Stress and Environmental Regulation of Gene Expression and Adaptation in Bacteria

1365 Pages·2016·189.72 MB·English

by  Frans J. de Bruijn

Stress and environmental
regulation of gene
expression and adaptation
in bacteria
Volume 1
Stress and environmental
regulation of gene
expression and adaptation
in bacteria
Volume 1
Editedby
Frans J. de Bruijn
INRA-CNRSLaboratoryofPlant-MicrobeInteractions(LIPM)
ChemindeBordeRouge-Auzeville
Castanet-Tolosan
France
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ISBN:9781119004882
Coverinsetfigure:CourtesyofMaudeGuillier.
Regulationofgeneexpressioninbacteriaplaysakeyroleintheiradaptationtoever-changingenvironments.Transcriptionisthefirst
levelofcontrolthathasbeendescribedanddecadesofresearchhaveledtoathoroughcharacterizationofthetranscriptional
network,atleastforsomeofthemodelbacteriasuchasEscherichiacoli.However,itisnowclearthatmanygenesaresubjectto
post-transcriptionalcontrolaswell,andsmallRNAsareamajorclassofpost-transcriptionalregulators.Manyfunctionsareinfact
controlledbymixedregulatorycircuitsencompassingbothtranscriptionalandpost-transcriptionalcontrolmediatedrespectivelyby
proteinsorRNAs.Thepropertiesofsuchcircuitsarejuststartingtobeelucidated.Intheregulatoryschemeshownonthecover,the
involvementofHfq-bindingsRNAsincontrolofmotilityandadhesioninenterobacteriaisdepicted.Positiveandnegativecontrols
areshownwithnormalandblunt-endarrowsrespectively.Asterisksindicateregulatoryinteractionspresumedtobedirect.Green
triangleshighlightfeedforwardregulatorymotifs.TheregulatoryschemeisfoundinFigure5.1.1inChapter5.1byMaudeGuillier
etal.FormoredetailsseeChapter5.1.
10 9 8 7 6 5 4 3 2 1
Thisworkisdedicatedtomywife,CathySenta-LoysdeBruijn,forhersupportandinterestinthe
book,andherloveandunderstandingduringthehecticeditingepisodes.
Contents
VOLUME 1 2.10 Transposableelements:atoolkitforstressand
environmentaladaptationinbacteria,137
Preface,xiii
AnnaUllastres,MiriamMerenciano,LainGuio,and
Acknowledgements,xiv JosefaGonza´lez
Listofcontributors,xv 2.11 CRISPR–Cassystem:anewparadigmforbacterial
stressresponsethroughgenomerearrangement,146
1 Introduction,1 JosephA.Hakim,HyunminKoo,JanD.vanElsas,
FransJ.deBruijn JackT.Trevors,andAsimK.Bej
2.12 Thecoppermetallomeinprokaryoticcells,161
Section2: Keyoverviewchapters,3
ChristopherRensing,HendA.Alwathnani,and
2.1 Stress-inducedchangesintranscriptstability,5 SylviaF.McDevitt
DvoraBiranandElioraZ.Ron
2.13 Ribonucleasesasmodulatorsofbacterialstress
2.2 StressChipformonitoringmicrobialstressresponsein response,174
theenvironment,9 Ca´tiaBa´rria,VaˆniaPobre,AfonsoM.Bravo,and
JoyD.VanNostrand,AifenZhouandJizhongZhou Cec´ıliaM.Arraiano
2.3 Arevolutionaryparadigmofbacterialgenome 2.14 Double-strand-breakrepair,mutagenesis,and
regulation,23 stress,185
AkiraIshihama ElizabethRogers,RaulCorrea,BrittanyBarreto,
Mar´ıaAnge´licaBravoNu´n˜ez,P.J.Minnick,Diana
2.4 Roleofchangesinσ70-driventranscriptionin
VeraCruz,JunXia,P.J.Hastings,andSusanM.
adaptationofE.colitoconditionsofstressor
Rosenberg
starvation,37
UmenderK.Sharma 2.15 SigmafactorcompetitioninEscherichiacoli:kinetic
andthermodynamicperspectives,196
2.5 ThedistributionandspatialorganizationofRNA
KuldeepkumarRamnareshGuptaand
polymeraseinEscherichiacoli:growthrateregulation
DipankarChatterji
andstressresponses,48
DingJunJin,CedricCagliero,JeromeIzard,Carmen 2.16 Ironhomeostasisandiron–sulfurclusterassemblyin
MataMartin,andYanNingZhou Escherichiacoli,203
HuangenDing
2.6 TheECFclassification:aphylogeneticreflectionofthe
regulatorydiversityintheextracytoplasmicfunctionσ 2.17 Mechanismsunderlyingtheantimicrobialcapacityof
factorproteinfamily,64 metals,215
DanielaPintoandThorstenMascher JoeA.LemireandRaymondJ.Turner
2.7 Toxin–antitoxinsystemsinbacteriaandarchaea,97 2.18 Acyl-homoserinelactone-basedquorumsensingin
YoshihiroYamaguchiandMasayoriInouye membersofthemarinebacterialRoseobacterclade:
complexcell-to-cellcommunicationcontrolsmultiple
2.8 BacterialsRNAs:regulationinstress,108
physiologies,225
MarimuthuCitartan,CarstenA.Raabe,Chee-Hock
AlisonBuchan,AprilMitchell,W.NathanCude,
Hoe,TimofeyS.Rozhdestvensky,andThean-Hock
andShawnCampagna
Tang
2.19 Nativeandsyntheticgeneregulationtonitrogen
2.9 Bacterialstressresponsesasdeterminantsof
limitationstress,234
antimicrobialresistance,115
Jo¨rgSchumacher
MichaelFruciandKeithPoole
vii
viii Contents
Section3: One-,two-,andthree-component 4.7 Posttranslationalregulationofantisigmafactorsof
regulatorysystemsandstressresponses,247 RpoE:acomparisonbetweentheEscherichiacoliand
Pseudomonasaeruginosasystems,361
3.1 Two-componentsystemsthatcontroltheexpressionof
SundarPandey,KyleL.Martins,andKalaiMathee
aromatichydrocarbondegradationpathways,249
TinoKrell
Section5: SmallnoncodingRNAsandstress
3.2 Cross-talkofglobalregulatorsinStreptomyces,257
responses,369
JuanF.Mart´ın,FernandoSantos-Beneit,Alberto
Sola-Landa,andPalomaLiras 5.1 BacterialsmallRNAsinmixedregulatorycircuits,371
JonathanJagodnik,DenisThieffry,andMaude
3.3 NO–H-NOX-regulatedtwo-componentsignaling,268
Guillier
DhruvP.Arora,SandhyaMuralidharan,and
ElizabethM.Boon 5.2 RoleofsmallRNAsinPseudomonasaeruginosa
virulenceandadaptation,383
3.4 Thetwo-componentCheYsysteminthechemotaxisof
HansiKumari,DeepakBalasubramanian,andKalai
Sinorhizobiummeliloti,277
Mathee
MartinHaslbeck
5.3 Physiologicaleffectsofposttranscriptionalregulation
3.5 Stimulusperceptionbyhistidinekinases,282
bythesmallRNASgrSduringmetabolicstressin
HannahSchramke,YangWang,RalfHeermann,and
Escherichiacoli,393
KirstenJung
GregoryR.Richards
Section4: Sigmafactorsandstressresponses,301 5.4 ThreerpoS-activatingsmallRNAsinpathways
contributingtoacidresistanceofEscherichiacoli,402
4.1 TheextracytoplasmicfunctionsigmafactorEcfO
GeunuBak,KookHan,DaunKim,Kwang-sunKim,
protectsBacteroidesfragilisagainstoxidativestress,303
andYounghoonLee
IvanC.Ndamukong,SamanthaPalethorpe,Michael
Betteken,andC.JeffreySmith 5.5 ThermalstressnoncodingRNAsinprokaryotesand
eukaryotes:acomparativeapproach,412
4.2 Regulationofenergymetabolismbythe
MercedesdelaFuenteandJose´Luis
extracytoplasmicfunction(ECF)σfactorsof
Mart´ınez-Guitarte
Arcobacterbutzleri,311
IratiMartinez-Malaxetxebarria,RudyMuts,Linda
vanDijk,CraigT.Parker,WilliamG.Miller,Steven
Section6: Toxin-antitoxinsystemsandstress
Huynh,WimGaastra,JosP.M.vanPutten,Aurora
responses,423
Fernandez-Astorga,andMarcM.S.MWo¨sten
6.1 Epigeneticsmediatedbyrestrictionmodification
4.3 Extracytoplasmicfunctionsigmafactorsandstress
systems,425
responsesinCorynebacterium
IwonaMrukandIchizoKobayashi
pseudotuberculosis,321
ThiagoL.P.Castro,NubiaSeyffert,AnneC.Pinto, 6.2 Toxin–antitoxinsystemsasregulatorsofbacterial
ArturSilva,VascoAzevedo,andLuisG.C.Pacheco fitnessandvirulence,437
BrittanyA.FlemingandMatthewA.Mulvey
4.4 Thecomplexrolesandregulationofstressresponseσ
factorsinStreptomycescoelicolor,328 6.3 Mechanismsofstress-activatedpersisterformationin
JanKormanec,BeatricaSevcikova,RenataNovakova, Escherichiacoli,446
DagmarHomerova,BronislavaRezuchova,andErik StephanieM.AmatoandMarkP.Brynildsen
Mingyar
6.4 IdentificationandcharacterizationoftypeII
4.5 Proteolyticactivationofextracytoplasmicfunction toxin–antitoxinsystemsintheopportunisticpathogen
(ECF)σfactors,344 Acinetobacterbaumannii,454
JessicaL.HastieandCraigD.Ellermeier EditaSuzˇiede˙liene˙,MildaJure˙naite˙,andJulija
Armalyte˙
4.6 TheECFfamilysigmafactorσHinCorynebacterium
glutamicumcontrolsthethiol-oxidativestress 6.5 Transcriptionalcontroloftoxin–antitoxinexpression:
response,352 keepingtoxinsunderwrapsuntilthetimeisright,463
TobiasBuscheandJo¨rnKalinowski BarbaraKeℷdzierskaandFinbarrHayes
Contents ix
6.6 OppositeeffectsofGraTtoxinonstresstolerance 9.3 HowalargegenenetworkcouplesmutagenicDNA
ofPseudomonasputida,473 breakrepairtostressinEscherichiacoli,570
RitaHo˜rakandHedvigTamman ElizabethRogers,P.J.Hastings,Mar´ıaAnge´licaBravo
Nu´n˜ez,andSusanM.Rosenberg
Section7: Stringentresponsetostress,479
9.4 Double-strandDNAbreakrepairinmycobacteria,577
7.1 PreferentialcellularaccumulationofppGpporpppGpp RichaGuptaandMichaelS.Glickman
inEscherichiacoli,481
K.PotrykusandM.Cashel
Section10: Adaptationtooxidativestress,587
7.2 GlobalRsh-dependenttranscriptionprofileofBrucella
10.1 Peroxide-sensingtranscriptionalregulatorsin
suisduringstringentresponseunravelsadaptationto
bacteria,589
nutrientstarvationandcross-talkwithotherstress
JamesM.DubbsandSkornMongkolsuk
responses,489
StephanKo¨hler,NabilHanna,Safia 10.2 Regulationofoxidativestress–relatedgenesimplicated
Ouahrani-Bettache,KennethL.Drake,L.Garry intheestablishmentofopportunisticinfectionsby
Adams,andAlessandraOcchialini Bacteroidesfragilis,603
FelipeLopesTeixeira,ReginaMariaCavalcanti
7.3 Thestringentresponseandantioxidantdefencesin
PilottoDomingues,andLeandroAraujoLobo
Pseudomonasaeruginosa,500
GowthamiSampathkumar,MalikaKhakimova,Tevy 10.3 Investigationintooxidativestressresponseof
Chan,andDaoNguyen Shewanellaoneidensisrevealsadistinctmechanism,609
JieYuan,FenWan,andHaichunGao
7.4 MolecularbasisofthestringentresponseinVibrio
cholerae,507 10.4 Anomicsviewontheresponsetosingletoxygen,619
ShreyaDasgupta,BhabatoshDas,PallabiBasu,and BorkA.BerghoffandGabrieleKlug
RupakK.Bhadra
10.5 Regulatorsofoxidativestressresponsegenesin
Escherichiacoliandtheirconservationinbacteria,632
Section8: ResponsestoUVirradiation,517
HerbE.Schellhorn,MohammadMohiuddin,Sarah
8.1 UVstress-responsivegenesassociatedwith M.Hammond,andStevenBotts
enterobacterialintegrativeconjugativeelementsofthe
10.6 HydrogenperoxideresistanceinBifidobacterium
ICESXT/R391group,519
animalissubsp.lactisandBifidobacteriumlongum,638
PatriciaArmshawandJ.TonyPembroke
TaylorS.ObergandJeffR.Broadbent
8.2 AlteredoutermembraneproteinsinresponsetoUVC
radiationinVibrioparahaemolyticus
andVibrioalginolyticus,528 Section11: Adaptationtoosmoticstress,647
FethiBenAbdallah
11.1 Interstrainvariationinthephysiologicaland
8.3 Ultraviolet-Bradiationeffectsonthecommunity, transcriptionalresponsesofPseudomonassyringae
physiology,andmineralizationofmagnetotactic toosmoticstress,649
bacteria,532 GwynA.Beattie,ChiliangChen,LindseyNielsen,
YingzhaoWangandYongxinPan andBrianC.Freeman
8.4 Nucleotideexcisionrepairsystemandgeneexpression 11.2 ManagementofosmoticstressbyBacillussubtilis:
inMycobacteriumsmegmatis,545 geneticsandphysiology,657
AngelinaCordone TamaraHoffmannandErhardBremer
11.3 HyperosmoticresponseofStreptococcusmutans:
Section9: SOSanddoublestrandedrepairsystems
frommicroscopicphysiologytotranscriptomic
andstress,551
profile,677
9.1 TheSOSresponsemodulatesbacterialpathogenesis,553 LuWangandXinXu
DarjaZˇgurBertok
11.4 Defectiveribosomematurationorfunctionmakes
9.2 RNAPsecondary-channelinteractorsinEscherichia Escherichiacolicellssalt-resistant,687
coli:makersandbreakersofgenomestability,561 HyoutaHimeno,TakefusaTarusawa,ShionIto,and
PriyaSivaramakrishnanandChristopheHerman SimonGoto
x Contents
Section12: Dessicationtoleranceanddrought 14.3 Coevolutionanalysisilluminatestheevolutionary
stress,693 plasticityofthechaperoninsystemGroES/L,796
MarioA.Fares
12.1 Consequencesofelevatedsaltconcentrationson
expressionprofilesintherhizobiumS.meliloti1021 14.4 ClpLATPase:anovelchaperoneinbacterialstress
likelyinvolvedinheatanddesiccationstress,695 responses,812
JanA.C.Vriezen,CarolineM.Finn,andKlaus PratickKharaandIndranilBiswas
Nu¨sslein
14.5 DuplicatedgroELgenesinMyxococcusxanthus
12.2 Genesinvolvedintheformationofdesiccation-
DK1622,820
resistantcystsinAzotobactervinelandii,709
YanWang,Xiao-jingChen,andYue-zhongLi
GuadalupeEsp´ın
12.3 OsmoticanddesiccationtoleranceinEscherichiacoli
Section15: Coldshockresponses,827
O157:H7andSalmonellaentericarequiresrpoS
(σ38),716 15.1 Generegulationbycoldshockproteinsvia
ZachPratt,MeganShiroda,AndrewJ.Stasic,Josh transcriptionantitermination,829
Lensmire,andC.W.Kaspar SangitaPhadtareandKonstantinSeverinov
12.4 DesiccationofSalmonellaentericainduces 15.2 Metagenomicanalysisofmicrobialcoldstressproteins
cross-tolerancetootherstresses,725 inpolarlacustrineecosystems,837
ShlomoSela(Saldinger)andChellaiahEdwardRaja HyunminKoo,JosephA.Hakim,and
Index,i1 AsimK.Bej
15.3 Roleoftwo-componentsystemsincoldtoleranceof
VOLUME 2 Clostridiumbotulinum,845
Yag˘murDerman,EliasDahlsten,andHannu
Preface,xiii
Korkeala
Acknowledgements,xiv
15.4 ColdshockCspAproteinproductionduringperiodic
Listofcontributors,xv temperaturecyclinginEscherichiacoli,854
DavidStoparandTinaIvancic
Section13: Heatshockresponses,737
13.1 Heatshockresponseinbacteriawithlargegenomes: 15.5 ColdshockresponseinEscherichiacoli:amodel
lessonsfromrhizobia,739 systemtostudyposttranscriptionalregulation,859
AnaAlexandreandSolangeOliveira AnnaMariaGiuliodori
13.2 Smallheatshockproteinsinbacteria,747 15.6 Newinsightintocoldshockproteins:
MartinHaslbeck RNA-bindingproteinsinvolvedinstressresponseand
13.3 Transcriptomeanalysisofbacterialresponsetoheat virulence,873
shockusingnext-generationsequencing,754 CharlotteMichauxandJean-Christophe
Kok-GanChan Giard
13.4 Comparativeanalysesofbacterialtranscriptome
15.7 Lightregulationofcoldstressresponsesin
reorganisationinresponsetotemperatureincrease,757
Synechocystis,881
Bei-WenYingandTetsuyaYomo
KirillS.MironovandDmitryA.Los
13.5 ParticipationofSer–Thrproteinkinasesinregulation
15.8 Escherichiacolicoldshockgeneprofilesinresponse
ofheatstressresponsesinSynechocystis,766
tooverexpressionordeletionofCsdA,RNaseR,and
AnnaA.Zorina,GalinaV.Novikova,and
PNPaseandrelevancetolow-temperatureRNA
DmitryA.Los
metabolism,890
Section14: Chaperoninsandstress,781 SangitaPhadtare
14.1 GroEL/ESchaperonin:unfoldingandrefolding
reactions,783 Section16: Adaptationtoacidstress,897
VictorV.Marchenkov,NataliyaA.Ryabova,Olga
16.1 Acid-adaptiveresponsesofStreptococcusmutans,
M.Selivanova,andGennadyV.Semisotnov
andmechanismsofintegrationwithoxidative
14.2 FunctionalcomparisonbetweentheDnaKchaperone stress,899
systemsofStreptococcusintermediusand RobertG.QuiveyJr.,RobertaC.Faustoferri,
Escherichiacoli,791 BrendalizSantiago,JonathonBaker,Benjamin
ToshifumiTomoyasuandHideakiNagamune Cross,andJinXiao
Contents xi
16.2 Acidsurvivalmechanismsinneutralophilic 18.3 Promiscuousfunctionsofcellenvelopestress-sensing
bacteria,911 systemsinKlebsiellapneumoniaeandAcinetobacter
EugeniaPennacchietti,FabioGiovannercole,and baumannii,1031
DanielaDeBiase VijayaBharathiSrinivasanandGovindan
Rajamohan
16.3 Two-componentsystemsinsensingandadaptingto
acidstressinEscherichiacoli,927 18.4 InfluenceofBrpAandPsroncellenvelope
YokoEguchiandRyutaroUtsumi homeostasisandvirulenceofStreptococcus
mutans,1043
16.4 Slr1909,anoveltwo-componentresponseregulator
ZezhangT.Wen,JacobP.Bitoun,SumeiLiao,and
involvedinacidtoleranceinSynechocystis
JacquelineAbranches
sp.PCC6803,935
LeiChen,QiangRen,JiangxinWang,andWeiwen 18.5 Modulatorsofthebacterialtwo-componentsystems
Zhang involvedinenvelopestress,transport,andvirulence,1055
RajeevMisra
16.5 Comparativemassspectrometry–basedproteomicsto
elucidatetheacidstressresponseinLactobacillus
Section19: Ironhomeostasis,1065
plantarum,944
TiaanHeunis,ShellyDeane,andLeonM.T.Dicks 19.1 Ironhomeostasisandenvironmentalresponsesin
cyanobacteria:regulatorynetworksinvolvingFur,1067
Section17: Adaptationtonitrosativestress,953 Mar´ıaLuisaPeleato,Mar´ıaTeresaBes,andMar´ıaF.
17.1 Transcriptionalregulationbythiol-basedsensorsof Fillat
oxidativeandnitrosativestress,955 19.2 InterplaybetweenO andironingeneexpression:
2
TimothyTapscott,MatthewA.Crawford,and environmentalsensingbyFNR,ArcA,andFurin
Andre´sVa´zquez-Torres bacteria,1079
17.2 HaemoglobinsofMycobacteriumtuberculosisand BryanTroxellandHosniM.Hassan
theirinvolvementinmanagementofenvironmental
19.3 Theiron–sulfurclusterbiosynthesisregulatorIscR
stress,967
contributestoironhomeostasisandresistanceto
KanakL.Dikshit
oxidantsinPseudomonasaeruginosa,1090
17.3 WhatisitaboutNOthatyoudon’tunderstand?The AdisakRomsang,JamesM.Dubbs,andSkorn
roleofhemeandHcpRinPorphyromonas Mongkolsuk
gingivalis’sresponsetonitrate(NO ),nitrite(NO ),
3 2 19.4 Transcriptionalanalysisofiron-responsiveregulatory
andnitricoxide(NO),976
networksinCaulobactercrescentus,1103
JaninaP.LewisandBenjaminR.Belvin
Jose´F.daSilvaNeto
17.4 Di-ironRICs:playersinnitrosative-oxidativestress
19.5 Protein–proteininteractionsregulatethereleaseof
defences,989
ironstoredinbacterioferritin,1109
L´ıgiaS.NobreandL´ıgiaM.Saraiva
HuiliYao,YanWang,andMarioRivera
17.5 TheVibriocholeraestressresponse:anelaborate
19.6 Proteindynamicsandiontrafficinbacterioferritin
systemgearedtowardovercominghostdefenses
function:amoleculardynamicssimulationstudyon
duringinfection,997
wild-typeandmutantPseudomonasaeruginosa
Karl-GustavRueggebergandJunZhu
BfrB,1118
17.6 Ensemblemodelingenablesquantitativeexploration HuanRui,MarioRivera,andWonpilIm
ofbacterialnitricoxidestressnetworks,1009
JonathanL.RobinsonandMarkP.Brynildsen Section20: Metalresistance,1131
Section18: Adaptationtocellenvelopestress,1015 20.1 Nickeltoxicity,regulation,andresistancein
bacteria,1133
18.1 TheCpxinnermembranestressresponse,1017
LeeMacomberandRobertP.Hausinger
RandiL.GuestandTracyL.Raivio
20.2 MetabolicnetworkstocounterAltoxicity
18.2 Newinsightsintostimulusdetectionandsignal
inPseudomonasfluorescens:aholisticview,1145
propagationbytheCpx-envelopestresssystem,1025
ChristopherAuger,NishmaD.Appanna,andVasu
PatrickHoernschemeyerandSabineHunke
D.Appanna