Evidence map›Paper›PMID 35641110›Full record

ArticleNucleic acids research2022

Mechanism of transcription modulation by the transcription-repair coupling factor.

Bishnu P Paudel, Zhi-Qiang Xu, Slobodan Jergic, Aaron J Oakley, Nischal Sharma, Simon H J Brown, James C Bouwer, Peter J Lewis, Nicholas E Dixon, Antoine M van Oijen and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

7 citing papers in PubMed.

  1. Predicting theLife (Basel, Switzerland) · 2025
    Article
  2. Article
  3. Dynamics of transcription-coupled repair of cyclobutane pyrimidine dimers and (6-4) photoproducts inProceedings of the National Academy of Sciences of the United States of America · 2024
    Article
  4. Review
  5. Review
  6. Review
  7. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Bishnu P PaudelMolecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.ORCID 0000-0003-3518-3882
Zhi-Qiang XuMolecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.ORCID 0000-0002-5884-0569
Slobodan JergicMolecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.ORCID 0000-0001-5252-0815
Aaron J OakleyMolecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.ORCID 0000-0002-4764-014X
Nischal SharmaMolecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.ORCID 0000-0003-3405-2741
Simon H J BrownMolecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.ORCID 0000-0003-3997-4614
James C BouwerMolecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.ORCID 0000-0003-2384-070X
Peter J LewisMolecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.ORCID 0000-0002-1992-062X
Nicholas E DixonMolecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.ORCID 0000-0002-5958-6945
Antoine M van OijenMolecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.ORCID 0000-0002-1794-5161
Harshad GhodkeMolecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.ORCID 0000-0002-6628-876X

Funding

Creation and Repair of Postreplicative DNA GapsRM1GM130450 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI Michael M. Cox, MYRON GOODMAN · 2019 to 2026
$10.4M
NIGMS NIH HHS RM1 GM130450
6 · The paper itself

Abstract

Elongation by RNA polymerase is dynamically modulated by accessory factors. The transcription-repair coupling factor (TRCF) recognizes paused/stalled RNAPs and either rescues transcription or initiates transcription termination. Precisely how TRCFs choose to execute either outcome remains unclear. With Escherichia coli as a model, we used single-molecule assays to study dynamic modulation of elongation by Mfd, the bacterial TRCF. We found that nucleotide-bound Mfd converts the elongation complex (EC) into a catalytically poised state, presenting the EC with an opportunity to restart transcription. After long-lived residence in this catalytically poised state, ATP hydrolysis by Mfd remodels the EC through an irreversible process leading to loss of the RNA transcript. Further, biophysical studies revealed that the motor domain of Mfd binds and partially melts DNA containing a template strand overhang. The results explain pathway choice determining the fate of the EC and provide a molecular mechanism for transcription modulation by TRCF.

Indexed as

Bacterial ProteinsDNA RepairEscherichia coliTranscription FactorsDNA-Directed RNA PolymerasesTranscription, GeneticBacterial ProteinsDNA-Directed RNA PolymerasesTranscription Factorstranscription repair coupling factor protein, Bacteria

Identifiers

PMID35641110
PMCPMC9177983

What OpenQuestion holds

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Registered trials

None linked

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.