Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

Title: RNA Sequencing Identifies New RNase III Cleavage Sites in Escherichia coli and Reveals Increased Regulation of mRNA

Abstract

ABSTRACT Ribonucleases facilitate rapid turnover of RNA, providing cells with another mechanism to adjust transcript and protein levels in response to environmental conditions. While many examples have been documented, a comprehensive list of RNase targets is not available. To address this knowledge gap, we compared levels of RNA sequencing coverage of Escherichia coli and a corresponding RNase III mutant to expand the list of known RNase III targets. RNase III is a widespread endoribonuclease that binds and cleaves double-stranded RNA in many critical transcripts. RNase III cleavage at novel sites found in aceEF , proP , tnaC , dctA , pheM , sdhC , yhhQ , glpT , aceK , and gluQ accelerated RNA decay, consistent with previously described targets wherein RNase III cleavage initiates rapid degradation of secondary messages by other RNases. In contrast, cleavage at three novel sites in the ahpF , pflB , and yajQ transcripts led to stabilized secondary transcripts. Two other novel sites in hisL and pheM overlapped with transcriptional attenuators that likely serve to ensure turnover of these highly structured RNAs. Many of the new RNase III target sites are located on transcripts encoding metabolic enzymes. For instance, two novel RNase III sites aremore » located within transcripts encoding enzymes near a key metabolic node connecting glycolysis and the tricarboxylic acid (TCA) cycle. Pyruvate dehydrogenase activity was increased in an rnc deletion mutant compared to the wild-type (WT) strain in early stationary phase, confirming the novel link between RNA turnover and regulation of pathway activity. Identification of these novel sites suggests that mRNA turnover may be an underappreciated mode of regulating metabolism. IMPORTANCE The concerted action and overlapping functions of endoribonucleases, exoribonucleases, and RNA processing enzymes complicate the study of global RNA turnover and recycling of specific transcripts. More information about RNase specificity and activity is needed to make predictions of transcript half-life and to design synthetic transcripts with optimal stability. RNase III does not have a conserved target sequence but instead recognizes RNA secondary structure. Prior to this study, only a few RNase III target sites in E. coli were known, so we used RNA sequencing to provide a more comprehensive list of cleavage sites and to examine the impact of RNase III on transcript degradation. With this added information on how RNase III participates in transcript regulation and recycling, a more complete picture of RNA turnover can be developed for E. coli . Similar approaches could be used to augment our understanding of RNA turnover in other bacteria.« less

Authors:
 [1];  [2];  [1];
+ Show Author Affiliations
  1. Department of Chemical and Biological Engineering, University of Wisconsin—Madison, Madison, Wisconsin, USA, Microbiology Doctoral Training Program, University of Wisconsin—Madison, Madison, Wisconsin, USA
  2. Department of Chemical and Biological Engineering, University of Wisconsin—Madison, Madison, Wisconsin, USA
Publication Date:
Research Org.:
Univ. of Wisconsin, Madison, WI (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Inst. of Health (NIH) (United States)
OSTI Identifier:
1618362
Alternate Identifier(s):
OSTI ID: 1368401
Grant/Contract Number:  
SC0010329; 5 T32 GM08349
Resource Type:
Published Article
Journal Name:
mBio
Additional Journal Information:
Journal Name: mBio Journal Volume: 8 Journal Issue: 2; Journal ID: ISSN 2161-2129
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Escherichia coli; RNA degradation; RNA sequencing; RNA stability; RNase III

Citation Formats

Gordon, Gina C., Cameron, Jeffrey C., Pfleger, Brian F., and Papoutsakis, ed., Eleftherios T. RNA Sequencing Identifies New RNase III Cleavage Sites in Escherichia coli and Reveals Increased Regulation of mRNA. United States: N. p., 2017. Web. doi:10.1128/mBio.00128-17.
Copy to clipboard
Gordon, Gina C., Cameron, Jeffrey C., Pfleger, Brian F., & Papoutsakis, ed., Eleftherios T. RNA Sequencing Identifies New RNase III Cleavage Sites in Escherichia coli and Reveals Increased Regulation of mRNA. United States. https://doi.org/10.1128/mBio.00128-17
Copy to clipboard
Gordon, Gina C., Cameron, Jeffrey C., Pfleger, Brian F., and Papoutsakis, ed., Eleftherios T. Wed . "RNA Sequencing Identifies New RNase III Cleavage Sites in Escherichia coli and Reveals Increased Regulation of mRNA". United States. https://doi.org/10.1128/mBio.00128-17.
Copy to clipboard
@article{osti_1618362,
title = {RNA Sequencing Identifies New RNase III Cleavage Sites in Escherichia coli and Reveals Increased Regulation of mRNA},
author = {Gordon, Gina C. and Cameron, Jeffrey C. and Pfleger, Brian F. and Papoutsakis, ed., Eleftherios T.},
abstractNote = {ABSTRACT Ribonucleases facilitate rapid turnover of RNA, providing cells with another mechanism to adjust transcript and protein levels in response to environmental conditions. While many examples have been documented, a comprehensive list of RNase targets is not available. To address this knowledge gap, we compared levels of RNA sequencing coverage of Escherichia coli and a corresponding RNase III mutant to expand the list of known RNase III targets. RNase III is a widespread endoribonuclease that binds and cleaves double-stranded RNA in many critical transcripts. RNase III cleavage at novel sites found in aceEF , proP , tnaC , dctA , pheM , sdhC , yhhQ , glpT , aceK , and gluQ accelerated RNA decay, consistent with previously described targets wherein RNase III cleavage initiates rapid degradation of secondary messages by other RNases. In contrast, cleavage at three novel sites in the ahpF , pflB , and yajQ transcripts led to stabilized secondary transcripts. Two other novel sites in hisL and pheM overlapped with transcriptional attenuators that likely serve to ensure turnover of these highly structured RNAs. Many of the new RNase III target sites are located on transcripts encoding metabolic enzymes. For instance, two novel RNase III sites are located within transcripts encoding enzymes near a key metabolic node connecting glycolysis and the tricarboxylic acid (TCA) cycle. Pyruvate dehydrogenase activity was increased in an rnc deletion mutant compared to the wild-type (WT) strain in early stationary phase, confirming the novel link between RNA turnover and regulation of pathway activity. Identification of these novel sites suggests that mRNA turnover may be an underappreciated mode of regulating metabolism. IMPORTANCE The concerted action and overlapping functions of endoribonucleases, exoribonucleases, and RNA processing enzymes complicate the study of global RNA turnover and recycling of specific transcripts. More information about RNase specificity and activity is needed to make predictions of transcript half-life and to design synthetic transcripts with optimal stability. RNase III does not have a conserved target sequence but instead recognizes RNA secondary structure. Prior to this study, only a few RNase III target sites in E. coli were known, so we used RNA sequencing to provide a more comprehensive list of cleavage sites and to examine the impact of RNase III on transcript degradation. With this added information on how RNase III participates in transcript regulation and recycling, a more complete picture of RNA turnover can be developed for E. coli . Similar approaches could be used to augment our understanding of RNA turnover in other bacteria.},
doi = {10.1128/mBio.00128-17},
journal = {mBio},
number = 2,
volume = 8,
place = {United States},
year = {2017},
month = {5}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1128/mBio.00128-17
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Citation Metrics:
Cited by: 32 works
Citation information provided by
Web of Science
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

Bacteriophage lambda N gene leader RNA. RNA processing and translational initiation signals.
journal, December 1987

Regulation of E. coli phenylalanyl-tRNA synthetase operon in vivo
journal, May 1984

  • Trudel, Marie; Springer, Mathias; Graffe, Monique
  • Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression, Vol. 782, Issue 1
  • DOI: 10.1016/0167-4781(84)90100-3

Attenuation and processing of RNA from the rplJL--rpoBC transcription unit of Escherichia coli.
journal, June 1980

  • Barry, G.; Squires, C.; Squires, C. L.
  • Proceedings of the National Academy of Sciences, Vol. 77, Issue 6
  • DOI: 10.1073/pnas.77.6.3331

Messenger RNA Degradation in Bacterial Cells
journal, November 2014

Ribonuclease III cleavage of bacteriophage T3RNA polymerase transcripts to late T3 mRNAs.
journal, November 1977

  • Majumder, H. K.; Bishayee, S.; Chakraborty, P. R.
  • Proceedings of the National Academy of Sciences, Vol. 74, Issue 11
  • DOI: 10.1073/pnas.74.11.4891

Proteins associated with RNase E in a multicomponent ribonucleolytic complex.
journal, April 1996

  • Miczak, A.; Kaberdin, V. R.; Wei, C. L.
  • Proceedings of the National Academy of Sciences, Vol. 93, Issue 9
  • DOI: 10.1073/pnas.93.9.3865

tmRNA regulates synthesis of the ArfA ribosome rescue factor: tmRNA regulates ArfA synthesis
journal, March 2011

Protein abundance profiling of the Escherichia coli cytosol
journal, January 2008

  • Ishihama, Yasushi; Schmidt, Thorsten; Rappsilber, Juri
  • BMC Genomics, Vol. 9, Issue 1
  • DOI: 10.1186/1471-2164-9-102

Transcriptional analysis of the gene encoding pyruvate formate-lyase-activating enzyme of Escherichia coli
journal, March 1990

RNase III Controls mltD mRNA Degradation in Escherichia coli
journal, December 2013

A protein complex mediating mRNA degradation in Escherichia coli
journal, November 1994

The Continuing Story of Endoribonuclease III
journal, January 2004

  • Drider, Djamel; Condon, Ciarán
  • Journal of Molecular Microbiology and Biotechnology, Vol. 8, Issue 4
  • DOI: 10.1159/000086700

Dihydrolipoamide Dehydrogenase Mutation Alters the NADH Sensitivity of Pyruvate Dehydrogenase Complex of Escherichia coli K-12
journal, March 2008

  • Kim, Y.; Ingram, L. O.; Shanmugam, K. T.
  • Journal of Bacteriology, Vol. 190, Issue 11, p. 3851-3858
  • DOI: 10.1128/JB.00104-08

Escherichia coli RNase III ( rnc ) autoregulation occurs independently of rnc gene translation
journal, December 1997

Mfold web server for nucleic acid folding and hybridization prediction
journal, July 2003

Integrative genomics viewer
journal, January 2011

  • Robinson, James T.; Thorvaldsdóttir, Helga; Winckler, Wendy
  • Nature Biotechnology, Vol. 29, Issue 1
  • DOI: 10.1038/nbt.1754

Nutrient Dependence of RNase E Essentiality in Escherichia coli
journal, December 2012

  • Tamura, M.; Moore, C. J.; Cohen, S. N.
  • Journal of Bacteriology, Vol. 195, Issue 6
  • DOI: 10.1128/JB.01558-12

RNase III initiates rapid degradation of proU mRNA upon hypo-osmotic stress in Escherichia coli
journal, January 2012

  • Kavalchuk, Kanstantsin; Madhusudan, Srinivasan; Schnetz, Karin
  • RNA Biology, Vol. 9, Issue 1
  • DOI: 10.4161/rna.9.1.18228

Investigation on the anaerobic propionate degradation by Escherichia coli K12 : Anaerobic propionate degradation by
journal, October 2016

  • Simonte, Francesca M.; Dötsch, Andreas; Galego, Lisete
  • Molecular Microbiology, Vol. 103, Issue 1
  • DOI: 10.1111/mmi.13541

The quantitative and condition-dependent Escherichia coli proteome
journal, December 2015

  • Schmidt, Alexander; Kochanowski, Karl; Vedelaar, Silke
  • Nature Biotechnology, Vol. 34, Issue 1
  • DOI: 10.1038/nbt.3418

Translation of the adhE transcript to produce ethanol dehydrogenase requires RNase III cleavage in Escherichia coli.
journal, July 1996

Enzymatic assembly of DNA molecules up to several hundred kilobases
journal, April 2009

  • Gibson, Daniel G.; Young, Lei; Chuang, Ray-Yuan
  • Nature Methods, Vol. 6, Issue 5, p. 343-345
  • DOI: 10.1038/nmeth.1318

Autoregulation of RNase III operon by mRNA processing.
journal, November 1989

The metabolic potential of Escherichia coli BL21 in defined and rich medium
journal, January 2014

  • Li, Zhaopeng; Nimtz, Manfred; Rinas, Ursula
  • Microbial Cell Factories, Vol. 13, Issue 1
  • DOI: 10.1186/1475-2859-13-45

CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III
journal, March 2011

  • Deltcheva, Elitza; Chylinski, Krzysztof; Sharma, Cynthia M.
  • Nature, Vol. 471, Issue 7340
  • DOI: 10.1038/nature09886

Polynucleotide Phosphorylase Activity May Be Modulated by Metabolites in Escherichia coli
journal, February 2011

  • Nurmohamed, Salima; Vincent, Helen A.; Titman, Christopher M.
  • Journal of Biological Chemistry, Vol. 286, Issue 16
  • DOI: 10.1074/jbc.M110.200741

Escherichia coli cell division inhibitor DicF-RNA of the dicB operon
journal, April 1990

  • Faubladier, Marlène; Cam, Kaymeuang; Bouché, Jean-Pierre
  • Journal of Molecular Biology, Vol. 212, Issue 3
  • DOI: 10.1016/0022-2836(90)90325-G

Accumulation of 30S preribosomal ribonucleic acid in an Escherichia coli mutant treated with chloramphenicol
journal, October 1974

  • Schlessinger, David; Ono, Mayumi; Nikolaev, N.
  • Biochemistry, Vol. 13, Issue 21
  • DOI: 10.1021/bi00718a004

RraA
journal, September 2003

Overexpression, Purification, and Properties of Escherichia coli Ribonuclease II
journal, January 1996

  • Coburn, Glen A.; Mackie, George A.
  • Journal of Biological Chemistry, Vol. 271, Issue 2
  • DOI: 10.1074/jbc.271.2.1048

The double-stranded transcriptome of Escherichia coli
journal, January 2014

  • Lybecker, M.; Zimmermann, B.; Bilusic, I.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 8
  • DOI: 10.1073/pnas.1315974111

RNase III stimulates the translation of the cIII gene of bacteriophage lambda.
journal, September 1987

  • Altuvia, S.; Locker-Giladi, H.; Koby, S.
  • Proceedings of the National Academy of Sciences, Vol. 84, Issue 18
  • DOI: 10.1073/pnas.84.18.6511

Cleavage by RNase III in the transcripts of the metY-nusA-infB operon of Escherichia coli releases the tRNA and initiates the decay of the downstream mRNA
journal, November 1989

RNase G-Dependent Degradation of the eno mRNA Encoding a Glycolysis Enzyme Enolase in Escherichia coli
journal, January 2002

  • Kaga, Naoko; Umitsuki, Genryou; Nagai, Kazuo
  • Bioscience, Biotechnology, and Biochemistry, Vol. 66, Issue 10
  • DOI: 10.1271/bbb.66.2216

The nuclear RNase III Drosha initiates microRNA processing
journal, September 2003

  • Lee, Yoontae; Ahn, Chiyoung; Han, Jinju
  • Nature, Vol. 425, Issue 6956
  • DOI: 10.1038/nature01957

In vivo and in vitro detection of the leader RNA of the histidine operon of Escherichia coli K-12.
journal, May 1981

  • Frunzio, R.; Bruni, C. B.; Blasi, F.
  • Proceedings of the National Academy of Sciences, Vol. 78, Issue 5
  • DOI: 10.1073/pnas.78.5.2767

Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays
journal, December 2010

  • Stead, Mark B.; Marshburn, Sarah; Mohanty, Bijoy K.
  • Nucleic Acids Research, Vol. 39, Issue 8
  • DOI: 10.1093/nar/gkq1242

Stability of the Osmoregulated Promoter-Derived proP mRNA Is Posttranscriptionally Regulated by RNase III in Escherichia coli
journal, February 2015

  • Lim, Boram; Lee, Kangseok
  • Journal of Bacteriology, Vol. 197, Issue 7
  • DOI: 10.1128/JB.02460-14

Function, mechanism and regulation of bacterial ribonucleases
journal, June 1999

Structure, mechanism and ensemble formation of the alkylhydroperoxide reductase subunits AhpC and AhpF from Escherichia coli
journal, October 2014

  • Dip, Phat Vinh; Kamariah, Neelagandan; Subramanian Manimekalai, Malathy Sony
  • Acta Crystallographica Section D Biological Crystallography, Vol. 70, Issue 11
  • DOI: 10.1107/S1399004714019233

Role for a bidentate ribonuclease in the initiation step of RNA interference
journal, January 2001

  • Bernstein, Emily; Caudy, Amy A.; Hammond, Scott M.
  • Nature, Vol. 409, Issue 6818
  • DOI: 10.1038/35053110

Differential degradation of the Escherichia coli polynucleotide phosphorylase mRNA
journal, January 1989

  • Takata, Renkichi; Izuhara, Mika; Planta, Rudi J.
  • Nucleic Acids Research, Vol. 17, Issue 18
  • DOI: 10.1093/nar/17.18.7441

A 5'-terminal stem-loop structure can stabilize mRNA in Escherichia coli.
journal, January 1992

  • Emory, S. A.; Bouvet, P.; Belasco, J. G.
  • Genes & Development, Vol. 6, Issue 1
  • DOI: 10.1101/gad.6.1.135

Complementary sequences 1700 nucleotides apart form a ribonuclease III cleavage site in Escherichia coli ribosomal precursor RNA.
journal, August 1978

  • Young, R. A.; Steitz, J. A.
  • Proceedings of the National Academy of Sciences, Vol. 75, Issue 8
  • DOI: 10.1073/pnas.75.8.3593

The Essential Function of B. subtilis RNase III Is to Silence Foreign Toxin Genes
journal, December 2012

Novel Activities of Glycolytic Enzymes in Bacillus subtilis : INTERACTIONS WITH ESSENTIAL PROTEINS INVOLVED IN mRNA PROCESSING
journal, February 2009

  • Commichau, Fabian M.; Rothe, Fabian M.; Herzberg, Christina
  • Molecular & Cellular Proteomics, Vol. 8, Issue 6
  • DOI: 10.1074/mcp.M800546-MCP200

Sequence and transcriptional pattern of the essential Escherichia coli secE-nusG operon.
journal, March 1990

RNase III cleavage is obligate for maturation but not for function of Escherichia coli pre-23S rRNA.
journal, January 1984

  • King, T. C.; Sirdeshmukh, R.; Schlessinger, D.
  • Proceedings of the National Academy of Sciences, Vol. 81, Issue 1
  • DOI: 10.1073/pnas.81.1.185

Comparing the predicted and observed properties of proteins encoded in the genome ofEscherichia coli K-12
journal, January 1997

  • Link, Andrew J.; Robison, Keith; Church, George M.
  • Electrophoresis, Vol. 18, Issue 8
  • DOI: 10.1002/elps.1150180807

Linkage map of Escherichia coli K-12, edition 6
journal, March 1980

RNase III Controls the Degradation of corA mRNA in Escherichia coli
journal, February 2012

  • Lim, B.; Sim, S. -H.; Sim, M.
  • Journal of Bacteriology, Vol. 194, Issue 9
  • DOI: 10.1128/JB.00099-12

T7 Early RNAs and Escherichia coli Ribosomal RNAs are Cut from Large Precursor RNAs In Vivo by Ribonuclease III
journal, December 1973

  • Dunn, J. J.; Studier, F. W.
  • Proceedings of the National Academy of Sciences, Vol. 70, Issue 12
  • DOI: 10.1073/pnas.70.12.3296

RNase III: Genetics and Function; Structure and Mechanism
journal, November 2013

YmdB: a stress-responsive ribonuclease-binding regulator of E. coli RNase III activity
journal, December 2008

  • Kim, K. -s.; Manasherob, R.; Cohen, S. N.
  • Genes & Development, Vol. 22, Issue 24
  • DOI: 10.1101/gad.1729508

RNase G complementation of rne null mutation identifies functional interrelationships with RNase E in Escherichia coli
journal, March 2002

Transcription and transcript processing in the sdh CDAB-sucABCD operon of Escherichia coli
journal, August 1998

    Sort by:
    [ × clear filter / sort ]

    Similar Records in DOE PAGES and OSTI.GOV collections: