Literature DB >> 34696836

Watching the bacterial RNA polymerase transcription reaction by time-dependent soak-trigger-freeze X-ray crystallography.

Yeonoh Shin1, Katsuhiko S Murakami2.   

Abstract

RNA polymerase (RNAP) is the central enzyme of gene expression, which transcribes DNA to RNA. All cellular organisms synthesize RNA with highly conserved multi-subunit DNA-dependent RNAPs, except mitochondrial RNA transcription, which is carried out by a single-subunit RNAP. Over 60 years of extensive research has elucidated the structures and functions of cellular RNAPs. In this review, we introduce a brief structural feature of bacterial RNAP, the most well characterized model enzyme, and a novel experimental approach known as "Time-dependent soak-trigger-freeze X-ray crystallography" which can be used to observe the RNA synthesis reaction at atomic resolution in real time. This principle methodology can be used for elucidating fundamental mechanisms of cellular RNAP transcription.
Copyright © 2021 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  RNA; RNA polymerase; Structural biology; Time-dependent soak-trigger-freeze X-ray crystallography; Transcription

Mesh:

Substances:

Year:  2021        PMID: 34696836      PMCID: PMC8965730          DOI: 10.1016/bs.enz.2021.06.009

Source DB:  PubMed          Journal:  Enzymes        ISSN: 1874-6047


  56 in total

Review 1.  The functional and regulatory roles of sigma factors in transcription.

Authors:  C A Gross; C Chan; A Dombroski; T Gruber; M Sharp; J Tupy; B Young
Journal:  Cold Spring Harb Symp Quant Biol       Date:  1998

2.  Architecture of RNA polymerase II and implications for the transcription mechanism.

Authors:  P Cramer; D A Bushnell; J Fu; A L Gnatt; B Maier-Davis; N E Thompson; R R Burgess; A M Edwards; P R David; R D Kornberg
Journal:  Science       Date:  2000-04-28       Impact factor: 47.728

3.  X-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides.

Authors:  Michael L Gleghorn; Elena K Davydova; Ritwika Basu; Lucia B Rothman-Denes; Katsuhiko S Murakami
Journal:  Proc Natl Acad Sci U S A       Date:  2011-02-14       Impact factor: 11.205

4.  Structural basis for rifamycin resistance of bacterial RNA polymerase by the three most clinically important RpoB mutations found in Mycobacterium tuberculosis.

Authors:  Vadim Molodtsov; Nathan T Scharf; Maxwell A Stefan; George A Garcia; Katsuhiko S Murakami
Journal:  Mol Microbiol       Date:  2017-01-10       Impact factor: 3.501

Review 5.  Genetics of eukaryotic RNA polymerases I, II, and III.

Authors:  J Archambault; J D Friesen
Journal:  Microbiol Rev       Date:  1993-09

Review 6.  Human mitochondrial RNA polymerase: structure-function, mechanism and inhibition.

Authors:  Jamie J Arnold; Eric D Smidansky; Ibrahim M Moustafa; Craig E Cameron
Journal:  Biochim Biophys Acta       Date:  2012-04-19

Review 7.  Archaeal RNA polymerase and transcription regulation.

Authors:  Sung-Hoon Jun; Matthew J Reichlen; Momoko Tajiri; Katsuhiko S Murakami
Journal:  Crit Rev Biochem Mol Biol       Date:  2011-02       Impact factor: 8.250

8.  Region 3.2 of the σ factor controls the stability of rRNA promoter complexes and potentiates their repression by DksA.

Authors:  Danil Pupov; Ivan Petushkov; Daria Esyunina; Katsuhiko S Murakami; Andrey Kulbachinskiy
Journal:  Nucleic Acids Res       Date:  2018-11-30       Impact factor: 16.971

Review 9.  The sigma70 family of sigma factors.

Authors:  Mark S B Paget; John D Helmann
Journal:  Genome Biol       Date:  2003-01-03       Impact factor: 13.583

10.  Mode of Action of Kanglemycin A, an Ansamycin Natural Product that Is Active against Rifampicin-Resistant Mycobacterium tuberculosis.

Authors:  Hamed Mosaei; Vadim Molodtsov; Bernhard Kepplinger; John Harbottle; Christopher William Moon; Rose Elizabeth Jeeves; Lucia Ceccaroni; Yeonoh Shin; Stephanie Morton-Laing; Emma Claire Louise Marrs; Corinne Wills; William Clegg; Yulia Yuzenkova; John David Perry; Joanna Bacon; Jeff Errington; Nicholas Edward Ellis Allenby; Michael John Hall; Katsuhiko S Murakami; Nikolay Zenkin
Journal:  Mol Cell       Date:  2018-09-20       Impact factor: 17.970

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