Literature DB >> 33122819

Diverse and unified mechanisms of transcription initiation in bacteria.

James Chen1, Hande Boyaci1, Elizabeth A Campbell2.   

Abstract

Transcription of DNA is a fundamental process in all cellular organisms. The enzyme responsible for transcription, RNA polymerase, is conserved in general architecture and catalytic function across the three domains of life. Diverse mechanisms are used among and within the different branches to regulate transcription initiation. Mechanistic studies of transcription initiation in bacteria are especially amenable because the promoter recognition and melting steps are much less complicated than in eukaryotes or archaea. Also, bacteria have critical roles in human health as pathogens and commensals, and the bacterial RNA polymerase is a proven target for antibiotics. Recent biophysical studies of RNA polymerases and their inhibition, as well as transcription initiation and transcription factors, have detailed the mechanisms of transcription initiation in phylogenetically diverse bacteria, inspiring this Review to examine unifying and diverse themes in this process.

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Year:  2020        PMID: 33122819      PMCID: PMC7855538          DOI: 10.1038/s41579-020-00450-2

Source DB:  PubMed          Journal:  Nat Rev Microbiol        ISSN: 1740-1526            Impact factor:   60.633


  161 in total

1.  Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution.

Authors:  A L Gnatt; P Cramer; J Fu; D A Bushnell; R D Kornberg
Journal:  Science       Date:  2001-04-19       Impact factor: 47.728

2.  Bacterial RNA polymerase can retain σ70 throughout transcription.

Authors:  Timothy T Harden; Christopher D Wells; Larry J Friedman; Robert Landick; Ann Hochschild; Jane Kondev; Jeff Gelles
Journal:  Proc Natl Acad Sci U S A       Date:  2016-01-05       Impact factor: 11.205

3.  Mechanism of bacterial transcription initiation: RNA polymerase - promoter binding, isomerization to initiation-competent open complexes, and initiation of RNA synthesis.

Authors:  Ruth M Saecker; M Thomas Record; Pieter L Dehaseth
Journal:  J Mol Biol       Date:  2011-03-01       Impact factor: 5.469

4.  The molecular topography of RNA polymerase-promoter interaction.

Authors:  R B Simpson
Journal:  Cell       Date:  1979-10       Impact factor: 41.582

5.  Stepwise Promoter Melting by Bacterial RNA Polymerase.

Authors:  James Chen; Courtney Chiu; Saumya Gopalkrishnan; Albert Y Chen; Paul Dominic B Olinares; Ruth M Saecker; Jared T Winkelman; Michael F Maloney; Brian T Chait; Wilma Ross; Richard L Gourse; Elizabeth A Campbell; Seth A Darst
Journal:  Mol Cell       Date:  2020-03-10       Impact factor: 17.970

6.  Structural Basis of Transcription Inhibition by CBR Hydroxamidines and CBR Pyrazoles.

Authors:  Yu Feng; David Degen; Xinyue Wang; Matthew Gigliotti; Shuang Liu; Yu Zhang; Deepankar Das; Trevor Michalchuk; Yon W Ebright; Meliza Talaue; Nancy Connell; Richard H Ebright
Journal:  Structure       Date:  2015-07-16       Impact factor: 5.006

7.  6S RNA Mimics B-Form DNA to Regulate Escherichia coli RNA Polymerase.

Authors:  James Chen; Karen M Wassarman; Shili Feng; Katherine Leon; Andrey Feklistov; Jared T Winkelman; Zongli Li; Thomas Walz; Elizabeth A Campbell; Seth A Darst
Journal:  Mol Cell       Date:  2017-10-05       Impact factor: 17.970

8.  Cycling of ribonucleic acid polymerase to produce oligonucleotides during initiation in vitro at the lac UV5 promoter.

Authors:  A J Carpousis; J D Gralla
Journal:  Biochemistry       Date:  1980-07-08       Impact factor: 3.162

9.  Heterogeneity of RNA polymerase in Bacillus subtilis: evidence for an additional sigma factor in vegetative cells.

Authors:  J L Wiggs; M Z Gilman; M J Chamberlin
Journal:  Proc Natl Acad Sci U S A       Date:  1981-05       Impact factor: 11.205

Review 10.  Molecular Mechanisms of Transcription Initiation-Structure, Function, and Evolution of TFE/TFIIE-Like Factors and Open Complex Formation.

Authors:  Fabian Blombach; Katherine L Smollett; Dina Grohmann; Finn Werner
Journal:  J Mol Biol       Date:  2016-04-20       Impact factor: 5.469

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  24 in total

1.  Transmission studies and the composition of prokaryotic communities associated with healthy and diseased Aplysina cauliformis sponges suggest that Aplysina Red Band Syndrome is a prokaryotic polymicrobial disease.

Authors:  Matteo Monti; Aurora Giorgi; Cole G Easson; Deborah J Gochfeld; Julie B Olson
Journal:  FEMS Microbiol Ecol       Date:  2022-01-11       Impact factor: 4.194

2.  How the antibiotic fidaxomicin targets an intestinal pathogen.

Authors: 
Journal:  Nature       Date:  2022-04-06       Impact factor: 49.962

3.  Structural basis of transcription activation by the global regulator Spx.

Authors:  Jing Shi; Fangfang Li; Aijia Wen; Libing Yu; Lu Wang; Fulin Wang; Yuanling Jin; Sha Jin; Yu Feng; Wei Lin
Journal:  Nucleic Acids Res       Date:  2021-10-11       Impact factor: 16.971

Review 4.  Bacterial transcription during growth arrest.

Authors:  Megan Bergkessel
Journal:  Transcription       Date:  2021-09-06

Review 5.  Bacterial Small Membrane Proteins: the Swiss Army Knife of Regulators at the Lipid Bilayer.

Authors:  Srujana S Yadavalli; Jing Yuan
Journal:  J Bacteriol       Date:  2021-09-13       Impact factor: 3.476

6.  RNA polymerase spoiled for choice as transcription begins.

Authors:  Stephen J W Busby
Journal:  Proc Natl Acad Sci U S A       Date:  2021-07-27       Impact factor: 11.205

7.  Universal functions of the σ finger in alternative σ factors during transcription initiation by bacterial RNA polymerase.

Authors:  Anastasiya Oguienko; Ivan Petushkov; Danil Pupov; Daria Esyunina; Andrey Kulbachinskiy
Journal:  RNA Biol       Date:  2021-02-25       Impact factor: 4.652

8.  Structural basis of transcriptional activation by the Mycobacterium tuberculosis intrinsic antibiotic-resistance transcription factor WhiB7.

Authors:  Mirjana Lilic; Seth A Darst; Elizabeth A Campbell
Journal:  Mol Cell       Date:  2021-06-24       Impact factor: 19.328

9.  Temperature effects on RNA polymerase initiation kinetics reveal which open complex initiates and that bubble collapse is stepwise.

Authors:  Dylan M Plaskon; Kate L Henderson; Lindsey C Felth; Cristen M Molzahn; Claire Evensen; Sarah Dyke; Irina A Shkel; M Thomas Record
Journal:  Proc Natl Acad Sci U S A       Date:  2021-07-27       Impact factor: 12.779

10.  Allosteric Activation of SARS-CoV-2 RNA-Dependent RNA Polymerase by Remdesivir Triphosphate and Other Phosphorylated Nucleotides.

Authors:  Bing Wang; Vladimir Svetlov; Yuri I Wolf; Eugene V Koonin; Evgeny Nudler; Irina Artsimovitch
Journal:  mBio       Date:  2021-06-22       Impact factor: 7.867

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