Literature DB >> 26884158

Conserved rates and patterns of transcription errors across bacterial growth states and lifestyles.

Charles C Traverse1, Howard Ochman2.   

Abstract

Errors that occur during transcription have received much less attention than the mutations that occur in DNA because transcription errors are not heritable and usually result in a very limited number of altered proteins. However, transcription error rates are typically several orders of magnitude higher than the mutation rate. Also, individual transcripts can be translated multiple times, so a single error can have substantial effects on the pool of proteins. Transcription errors can also contribute to cellular noise, thereby influencing cell survival under stressful conditions, such as starvation or antibiotic stress. Implementing a method that captures transcription errors genome-wide, we measured the rates and spectra of transcription errors in Escherichia coli and in endosymbionts for which mutation and/or substitution rates are greatly elevated over those of E. coli Under all tested conditions, across all species, and even for different categories of RNA sequences (mRNA and rRNAs), there were no significant differences in rates of transcription errors, which ranged from 2.3 × 10(-5) per nucleotide in mRNA of the endosymbiont Buchnera aphidicola to 5.2 × 10(-5) per nucleotide in rRNA of the endosymbiont Carsonella ruddii The similarity of transcription error rates in these bacterial endosymbionts to that in E. coli (4.63 × 10(-5) per nucleotide) is all the more surprising given that genomic erosion has resulted in the loss of transcription fidelity factors in both Buchnera and Carsonella.

Entities:  

Keywords:  RNA polymerase fidelity; base substitutions; transcription errors

Mesh:

Substances:

Year:  2016        PMID: 26884158      PMCID: PMC4812759          DOI: 10.1073/pnas.1525329113

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  65 in total

1.  Stationary-phase mutation in the bacterial chromosome: recombination protein and DNA polymerase IV dependence.

Authors:  H J Bull; M J Lombardo; S M Rosenberg
Journal:  Proc Natl Acad Sci U S A       Date:  2001-07-17       Impact factor: 11.205

2.  An aerobic recA-, umuC-dependent pathway of spontaneous base-pair substitution mutagenesis in Escherichia coli.

Authors:  S Bhamre; B B Gadea; C A Koyama; S J White; R G Fowler
Journal:  Mutat Res       Date:  2001-02-20       Impact factor: 2.433

3.  Dps protects cells against multiple stresses during stationary phase.

Authors:  Sudha Nair; Steven E Finkel
Journal:  J Bacteriol       Date:  2004-07       Impact factor: 3.490

4.  Generation and characterization of new highly thermostable and processive M-MuLV reverse transcriptase variants.

Authors:  Aurimas Baranauskas; Sigitas Paliksa; Gediminas Alzbutas; Mindaugas Vaitkevicius; Judita Lubiene; Virginija Letukiene; Sigitas Burinskas; Giedrius Sasnauskas; Remigijus Skirgaila
Journal:  Protein Eng Des Sel       Date:  2012-06-12       Impact factor: 1.650

5.  Visualizing high error levels during gene expression in living bacterial cells.

Authors:  Mor Meyerovich; Gideon Mamou; Sigal Ben-Yehuda
Journal:  Proc Natl Acad Sci U S A       Date:  2010-06-07       Impact factor: 11.205

Review 6.  Stress responses and genetic variation in bacteria.

Authors:  Patricia L Foster
Journal:  Mutat Res       Date:  2005-01-06       Impact factor: 2.433

7.  A sensitive genetic assay for the detection of cytosine deamination: determination of rate constants and the activation energy.

Authors:  L A Frederico; T A Kunkel; B R Shaw
Journal:  Biochemistry       Date:  1990-03-13       Impact factor: 3.162

8.  Growth phase dependent stop codon readthrough and shift of translation reading frame in Escherichia coli.

Authors:  A M Wenthzel; M Stancek; L A Isaksson
Journal:  FEBS Lett       Date:  1998-01-16       Impact factor: 4.124

9.  Bacterial global regulators DksA/ppGpp increase fidelity of transcription.

Authors:  Mohammad Roghanian; Nikolay Zenkin; Yulia Yuzenkova
Journal:  Nucleic Acids Res       Date:  2015-01-20       Impact factor: 16.971

10.  Protein mistranslation protects bacteria against oxidative stress.

Authors:  Yongqiang Fan; Jiang Wu; Matthew H Ung; Nicholas De Lay; Chao Cheng; Jiqiang Ling
Journal:  Nucleic Acids Res       Date:  2015-01-10       Impact factor: 16.971

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  29 in total

1.  Trends in Symbiont-Induced Host Cellular Differentiation.

Authors:  Shelbi L Russell; Jennie Ruelas Castillo
Journal:  Results Probl Cell Differ       Date:  2020

2.  Deoxyuridine in DNA has an inhibitory and promutagenic effect on RNA transcription by diverse RNA polymerases.

Authors:  Junru Cui; Anthony Gizzi; James T Stivers
Journal:  Nucleic Acids Res       Date:  2019-05-07       Impact factor: 16.971

3.  Drift Barriers to Quality Control When Genes Are Expressed at Different Levels.

Authors:  Kun Xiong; Jay P McEntee; David J Porfirio; Joanna Masel
Journal:  Genetics       Date:  2016-11-11       Impact factor: 4.562

Review 4.  How Acts of Infidelity Promote DNA Break Repair: Collision and Collusion Between DNA Repair and Transcription.

Authors:  Priya Sivaramakrishnan; Alasdair J E Gordon; Jennifer A Halliday; Christophe Herman
Journal:  Bioessays       Date:  2018-08-09       Impact factor: 4.345

5.  Transcriptional errors and the drift barrier.

Authors:  David M McCandlish; Joshua B Plotkin
Journal:  Proc Natl Acad Sci U S A       Date:  2016-03-10       Impact factor: 11.205

6.  Transcriptional fidelities of human mitochondrial POLRMT, yeast mitochondrial Rpo41, and phage T7 single-subunit RNA polymerases.

Authors:  Shemaila Sultana; Mihai Solotchi; Aparna Ramachandran; Smita S Patel
Journal:  J Biol Chem       Date:  2017-09-07       Impact factor: 5.157

Review 7.  Transcription fidelity: New paradigms in epigenetic inheritance, genome instability and disease.

Authors:  Catherine C Bradley; Alasdair J E Gordon; Jennifer A Halliday; Christophe Herman
Journal:  DNA Repair (Amst)       Date:  2019-07-08

Review 8.  Detecting Rare Mutations and DNA Damage with Sequencing-Based Methods.

Authors:  Daniel B Sloan; Amanda K Broz; Joel Sharbrough; Zhiqiang Wu
Journal:  Trends Biotechnol       Date:  2018-03-14       Impact factor: 19.536

9.  Universally high transcript error rates in bacteria.

Authors:  Weiyi Li; Michael Lynch
Journal:  Elife       Date:  2020-05-29       Impact factor: 8.140

10.  Catalytic properties of RNA polymerases IV and V: accuracy, nucleotide incorporation and rNTP/dNTP discrimination.

Authors:  Michelle Marasco; Weiyi Li; Michael Lynch; Craig S Pikaard
Journal:  Nucleic Acids Res       Date:  2017-11-02       Impact factor: 16.971

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