Literature DB >> 21326898

Modulation of RNA polymerase activity through the trigger loop folding.

Nataliya Miropolskaya1, Vadim Nikiforov, Saulius Klimasauskas, Irina Artsimovitch, Andrey Kulbachinskiy.   

Abstract

Folding of the trigger loop of RNA polymerase promotes nucleotide addition through creating a closed, catalytically competent conformation of the active center. Here, we discuss the impact of adjacent RNA polymerase elements, including the F loop and the jaw domain, as well as external regulatory factors on the trigger loop folding and catalysis.

Keywords:  RNA polymerase; nucleotide discrimination; temperature adaptation; transcription elongation complex; trigger loop

Mesh：

Substances：

Year:  2010        PMID： 21326898      PMCID： PMC3023635          DOI： 10.4161/trns.1.2.12544

Source DB:  PubMed          Journal:  Transcription        ISSN： 2154-1272


  28 in total

1.  Swing-gate model of nucleotide entry into the RNA polymerase active center.

Authors:  Vitaliy Epshtein; Arkady Mustaev; Vadim Markovtsov; Oxana Bereshchenko; Vadim Nikiforov; Alex Goldfarb
Journal:  Mol Cell       Date:  2002-09       Impact factor: 17.970

2.  A new class of bacterial RNA polymerase inhibitor affects nucleotide addition.

Authors:  Irina Artsimovitch; Clement Chu; A Simon Lynch; Robert Landick
Journal:  Science       Date:  2003-10-24       Impact factor: 47.728

3.  The downstream DNA jaw of bacterial RNA polymerase facilitates both transcriptional initiation and pausing.

Authors:  Josefine Ederth; Irina Artsimovitch; Leif A Isaksson; Robert Landick
Journal:  J Biol Chem       Date:  2002-07-29       Impact factor: 5.157

4.  A ratchet mechanism of transcription elongation and its control.

Authors:  Gil Bar-Nahum; Vitaly Epshtein; Andrei E Ruckenstein; Ruslan Rafikov; Arkady Mustaev; Evgeny Nudler
Journal:  Cell       Date:  2005-01-28       Impact factor: 41.582

5.  Cold sensitivity of thermophilic and mesophilic RNA polymerases.

Authors:  A Kulbachinskiy; I Bass; E Bogdanova; A Goldfarb; V Nikiforov
Journal:  J Bacteriol       Date:  2004-11       Impact factor: 3.490

6.  Yeast RNA polymerase II subunit RPB9. Mapping of domains required for transcription elongation.

Authors:  S A Hemming; A M Edwards
Journal:  J Biol Chem       Date:  2000-01-28       Impact factor: 5.157

7.  Stimulation of transcription by mutations affecting conserved regions of RNA polymerase II.

Authors:  J Archambault; D B Jansma; J H Kawasoe; K T Arndt; J Greenblatt; J D Friesen
Journal:  J Bacteriol       Date:  1998-05       Impact factor: 3.490

8.  Streptolydigin-resistant mutants in an evolutionarily conserved region of the beta' subunit of Escherichia coli RNA polymerase.

Authors:  K Severinov; D Markov; E Severinova; V Nikiforov; R Landick; S A Darst; A Goldfarb
Journal:  J Biol Chem       Date:  1995-10-13       Impact factor: 5.157

9.  Stepwise mechanism for transcription fidelity.

Authors:  Yulia Yuzenkova; Aleksandra Bochkareva; Vasisht R Tadigotla; Mohammad Roghanian; Savva Zorov; Konstantin Severinov; Nikolay Zenkin
Journal:  BMC Biol       Date:  2010-05-07       Impact factor: 7.431

10.  Termination-altering amino acid substitutions in the beta' subunit of Escherichia coli RNA polymerase identify regions involved in RNA chain elongation.

Authors:  R Weilbaecher; C Hebron; G Feng; R Landick
Journal:  Genes Dev       Date:  1994-12-01       Impact factor: 11.361
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  7 in total

1.  CBR antimicrobials inhibit RNA polymerase via at least two bridge-helix cap-mediated effects on nucleotide addition.

Authors:  Brian Bae; Dhananjaya Nayak; Ananya Ray; Arkady Mustaev; Robert Landick; Seth A Darst
Journal:  Proc Natl Acad Sci U S A       Date:  2015-07-20       Impact factor: 11.205

Review 2.  The Mechanisms of Substrate Selection, Catalysis, and Translocation by the Elongating RNA Polymerase.

Authors:  Georgiy A Belogurov; Irina Artsimovitch
Journal:  J Mol Biol       Date:  2019-05-31       Impact factor: 5.469

3.  Direct interactions between the coiled-coil tip of DksA and the trigger loop of RNA polymerase mediate transcriptional regulation.

Authors:  Christopher W Lennon; Wilma Ross; Stephen Martin-Tumasz; Innokenti Toulokhonov; Catherine E Vrentas; Steven T Rutherford; Jeong-Hyun Lee; Samuel E Butcher; Richard L Gourse
Journal:  Genes Dev       Date:  2012-12-01       Impact factor: 11.361

4.  Lineage-specific variations in the trigger loop modulate RNA proofreading by bacterial RNA polymerases.

Authors:  Daria Esyunina; Matti Turtola; Danil Pupov; Irina Bass; Saulius Klimašauskas; Georgiy Belogurov; Andrey Kulbachinskiy
Journal:  Nucleic Acids Res       Date:  2016-01-04       Impact factor: 16.971

5.  Cys-pair reporters detect a constrained trigger loop in a paused RNA polymerase.

Authors:  Dhananjaya Nayak; Michael Voss; Tricia Windgassen; Rachel Anne Mooney; Robert Landick
Journal:  Mol Cell       Date:  2013-06-13       Impact factor: 17.970

6.  Trigger-helix folding pathway and SI3 mediate catalysis and hairpin-stabilized pausing by Escherichia coli RNA polymerase.

Authors:  Tricia A Windgassen; Rachel Anne Mooney; Dhananjaya Nayak; Murali Palangat; Jinwei Zhang; Robert Landick
Journal:  Nucleic Acids Res       Date:  2014-10-21       Impact factor: 16.971

7.  Interplay between the trigger loop and the F loop during RNA polymerase catalysis.

Authors:  Nataliya Miropolskaya; Daria Esyunina; Saulius Klimasauskas; Vadim Nikiforov; Irina Artsimovitch; Andrey Kulbachinskiy
Journal:  Nucleic Acids Res       Date:  2013-10-01       Impact factor: 16.971
  7 in total

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