1 B-reader loop (residues 67-79) and a new 'B-reader strand' (residues 80-83). The B-reader loop does not reach the active site, but instead interacts with the Pol II rudder and fork loop ...

show abstract

Architecture of the RNA polymerase II–TFIIF complex revealed by cross-linking and mass spectrometry

Cited by 365 publications

References 69 publications

Conserved architecture of the core RNA polymerase II initiation complex

Conserved architecture of the core RNA polymerase II initiation complex

RNA polymerase I structure and transcription regulation

Structure and function of the initially transcribing RNA polymerase II–TFIIB complex

Contact Info

Product

Resources

About