scholarly journals Contacts between mammalian RNA polymerase II and the template DNA in a ternary elongation complex

1993 ◽  
Vol 21 (1) ◽  
pp. 113-118 ◽  
Author(s):  
Gretchen A. Rice ◽  
Michael J. Chamberlin ◽  
Caroline M. Kane
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Elongation Complex ◽  
Template Dna

Allosteric transcription stimulation by RNA polymerase II super elongation complex

2021 ◽  
Author(s):  
Ying Chen ◽  
Seychelle M. Vos ◽  
Christian Dienemann ◽  
Momchil Ninov ◽  
Henning Urlaub ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Elongation Complex ◽  
Super Elongation Complex

Structure of the complete elongation complex of RNA polymerase II with basal factors

Science ◽  
2017 ◽  
Vol 357 (6354) ◽  
pp. 921-924 ◽  
Author(s):  
Haruhiko Ehara ◽  
Takeshi Yokoyama ◽  
Hideki Shigematsu ◽  
Shigeyuki Yokoyama ◽  
Mikako Shirouzu ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Elongation Complex

scholarly journals Nano positioning system reveals the course of upstream and nontemplate DNA within the RNA polymerase II elongation complex

2009 ◽  
Vol 37 (17) ◽  
pp. 5803-5809 ◽  
Author(s):  
Joanna Andrecka ◽  
Barbara Treutlein ◽  
Maria Angeles Izquierdo Arcusa ◽  
Adam Muschielok ◽  
Robert Lewis ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Positioning System ◽  
Elongation Complex

scholarly journals Role of the mammalian transcription factors IIF, IIS, and IIX during elongation by RNA polymerase II.

1991 ◽  
Vol 11 (3) ◽  
pp. 1195-1206 ◽  
Author(s):  
E Bengal ◽  
O Flores ◽  
A Krauskopf ◽  
D Reinberg ◽  
Y Aloni
Keyword(s):  
Transcription Factors ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Gel Filtration ◽  
Late Promoter ◽  
Elongation Complex ◽  
Cell Extracts ◽  
Adenovirus Major Late Promoter ◽  
Major Late Promoter ◽  
Transcription Complexes

We have used a recently developed system that allows the isolation of complexes competent for RNA polymerase II elongation (E. Bengal, A. Goldring, and Y. Aloni, J. Biol. Chem. 264:18926-18932, 1989). Pulse-labeled transcription complexes were formed at the adenovirus major late promoter with use of HeLa cell extracts. Elongation-competent complexes were purified from most of the proteins present in the extract, as well as from loosely bound elongation factors, by high-salt gel filtration chromatography. We found that under these conditions the nascent RNA was displaced from the DNA during elongation. These column-purified complexes were used to analyze the activities of different transcription factors during elongation by RNA polymerase II. We found that transcription factor IIS (TFIIS), TFIIF, and TFIIX affected the efficiency of elongation through the adenovirus major late promoter attenuation site and a synthetic attenuation site composed of eight T residues. These factors have distinct activities that depend on whether they are added before RNA polymerase has reached the attenuation site or at the time when the polymerase is pausing at the attenuation site. TFIIS was found to have antiattenuation activity, while TFIIF and TFIIX stimulated the rate of elongation. In comparison with TFIIF, TFIIS is loosely bound to the elongation complex. We also found that the activities of the factors are dependent on the nature of the attenuator. These results indicate that at least three factors play a major role during elongation by RNA polymerase II.

NTP-driven translocation and regulation of downstream template opening by multi-subunit RNA polymerases

2005 ◽  
Vol 83 (4) ◽  
pp. 486-496 ◽  
Author(s):  
Zachary F Burton ◽  
Michael Feig ◽  
Xue Q Gong ◽  
Chunfen Zhang ◽  
Yuri A Nedialkov ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Active Site ◽  
Binding Sites ◽  
Rna Synthesis ◽  
Rna Polymerases ◽  
Phosphoryl Transfer ◽  
Elongation Complex ◽  
Detailed Model ◽  
Loop 2

Multi-subunit RNA polymerases bind nucleotide triphosphate (NTP) substrates in the pretranslocated state and carry the dNMP–NTP base pair into the active site for phosphoryl transfer. NTP-driven translocation requires that NTP substrates enter the main-enzyme channel before loading into the active site. Based on this model, a new view of fidelity and efficiency of RNA synthesis is proposed. The model predicts that, during processive elongation, NTP-driven translocation is coupled to a protein conformational change that allows pyrophosphate release: coupling the end of one bond-addition cycle to substrate loading and translocation for the next. We present a detailed model of the RNA polymerase II elongation complex based on 2 low-affinity NTP binding sites located in the main-enzyme channel. This model posits that NTP substrates, elongation factors, and the conserved Rpb2 subunit fork loop 2 cooperate to regulate opening of the downstream transcription bubble.Key words: RNA polymerase, NTP-driven translocation, transcriptional fidelity, transcriptional efficiency, α-amanitin.

scholarly journals The RAP74 Subunit of Human Transcription Factor IIF Has Similar Roles in Initiation and Elongation

1999 ◽  
Vol 19 (12) ◽  
pp. 8372-8382 ◽  
Author(s):  
Lei Lei ◽  
Delin Ren ◽  
Zachary F. Burton
Keyword(s):  
Transcription Factor ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Active Form ◽  
Elongation Complex ◽  
Allosteric Effector ◽  
Full Turn ◽  
Activated State ◽  
Transcription Factor Iif ◽  
Promoter Dna

ABSTRACT Transcription factor IIF (TFIIF) is a protein allosteric effector for RNA polymerase II during the initiation and elongation phases of the transcription cycle. In initiation, TFIIF induces promoter DNA to wrap almost a full turn around RNA polymerase II in a complex that includes the general transcription factors TATA-binding protein, TFIIB, and TFIIE. During elongation, TFIIF also supports a more active conformation of RNA polymerase II. This conformational model for elongation is supported by three lines of experimental evidence. First, a region within the RNA polymerase II-associating protein 74 (RAP74) subunit of TFIIF (amino acids T154 to M177), a region that is critical for isomerization of the preinitiation complex, is also critical for elongation stimulation. Amino acid substitutions within this region are shown to have very similar effects on initiation and elongation, and mutagenic analysis indicates that L155, W164, N172, I176, and M177 are the most important residues in this region for transcription. Second, TFIIF is shown to have a higher affinity for rapidly elongating RNA polymerase II than for the stalled elongation complex, indicating that RNA polymerase II alternates between active and inactive states during elongation and that TFIIF stimulates elongation by supporting the active conformational state of RNA polymerase II. The deleterious I176A substitution in the critical region of RAP74 decreases the affinity of TFIIF for the active form of the elongation complex. Third, TFIIF is shown by Arrhenius analysis to stimulate elongation by populating an activated state of RNA polymerase II.

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