ArticleThe Journal of biological chemistry2011
Interaction of RNA polymerase II fork loop 2 with downstream non-template DNA regulates transcription elongation.
Article in The Journal of biological chemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 27 citations in OpenAlex.
- Recent advances in mycobacterial transcription: insights beyond the general pathway.Journal of bacteriology · 2025Review
- Transient-State Kinetic Analysis of the RNA Polymerase II Nucleotide Incorporation Mechanism.Biochemistry · 2023Article
- Structure and RNA template requirements ofProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Transient-state kinetic analysis of multi-nucleotide addition catalyzed by RNA polymerase I.Biophysical journal · 2021Article
- The Mechanisms of Substrate Selection, Catalysis, and Translocation by the Elongating RNA Polymerase.Journal of molecular biology · 2019Review
- Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Production and characterization of a highly pure RNA polymerase holoenzyme from Mycobacterium tuberculosis.Protein expression and purification · 2017Article
- CBR antimicrobials inhibit RNA polymerase via at least two bridge-helix cap-mediated effects on nucleotide addition.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Resection is responsible for loss of transcription around a double-strand break in Saccharomyces cerevisiae.eLife · 2015Article
- Mutations in the CRE pocket of bacterial RNA polymerase affect multiple steps of transcription.Nucleic acids research · 2015Article
- Productive mRNA stem loop-mediated transcriptional slippage: Crucial features in common with intrinsic terminators.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Review
- Regulation of Transcript Elongation.Annual review of microbiology · 2015Review
- Coliphage HK022 Nun protein inhibits RNA polymerase translocation.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Intrinsic translocation barrier as an initial step in pausing by RNA polymerase II.Journal of molecular biology · 2013Article
- RNA polymerase II mutations conferring defects in poly(A) site cleavage and termination in Saccharomyces cerevisiae.G3 (Bethesda, Md.) · 2013Article
- Basic mechanisms of RNA polymerase II activity and alteration of gene expression in Saccharomyces cerevisiae.Biochimica et biophysica acta · 2013Review
- Structural basis of transcription initiation.Science (New York, N.Y.) · 2012Article
- Sensitivity of mitochondrial transcription and resistance of RNA polymerase II dependent nuclear transcription to antiviral ribonucleosides.PLoS pathogens · 2012Article
- A comprehensive mechanism for 5-carboxylcytosine-induced transcriptional pausing revealed by Markov state models.The Journal of biological chemistryArticle
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 2 countries.
Funding
Abstract
Fork loop 2 is a small semiconservative segment of the larger fork domain in the second largest Rpb2 subunit of RNA polymerase II (Pol II). This flexible loop, juxtaposed at the leading edge of transcription bubble, has been proposed to participate in DNA strand separation, translocation along DNA, and NTP loading to Pol II during elongation. Here we show that the Rpb2 mutant carrying a deletion of the flexible part of the loop is not lethal in yeast. The mutation exhibits no defects in DNA melting and translocation in vitro but confers a moderate decrease of the catalytic activity of the enzyme caused by the impaired sequestration of the NTP substrate in the active center prior to catalysis. In the structural model of the Pol II elongation complex, fork loop 2 directly interacts with an unpaired DNA residue in the non-template DNA strand one nucleotide ahead from the active center (the i+2 position). We showed that elimination of this putative interaction by replacement of the i+2 residue with an abasic site inhibits Pol II activity to the same degree as the deletion of fork loop 2. This replacement has no detectable effect on the activity of the mutant enzyme. We provide direct evidence that interaction of fork loop 2 with the non-template DNA strand facilitates NTP sequestration through interaction with the adjacent segment of the fork domain involved in the active center of Pol II.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.