Literature DB >> 23855603

RNA polymerase: in search of promoters.

Andrey Feklistov1.   

Abstract

Transcription initiation is a key event in the regulation of gene expression. RNA polymerase (RNAP), the central enzyme of transcription, is able to efficiently locate promoters in the genome, carry out promoter opening, and initiate RNA synthesis. All the substeps of transcription initiation are subject to complex cellular regulation. Understanding the molecular details of each step in the promoter-opening pathway is essential for a complete mechanistic and quantitative picture of gene expression. In this minireview, primarily using bacterial RNAP as an example, I briefly summarize some of the key recent advances in our understanding of the mechanisms of promoter search and promoter opening.
© 2013 New York Academy of Sciences.

Entities:  

Keywords:  RNA polymerase; promoter; protein-DNA recognition; transcription

Mesh:

Substances:

Year:  2013        PMID: 23855603      PMCID: PMC3740395          DOI: 10.1111/nyas.12197

Source DB:  PubMed          Journal:  Ann N Y Acad Sci        ISSN: 0077-8923            Impact factor:   5.691


  58 in total

Review 1.  Bacterial RNA polymerases: the wholo story.

Authors:  Katsuhiko S Murakami; Seth A Darst
Journal:  Curr Opin Struct Biol       Date:  2003-02       Impact factor: 6.809

Review 2.  Multiple sigma subunits and the partitioning of bacterial transcription space.

Authors:  Tanja M Gruber; Carol A Gross
Journal:  Annu Rev Microbiol       Date:  2003       Impact factor: 15.500

Review 3.  Activating transcription in bacteria.

Authors:  David J Lee; Stephen D Minchin; Stephen J W Busby
Journal:  Annu Rev Microbiol       Date:  2012-06-15       Impact factor: 15.500

Review 4.  Facilitated target location in biological systems.

Authors:  P H von Hippel; O G Berg
Journal:  J Biol Chem       Date:  1989-01-15       Impact factor: 5.157

5.  Real-time characterization of intermediates in the pathway to open complex formation by Escherichia coli RNA polymerase at the T7A1 promoter.

Authors:  Bianca Sclavi; Evgeny Zaychikov; Anastasia Rogozina; Ferdinand Walther; Malcolm Buckle; Hermann Heumann
Journal:  Proc Natl Acad Sci U S A       Date:  2005-02-28       Impact factor: 11.205

6.  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

7.  Molecular mechanism of promoter selection in gene transcription. II. Kinetic evidence for promoter search by a one-dimensional diffusion of RNA polymerase molecule along the DNA template.

Authors:  C S Park; F Y Wu; C W Wu
Journal:  J Biol Chem       Date:  1982-06-25       Impact factor: 5.157

8.  Opening and closing of the bacterial RNA polymerase clamp.

Authors:  Anirban Chakraborty; Dongye Wang; Yon W Ebright; You Korlann; Ekaterine Kortkhonjia; Taiho Kim; Saikat Chowdhury; Sivaramesh Wigneshweraraj; Herbert Irschik; Rolf Jansen; B Tracy Nixon; Jennifer Knight; Shimon Weiss; Richard H Ebright
Journal:  Science       Date:  2012-08-03       Impact factor: 47.728

9.  A new basal promoter element recognized by RNA polymerase core enzyme.

Authors:  Yulia Yuzenkova; Vasisht R Tadigotla; Konstantin Severinov; Nikolay Zenkin
Journal:  EMBO J       Date:  2011-07-26       Impact factor: 11.598

10.  Anatomy of Escherichia coli sigma70 promoters.

Authors:  Ryan K Shultzaberger; Zehua Chen; Karen A Lewis; Thomas D Schneider
Journal:  Nucleic Acids Res       Date:  2006-12-22       Impact factor: 16.971

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  11 in total

1.  Structural basis for -10 promoter element melting by environmentally induced sigma factors.

Authors:  Sébastien Campagne; May E Marsh; Guido Capitani; Julia A Vorholt; Frédéric H-T Allain
Journal:  Nat Struct Mol Biol       Date:  2014-02-16       Impact factor: 15.369

2.  Characterization of molecular interactions between Escherichia coli RNA polymerase and topoisomerase I by molecular simulations.

Authors:  Purushottam B Tiwari; Prem P Chapagain; Srikanth Banda; Yesim Darici; Aykut Üren; Yuk-Ching Tse-Dinh
Journal:  FEBS Lett       Date:  2016-08-04       Impact factor: 4.124

Review 3.  Studying transcription initiation by RNA polymerase with diffusion-based single-molecule fluorescence.

Authors:  Yazan Alhadid; SangYoon Chung; Eitan Lerner; Dylan J Taatjes; Sergei Borukhov; Shimon Weiss
Journal:  Protein Sci       Date:  2017-04-02       Impact factor: 6.993

4.  A Conserved Pattern of Primer-Dependent Transcription Initiation in Escherichia coli and Vibrio cholerae Revealed by 5' RNA-seq.

Authors:  Sergey Y Druzhinin; Ngat T Tran; Kyle S Skalenko; Seth R Goldman; Jared G Knoblauch; Simon L Dove; Bryce E Nickels
Journal:  PLoS Genet       Date:  2015-07-01       Impact factor: 5.917

Review 5.  Bacterial RNA Polymerase-DNA Interaction-The Driving Force of Gene Expression and the Target for Drug Action.

Authors:  Jookyung Lee; Sergei Borukhov
Journal:  Front Mol Biosci       Date:  2016-11-09

6.  Structure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA.

Authors:  Elizabeth A Hubin; Allison Fay; Catherine Xu; James M Bean; Ruth M Saecker; Michael S Glickman; Seth A Darst; Elizabeth A Campbell
Journal:  Elife       Date:  2017-01-09       Impact factor: 8.140

7.  Insights into Transcriptional Repression of the Homologous Toxin-Antitoxin Cassettes yefM-yoeB and axe-txe.

Authors:  Barbara Kędzierska; Katarzyna Potrykus; Agnieszka Szalewska-Pałasz; Beata Wodzikowska
Journal:  Int J Mol Sci       Date:  2020-11-28       Impact factor: 5.923

8.  bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria and Escherichia coli.

Authors:  Ilham Ayub Shahmuradov; Rozaimi Mohamad Razali; Salim Bougouffa; Aleksandar Radovanovic; Vladimir B Bajic
Journal:  Bioinformatics       Date:  2017-02-01       Impact factor: 6.937

9.  High-throughput detection of RNA processing in bacteria.

Authors:  Erin E Gill; Luisa S Chan; Geoffrey L Winsor; Neil Dobson; Raymond Lo; Shannan J Ho Sui; Bhavjinder K Dhillon; Patrick K Taylor; Raunak Shrestha; Cory Spencer; Robert E W Hancock; Peter J Unrau; Fiona S L Brinkman
Journal:  BMC Genomics       Date:  2018-03-27       Impact factor: 3.969

Review 10.  Multisubunit RNA Polymerases of Jumbo Bacteriophages.

Authors:  Maria L Sokolova; Inna Misovetc; Konstantin V Severinov
Journal:  Viruses       Date:  2020-09-23       Impact factor: 5.048

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