ArticleJournal of molecular biology2013
An insertion in the catalytic trigger loop gates the secondary channel of RNA polymerase.
Article in Journal of molecular biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 41 citations in OpenAlex.
- RNA polymerase SI3 domain modulates global transcriptional pausing and pause-site fluctuations.Nucleic acids research · 2024Article
- DksA, ppGpp, and RegAB Regulate Nitrate Respiration in Paracoccus denitrificans.Journal of bacteriology · 2023Article
- High-throughput, fluorescent-aptamer-based measurements of steady-state transcription rates forbioRxiv : the preprint server for biology · 2023Article
- A non-native C-terminal extension of the β' subunit compromises RNA polymerase and Rho functions.Molecular microbiology · 2022Article
- The δ subunit and NTPase HelD institute a two-pronged mechanism for RNA polymerase recycling.Nature communications · 2020Article
- Role of the trigger loop in translesion RNA synthesis by bacterial RNA polymerase.The Journal of biological chemistry · 2020Article
- DksA and DNA double-strand break repair.Current genetics · 2019Review
- The Mechanisms of Substrate Selection, Catalysis, and Translocation by the Elongating RNA Polymerase.Journal of molecular biology · 2019Review
- Structural Basis of Transcription: RNA Polymerase Backtracking and Its Reactivation.Molecular cell · 2019Article
- DksA Controls the Response of the Lyme Disease SpirocheteJournal of bacteriology · 2019Article
- Delayed inhibition mechanism for secondary channel factor regulation of ribosomal RNA transcription.eLife · 2019Article
- Transcriptional Responses to ppGpp and DksA.Annual review of microbiology · 2018Review
- Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA.Molecular cell · 2018Article
- TraR directly regulates transcription initiation by mimicking the combined effects of the global regulators DksA and ppGpp.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Dynamics of GreB-RNA polymerase interaction allow a proofreading accessory protein to patrol for transcription complexes needing rescue.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- ppGpp Binding to a Site at the RNAP-DksA Interface Accounts for Its Dramatic Effects on Transcription Initiation during the Stringent Response.Molecular cell · 2016Article
- Contributions of Sinorhizobium meliloti Transcriptional Regulator DksA to Bacterial Growth and Efficient Symbiosis with Medicago sativa.Journal of bacteriology · 2016Article
- Lineage-specific variations in the trigger loop modulate RNA proofreading by bacterial RNA polymerases.Nucleic acids research · 2016Article
- DksA regulates RNA polymerase in Escherichia coli through a network of interactions in the secondary channel that includes Sequence Insertion 1.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- DksA involvement in transcription fidelity buffers stochastic epigenetic change.Nucleic acids research · 2015Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
Abstract
Escherichia coli DksA and GreB bind to RNA polymerase (RNAP), reaching inside the secondary channel, with similar affinities but have different cellular functions. DksA destabilizes promoter complexes whereas GreB facilitates RNA cleavage in arrested elongation complexes (ECs). Although the less abundant GreB may not interfere with DksA regulation during initiation, reports that DksA acts during elongation and termination suggest that it may exclude GreB from arrested complexes, potentially triggering genome instability. Here, we show that GreB does not compete with DksA during termination whereas DksA, even when present in several hundredfold molar excess, does not inhibit GreB-mediated cleavage of the nascent RNA. Our findings that DksA does not bind to backtracked or active ECs provide an explanation for the lack of DksA activity on most ECs that we reported previously, raising a question of what makes a transcription complex susceptible to DksA. Structural modeling suggests that i6, an insertion in the catalytic trigger loop, hinders DksA access into the channel, restricting DksA action to a subset of transcription complexes. In support of this hypothesis, we demonstrate that deletion of i6 permits DksA binding to ECs and that the distribution of DksA and i6 in bacterial genomes is strongly concordant. We hypothesize that DksA binds to transcription complexes in which i6 becomes mobile, for example, as a consequence of weakened RNAP interactions with the downstream duplex DNA.
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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.