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Title: Distinct and redundant functions of three homologs of RNase III in the cyanobacterium Synechococcus sp. strain PCC 7002

Abstract

RNase III is a ribonuclease that recognizes and cleaves double-stranded RNA. Across bacteria, RNase III is involved in rRNA maturation, CRISPR RNA maturation, controlling gene expression, and turnover of messenger RNAs. Many organisms have only one RNase III while others have both a full-length RNase III and another version that lacks a double-stranded RNA binding domain (mini-III). The genome of the cyanobacterium Synechococcus sp. strain PCC 7002 (PCC 7002) encodes three homologs of RNase III, two full-length and one mini-III, that are not essential even when deleted in combination. To discern if each enzyme had distinct responsibilities, we collected and sequenced global RNA samples from the wild type strain, the single, double, and triple RNase III mutants. Approximately 20% of genes were differentially expressed in various mutants with some operons and regulons showing complex changes in expression levels between mutants. Two RNase III's had a role in 23S rRNA maturation and the third was involved in copy number regulation one of six native plasmids. In vitro, purified RNase III enzymes were capable of cleaving some of the known Escherichia coli RNase III target sequences, highlighting the remarkably conserved substrate specificity between organisms yet complex regulation of gene expression.

Authors:
 [1];  [2]; ORCiD logo [1]
  1. Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA, Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706, USA
  2. Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
Publication Date:
Research Org.:
Univ. of Wisconsin, Madison, WI (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1430778
Alternate Identifier(s):
OSTI ID: 1502458
Grant/Contract Number:  
SC0010329
Resource Type:
Published Article
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Name: Nucleic Acids Research Journal Volume: 46 Journal Issue: 4; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Gordon, Gina C., Cameron, Jeffrey C., and Pfleger, Brian F. Distinct and redundant functions of three homologs of RNase III in the cyanobacterium Synechococcus sp. strain PCC 7002. United Kingdom: N. p., 2018. Web. https://doi.org/10.1093/nar/gky041.
Gordon, Gina C., Cameron, Jeffrey C., & Pfleger, Brian F. Distinct and redundant functions of three homologs of RNase III in the cyanobacterium Synechococcus sp. strain PCC 7002. United Kingdom. https://doi.org/10.1093/nar/gky041
Gordon, Gina C., Cameron, Jeffrey C., and Pfleger, Brian F. Wed . "Distinct and redundant functions of three homologs of RNase III in the cyanobacterium Synechococcus sp. strain PCC 7002". United Kingdom. https://doi.org/10.1093/nar/gky041.
@article{osti_1430778,
title = {Distinct and redundant functions of three homologs of RNase III in the cyanobacterium Synechococcus sp. strain PCC 7002},
author = {Gordon, Gina C. and Cameron, Jeffrey C. and Pfleger, Brian F.},
abstractNote = {RNase III is a ribonuclease that recognizes and cleaves double-stranded RNA. Across bacteria, RNase III is involved in rRNA maturation, CRISPR RNA maturation, controlling gene expression, and turnover of messenger RNAs. Many organisms have only one RNase III while others have both a full-length RNase III and another version that lacks a double-stranded RNA binding domain (mini-III). The genome of the cyanobacterium Synechococcus sp. strain PCC 7002 (PCC 7002) encodes three homologs of RNase III, two full-length and one mini-III, that are not essential even when deleted in combination. To discern if each enzyme had distinct responsibilities, we collected and sequenced global RNA samples from the wild type strain, the single, double, and triple RNase III mutants. Approximately 20% of genes were differentially expressed in various mutants with some operons and regulons showing complex changes in expression levels between mutants. Two RNase III's had a role in 23S rRNA maturation and the third was involved in copy number regulation one of six native plasmids. In vitro, purified RNase III enzymes were capable of cleaving some of the known Escherichia coli RNase III target sequences, highlighting the remarkably conserved substrate specificity between organisms yet complex regulation of gene expression.},
doi = {10.1093/nar/gky041},
journal = {Nucleic Acids Research},
number = 4,
volume = 46,
place = {United Kingdom},
year = {2018},
month = {1}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1093/nar/gky041

Citation Metrics:
Cited by: 1 work
Citation information provided by
Web of Science

Figures / Tables:

Figure 1 Figure 1: Role of RNase III in rRNA processing. (A) BioAnalyzer traces of RNA extracted from WT and select RNase III mutants. (B) Extensions of 23S rRNA at the 5′ and 3′ ends in A0061 A2542 A0384. A diagram of the rRNA operon shows primers used to amplify cDNA mademore » from WT and A0384 and triple strains. Controls using WT PCC 7002 DNA as a template (DNA), no template (X), and 2 log DNA ladder (L) are also shown. (C) Proposed rRNA species seen in the BioAnalyzer traces.The 23S peak (labeled as A) breaks into two fragments B (524 bases) and C (2289 bases). rRNA species from the triple mutant with 5′ and 3′ extensions are labeled with an asterisk.« less

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Works referenced in this record:

Bacterial ribosomal RNA in pieces: rRNA fragmentation in bacteria
journal, May 2005


Tunable protein degradation in bacteria
journal, November 2014

  • Cameron, D. Ewen; Collins, James J.
  • Nature Biotechnology, Vol. 32, Issue 12
  • DOI: 10.1038/nbt.3053

How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?
journal, January 2012


Secondary structure and domain architecture of the 23S and 5S rRNAs
journal, June 2013

  • Petrov, Anton S.; Bernier, Chad R.; Hershkovits, Eli
  • Nucleic Acids Research, Vol. 41, Issue 15
  • DOI: 10.1093/nar/gkt513

RNase III Cleaves Eukaryotic Preribosomal RNA at a U3 snoRNP-Dependent Site
journal, April 1996


Arabidopsis Chloroplast Mini-Ribonuclease III Participates in rRNA Maturation and Intron Recycling
journal, February 2015

  • Hotto, Amber M.; Castandet, Benoît; Gilet, Laetitia
  • The Plant Cell, Vol. 27, Issue 3
  • DOI: 10.1105/tpc.114.134452

Artificial repressors for controlling gene expression in bacteria
journal, January 2013

  • Politz, Mark C.; Copeland, Matthew F.; Pfleger, Brian F.
  • Chem. Commun., Vol. 49, Issue 39
  • DOI: 10.1039/C2CC37107C

Recombinant organisms for production of industrial products
journal, March 2010


The Phyre2 web portal for protein modeling, prediction and analysis
journal, May 2015

  • Kelley, Lawrence A.; Mezulis, Stefans; Yates, Christopher M.
  • Nature Protocols, Vol. 10, Issue 6
  • DOI: 10.1038/nprot.2015.053

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


Microbial engineering for the production of advanced biofuels
journal, August 2012

  • Peralta-Yahya, Pamela P.; Zhang, Fuzhong; del Cardayre, Stephen B.
  • Nature, Vol. 488, Issue 7411
  • DOI: 10.1038/nature11478

Alterations in Global Patterns of Gene Expression in Synechocystis sp. PCC 6803 in Response to Inorganic Carbon Limitation and the Inactivation of ndhR , a LysR Family Regulator
journal, November 2003

  • Wang, Hong-Liang; Postier, Bradley L.; Burnap, Robert L.
  • Journal of Biological Chemistry, Vol. 279, Issue 7
  • DOI: 10.1074/jbc.M311336200

Characterization of the biochemical properties of Campylobacter jejuni RNase III
journal, November 2013

  • Haddad, Nabila; Saramago, Margarida; Matos, Rute G.
  • Bioscience Reports, Vol. 33, Issue 6
  • DOI: 10.1042/BSR20130090

Metabolic Engineering for the Production of Natural Products
journal, July 2011


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

Divergent mechanisms of 5' 23S rRNA IVS processing in the alpha-proteobacteria
journal, December 2000


Feedback regulation of ribosomal protein gene expression in Escherichia coli: structural homology of ribosomal RNA and ribosomal protein MRNA.
journal, December 1980

  • Nomura, M.; Yates, J. L.; Dean, D.
  • Proceedings of the National Academy of Sciences, Vol. 77, Issue 12
  • DOI: 10.1073/pnas.77.12.7084

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


Gene-expression tools for the metabolic engineering of bacteria
journal, November 1999


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

PNPase autocontrols its expression by degrading a double-stranded structure in the pnp mRNA leader
journal, December 2001


edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
journal, November 2009


Replication of the streptococcal plasmid pMV158 and derivatives in cell-free extracts of Escherichia coli
journal, March 1987

  • del Solar, Gloria; Diaz, Ramon; Espinosa, Manuel
  • Molecular and General Genetics MGG, Vol. 206, Issue 3
  • DOI: 10.1007/BF00428882

HTSeq--a Python framework to work with high-throughput sequencing data
journal, September 2014


Genetic and genomic analysis of RNases in model cyanobacteria
journal, January 2015

  • Cameron, Jeffrey C.; Gordon, Gina C.; Pfleger, Brian F.
  • Photosynthesis Research, Vol. 126, Issue 1
  • DOI: 10.1007/s11120-015-0076-2

Network analysis of transcriptomics expands regulatory landscapes in Synechococcus sp. PCC 7002
journal, August 2016

  • McClure, Ryan S.; Overall, Christopher C.; McDermott, Jason E.
  • Nucleic Acids Research, Vol. 44, Issue 18
  • DOI: 10.1093/nar/gkw737

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

Analysis of current and alternative phenol based RNA extraction methodologies for cyanobacteria
journal, January 2009

  • Pinto, Fernando; Thapper, Anders; Sontheim, Wolfgang
  • BMC Molecular Biology, Vol. 10, Issue 1
  • DOI: 10.1186/1471-2199-10-79

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

Global Regulatory Functions of the Staphylococcus aureus Endoribonuclease III in Gene Expression
journal, June 2012


A Prophage-Encoded Small RNA Controls Metabolism and Cell Division in Escherichia coli
journal, December 2015


A renaissance in RNA synthetic biology: new mechanisms, applications and tools for the future
journal, October 2015

  • Chappell, James; Watters, Kyle E.; Takahashi, Melissa K.
  • Current Opinion in Chemical Biology, Vol. 28
  • DOI: 10.1016/j.cbpa.2015.05.018

Autoregulation of AbsB (RNase III) Expression in Streptomyces coelicolor by Endoribonucleolytic Cleavage of absB Operon Transcripts
journal, June 2008

  • Xu, W.; Huang, J.; Cohen, S. N.
  • Journal of Bacteriology, Vol. 190, Issue 15
  • DOI: 10.1128/JB.00558-08

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

Direct regulation of Escherichia coli ribosomal protein promoters by the transcription factors ppGpp and DksA
journal, March 2011

  • Lemke, J. J.; Sanchez-Vazquez, P.; Burgos, H. L.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 14
  • DOI: 10.1073/pnas.1019383108

Synthetic Riboswitches That Induce Gene Expression in Diverse Bacterial Species
journal, October 2010

  • Topp, S.; Reynoso, C. M. K.; Seeliger, J. C.
  • Applied and Environmental Microbiology, Vol. 76, Issue 23
  • DOI: 10.1128/AEM.01537-10

Coordinated, Differential Expression of Two Genes through Directed mRNA Cleavage and Stabilization by Secondary Structures
journal, December 2000


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


Engineering mRNA stability inE. coli by the addition of synthetic hairpins using a 5′ cassette system
journal, August 1997


Translation initiation of the replication initiator repB gene of promiscuous plasmid pMV158 is led by an extended non-SD sequence
journal, July 2013


RNA Sequencing Identifies New RNase III Cleavage Sites in Escherichia coli and Reveals Increased Regulation of mRNA
journal, March 2017

  • Gordon, Gina C.; Cameron, Jeffrey C.; Pfleger, Brian F.
  • mBio, Vol. 8, Issue 2
  • DOI: 10.1128/mBio.00128-17

Synthetic RNA modules for fine-tuning gene expression levels in yeast by modulating RNase III activity
journal, July 2011

  • Babiskin, Andrew H.; Smolke, Christina D.
  • Nucleic Acids Research, Vol. 39, Issue 19
  • DOI: 10.1093/nar/gkr445

Efficient engineering of chromosomal ribosome binding site libraries in mismatch repair proficient Escherichia coli
journal, September 2017


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

Mini-III, an unusual member of the RNase III family of enzymes, catalyses 23S ribosomal RNA maturation in B. subtilis
journal, June 2008


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 III-Dependent Expression of the rpsO-pnpOperon of Streptomyces coelicolor
journal, July 2011

  • Gatewood, M. L.; Bralley, P.; Jones, G. H.
  • Journal of Bacteriology, Vol. 193, Issue 17
  • DOI: 10.1128/JB.00452-11

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