title: Stochastic induction of persister cells by HipA through (p)ppGpp-mediated activation of mRNA endonucleases.
abstract: The model organism Escherichia coli codes for at least 11 type II toxin-antitoxin (TA) modules, all implicated in bacterial persistence (multidrug tolerance). Ten of these encode messenger RNA endonucleases (mRNases) inhibiting translation by catalytic degradation of mRNA, and the 11th module, hipBA, encodes HipA (high persister protein A) kinase, which inhibits glutamyl tRNA synthetase (GltX). In turn, inhibition of GltX inhibits translation and induces the stringent response and persistence. Previously, we presented strong support for a model proposing (p)ppGpp (guanosine tetra and penta-phosphate) as the master regulator of persistence. Stochastic variation of [(p)ppGpp] in single cells induced TA-encoded mRNases via a pathway involving polyphosphate and Lon protease. Polyphosphate activated Lon to degrade all known type II antitoxins of E. coli. In turn, the activated mRNases induced persistence and multidrug tolerance. However, even though it was known that activation of HipA stimulated (p)ppGpp synthesis, our model did not explain how hipBA induced persistence. Here we show that, in support of and consistent with our initial model, HipA-induced persistence depends not only on (p)ppGpp but also on the 10 mRNase-encoding TA modules, Lon protease, and polyphosphate. Importantly, observations with single cells convincingly show that the high level of (p)ppGpp caused by activation of HipA does not induce persistence in the absence of TA-encoded mRNases. Thus, slow growth per se does not induce persistence in the absence of TA-encoded toxins, placing these genes as central effectors of bacterial persistence.
authors.affiliation: Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark; and Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, NE2 4AX, Newcastle upon Tyne, United Kingdom.
authors.forename: Elsa
authors.initials: E
authors.lastname: Germain
authors.affiliation: Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark; and Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, NE2 4AX, Newcastle upon Tyne, United Kingdom.
authors.forename: Mohammad
authors.initials: M
authors.lastname: Roghanian
authors.affiliation: Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark; and Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, NE2 4AX, Newcastle upon Tyne, United Kingdom kgerdes@bio.ku.dk e.maisonneuve@bio.ku.dk.
authors.forename: Kenn
authors.initials: K
authors.lastname: Gerdes
authors.affiliation: Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark; and Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, NE2 4AX, Newcastle upon Tyne, United Kingdom kgerdes@bio.ku.dk e.maisonneuve@bio.ku.dk.
authors.forename: Etienne
authors.initials: E
authors.lastname: Maisonneuve
mesh_terms: D000483:Alleles; D000992:Antitoxins / Q000378:metabolism; D001427:Bacterial Toxins / Q000378:metabolism; D004720:Endonucleases / Q000378:metabolism*; D004789:Enzyme Activation; D029968:Escherichia coli Proteins / Q000378:metabolism*; D006158:Guanosine Pentaphosphate / Q000378:metabolism*; D006159:Guanosine Tetraphosphate / Q000378:metabolism*; D008958:Models, Molecular; D012333:RNA, Messenger / Q000378:metabolism; D013269:Stochastic Processes; D059008:Time-Lapse Imaging
chemical_list: D000992:Antitoxins; D001427:Bacterial Toxins; D029968:Escherichia coli Proteins; D012333:RNA, Messenger; C070741:hipA protein, E coli; D006159:Guanosine Tetraphosphate; D006158:Guanosine Pentaphosphate; D004720:Endonucleases
keywords: (p)ppGpp; HipA; bacterial persistence; single-cell analysis; toxin–antitoxin
references.citation: Mol Cell. 2003 Oct;12(4):913-23
references.pmid: 14580342
references.citation: Mol Microbiol. 2003 Jun;48(5):1389-400
references.pmid: 12787364
references.citation: FEMS Microbiol Lett. 2004 Jan 15;230(1):13-8
references.pmid: 14734160
references.citation: Mol Microbiol. 2002 Jul;45(2):501-10
references.pmid: 12123459
references.citation: Proc Natl Acad Sci U S A. 2010 Jul 13;107(28):12541-6
references.pmid: 20616060
references.citation: Cell. 2004 Aug 6;118(3):311-22
references.pmid: 15294157
references.citation: Science. 2004 Sep 10;305(5690):1622-5
references.pmid: 15308767
references.citation: J Bacteriol. 1983 Aug;155(2):768-75
references.pmid: 6348026
references.citation: J Biol Chem. 1984 Feb 10;259(3):1951-7
references.pmid: 6363418
references.citation: J Gen Microbiol. 1986 May;132(5):1297-304
references.pmid: 3534137
references.citation: J Biol Chem. 1997 Aug 22;272(34):21240-3
references.pmid: 9261133
references.citation: J Bacteriol. 2004 Dec;186(24):8172-80
references.pmid: 15576765
references.citation: Science. 2005 Sep 23;309(5743):2075-8
references.pmid: 16123265
references.citation: J Bacteriol. 2006 May;188(10):3494-7
references.pmid: 16672603
references.citation: J Bacteriol. 2006 Jun;188(11):3826-36
references.pmid: 16707675
references.citation: Nat Rev Microbiol. 2006 Jul;4(7):556-62
references.pmid: 16778840
references.citation: BMC Microbiol. 2006;6:53
references.pmid: 16768798
references.citation: J Bacteriol. 2006 Dec;188(24):8360-7
references.pmid: 17041039
references.citation: J Bacteriol. 2010 Dec;192(23):6191-9
references.pmid: 20935098
references.citation: Proc Natl Acad Sci U S A. 2011 Apr 5;108(14):5712-7
references.pmid: 21402902
references.citation: Nature. 2011 May 12;473(7346):216-20
references.pmid: 21562562
references.citation: Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):13206-11
references.pmid: 21788497
references.citation: Annu Rev Microbiol. 2010;64:357-72
references.pmid: 20528688
references.citation: EMBO Rep. 2012 Sep;13(9):835-9
references.pmid: 22814757
references.citation: Cell Rep. 2012 Sep 27;2(3):518-25
references.pmid: 22999936
references.citation: Mol Cell. 2013 May 23;50(4):475-87
references.pmid: 23665232
references.citation: J Bacteriol. 2013 Jul;195(14):3173-82
references.pmid: 23667235
references.citation: J Biol Chem. 2013 Jul 19;288(29):21055-64
references.pmid: 23749992
references.citation: Antimicrob Agents Chemother. 2013 Sep;57(9):4398-409
references.pmid: 23817376
references.citation: Cell. 2013 Aug 29;154(5):1140-50
references.pmid: 23993101
references.citation: Mol Cell. 2013 Oct 24;52(2):248-54
references.pmid: 24095282
references.citation: Nat Commun. 2013;4:3001
references.pmid: 24343429
references.citation: PLoS One. 2014;9(3):e93110
references.pmid: 24667358
references.citation: Cell. 2014 Apr 24;157(3):539-48
references.pmid: 24766804
references.citation: Nucleic Acids Res. 2014 Sep;42(15):10134-47
references.pmid: 25056321
references.citation: Nat Rev Microbiol. 2007 Jan;5(1):48-56
references.pmid: 17143318
references.citation: Science. 2008 Apr 4;320(5872):65-8
references.pmid: 18388284
references.citation: Annu Rev Microbiol. 2008;62:193-210
references.pmid: 18537474
references.citation: Science. 2009 Jan 16;323(5912):396-401
references.pmid: 19150849
references.citation: Antimicrob Agents Chemother. 2010 Jan;54(1):39-44
references.pmid: 19841146
references.citation: Mol Microbiol. 2009 Dec;74(6):1368-79
references.pmid: 19889089
references.citation: Mol Microbiol. 2010 Jan;75(2):333-48
references.pmid: 19943910
references.citation: Biochem Biophys Res Commun. 2010 Jan 1;391(1):209-13
references.pmid: 19909729
references.citation: PLoS Biol. 2010 Feb;8(2):e1000317
references.pmid: 20186264
references.citation: Mol Microbiol. 2003 Nov;50(4):1199-213
references.pmid: 14622409