The positions of TFIIF and TFIIE in the RNA polymerase II transcription preinitiation complex

Chen, Hung-Ta; Warfield, Linda; Hahn, Steven

doi:10.1038/nsmb1272

Cited by 159 publications

(213 citation statements)

References 43 publications

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“…Our crosslinking data and detailed architectural model of the core yeast ITC agree with previous site-specific protein cleavage mapping of the yeast PIC 4,5,28 . Our model further agrees with structural analysis of human Pol II PIC intermediates by EM 7 .…”

Section: Discussionsupporting

confidence: 78%

“…Endogenous S. cerevisiae 12-subunit Pol II was prepared as described 29 . Full-length TFIIB 11 , TFIIF (S. mikatae Tfg1, S. cerevisiae Tfg2) 4 and TBP 30 (residues 61-240) were prepared as described. Pol II (0.77 mg, 3.5 mg ml À 1 ) was incubated with a fourfold molar excess of TFIIF, TFIIB and TBP, and a twofold molar excess of DNA-RNA scaffold (Fig.…”

Section: Methodsmentioning

confidence: 99%

“…Architectural models of the yeast Pol II PIC were obtained by site-specific protein cleavage mapping [4][5][6] . The architecture of the human PIC was obtained by electron microscopy (EM) 7 , and generally resembled that of the yeast PIC.…”

mentioning

confidence: 99%

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Conserved architecture of the core RNA polymerase II initiation complex

et al. 2014

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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.

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Section: Discussionsupporting

confidence: 78%

Section: Methodsmentioning

confidence: 99%

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Conserved architecture of the core RNA polymerase II initiation complex

et al. 2014

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“…On the Rpb2 side of the cleft, a series of loops protruding from the ''lobe'' domain had different conformations in S. pombe. Loop ␤9-␤10, which can be cross-linked to TFIIF in S. cerevisiae (30), and loop ␤7-␤8 were shifted toward downstream DNA in S. pombe. Fork loop 2, only seen in its entirety in S. cerevisiae after an advanced refinement approach (31), could be completely built in S. pombe, in a location where it would block the path of the nontemplate DNA strand in a transcribing complex, and thus contribute to the formation of the downstream edge of the transcription bubble (3,32).…”

Section: Clamp Headmentioning

confidence: 99%

“…The Rpb1 ''clamp head,'' which can be cross-linked to TFIIE in S. cerevisiae (30), adopted a different conformation in S. pombe (Fig. 2).…”

Section: Clamp Headmentioning

confidence: 99%

Schizosacharomyces pombe RNA polymerase II at 3.6-Å resolution

Spåhr

Calero

Bushnell

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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The second structure of a eukaryotic RNA polymerase II so far determined, that of the enzyme from the fission yeast Schizosaccharomyces pombe, is reported here. Comparison with the previous structure of the enzyme from the budding yeast Saccharomyces cerevisiae reveals differences in regions implicated in start site selection and transcription factor interaction. These aspects of the transcription mechanism differ between S. pombe and S. cerevisiae, but are conserved between S. pombe and humans. Amino acid changes apparently responsible for the structural differences are also conserved between S. pombe and humans, suggesting that the S. pombe structure may be a good surrogate for that of the human enzyme. molecular replacement ͉ X-ray crystallography ͉ yeast X -ray crystal structures of RNA polymerases from bacteria and Archaea, and of RNA polymerase II (pol II) from the budding yeast Saccharomyces cerevisiae, have given insight into the fundamental mechanism of transcription (1-7). The structures are closely similar in the catalytic core of the enzyme, where mobile elements interact with nucleic acids during transcription. The bacterial and S. cerevisiae structures differ in the periphery, where the enzymes interact with accessory factors, most notably the general transcription factors and Mediator of eukaryotes. One of the general factors, transcription factor II B (TFIIB), exhibits a degree of conservation with bacterial sigma factor and has a counterpart in Archaea, and a subunit of another general factor, the TATA-binding protein, occurs in Archaea as well, but the remaining general factors and Mediator are unique to eukaryotes.Conserved elements of the catalytic core include ''switch regions'' at the base of a swinging clamp, which interact with the DNA-RNA hybrid and downstream DNA during transcription (2, 3) and may be involved in transcription start site determination (8, 9). A so-called ''trigger loop'' interacts with the substrate nucleoside triphosphate to achieve the high fidelity of transcription (10)(11)(12)(13)(14). A ''bridge helix'' interacts with the coding base in the template strand of the DNA and is believed to play a role in the translocation step of transcription.Peripheral, more divergent elements of pol II include subunits Rpb4 and Rpb7, which form a dimer protruding from the enzyme surface (15, 16) and may be involved in RNA binding. Nearby lies the C terminus of Rpb1, from which extends a flexible linker, followed by Ͼ20 repeats of a 7-aa sequence [the C-terminal domain (CTD)], which interact not only with Mediator but also with capping, splicing, and cleavage/polyadenylation factors during transcription (17).Pol II is 53% identical in amino acid sequence between S. cerevisiae and humans, assuring a high degree of structural similarity. Notable differences in transcription have nevertheless emerged, including differences in promoter structure and interactions with accessory factors. In these respects, the fission yeast Schizosaccharomyces pombe more closely resembles the human system....

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Evolution of Eukaryotic RNA Polymerases

Drouin

Robert

2010

Encyclopedia of Life Sciences

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Ribonucleic acid (RNA) polymerases are responsible for the transcription of deoxyribonucleic acid (DNA) into RNA. The number of protein subunits making up these enzymes has increased during evolution from 5 in Eubacteria to 12 in the common ancestor of Archaea and eukaryotes. Eukaryotes have three RNA polymerases , each transcribing a particular subset of genes. RNA polymerase I transcribes ribosomal RNA genes, RNA polymerase II transcribes messenger RNA genes and RNA polymerase III transcribes 5S and transfer RNA genes. Although RNA polymerase II is still made up of 12 subunits, the number of subunits has increased to 14 in RNA polymerase I and to 17 in RNA polymerase III . These new subunits originated from the permanent recruitment of pre‐existing general transcription factors. Interestingly, the evolution of the three eukaryotic RNA polymerases has been affected not only by adaptive forces but also by the nonadaptive forces due to the concerted evolution of the genes they transcribe. Key Concepts: The larger numbers of protein subunits found in RNA polymerases I and III, relative to RNA polymerase II, are due to the permanent recruitment of general transcription factors. The three universal eukaryotic RNA polymerases have specific functional differences near their respective active sites. During evolution, the three eukaryotic RNA polymerase have been selected to better perform their specific tasks. The rate of evolution of RNA polymerases is proportional to the amount of homogenisation (concerted evolution) experienced by the genes they transcribe. Nonadaptive processes therefore also affect the rate of evolution of RNA polymerase genes.

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The positions of TFIIF and TFIIE in the RNA polymerase II transcription preinitiation complex

Cited by 159 publications

References 43 publications

Conserved architecture of the core RNA polymerase II initiation complex

Conserved architecture of the core RNA polymerase II initiation complex

Schizosacharomyces pombe RNA polymerase II at 3.6-Å resolution

Evolution of Eukaryotic RNA Polymerases

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