Literature DB >> 23117822

A new way to start: nanoRNA-mediated priming of transcription initiation.

Bryce E Nickels1.   

Abstract

A recent study provides evidence that RNA polymerase uses 2- to ~4-nt RNAs, species termed "nanoRNAs," to prime transcription initiation in Escherichia coli. Priming of transcription initiation with nanoRNAs represents a previously undocumented component of transcription start site selection and gene expression.

Entities:  

Keywords:  RNA polymerase; RNA-seq; gene expression; small RNA; start site selection; stationary phase

Mesh：

Substances：

Year:  2012        PMID： 23117822      PMCID： PMC3630185          DOI： 10.4161/trns.21903

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


  29 in total

Review 1.  All things must pass: contrasts and commonalities in eukaryotic and bacterial mRNA decay.

Authors:  Joel G Belasco
Journal:  Nat Rev Mol Cell Biol       Date:  2010-06-03       Impact factor: 94.444

2.  YcfR (BhsA) influences Escherichia coli biofilm formation through stress response and surface hydrophobicity.

Authors:  Xue-Song Zhang; Rodolfo García-Contreras; Thomas K Wood
Journal:  J Bacteriol       Date:  2007-02-09       Impact factor: 3.490

3.  Oligoribonuclease is an essential component of the mRNA decay pathway.

Authors:  S Ghosh; M P Deutscher
Journal:  Proc Natl Acad Sci U S A       Date:  1999-04-13       Impact factor: 11.205

4.  Axiom of determining transcription start points by RNA polymerase in Escherichia coli.

Authors:  Dale E A Lewis; Sankar Adhya
Journal:  Mol Microbiol       Date:  2004-11       Impact factor: 3.501

5.  Characterization of nucleotide pools as a function of physiological state in Escherichia coli.

Authors:  Michael H Buckstein; Jian He; Harvey Rubin
Journal:  J Bacteriol       Date:  2007-10-26       Impact factor: 3.490

6.  Start site selection at lacUV5 promoter affected by the sequence context around the initiation sites.

Authors:  W Jeong; C Kang
Journal:  Nucleic Acids Res       Date:  1994-11-11       Impact factor: 16.971

7.  Regulation of pyrBI operon expression in Escherichia coli by UTP-sensitive reiterative RNA synthesis during transcriptional initiation.

Authors:  C Liu; L S Heath; C L Turnbough
Journal:  Genes Dev       Date:  1994-12-01       Impact factor: 11.361

Review 8.  Degradation of RNA in bacteria: comparison of mRNA and stable RNA.

Authors:  Murray P Deutscher
Journal:  Nucleic Acids Res       Date:  2006-02-01       Impact factor: 16.971

9.  The crystal structure of the Escherichia coli RNase E apoprotein and a mechanism for RNA degradation.

Authors:  Daniel J Koslover; Anastasia J Callaghan; Maria J Marcaida; Elspeth F Garman; Monika Martick; William G Scott; Ben F Luisi
Journal:  Structure       Date:  2008-08-06       Impact factor: 5.006

10.  Protein translation and cell death: the role of rare tRNAs in biofilm formation and in activating dormant phage killer genes.

Authors:  Rodolfo García-Contreras; Xue-Song Zhang; Younghoon Kim; Thomas K Wood
Journal:  PLoS One       Date:  2008-06-11       Impact factor: 3.240
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  11 in total

1.  Analysis of Bacterial Transcription by "Massively Systematic Transcript End Readout," MASTER.

Authors:  Irina O Vvedenskaya; Seth R Goldman; Bryce E Nickels
Journal:  Methods Enzymol       Date:  2018-10-12       Impact factor: 1.600

2.  Mechanism of transcription initiation and promoter escape by E. coli RNA polymerase.

Authors:  Kate L Henderson; Lindsey C Felth; Cristen M Molzahn; Irina Shkel; Si Wang; Munish Chhabra; Emily F Ruff; Lauren Bieter; Joseph E Kraft; M Thomas Record
Journal:  Proc Natl Acad Sci U S A       Date:  2017-03-27       Impact factor: 11.205

3.  RNA polymerase spoiled for choice as transcription begins.

Authors:  Stephen J W Busby
Journal:  Proc Natl Acad Sci U S A       Date:  2021-07-27       Impact factor: 11.205

4.  A Conserved Pattern of Primer-Dependent Transcription Initiation in Escherichia coli and Vibrio cholerae Revealed by 5' RNA-seq.

Authors:  Sergey Y Druzhinin; Ngat T Tran; Kyle S Skalenko; Seth R Goldman; Jared G Knoblauch; Simon L Dove; Bryce E Nickels
Journal:  PLoS Genet       Date:  2015-07-01       Impact factor: 5.917

5.  Intracellular Concentrations of Borrelia burgdorferi Cyclic Di-AMP Are Not Changed by Altered Expression of the CdaA Synthase.

Authors:  Christina R Savage; William K Arnold; Alexandra Gjevre-Nail; Benjamin J Koestler; Eric L Bruger; Jeffrey R Barker; Christopher M Waters; Brian Stevenson
Journal:  PLoS One       Date:  2015-04-23       Impact factor: 3.240

6.  Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli.

Authors:  Kyle S Skalenko; Lingting Li; Yuanchao Zhang; Irina O Vvedenskaya; Jared T Winkelman; Alexander L Cope; Deanne M Taylor; Premal Shah; Richard H Ebright; Justin B Kinney; Yu Zhang; Bryce E Nickels
Journal:  Proc Natl Acad Sci U S A       Date:  2021-07-06       Impact factor: 11.205

7.  C-di-GMP hydrolysis by Pseudomonas aeruginosa HD-GYP phosphodiesterases: analysis of the reaction mechanism and novel roles for pGpG.

Authors:  Valentina Stelitano; Giorgio Giardina; Alessandro Paiardini; Nicoletta Castiglione; Francesca Cutruzzolà; Serena Rinaldo
Journal:  PLoS One       Date:  2013-09-16       Impact factor: 3.240

Review 8.  The cyclic-di-GMP signaling pathway in the Lyme disease spirochete, Borrelia burgdorferi.

Authors:  Elizabeth A Novak; Syed Z Sultan; Md A Motaleb
Journal:  Front Cell Infect Microbiol       Date:  2014-05-01       Impact factor: 5.293

9.  Structural Basis for the Bidirectional Activity of Bacillus nanoRNase NrnA.

Authors:  Brad J Schmier; Claudiu M Nelersa; Arun Malhotra
Journal:  Sci Rep       Date:  2017-09-11       Impact factor: 4.379

10.  Identification and Characterization of c-di-GMP Metabolic Enzymes of Leptospira interrogans and c-di-GMP Fluctuations After Thermal Shift and Infection.

Authors:  Guohui Xiao; Liangliang Kong; Rongbo Che; Yusi Yi; Qinchao Zhang; Jie Yan; Xu'ai Lin
Journal:  Front Microbiol       Date:  2018-04-20       Impact factor: 5.640
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