title: RalR (a DNase) and RalA (a small RNA) form a type I toxin-antitoxin system in Escherichia coli.
abstract: For toxin/antitoxin (TA) systems, no toxin has been identified that functions by cleaving DNA. Here, we demonstrate that RalR and RalA of the cryptic prophage rac form a type I TA pair in which the antitoxin RNA is a trans-encoded small RNA with 16 nucleotides of complementarity to the toxin mRNA. We suggest the newly discovered antitoxin gene be named ralA for RalR antitoxin. Toxin RalR functions as a non-specific endonuclease that cleaves methylated and unmethylated DNA. The RNA chaperone Hfq is required for RalA antitoxin activity and appears to stabilize RalA. Also, RalR/RalA is beneficial to the Escherichia coli host for responding to the antibiotic fosfomycin. Hence, our results indicate that cryptic prophage genes can be functionally divergent from their active phage counterparts after integration into the host genome.
authors.affiliation: Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China.
authors.forename: Yunxue
authors.initials: Y
authors.lastname: Guo
authors.affiliation: Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802-4400, USA.
authors.forename: Cecilia
authors.initials: C
authors.lastname: Quiroga
authors.affiliation: Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802-4400, USA.
authors.forename: Qin
authors.initials: Q
authors.lastname: Chen
authors.affiliation: Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802-4400, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: McAnulty
authors.affiliation: Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802-4400, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Benedik
authors.affiliation: Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802-4400, USA Department of Biology, Texas A & M University, College Station, TX 77843-3258, USA xxwang@scsio.ac.cn.
authors.forename: Thomas K
authors.initials: TK
authors.lastname: Wood
authors.affiliation: Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China xxwang@scsio.ac.cn.
authors.forename: Xiaoxue
authors.initials: X
authors.lastname: Wang
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001427:Bacterial Toxins / Q000096:biosynthesis / Q000235:genetics / Q000378:metabolism*; D020029:Base Pairing; D024881:Drug Resistance, Bacterial; D004706:Endodeoxyribonucleases / Q000096:biosynthesis / Q000235:genetics / Q000378:metabolism*; D004926:Escherichia coli / Q000187:drug effects / Q000201:enzymology* / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000096:biosynthesis / Q000235:genetics / Q000378:metabolism* / Q000502:physiology; D005578:Fosfomycin / Q000494:pharmacology; D035001:Host Factor 1 Protein / Q000502:physiology; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000737:chemistry; D058727:RNA, Small Untranslated / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D014157:Transcription Factors / Q000096:biosynthesis / Q000235:genetics / Q000378:metabolism*
chemical_list: D000900:Anti-Bacterial Agents; D001427:Bacterial Toxins; D029968:Escherichia coli Proteins; C087373:Hfq protein, E coli; D035001:Host Factor 1 Protein; D012333:RNA, Messenger; D058727:RNA, Small Untranslated; C584789:RalR protein, E coli; D014157:Transcription Factors; D005578:Fosfomycin; D004706:Endodeoxyribonucleases
references.citation: J Bacteriol. 2003 Nov;185(22):6600-8
references.pmid: 14594833
references.citation: Mol Genet Genomics. 2004 Sep;272(2):227-34
references.pmid: 15316771
references.citation: Mol Microbiol. 2004 Mar;51(6):1525-33
references.pmid: 15009882
references.citation: J Bacteriol. 2009 Feb;191(4):1258-67
references.pmid: 19060153
references.citation: Mol Cell. 2011 Mar 18;41(6):625-35
references.pmid: 21419338
references.citation: Nat Chem Biol. 2012 Oct;8(10):855-61
references.pmid: 22941047
references.citation: Mol Microbiol. 1995 May;16(4):769-77
references.pmid: 7476171
references.citation: Mol Gen Genet. 1980;179(1):63-73
references.pmid: 6256607
references.citation: Clin Microbiol Infect. 2012 Jan;18(1):4-7
references.pmid: 21914036
references.citation: Nucleic Acids Res. 2014 Jan;42(1):70-86
references.pmid: 23945938
references.citation: J Bacteriol. 1996 Apr;178(7):2044-50
references.pmid: 8606182
references.citation: Trends Genet. 2005 Jul;21(7):399-404
references.pmid: 15913835
references.citation: J Virol. 1981 May;38(2):621-31
references.pmid: 6264133
references.citation: Nucleic Acids Res. 2014 Feb;42(3):1930-46
references.pmid: 24203704
references.citation: Mol Microbiol. 2012 Jun;84(5):979-89
references.pmid: 22515815
references.citation: Cell. 2009 Feb 20;136(4):615-28
references.pmid: 19239884
references.citation: Appl Environ Microbiol. 2011 Aug 15;77(16):5577-83
references.pmid: 21685157
references.citation: RNA Biol. 2012 Dec;9(12):1520-7
references.pmid: 23131729
references.citation: Proc Natl Acad Sci U S A. 2009 Jan 20;106(3):894-9
references.pmid: 19124776
references.citation: Science. 1997 Sep 5;277(5331):1453-62
references.pmid: 9278503
references.citation: Microbiol Mol Biol Rev. 2008 Dec;72(4):579-89, Table of Contents
references.pmid: 19052321
references.citation: Curr Biol. 2001 Jun 26;11(12):941-50
references.pmid: 11448770
references.citation: Mol Syst Biol. 2006;2:2006.0008
references.pmid: 16738554
references.citation: Environ Microbiol. 2007 Feb;9(2):332-46
references.pmid: 17222132
references.citation: J Bacteriol. 2006 Jan;188(1):305-16
references.pmid: 16352847
references.citation: Proc Natl Acad Sci U S A. 2004 May 11;101(19):7287-92
references.pmid: 15123812
references.citation: Mol Microbiol. 2008 Oct;70(1):258-70
references.pmid: 18761622
references.citation: Nat Protoc. 2006;1(1):16-22
references.pmid: 17406207
references.citation: Nat Rev Microbiol. 2005 May;3(5):371-82
references.pmid: 15864262
references.citation: RNA Biol. 2012 Dec;9(12):1504-12
references.pmid: 23182878
references.citation: Environ Microbiol. 2012 Mar;14(3):669-79
references.pmid: 22026739
references.citation: Genetics. 2011 Jan;187(1):123-30
references.pmid: 20980243
references.citation: Nature. 2001 Jan 25;409(6819):529-33
references.pmid: 11206551
references.citation: PLoS Biol. 2010 Feb 23;8(2):e1000317
references.pmid: 20186264
references.citation: J Mol Biol. 2009 Aug 28;391(4):717-28
references.pmid: 19538972
references.citation: DNA Res. 2005;12(5):291-9
references.pmid: 16769691
references.citation: Appl Microbiol Biotechnol. 2004 May;64(4):515-24
references.pmid: 14727089
references.citation: Cell. 2003 Jan 10;112(1):131-40
references.pmid: 12526800
references.citation: Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6640-5
references.pmid: 10829079
references.citation: Biotechnol Bioeng. 2004 Sep 20;87(6):779-90
references.pmid: 15329936
references.citation: J Bacteriol. 2005 Oct;187(19):6641-50
references.pmid: 16166525
references.citation: J Bacteriol. 2011 Feb;193(3):611-9
references.pmid: 21115657
references.citation: Mol Microbiol. 1999 Jun;32(5):1090-102
references.pmid: 10361310
references.citation: Biochem Biophys Res Commun. 2010 Jan 1;391(1):209-13
references.pmid: 19909729
references.citation: Environ Microbiol. 2014 Jun;16(6):1741-54
references.pmid: 24373067
references.citation: Nucleic Acids Res. 2010 Jun;38(11):3743-59
references.pmid: 20156992
references.citation: Environ Microbiol. 2013 Jun;15(6):1734-44
references.pmid: 23289863
references.citation: Cell. 2011 Jan 7;144(1):143-56
references.pmid: 21185072
references.citation: J Bacteriol. 1996 Sep;178(17):5100-4
references.pmid: 8752325
references.citation: Crit Rev Biochem Mol Biol. 2011 Oct;46(5):386-408
references.pmid: 21819231
references.citation: Nat Chem Biol. 2011 Jun;7(6):359-66
references.pmid: 21516113
references.citation: Nature. 2010 Jul 15;466(7304):334-8
references.pmid: 20631792
references.citation: Nucleic Acids Res. 2011 Jul;39(13):5744-56
references.pmid: 21421561
references.citation: J Biol Chem. 1961 Dec;236:3312-6
references.pmid: 13924728
references.citation: J Bacteriol. 2012 May;194(9):2152-64
references.pmid: 22343303
references.citation: Genome Biol. 2007;8(8):R155
references.pmid: 17678530
references.citation: Nat Commun. 2010;1:147
references.pmid: 21266997
references.citation: RNA Biol. 2012 Dec;9(12):1488-90
references.pmid: 23324552
references.citation: Appl Environ Microbiol. 1995 Nov;61(11):4083-8
references.pmid: 8526522