Literature DB >> 19398005

Millisecond phase kinetic analysis of elongation catalyzed by human, yeast, and Escherichia coli RNA polymerase.

Maria Kireeva1, Yuri A Nedialkov, Xue Qian Gong, Chunfen Zhang, Yalin Xiong, Woo Moon, Zachary F Burton, Mikhail Kashlev.   

Abstract

Strategies for assembly and analysis of human, yeast, and bacterial RNA polymerase elongation complexes are described, and methods are shown for millisecond phase kinetic analyses of elongation using rapid chemical quench flow. Human, yeast, and bacterial RNA polymerases function very similarly in NTP-Mg2+ commitment and phosphodiester bond formation. A "running start, two-bond, double-quench" protocol is described and its advantages discussed. These studies provide information about stable NTP-Mg2+ loading, phosphodiester bond synthesis, the processive transition between bonds, and sequence-specific effects on transcription elongation dynamics.

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Year:  2009        PMID： 19398005      PMCID： PMC2721912          DOI： 10.1016/j.ymeth.2009.04.008

Source DB:  PubMed          Journal:  Methods        ISSN： 1046-2023            Impact factor:   3.608


  44 in total

1.  Kinetic investigation of Escherichia coli RNA polymerase mutants that influence nucleotide discrimination and transcription fidelity.

Authors:  Shannon F Holmes; Thomas J Santangelo; Candice K Cunningham; Jeffrey W Roberts; Dorothy A Erie
Journal:  J Biol Chem       Date:  2006-04-18       Impact factor: 5.157

2.  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

3.  Properties of RNA polymerase II elongation complexes before and after the P-TEFb-mediated transition into productive elongation.

Authors:  Bo Cheng; David H Price
Journal:  J Biol Chem       Date:  2007-06-04       Impact factor: 5.157

4.  Hepatitis delta antigen binds to the clamp of RNA polymerase II and affects transcriptional fidelity.

Authors:  Yuki Yamaguchi; Takashi Mura; Sittinan Chanarat; Sachiko Okamoto; Hiroshi Handa
Journal:  Genes Cells       Date:  2007-07       Impact factor: 1.891

Review 5.  Single-molecule studies of RNA polymerase: motoring along.

Authors:  Kristina M Herbert; William J Greenleaf; Steven M Block
Journal:  Annu Rev Biochem       Date:  2008       Impact factor: 23.643

Review 6.  NTP-driven translocation and regulation of downstream template opening by multi-subunit RNA polymerases.

Authors:  Zachary F Burton; Michael Feig; Xue Q Gong; Chunfen Zhang; Yuri A Nedialkov; Yalin Xiong
Journal:  Biochem Cell Biol       Date:  2005-08       Impact factor: 3.626

7.  Dynamic error correction and regulation of downstream bubble opening by human RNA polymerase II.

Authors:  Xue Q Gong; Chunfen Zhang; Michael Feig; Zachary F Burton
Journal:  Mol Cell       Date:  2005-05-13       Impact factor: 17.970

8.  Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis.

Authors:  Dong Wang; David A Bushnell; Kenneth D Westover; Craig D Kaplan; Roger D Kornberg
Journal:  Cell       Date:  2006-12-01       Impact factor: 41.582

9.  Diffusion of nucleoside triphosphates and role of the entry site to the RNA polymerase II active center.

Authors:  Nizar N Batada; Kenneth D Westover; David A Bushnell; Michael Levitt; Roger D Kornberg
Journal:  Proc Natl Acad Sci U S A       Date:  2004-12-01       Impact factor: 11.205

10.  A tunable ratchet driving human RNA polymerase II translocation adjusted by accurately templated nucleoside triphosphates loaded at downstream sites and by elongation factors.

Authors:  Yalin Xiong; Zachary F Burton
Journal:  J Biol Chem       Date:  2007-09-17       Impact factor: 5.157
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  20 in total

1.  RNA polymerase II with open and closed trigger loops: active site dynamics and nucleic acid translocation.

Authors:  Michael Feig; Zachary F Burton
Journal:  Biophys J       Date:  2010-10-20       Impact factor: 4.033

2.  Fluorescence-based assay to measure the real-time kinetics of nucleotide incorporation during transcription elongation.

Authors:  Guo-Qing Tang; Vasanti S Anand; Smita S Patel
Journal:  J Mol Biol       Date:  2010-10-28       Impact factor: 5.469

3.  Coliphage HK022 Nun protein inhibits RNA polymerase translocation.

Authors:  Christal L Vitiello; Maria L Kireeva; Lucyna Lubkowska; Mikhail Kashlev; Max Gottesman
Journal:  Proc Natl Acad Sci U S A       Date:  2014-05-22       Impact factor: 11.205

4.  Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase.

Authors:  Steve A Seibold; Badri Nath Singh; Chunfen Zhang; Maria Kireeva; Céline Domecq; Annie Bouchard; Anthony M Nazione; Michael Feig; Robert I Cukier; Benoit Coulombe; Mikhail Kashlev; Michael Hampsey; Zachary F Burton
Journal:  Biochim Biophys Acta       Date:  2010-05-15

5.  Interaction of RNA polymerase II fork loop 2 with downstream non-template DNA regulates transcription elongation.

Authors:  Maria L Kireeva; Céline Domecq; Benoit Coulombe; Zachary F Burton; Mikhail Kashlev
Journal:  J Biol Chem       Date:  2011-07-05       Impact factor: 5.157

Review 6.  Molecular basis of transcriptional fidelity and DNA lesion-induced transcriptional mutagenesis.

Authors:  Liang Xu; Linati Da; Steven W Plouffe; Jenny Chong; Eric Kool; Dong Wang
Journal:  DNA Repair (Amst)       Date:  2014-04-21

7.  Templated nucleoside triphosphate binding to a noncatalytic site on RNA polymerase regulates transcription.

Authors:  Scott R Kennedy; Dorothy A Erie
Journal:  Proc Natl Acad Sci U S A       Date:  2011-03-29       Impact factor: 11.205

8.  RNA polymerase structure, function, regulation, dynamics, fidelity, and roles in gene expression.

Authors:  Maria L Kireeva; Mikhail Kashlev; Zachary F Burton
Journal:  Chem Rev       Date:  2013-11-13       Impact factor: 60.622

9.  Isolation and characterization of RNA polymerase rpoB mutations that alter transcription slippage during elongation in Escherichia coli.

Authors:  Yan Ning Zhou; Lucyna Lubkowska; Monica Hui; Carolyn Court; Shuo Chen; Donald L Court; Jeffrey Strathern; Ding Jun Jin; Mikhail Kashlev
Journal:  J Biol Chem       Date:  2012-12-05       Impact factor: 5.157

Review 10.  Macromolecular micromovements: how RNA polymerase translocates.

Authors:  Vladimir Svetlov; Evgeny Nudler
Journal:  Curr Opin Struct Biol       Date:  2009-11-02       Impact factor: 6.809
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