A Genome-Wide Assay Specifies Only GreA as a Transcription Fidelity Factor in Escherichia coli

G3 : Genes - Genomes - Genetics
Charles C Traverse, Howard Ochman

Abstract

Although mutations are the basis for adaptation and heritable genetic change, transient errors occur during transcription at rates that are orders of magnitude higher than the mutation rate. High rates of transcription errors can be detrimental by causing the production of erroneous proteins that need to be degraded. Two transcription fidelity factors, GreA and GreB, have previously been reported to stimulate the removal of errors that occur during transcription, and a third fidelity factor, DksA, is thought to decrease the error rate through an unknown mechanism. Because the majority of transcription-error assays of these fidelity factors were performed in vitro and on individual genes, we measured the in vivo transcriptome-wide error rates in all possible combinations of mutants of the three fidelity factors. This method expands measurements of these fidelity factors to the full spectrum of errors across the entire genome. Our assay shows that GreB and DksA have no significant effect on transcription error rates, and that GreA only influences the transcription error rate by reducing G-to-A errors.

References

Oct 5, 1975·Journal of Molecular Biology·C F Springgate, L A Loeb
Oct 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·S BorukhovA Goldfarb
Jan 1, 1981·Molecular & General Genetics : MGG·R F Rosenberger, G Foskett
May 9, 1995·Proceedings of the National Academy of Sciences of the United States of America·M OrlovaS Borukhov
Feb 12, 1993·Cell·S BorukhovA Goldfarb
Dec 5, 1995·Proceedings of the National Academy of Sciences of the United States of America·L M HsuM J Chamberlin
Mar 4, 1997·Proceedings of the National Academy of Sciences of the United States of America·N Komissarova, M Kashlev
Jun 19, 1998·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·R D'Ari, J Casadesús
Sep 6, 2002·Biochimica Et Biophysica Acta·Rachel N Fish, Caroline M Kane
May 3, 2003·The EMBO Journal·Vasily SosunovAlex Goldfarb
Feb 22, 2005·Molecular Microbiology·Sergei BorukhovOleg Laptenko
May 19, 2005·Proceedings of the National Academy of Sciences of the United States of America·Brian J PaulRichard L Gourse
Apr 7, 2006·The Journal of Biological Chemistry·Katarzyna PotrykusMichael Cashel
Jul 29, 2006·Science·Nikolay ZenkinKonstantin Severinov
Feb 27, 2009·PLoS Biology·Alasdair J E GordonChristophe Herman
Jun 11, 2010·Proceedings of the National Academy of Sciences of the United States of America·Yulia Yuzenkova, Nikolay Zenkin
Jun 11, 2010·Proceedings of the National Academy of Sciences of the United States of America·Mor MeyerovichSigal Ben-Yehuda
Dec 25, 2010·Proceedings of the National Academy of Sciences of the United States of America·Robert S Washburn, Max E Gottesman
Jan 21, 2011·Nature·L Stirling Churchman, Jonathan S Weissman
Feb 25, 2011·Nature Reviews. Cancer·Damien Brégeon, Paul W Doetsch
Jul 24, 2012·Nucleic Acids Research·Mark B SteadSidney R Kushner
Jul 5, 2013·PLoS Genetics·Alasdair J E GordonChristophe Herman
Aug 9, 2013·Nucleic Acids Research·Masahiko ImashimizuMikhail Kashlev
Jun 27, 2014·Nature Protocols·Ashley Acevedo, Raul Andino
Jan 22, 2015·Nucleic Acids Research·Mohammad RoghanianYulia Yuzenkova
Feb 1, 2015·Current Opinion in Microbiology·Alasdair J E GordonChristophe Herman
Aug 26, 2015·Nucleic Acids Research·Dominik SatoryChristophe Herman
Feb 18, 2016·Proceedings of the National Academy of Sciences of the United States of America·Charles C Traverse, Howard Ochman
Jan 11, 2017·Transcription·Pamela GambaNikolay Zenkin
Jun 14, 2017·Proceedings of the National Academy of Sciences of the United States of America·Tatiana V MishaninaRobert Landick
Oct 5, 2017·Nature·Priya SivaramakrishnanChristophe Herman

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Citations

Nov 27, 2018·Microbial Cell Factories·Dawid KoscielniakMarian Sektas
Dec 17, 2019·Genome Biology and Evolution·Kendra M MeerJoanna Masel
Oct 28, 2019·International Journal of Molecular Sciences·Maciej DylewskiKatarzyna Potrykus
May 30, 2020·ELife·Weiyi Li, Michael Lynch

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Datasets Mentioned

BETA
PRJNA417942

Methods Mentioned

BETA
in vitro transcription
CirSeq
Illumina sequencing
NET-seq

Software Mentioned

seq
GreB
GreAB
NET
CirSeq
GreA

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