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ResearcharticleThecompletegenomeofZunongwangiaprofundaSM-A87revealsitsadaptationtothedeep-seaenvironmentandecologicalroleinsedimentaryorganicnitrogendegradationQi-LongQin1,Xi-YingZhang1,Xu-MinWang2,Gui-MingLiu2,Xiu-LanChen1,Bin-BinXie1,Hong-YueDang3,Bai-ChengZhou1,JunYu2andYu-ZhongZhang*1AbstractBackground:ZunongwangiaprofundaSM-A87,whichwasisolatedfromdeep-seasediment,isanaerobic,gram-negativebacteriumthatrepresentsanewgenusofFlavobacteriaceae.
Thisisthefirstsequencedgenomeofadeep-seabacteriumfromthephylumBacteroidetes.
Results:TheZ.
profundaSM-A87genomehasasingle5128187-bpcircularchromosomewithnoextrachromosomalelementsandharbors4653predictedprotein-codinggenes.
SM-A87producesalargeamountofcapsularpolysaccharidesandpossessestwopolysaccharidebiosynthesisgeneclusters.
Ithasatotalof130peptidases,61ofwhichhavesignalpeptides.
Inadditiontoextracellularpeptidases,SM-A87alsohasvariousextracellularenzymesforcarbohydrate,lipidandDNAdegradation.
Theseextracellularenzymessuggestthatthebacteriumisabletohydrolyzeorganicmaterialsinthesediment,especiallycarbohydratesandproteinaceousorganicnitrogen.
Therearetwoclusteredregularlyinterspacedshortpalindromicrepeatsinthegenome,buttheirspacersdonotmatchanysequencesinthepublicsequencedatabases.
SM-A87isamoderatehalophile.
Ourproteinisoelectricpointanalysisindicatesthatextracellularproteinshavelowerpredictedisoelectricpointsthanintracellularproteins.
SM-A87accumulatesorganicosmolytesinthecell,soitsextracelluarproteinsaremorehalophilicthanitsintracellularproteins.
Conclusion:Here,wepresentthefirstcompletegenomeofadeep-seasedimentarybacteriumfromthephylumBacteroidetes.
ThegenomeanalysisshowsthatSM-A87hassomecommonfeaturesofdeep-seabacteria,aswellasanimportantcapacitytohydrolyzesedimentaryorganicnitrogen.
BackgroundTheaveragedepthoftheoceansisabout3800m,andalmost60%oftheearth'ssurfaceisdeep-seafloor(waterdepthgreaterthan2000m)[1].
Althoughmostofthedeep-seafloorenvironmentischaracterizedbydarkness,highhydrostaticpressureandlowtemperatures,morethanhalfoftheworld'sprokaryotesliveinsub-seafloorsediments[2-4],whichplayamajorroleinmarinebio-geochemicalcycling[5].
Everyyear,massiveamountsofparticulateorganicmatter(POM)aretransportedtothedeeplayersoftheoceanfloor,formingalargepoolofcar-bonandnitrogen[6].
However,howthisorganicmaterialisdegraded,aswellasthetypesofbacteriainvolvedandtheenzymesused,arestillunclear,especiallyforthedeg-radationofsedimentaryorganicnitrogen(SON)[7].
Todate,numerouseffortshavebeenmadetoclarifythemechanismofSONdegradation,includinginvestigationsofthediversityofbacteriaandproteasesinvolvedinSONdegradation[8,9].
ResearchershavealsocharacterizedsomeextracellularproteasesfromsedimentarybacteriaandelucidatedtheirecologicalroleinSONdegradation[10-13].
However,theroleofdeep-seabacteriainSONdegradationandcyclinghasneverbeenanalyzedatagenomiclevel.
Genomeanalysesofdeep-seahet-*Correspondence:zhangyz@sdu.
edu.
cn1StateKeyLabofMicrobialTechnology,MarineBiotechnologyResearchCenter,ShandongUniversity,Jinan250100,PRChinaContributedequallyFulllistofauthorinformationisavailableattheendofthearticleQinetal.
BMCGenomics2010,11:247http://www.
biomedcentral.
com/1471-2164/11/247Page2of10erotrophicbacteriawouldprovideabetterunderstandingofthedeep-seanitrogencycle,andrevealtowhatextentbacteriaaffectthedeep-seaenvironment[14].
Bacteroidetes(formerlyCytophaga-Flavobacterium-Bacteroides(CFB))areawidespreadanddiversegroupofbacteriathatcanbefoundthroughoutthesea,fromsur-facewatertodeep-seasediment.
Studiesofbothculti-vatedanduncultivatedmarineBacteroideteshaveshownthatBacteroidetesareabletoefficientlyconsumebiopoly-merssuchasproteinandchitin[15,16],whichmakeupasignificantfractionofthehigh-molecular-weightdis-solvedorganicmatter(HMWDOM)poolintheocean[17].
Biopolymerdegradationisconsideredtobetherate-limitingstepinDOMmineralizationbymarinemicroor-ganisms,andBacteroidetesarehypothesizedtoplayakeyroleinthisprocessintheoceans[7].
GenomesequencedatahavebeenextremelyhelpfulinthedevelopmentofdetailedhypothesesontheroleofspecificBacteroidetesmembersinmarinebiogeochemicalcycling.
AnanalysisofthegenomeofBacteroidetes'Gramellaforsetii'KT0803,abacterioplanktonisolatedfromNorthSeasur-facewatersduringaphytoplanktonbloom,indicatedthatitisefficientatdegradingbiopolymers,especiallypro-teins[18,19].
MetagenomicstudieshavealsoreportedthedistributionandfunctionalanalysisofspecificCytophaga-likehydrolasesintheSargassoSeaandwest-ernArcticOceananddescribedhydrolase-containinggenomefragmentsofAntarcticmarineBacteroidetes[20,21].
However,whileBacteroideteshavebeenfre-quentlyencounteredintheanalysisofsedimentarybacte-rialdiversity,nocompletegenomeanalysisofadeep-seasedimentaryBacteroideteshasyetbeenpublished[15,16].
Thistypeofanalysiscouldbeusedtoaddresshowtheorganisms'geneticinventoriesreflectboththeirSONremineralizationcapabilitiesandtheiradaptationtothedeep-seaenvironment.
WangiaprofundaSM-A87(hereaftercalledSM-A87),isolatedatadepthof1245mfromdeep-seasedimentinthesouthernOkinawaTroughwithinsitutemperatureof4.
7°C,isanewlydescribedspeciesofBacteroidetesandrepresentsanewgenusofFlavobacteriaceae[22].
ItwasrenamedZunongwangiaprofundaintheInternationalJournalofSystematicandEvolutionaryMicrobiology(IJSEM)ValidationListno.
116.
Inthisstudy,wereportitscompletegenomesequence,whichrepresentsthefirstgenomeofadeep-seabacteriumofthephylumBacteroi-detes.
Inaddition,weperformedagenomiccomparisonwithtwobacteriaofthefamilyofFlavobacteriaceaefromsurfaceseawater,andtwobacteriafromacolddeep-seaenvironment.
OurgenomicanalysisofstrainSM-A87indicatesthatitiscapableofdegradingbiopolymersourcesandshedslightonitsadaptationtothedeep-seaenvironment.
ResultsanddiscussionGeneralgenomefeaturesGeneralfeaturesoftheZ.
profundaSM-A87genomearesummarizedinTable1.
Thegenomehasasingle5.
1-Mbpcircularchromosomewithnoextrachromosomalele-ments.
TheG+Ccontentofthegenomeis36.
2%,whichisslightlyhigherthantheexperimentallydetermined35.
8%[22].
Thegenomeharbors4653predictedopenreadingframes(ORFs),ofwhich69.
4%areannotatedwithknownorpredictedfunctions.
About50%ofSM-A87ORFshavethehighestsimilaritytothoseinthepublishedgenomeofG.
forsetiiKT0803.
SM-A87has47tRNAgenesandthree16S-23S-5Soperons.
Figure1showstheproportionsofproteinsbelongingtoclustersoforthologousgroups(COGs)inSM-A87andseveralotherbacterialgroups.
Thedeep-seabacteria(SM-A87,PhotobacteriumprofundumSS9andShe-wanellapiezotoleransWP3)haveanaverageof2.
35%moreproteinsbelongingtoCOGK(transcription),and2.
11%moreproteinsbelongingtoCOGT(signaltrans-ductionmechanisms)thantheshallow-waterbacteria(FlavobacteriumpsychrophilumandGramellaforsetiiKT0803).
Thesedifferencesarestatisticallysignificant(p<0.
05).
GeneralmetabolismSM-A87hasafullsetofgenesforglycolysis,thepentosephosphatepathwayandthetricarboxylic/citricacidcycle.
Thestrainhasfivepredictedlactatedehydrogenases,twoL-andthreeD-,andalsocontainspredictedethanol-pro-ducingenzymesincludingaldehydedehydrogenase(ZPR_1384,ZPR_3649)andalcoholdehydrogenase(ZPR_4362).
Theseenzymesmayhelpthebacteriumtosurviveinthelow-oxygenenvironmentofthedeepsea.
SM-A87containspredictedcytochromebdubiquinoloxidasesubunitsI(ZPR_1985)andII(ZPR_1985).
Thisoxidaseisrelatedtoadaptationtomicroaerobiccondi-tionsinthedeepsea[23].
AccordingtotheKyotoEncy-clopediaofGenesandGenomes(KEGG)pathwaymapofTable1:GeneralfeaturesoftheZ.
profundaSM-A87genome.
Size(bp)5128187G+Ccontent36.
2%NumberofpredictedORFs4653AverageORFlength(bp)960Codingdensity87.
4%tRNAs47rRNAoperons3Conservedhypotheticalproteins%17.
1%Hypotheticalproteins%13.
5%Qinetal.
BMCGenomics2010,11:247http://www.
biomedcentral.
com/1471-2164/11/247Page3of10SM-A87,fructoseandmannosecanbeconvertedtofruc-tose-6p,andgalactosecanbeconvertedtoglucose-1p;bothfructose-6pandglucose-1parethendegradedthroughglycolysis.
SM-A87harborsapredictedketo-deoxy-phosphogluconatealdolase(ZPR_2957),whichisthekeyenzymeoftheEntner-Doudoroffmetabolicpath-way.
Thisstrainalsocontainstheenzymesthatutilizemostaminoacids.
AllthesefeaturesconferametabolicversatilitytoSM-A87thatallowsittoutilizesparseandsporadicnutrientsinthedeep-seaenvironment.
SM-A87hasallthegenesrequiredforfattyacidoxida-tion.
However,3R-hydroxymyristoylACPdehydrase,acomponentofthefattyacidbiosynthesispathway,wasnotfoundbygenomeannotation.
Thisabsencemaybeduetothelowsimilarityofthisgenetothoseinthedata-basesortoconvergentevolutionfromotherfunctionallysimilarenzymeswithdivergentsequences.
Phosphati-dylethanolamineistheonlyphospholipidthathasbeenexperimentallyidentifiedinZunongwangiaprofunda[22].
Thegenomeanalysissuggeststhatphosphatidyleth-anolamineisderivedfromphosphatidylserine,whichissynthesizedfromglycerate.
SM-A87hasallofthecomponentsoftheoxidativephosphorylationpathwaybutdoesnotcontainanyrho-dopsinorretinalgenes,consistentwiththedarkdeep-seaenvironmentinwhichthestrainthrives.
SensingsystemMostnutrientsarriveinthedeepseainanannualpulse,andthebacteriainthedeepseacansensethisfoodpulseandrespondaccordingly[24].
Awidespreadsensingsys-temusedbybacteriaisthetwo-componentsignaltrans-ductionsystem,whichconsistsofasignalsensorhistidinekinaseandaresponseregulator[25,26].
SM-A87harbors47predictedsensorhistidinekinases,themostofanyofthecomparedstrains(Table2),whichindi-catesitsstrongabilitytosenseenvironmentsignals.
SM-A87hasninepredictedtwo-componentoperons,eachofwhichiscomposedofahistidinekinaseandaresponseregulatorthatmayformaone-to-onephosphotransferpair.
SM-A87hasthreerRNAoperons,suggestingthatitcanrespondtonutrientenrichmentrapidlyandgrowquickly[27].
SM-A87canformcoloniesof1-3mmindiameteronarichmediumafter48hofcultivationat28°C[22].
Figure1COGcategorypercentageofZ.
profundaSM-A87andothercomparedbacteria.
Qinetal.
BMCGenomics2010,11:247http://www.
biomedcentral.
com/1471-2164/11/247Page4of10SM-A87contains22genesencodingRagB/SusDfamilyproteinsinitsgenome,whiletheothercomparedgenomeshavefewerornone(Table2).
RagBisaproteininvolvedinsignalingandSusDisanoutermembraneproteininvolvedinnutrientbinding[28,29].
NineteenoftheRagB/SusDfamilyproteingenesareeachadjacenttoaTonB-dependentreceptorgene,forming19predictedoperons.
Ofthe19predictedoperons,12areadjacenttopredictedglycosylhydrolasesorpeptidases[seeAddi-tionalfile1].
SpecificallyforthegenesfromZPR_1020toZPR_1033,therearetwoglycosidasegenes,twoesterasegenes,onexylanasegeneandsevenglycosylhydrolasegenesnexttotheoperon,implyingthatSM-A87cansenseandrespondtosugarsources.
Thegenomealsocontains27putativeoutermembraneproteingenes,whichareprobablyinvolvedinnutrientbinding.
AllthesefeaturesimplythatSM-A87hastheabilitytosenseextra-cellularnutrientssuchassugarsandproteins.
PolysaccharidesynthesisManydeep-seabacteriaproduceexopolysaccharidesthathelpthemsurviveintheextremedeep-seaenvironment[30].
Reportssuggestthatthesepolysaccharideshelpthebacteriaconcentrateorganicmatter,absorbmetalions,andformbiofilmsinthemarineenvironment[31,32].
Differentglycosyltransferasescancontributetothebio-synthesisofdisaccharides,oligosaccharides,andpolysac-charides[33].
OurexperimentalresultsshowthatstrainSM-A87canproducelargequantitiesofcapsularpolysac-charide(datanotshown).
ThegenomeanalysisshowsthatSM-A87contains46predictedglycosyltransferases,ofwhich13belongtofamilytwoand10belongtofamilyone.
SM-A87containstwoglycosyltransferases(ZPR_0565andZPR_1126)thataresimilartoWbaPfromSalmonellaenterica.
WbaPisresponsiblefortheinitia-tionofpolysaccharidesynthesis,transferringthefirstsugartoundecaprenylphosphate(Und-P)[34].
SimilartoWbaP,ZPR_1126has462aminoacidresiduesandfivepredictedtransmembraneregions.
Thetopologicalorga-nizationofthetransmembraneregionsofthesetwoenzymesissimilar:therearefourtransmembraneregionsattheN-terminusandonetransmembranedomainwithsugar-phosphatetransferaseactivityattheC-terminus.
ZPR_0565consistsof339aminoacidresiduesandhasonlyonetransmembranedomain.
Amultiplesequencealignment[seeAdditionalfile2]showsthatZPR_0565correspondstotheC-terminusofWbaPandotherinitialglycosyltransferases;inaddition,theyallcontainthehighlyconservedaminoacidmotifsKFRSM,DELPQ,andPGITG[35].
ThisimpliesthatZPR_0565containsonlyTable2:ComparisonofthenumbersofselectedproteinsbetweenSM-A87andotherfourmarinebacteria.
SM-A87P.
profundumSS9S.
piezotoleransWP3G.
forsetiiKT0803F.
psychrophilumSensingcomponentsHistidinekinase4720463713RagB/susDfamilyprotein2200140EnzymesfordegradationPeptidase1130(60)74(18)129(50)94(47)59(42)Glucosidase110550Xylanase60000Xylosidase30010Beta-galactosidase53240Amylase32430Chitinase23200Otherglycosidase5046212Lipase1411793Esterase462032227TransportorsABC-typetransporter40155642840TonB-dependentreceptor4003340221Inparenthesesisthenumberofproteinswithsignalpeptides.
Qinetal.
BMCGenomics2010,11:247http://www.
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com/1471-2164/11/247Page5of10theglycosyltransferasecatalyticdomain.
Genesencodingotherglycosyltransferasesandpolysaccharideexportpro-teinsarefoundclosetoZPR_0565andZPR_1126;together,thesegenesformtwogeneclustersforpolysac-charidesynthesisandexport[seeAdditionalfile3].
ZPR_1123,whichisupstreamofZPR_1126,ispredictedtoencodeanO-antigenpolymerase,implyingthatpoly-saccharidesaresynthesizedthroughtheWzy-dependentpathwayinSM-A87[36].
SM-A87harborstwopredictedcapsularpolysaccharidebiosynthesisproteinsthatareprobablyinvolvedinthesynthesisofcapsularpolysaccha-rides.
TheproductionofcapsularpolysaccharideisadvantageousforSM-A87tothriveinthemarineenvi-ronment.
HydrolysisabilitySignalpeptideanalysissuggeststhatSM-A87cansecretealargenumberofhydrolysisenzymes,andithasmoreexportedpeptidasesthantheothercomparedstrains(Table2),reflectingitsunusualabilitytodegradeorganicnitrogen.
SM-A87contains130predictedpeptidases,61ofwhichhavesignalpeptides.
Thepeptidaseswithsignalpeptideshavemoreasparticacidsandahigherratioofacidicresiduestobasicresidues.
Additionally,theyhavealowerpredictedisoelectricpoint(pI)thanthepeptidaseswithoutsignalpeptides(Table3),adifferencethatissta-tisticallysignificant(p<0.
05).
Thus,theextracellularpeptidasesaremorehalophilicthantheintracellularpep-tidases,ashighnumbersofacidicresiduesandlowpIsarekeyfeaturesofhalophilicproteins[37].
Thehalophi-licityoftheextracellularpeptidaseshelpsthemfunctioninsalineenvironmentsanddecomposeextracellularorganicnitrogenmatterinthemarinesaltycondition.
Fifty-twooftheSM-A87peptidaseswithsignalpep-tidescanbeassignedtodifferentfamiliesintheMEROPSpeptidasedatabase[38].
AsshowninFigure2,thepepti-dasesmainlybelongtofamiliesofmetallopeptidasesandserinepeptidases,consistentwithourpreviousstudythattheextracellularpeptidasesofmarinesedimentarybacte-riaaremainlyserineproteasesandmetalloproteases[9].
ComparedtoG.
forsetiiKT0803,deep-seabacteriaSM-A87andS.
piezotoleransWP3havemorepeptidasesinfamiliesS09andS41,butfewerinfamilyM14(Figure2).
ThevarietyofextracellularpeptidasessuggeststhatSM-A87hasthecapacitytodecomposediversepeptidesandproteinsfromitssurroundings.
Forinstance,SM-A87hassixexportedfamilyM01peptidases,whichareamino-peptidases.
Ithasbeenreportedthatwhenmarinebacte-riagrowonHMWdissolvedorganicnitrogen(DON)asthesolenitrogensource,aminopeptidaseactivityisgreatlyenhanced[39].
Aminopeptidaseactivityinthedeep-seasedimentishigherthanthatinthesurfacesea-water;however,thisisnotthecaseforotherhydrolysisenzymes[40].
ThelargenumberofaminopeptidasessecretedbySM-A87maycontributetothehighamino-peptidaseactivityinthedeep-seasediment,andsuggeststhatSM-A87maybeabletorespondtoHMWDONanddecomposeit.
SM-A87secretessevenS09peptidases,whichareprolyloligopeptidasesthatcannotdegradepeptidesofmorethan30residuesinlength[41].
There-fore,theS09peptidasesspecificallyhydrolyzeoligopep-tides.
Notably,therearesixexportedpeptidasesthatcontainaPDZdomain,whichisknowntobeinvolvedinpeptidebinding[42].
ThelargenumberofPDZdomain-containingpeptidasessecretedbySM-A87suggestsastrategyforbindinganddegradingproteins,similartothePKDdomainsofexportedproteinsinG.
forsetiiKT0803[19].
Inthedeep-seasedimentarynitrogencycle,thepro-cessbywhichparticulateorganicnitrogenisconvertedtoNH4+isknowntobedominatedbybacteriabutispoorlycharacterized[1,14].
ThesecretedpeptidasesofSM-A87mayplayanimportantroleinthisprocess.
Amongthecomparedstrains,SM-A87hasthelargestproportionofproteinsbelongingtocarbohydratetrans-portandmetabolismCOGs(Figure1).
Accordingly,ithasmanygenesencodingenzymesthatdegradeoligo-andpolysaccharides(Table2)[Additionalfile4].
SM-A87hasTable3:Propertiesofpeptidaseswithandwithoutsignalpeptides.
WithsignalpeptidesWithoutsignalpeptidesNumber6169G+Ccontent(%)37.
536.
8Asp(percentage)6.
66.
0Glu(percentage)7.
27.
2Lys(percentage)8.
08.
1Arg(percentage)3.
63.
5(Asp+Glu)/(Lys+Arg)1.
21.
1pI16.
0±1.
76.
7±2.
01pI,predictedisoelectricpoint.
Thedataareaverageswithstandarddeviation.
Qinetal.
BMCGenomics2010,11:247http://www.
biomedcentral.
com/1471-2164/11/247Page6of1050annotatedglycosidases,17ofwhichhavesignalpep-tides,suggestingthatSM-A87canhydrolyzeextracellularcarbohydrates.
Itdoesnotcontainanypredictedcellu-lases,agreeingwiththeexperimentalresultthatitcannothydrolyzecellulose.
AlthoughSM-A87hasageneforexportedchitinase(ZPR_1703),experimentssuggestthatitdoesnotdegradechitin.
SM-A87harborssixxylanasegenesandthreexylosidasegenes,ofwhichthreexyla-nasesandtwoxylosidaseshavesignalpeptides,indicatingthatthestrainshouldhavetheabilitytodegradexylan.
Thegenomealsohasfourgenesencodingexportedbeta-galactosidases;correspondingly,beta-galactosidaseactiv-ityhasbeendetectedinthisstrain[22].
SM-A87contains11predictedglucosidases,ofwhichsevenhavesignalpeptides.
Glucosidaseproductioncanbeinducedbydissolvedpolymericglucose[43].
ThelargenumberofglucosidasesinSM-A87indicatesthatitisabletodecomposetheeasilyusedpolymericsugarintheenvi-ronment.
Thecarbohydrate-hydrolyzingenzymesmen-tionedaboveimplythatSM-A87isabletouseavarietyofcarbohydratesintheenvironmentascarbonandenergysources.
SM-A87harborssevengenesencodingextracellularlipases,includingonephospholipaseA1(ZPR_0295)andtwoGDSLfamilylipases.
Thestraincontains20genesencodingesteraseswithsignalpeptides,ofwhichfivearecarboxylesterasesandsixarephosphoesterases.
TheseenzymesmayallowSM-A87todegradevariousphospho-lipidsandcarboxylestersintheenvironmentascarbonandphosphorussources.
DNAisabundantinthedeep-seasediment,andmostofitisextracellular.
Morethanhalfofthetotalextracellu-larDNAcanberapidlydegradedbyenzymes[44].
DNAcanbeutilizedbybacteriaasasourceofcarbon,nitrogen,andphosphorous,contributingtophosphaterecycling[44].
SM-A87harborstwopredictedextracellularendo-nucleases(ZPR_0199,ZPR_1186),implyingthatitcanobtainnutrientelementsbydegradingextracellularDNA.
Ithasbeenreportedthatsedimentarycarbohydrateishydrolyzedmoreeasilywhenitistreatedwithfourenzymes,α-amylase,β-glucosidase,proteaseandlipase,thanwhenitistreatedwithonlyoneenzyme[45].
SM-A87containsthesefourkindsofextracellularenzymes,implyingthatthestraincanhydrolyzesedimentarycar-bohydrateseasily.
ThevarietyofexportedpeptidasesandotherhydrolysisenzymesintheSM-A87genomewouldallowthebacteriumtodegradesedimentarybiopoly-mericmaterialsintosmallmoleculesthatcanbeabsorbedbythecell.
ApreviousgenomeanalysisrevealedthatG.
forsetiiKT0803fromsurfaceseawaterisgoodatdegradingpolymericorganicmaterials[19].
OuranalysisoftheSM-A87genomeindicatesthatthisdeep-seasedi-mentBacteroidetesspeciesalsohastheunusualabilitytodecomposepolymericorganicmaterials,whichcouldcontributeconsiderablytodeep-seasedimentarybiogeo-chemistrycycles.
NitrogenandsulfurmetabolismAccordingtotheKEGGpathwaymap,nitritereductasecancatalyzetheconversionofnitritetoammonia[46].
Twonitritereductases(ZPR_3631,ZPR_4195)couldberesponsiblefortheconversionofnitritetoammoniainSM-A87.
Oneformate/nitritetransporter(ZPR_2292)andthreeputativenitrate/nitriteDNA-bindingresponseregulatorsinthegenomeindicatethatSM-A87canabsorbnitritefromtheenvironment.
Alloftheaboveevi-dencesuggeststhatthestraincanuseinorganicnitrogen.
TheSM-A87genomeencodesonesulfatetransporter(ZPR_0777)andtwosodium:sulfatesymporters(ZPR_0364,ZPR_4168)thatcantransportsulfateionsintothecell.
Italsohascorrespondingenzymestoutilizesulfate.
TherearethreeadjacentORFsthatencodeadeny-lylsulfatekinase(ZPR_0539)andtwosubunitsofsulfateadenylyltransferase(ZPR_0540,ZPR_0541),whichcon-vertsulfatetoadenylylsulfate(APS)andsubsequentlyto3'-phosphoadenylylsulfate(PAPS).
Phosphoadenosinephosphosulfatereductase(ZPR_3632)canconvertPAPSintosulfite,andthenhydrogensulfide(H2S)couldbeproducedfromsulfitebythesulfitereductases(ZPR_0424,ZPR_4048).
However,ourpreviousexperi-mentsshowedthatSM-A87doesnotsecreteH2S(22).
Thus,H2Sisprobablyusedtoproduceacetateviacysteinesynthase(ZPR_2076),whichconverts3-O-acetyl-L-serine(fromserine)andH2Stoacetate.
SubstratetransportsystemsSinceSM-A87hasmanyextracellularhydrolyticenzymes,theremustberelatedsystemstotransportthenutrientproductsintothecell.
TheATP-bindingcassetteFigure2TheMEROPScategoryoftheextracellularpeptidasesfromZ.
profundaSM-A87,G.
forsetiiKT0803andS.
piezotoleransWP3.
Qinetal.
BMCGenomics2010,11:247http://www.
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com/1471-2164/11/247Page7of10(ABC)transporters,whicharewidespreadamongbacte-ria,cancoupleATPhydrolysistothetransportofavari-etyofsubstratesintoandoutofthecell[47].
AnexaminationofSM-A87genomeidentifiedmanygenesencodingpossibleABCtransporters(Table2),whichisconsistentwiththereportthatthereisanenrichmentofABCtransportergenesinthegenomesofdeep-seamicroorganisms[48].
SM-A87hasthreepredictedaminoacidpermeasesandthreeaminoacidtransporters,whichmakeitpossibleforthestraintoabsorbaminoacidsandoligopeptides.
AccordingtotheKEGGpathwaymap,thestrainmaybeabletotransportmolybdate,ironcom-plexes,lipopolysaccharidesandlipoproteins.
Inaddition,thepresenceofgenesencodingxylosepermease(ZPR_0446),fucosepermease(ZPR_4359)andglucose/galactosetransporter(ZPR_0518)maycorrespondtothecarbohydratetransportabilityofSM-A87.
TheTonB-dependenttransportsystemcantakeuplargesubstratemolecules,suchassiderophoresandvita-mins,intothecellfromtheenvironment[49].
Thegenomeanalysisshowedthat40TonB-dependentrecep-torgenesand5TonBproteingenesarepresentinSM-A87.
Consistentwithpreviousreports,therearefewerTonBproteinsthanTonBreceptors[50].
ThepredictedTonB-dependentsiderophorereceptors(ZPR_0148,ZPR_2532)arelikelytobeinvolvedintheenrichmentandtransportofironintothecell.
MobileelementsSM-A87ispredictedtocarrymanytransposases,sup-portingtheideathattransposasesareabundantinthedeep-seaenvironment[5,48].
TwopredictedputativetransposonswereidentifiedintheSM-A87genome.
OneiscomposedofZPR_3981,ZPR_3982andZPR_3983,ofwhichZPR_3981andZPR_3983belongtotheIS66fam-ilyoftransposases.
Surprisingly,ZPR_3982ispredictedtobeanRNA-directedDNApolymerase(reversetran-scriptase),implyingthattheDNAsegmentofZPR_3982mayhavecomefromanRNAvirus.
Thesecondtranspo-soniscomposedofZPR_1509,ZPR_1511andZPR_1512,ofwhichZPR_1509isanIS3familytransposaseandZPR_1512isaIS116/IS110/IS902familytransposase.
ZPR_1511encodesaglyoxalasefamilyproteinwiththehighestaminoacidsimilarity(63%)toaglyoxalasefromMyxococcusxanthus.
CRISPRClusteredregularlyinterspacedshortpalindromicrepeat(CRISPR)elementsarecommoninbacteriaandarchaea.
ACRISPRischaracterizedbydirectrepeats(DR)thatareseparatedbysimilarlysizednon-repetitivespacers.
TherearealsoCRISPR-associated(CAS)genesandaleadersequencebeforetherepeatarea.
CRISPRelementscanbedescribedasfollows:CASgenes-leader-DR1-spacer1-DR2-spacer2.
.
.
DRn-1-spacern-1-DRn,wherenisthenum-berofrepeats[51,52].
AsingleCRISPRlocushasbeendetectedinmanybacterialgenomes[52].
However,therearetwopredictedCRISPRlociintheSM-A87genome.
Thefirstlocusis5594bpinlength(bp1642261tobp1647855).
Inthefirstlocus,theDRsequenceis37bpinlengthwith76spacers.
SixCASgenesofthecas1,cas2,cas3andcas5familiesweredetectedupstreamofthefirstlocus.
Thesecondlocusis2114bpinlength(bp4768893tobp4771007),witha47-bpDRsequenceand26spacers.
ThereareonlytwoCASgenesupstreamofthesecondlocus,onebelongingtothecas1familyandonetothecas2family.
ThetwoCASsystemsareclassifiedasdifferenttypesaccordingtothefamilyandarrangementoftheCASgenes.
CRISPRisthoughttofunctionasananti-phagedefensesystemviaanRNA-silencing-likemechanism,andthespacersareoftenfoundtosharehighsequencesimilari-tieswithphagesequences[52].
However,ourBLASTsearchesresultedinnohitsinthepublicdatabases,prob-ablybecauseonlyasmallfractionofphagesequencesaredepositedinthedatabases.
Intheocean,thequantityofphagesisabout5-10timesmorethanthatofbacteria[53].
SM-A87'sCRISPRsmayhelpdefendagainstinfec-tionbyunknownphagesinthedeepsea.
AdaptationtosaltandcoldHalophileshavetwodifferentwaystomaintaintheircel-lularosmoticbalanceinsaltyenvironments:byaccumu-latingorganiccompatiblesolutesorbymaintainingahighconcentrationofionssuchaspotassiuminthecell[54,55].
SM-A87isamoderatehalophileandcantolerate0-12%NaCl[22].
ToanalyzethemechanismofSM-A87'sadaptationtothemarinesaltyenvironment,wepredictedandcomparedthepIsofintracellularandextracellularproteinsfromSM-A87,G.
forsetiiKT0803,hyperhalo-philicbacteriumSalinibacterruber,nonhalophilicbacte-riumEscherichiacoliandBacteroidetessoilbacteriumCytophagahutchinsonii(Table4).
HalophilicproteinscontainmoreacidicresiduesandhavelowerpIsthannonhalophilicproteins[55].
E.
coliisnothalophilic,andthereisnostatisticallysignificantdifferencebetweenthepIsofitsintracellularandextracellularproteins.
S.
ruberisahyperhalophilicbacteriumthathasahighintracellu-larpotassiumconcentrationtomaintainitscellularosmoticbalance[55];thus,theionconcentrationsinsideandoutsideofthecellarebothhigh.
ThepIsofboththeintracellularandextracellularproteinsofS.
ruberaremuchlowerthanthoseofE.
coliandC.
hutchinsonii(Table4),suggestingthattheS.
ruberproteinsareallhalophilic.
ForthemarinebacteriaSM-A87andG.
forsetiiKT0803,theintracellularproteinpIsarehigherthanthoseoftheextracellularproteins,withastatisticallysignificantdifference(p<0.
01forallproteins,p<0.
05forQinetal.
BMCGenomics2010,11:247http://www.
biomedcentral.
com/1471-2164/11/247Page8of10peptidases).
ThisindicatesthattheintracellularproteinsofSM-A87havepoorsalt-tolerance,anditisthereforeimpossibleforSM-A87tomaintainhighionconcentra-tionsinthecellforosmoticbalance.
Instead,SM-A87hasaglycinebetainetransporter(ZPR_3842).
Glycinebetaineisawell-knownosmoregulator,implyingthatSM-A87mayuseorganiccompatiblesolutesratherthanionstomaintainitscellularosmoticbalance.
Thus,theintracellularproteinsofSM-A87arenothalophilicandhavehigherpIs.
Incontrast,theextracellularproteinsofSM-A87mustfacethemoderatelyhighionconcentration(~3%)ofthesea,sotheseproteinsarehalophilicandhavelowpIs.
ThisisalsothecaseforG.
forsetiiKT0803,whichalsocontainsglycinebetainetransporter.
Thesalt-toler-anceoftheextracellularproteinsofSM-A87andtheirlowerpIsareindicativeoftheiradaptationtothesaltymarineenvironment.
Unsaturatedfattyacidscanincreasethefluidityofthemembrane,whichisacommonstrategyusedbybacteriatoadapttoacoldenvironment.
Themembranesofdeep-seabacteriacontainahighproportionofmonounsatu-ratedfattyacids,whichareveryimportantformaintain-ingbacterialmembranefluidity[56].
SM-A87hasfivefattyaciddesaturasegenes,whichmaycontributetohighmembranefluidity,andthuscoldadaptation.
InadditiontothechaperonesGroELandDnaJ,SM-A87hasfourcoldshockproteingenesandoneheatshockproteingene,whichmayhelpthestrainsurviveinthecolddeep-seaenvironment.
SM-A87alsohasgenesencodingthepyruvatedehydrogenasecomplexandtrehalosephos-phatesynthase(ZPR_2459),whicharebothassociatedwithcoldadaptation[57].
ConclusionThisworkpresentsthefirstcompletedeep-seabacterialgenomeofamemberofthephylumBacteroidetes.
SM-A87hassomefeaturesthatarecommonindeep-seabac-teria,suchasnumeroustransposasesandABC-typetransporters.
Ourgenomesurveyalsorevealsitsmeta-bolicversatilityandextensivehydrolyticcapabilities.
Additionally,basedonthecontentsofitsgenome,SM-A87cansensenutrientpulses,synthesizeexopolysaccha-ridestoabsorbnutrients,exportavarietyofenzymestodegradematerials,transportsubstratesintothecelleffi-cientlyandutilizeresourcesviaversatilemetabolicpath-ways.
Withthesefeatures,SM-A87canthriveinthedeep-seaenvironment.
MethodsStrainSM-A87,originallyisolatedfromdeep-seasedi-mentinthesouthernOkinawaTrough,wasculturedaspreviouslydescribed[22].
Thecellswereharvestedbycentrifugationat12000gat10°Cfor30min.
GenomicDNAwaspreparedbyusingagenomicDNAextractionkit(BioTeke,China)accordingtothemanufacturer'sinstructions.
ThegenomesequenceofstrainSM-A87wasdeter-minedusingacombinedstrategyofSangersequencingand454pyrosequencing.
About100megabasesofdatawereobtainedfromone454(GS-FLX)sequencingrun.
Thesequenceswereassembledinto144largecontigsthatwereorientedbySangersequencingreadsfrompairedendsofplasmidandfosmidlibrarieswithinsertsizesvaryingfrom3kband5kbto40kb.
ThegapswereclosedbyprimerwalkingandPCRsegmentsequencing.
Thephred-phrap-consedpackagewasusedfortheassemblyandfinishing[58],andthefinishedgenomewasvalidatedfurtherby10-kblongPCR.
ThetRNAgeneswerepredictedbytRNAscan-SE[59].
TherRNAgeneswereidentifiedbyBLASTsearchagainstRfam[60].
Theopenreadingframes(ORFs)werefoundbyusingGLIMMER3.
0[61].
ThepredictedORFswereannotatedbysimilaritysearchesagainstdatabasesofnonredundantproteinsequencesfromNCBI,SWIS-SPROT,Pfam[62],COG[63],KEGGandInterPro[64].
TheannotationofORFswasmanuallycuratedwithArtemis[65].
TransmembraneregionsofthepredictedproteinswerepredictedwithTMHMM2.
0http://www.
cbs.
dtu.
dk/services/TMHMM/.
Signalpeptidepre-dictionwasdonewithSignalP3.
0[66].
Clusteredregu-larlyinterspacedshortpalindromicrepeats(CRISPR)werefoundwithCRISPR-finderhttp://crispr.
u-psud.
fr/Server/CRISPRfinder.
php.
ThesequencealignmentwasdonewithClustalX[67].
Table4:PredictedisoelectricpointsoftheproteinsofSM-A87andcomparedstrains1.
SM-A87G.
forsetiiKT0803E.
coliC.
hutchinsoniiS.
rubberWithsignalpeptidesWithoutsignalpeptidesWithsignalpeptidesWithoutsignalpeptidesWithsignalpeptidesWithoutsignalpeptidesWithsignalpeptidesWithoutsignalpeptidesWithsignalpeptidesWithoutsignalpeptidesAllproteins6.
29±2.
087.
28±2.
215.
73±1.
907.
07±2.
207.
22±2.
177.
20±2.
117.
45±1.
506.
47±1.
426.
58±2.
525.
79±2.
15Peptidases5.
96±1.
656.
65±2.
025.
29±1.
435.
93±1.
667.
54±2.
387.
33±2.
137.
65±1.
957.
35±1.
935.
76±1.
905.
91±2.
171Thedataareaverageswithstandarddeviation.
Qinetal.
BMCGenomics2010,11:247http://www.
biomedcentral.
com/1471-2164/11/247Page9of10ThecomparedgenomesequenceswereobtainedfromtheNCBIdatabaseFTPsite:ftp://ftp.
ncbi.
nih.
gov/genomes/Bacteria/.
AminoacidcompositionandproteinisoelectricpointswerepredictedbytheEMBOSSPep-statsprogram.
Thecomparedproteinnumberswerecountedbysearchingthegenomeannotationfileusingtheproteinnamewithnofurtherrefinementoftheanno-tation.
COGfunctionalcategorieswereassignedbyusingablastpprogramtosearchtheCOGdatabasewithallSM-A87proteins,andthefinalresultswerecompiledusingcustom-madePerlscripts.
ThecompletegenomesequenceofstrainSM-A87wasdepositedinGenBankundertheaccessionno.
CP001650.
AdditionalmaterialAuthors'contributionsXZcoordinatedthestudy.
YZ,BZandJYdesignedtheproject;HDproviedthestrain;QQpreparedtheDNA;XWandGLcarriedoutthesequencingandassembly;QQandXZfinishedthegenome;QQ,GL,BXandXZanalyzedthedata;QQwrotethepaper;YZandXCcriticallyreviewedthepaper.
Allauthorsapprovedthefinalmanuscript.
AcknowledgementsWethankHaiboSunforhishelpinsequenceassembly.
Theworkwassup-portedbyNationalNaturalScienceFoundationofChina(30770040,40706001),Hi-TechResearchandDevelopmentprogramofChina(2007AA091903,2007AA021306),andCOMRAProgram(DYXM-115-02-2-6).
AuthorDetails1StateKeyLabofMicrobialTechnology,MarineBiotechnologyResearchCenter,ShandongUniversity,Jinan250100,PRChina,2CASKeyLaboratoryofGenomeSciencesandInformation,BeijingInstituteofGenomics,ChineseAcademyofSciences,Beijing,100029,PRChinaand3CentreforBioengineeringandBiotechnology,ChinaUniversityofPetroleum(EastChina),Qingdao266555,PRChinaReferences1.
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Additionalfile2SequencealignmentofZPR_0565andZPR_1126withotherinitialglycosyltransferases.
CpsE(CAC18355),EpsE(AAC44012),EpsT(EF362569),ExoY(Q02731),GumD(AAA86372),RfbP(P26406),WbaP(AAD21565),WchA(AAK20699).
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Additionalfile4Summaryofthecarbohydrate-degradingenzymesfromZ.
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Received:26September2009Accepted:17April2010Published:17April2010Thisarticleisavailablefrom:http://www.
biomedcentral.
com/1471-2164/11/2472010Qinetal;licenseeBioMedCentralLtd.
ThisisanOpenAccessarticledistributedunderthetermsoftheCreativeCommonsAttributionLicense(http://creativecommons.
org/licenses/by/2.
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doi:10.
1186/1471-2164-11-247Citethisarticleas:Qinetal.
,ThecompletegenomeofZunongwangiapro-fundaSM-A87revealsitsadaptationtothedeep-seaenvironmentandeco-logicalroleinsedimentaryorganicnitrogendegradationBMCGenomics2010,11:247
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ResearcharticleThecompletegenomeofZunongwangiaprofundaSM-A87revealsitsadaptationtothedeep-seaenvironmentandecologicalroleinsedimentaryorganicnitrogendegradationQi-LongQin1,Xi-YingZhang1,Xu-MinWang2,Gui-MingLiu2,Xiu-LanChen1,Bin-BinXie1,Hong-YueDang3,Bai-ChengZhou1,JunYu2andYu-ZhongZhang*1AbstractBackground:ZunongwangiaprofundaSM-A87,whichwasisolatedfromdeep-seasediment,isanaerobic,gram-negativebacteriumthatrepresentsanewgenusofFlavobacteriaceae.
Thisisthefirstsequencedgenomeofadeep-seabacteriumfromthephylumBacteroidetes.
Results:TheZ.
profundaSM-A87genomehasasingle5128187-bpcircularchromosomewithnoextrachromosomalelementsandharbors4653predictedprotein-codinggenes.
SM-A87producesalargeamountofcapsularpolysaccharidesandpossessestwopolysaccharidebiosynthesisgeneclusters.
Ithasatotalof130peptidases,61ofwhichhavesignalpeptides.
Inadditiontoextracellularpeptidases,SM-A87alsohasvariousextracellularenzymesforcarbohydrate,lipidandDNAdegradation.
Theseextracellularenzymessuggestthatthebacteriumisabletohydrolyzeorganicmaterialsinthesediment,especiallycarbohydratesandproteinaceousorganicnitrogen.
Therearetwoclusteredregularlyinterspacedshortpalindromicrepeatsinthegenome,buttheirspacersdonotmatchanysequencesinthepublicsequencedatabases.
SM-A87isamoderatehalophile.
Ourproteinisoelectricpointanalysisindicatesthatextracellularproteinshavelowerpredictedisoelectricpointsthanintracellularproteins.
SM-A87accumulatesorganicosmolytesinthecell,soitsextracelluarproteinsaremorehalophilicthanitsintracellularproteins.
Conclusion:Here,wepresentthefirstcompletegenomeofadeep-seasedimentarybacteriumfromthephylumBacteroidetes.
ThegenomeanalysisshowsthatSM-A87hassomecommonfeaturesofdeep-seabacteria,aswellasanimportantcapacitytohydrolyzesedimentaryorganicnitrogen.
BackgroundTheaveragedepthoftheoceansisabout3800m,andalmost60%oftheearth'ssurfaceisdeep-seafloor(waterdepthgreaterthan2000m)[1].
Althoughmostofthedeep-seafloorenvironmentischaracterizedbydarkness,highhydrostaticpressureandlowtemperatures,morethanhalfoftheworld'sprokaryotesliveinsub-seafloorsediments[2-4],whichplayamajorroleinmarinebio-geochemicalcycling[5].
Everyyear,massiveamountsofparticulateorganicmatter(POM)aretransportedtothedeeplayersoftheoceanfloor,formingalargepoolofcar-bonandnitrogen[6].
However,howthisorganicmaterialisdegraded,aswellasthetypesofbacteriainvolvedandtheenzymesused,arestillunclear,especiallyforthedeg-radationofsedimentaryorganicnitrogen(SON)[7].
Todate,numerouseffortshavebeenmadetoclarifythemechanismofSONdegradation,includinginvestigationsofthediversityofbacteriaandproteasesinvolvedinSONdegradation[8,9].
ResearchershavealsocharacterizedsomeextracellularproteasesfromsedimentarybacteriaandelucidatedtheirecologicalroleinSONdegradation[10-13].
However,theroleofdeep-seabacteriainSONdegradationandcyclinghasneverbeenanalyzedatagenomiclevel.
Genomeanalysesofdeep-seahet-*Correspondence:zhangyz@sdu.
edu.
cn1StateKeyLabofMicrobialTechnology,MarineBiotechnologyResearchCenter,ShandongUniversity,Jinan250100,PRChinaContributedequallyFulllistofauthorinformationisavailableattheendofthearticleQinetal.
BMCGenomics2010,11:247http://www.
biomedcentral.
com/1471-2164/11/247Page2of10erotrophicbacteriawouldprovideabetterunderstandingofthedeep-seanitrogencycle,andrevealtowhatextentbacteriaaffectthedeep-seaenvironment[14].
Bacteroidetes(formerlyCytophaga-Flavobacterium-Bacteroides(CFB))areawidespreadanddiversegroupofbacteriathatcanbefoundthroughoutthesea,fromsur-facewatertodeep-seasediment.
Studiesofbothculti-vatedanduncultivatedmarineBacteroideteshaveshownthatBacteroidetesareabletoefficientlyconsumebiopoly-merssuchasproteinandchitin[15,16],whichmakeupasignificantfractionofthehigh-molecular-weightdis-solvedorganicmatter(HMWDOM)poolintheocean[17].
Biopolymerdegradationisconsideredtobetherate-limitingstepinDOMmineralizationbymarinemicroor-ganisms,andBacteroidetesarehypothesizedtoplayakeyroleinthisprocessintheoceans[7].
GenomesequencedatahavebeenextremelyhelpfulinthedevelopmentofdetailedhypothesesontheroleofspecificBacteroidetesmembersinmarinebiogeochemicalcycling.
AnanalysisofthegenomeofBacteroidetes'Gramellaforsetii'KT0803,abacterioplanktonisolatedfromNorthSeasur-facewatersduringaphytoplanktonbloom,indicatedthatitisefficientatdegradingbiopolymers,especiallypro-teins[18,19].
MetagenomicstudieshavealsoreportedthedistributionandfunctionalanalysisofspecificCytophaga-likehydrolasesintheSargassoSeaandwest-ernArcticOceananddescribedhydrolase-containinggenomefragmentsofAntarcticmarineBacteroidetes[20,21].
However,whileBacteroideteshavebeenfre-quentlyencounteredintheanalysisofsedimentarybacte-rialdiversity,nocompletegenomeanalysisofadeep-seasedimentaryBacteroideteshasyetbeenpublished[15,16].
Thistypeofanalysiscouldbeusedtoaddresshowtheorganisms'geneticinventoriesreflectboththeirSONremineralizationcapabilitiesandtheiradaptationtothedeep-seaenvironment.
WangiaprofundaSM-A87(hereaftercalledSM-A87),isolatedatadepthof1245mfromdeep-seasedimentinthesouthernOkinawaTroughwithinsitutemperatureof4.
7°C,isanewlydescribedspeciesofBacteroidetesandrepresentsanewgenusofFlavobacteriaceae[22].
ItwasrenamedZunongwangiaprofundaintheInternationalJournalofSystematicandEvolutionaryMicrobiology(IJSEM)ValidationListno.
116.
Inthisstudy,wereportitscompletegenomesequence,whichrepresentsthefirstgenomeofadeep-seabacteriumofthephylumBacteroi-detes.
Inaddition,weperformedagenomiccomparisonwithtwobacteriaofthefamilyofFlavobacteriaceaefromsurfaceseawater,andtwobacteriafromacolddeep-seaenvironment.
OurgenomicanalysisofstrainSM-A87indicatesthatitiscapableofdegradingbiopolymersourcesandshedslightonitsadaptationtothedeep-seaenvironment.
ResultsanddiscussionGeneralgenomefeaturesGeneralfeaturesoftheZ.
profundaSM-A87genomearesummarizedinTable1.
Thegenomehasasingle5.
1-Mbpcircularchromosomewithnoextrachromosomalele-ments.
TheG+Ccontentofthegenomeis36.
2%,whichisslightlyhigherthantheexperimentallydetermined35.
8%[22].
Thegenomeharbors4653predictedopenreadingframes(ORFs),ofwhich69.
4%areannotatedwithknownorpredictedfunctions.
About50%ofSM-A87ORFshavethehighestsimilaritytothoseinthepublishedgenomeofG.
forsetiiKT0803.
SM-A87has47tRNAgenesandthree16S-23S-5Soperons.
Figure1showstheproportionsofproteinsbelongingtoclustersoforthologousgroups(COGs)inSM-A87andseveralotherbacterialgroups.
Thedeep-seabacteria(SM-A87,PhotobacteriumprofundumSS9andShe-wanellapiezotoleransWP3)haveanaverageof2.
35%moreproteinsbelongingtoCOGK(transcription),and2.
11%moreproteinsbelongingtoCOGT(signaltrans-ductionmechanisms)thantheshallow-waterbacteria(FlavobacteriumpsychrophilumandGramellaforsetiiKT0803).
Thesedifferencesarestatisticallysignificant(p<0.
05).
GeneralmetabolismSM-A87hasafullsetofgenesforglycolysis,thepentosephosphatepathwayandthetricarboxylic/citricacidcycle.
Thestrainhasfivepredictedlactatedehydrogenases,twoL-andthreeD-,andalsocontainspredictedethanol-pro-ducingenzymesincludingaldehydedehydrogenase(ZPR_1384,ZPR_3649)andalcoholdehydrogenase(ZPR_4362).
Theseenzymesmayhelpthebacteriumtosurviveinthelow-oxygenenvironmentofthedeepsea.
SM-A87containspredictedcytochromebdubiquinoloxidasesubunitsI(ZPR_1985)andII(ZPR_1985).
Thisoxidaseisrelatedtoadaptationtomicroaerobiccondi-tionsinthedeepsea[23].
AccordingtotheKyotoEncy-clopediaofGenesandGenomes(KEGG)pathwaymapofTable1:GeneralfeaturesoftheZ.
profundaSM-A87genome.
Size(bp)5128187G+Ccontent36.
2%NumberofpredictedORFs4653AverageORFlength(bp)960Codingdensity87.
4%tRNAs47rRNAoperons3Conservedhypotheticalproteins%17.
1%Hypotheticalproteins%13.
5%Qinetal.
BMCGenomics2010,11:247http://www.
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com/1471-2164/11/247Page3of10SM-A87,fructoseandmannosecanbeconvertedtofruc-tose-6p,andgalactosecanbeconvertedtoglucose-1p;bothfructose-6pandglucose-1parethendegradedthroughglycolysis.
SM-A87harborsapredictedketo-deoxy-phosphogluconatealdolase(ZPR_2957),whichisthekeyenzymeoftheEntner-Doudoroffmetabolicpath-way.
Thisstrainalsocontainstheenzymesthatutilizemostaminoacids.
AllthesefeaturesconferametabolicversatilitytoSM-A87thatallowsittoutilizesparseandsporadicnutrientsinthedeep-seaenvironment.
SM-A87hasallthegenesrequiredforfattyacidoxida-tion.
However,3R-hydroxymyristoylACPdehydrase,acomponentofthefattyacidbiosynthesispathway,wasnotfoundbygenomeannotation.
Thisabsencemaybeduetothelowsimilarityofthisgenetothoseinthedata-basesortoconvergentevolutionfromotherfunctionallysimilarenzymeswithdivergentsequences.
Phosphati-dylethanolamineistheonlyphospholipidthathasbeenexperimentallyidentifiedinZunongwangiaprofunda[22].
Thegenomeanalysissuggeststhatphosphatidyleth-anolamineisderivedfromphosphatidylserine,whichissynthesizedfromglycerate.
SM-A87hasallofthecomponentsoftheoxidativephosphorylationpathwaybutdoesnotcontainanyrho-dopsinorretinalgenes,consistentwiththedarkdeep-seaenvironmentinwhichthestrainthrives.
SensingsystemMostnutrientsarriveinthedeepseainanannualpulse,andthebacteriainthedeepseacansensethisfoodpulseandrespondaccordingly[24].
Awidespreadsensingsys-temusedbybacteriaisthetwo-componentsignaltrans-ductionsystem,whichconsistsofasignalsensorhistidinekinaseandaresponseregulator[25,26].
SM-A87harbors47predictedsensorhistidinekinases,themostofanyofthecomparedstrains(Table2),whichindi-catesitsstrongabilitytosenseenvironmentsignals.
SM-A87hasninepredictedtwo-componentoperons,eachofwhichiscomposedofahistidinekinaseandaresponseregulatorthatmayformaone-to-onephosphotransferpair.
SM-A87hasthreerRNAoperons,suggestingthatitcanrespondtonutrientenrichmentrapidlyandgrowquickly[27].
SM-A87canformcoloniesof1-3mmindiameteronarichmediumafter48hofcultivationat28°C[22].
Figure1COGcategorypercentageofZ.
profundaSM-A87andothercomparedbacteria.
Qinetal.
BMCGenomics2010,11:247http://www.
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com/1471-2164/11/247Page4of10SM-A87contains22genesencodingRagB/SusDfamilyproteinsinitsgenome,whiletheothercomparedgenomeshavefewerornone(Table2).
RagBisaproteininvolvedinsignalingandSusDisanoutermembraneproteininvolvedinnutrientbinding[28,29].
NineteenoftheRagB/SusDfamilyproteingenesareeachadjacenttoaTonB-dependentreceptorgene,forming19predictedoperons.
Ofthe19predictedoperons,12areadjacenttopredictedglycosylhydrolasesorpeptidases[seeAddi-tionalfile1].
SpecificallyforthegenesfromZPR_1020toZPR_1033,therearetwoglycosidasegenes,twoesterasegenes,onexylanasegeneandsevenglycosylhydrolasegenesnexttotheoperon,implyingthatSM-A87cansenseandrespondtosugarsources.
Thegenomealsocontains27putativeoutermembraneproteingenes,whichareprobablyinvolvedinnutrientbinding.
AllthesefeaturesimplythatSM-A87hastheabilitytosenseextra-cellularnutrientssuchassugarsandproteins.
PolysaccharidesynthesisManydeep-seabacteriaproduceexopolysaccharidesthathelpthemsurviveintheextremedeep-seaenvironment[30].
Reportssuggestthatthesepolysaccharideshelpthebacteriaconcentrateorganicmatter,absorbmetalions,andformbiofilmsinthemarineenvironment[31,32].
Differentglycosyltransferasescancontributetothebio-synthesisofdisaccharides,oligosaccharides,andpolysac-charides[33].
OurexperimentalresultsshowthatstrainSM-A87canproducelargequantitiesofcapsularpolysac-charide(datanotshown).
ThegenomeanalysisshowsthatSM-A87contains46predictedglycosyltransferases,ofwhich13belongtofamilytwoand10belongtofamilyone.
SM-A87containstwoglycosyltransferases(ZPR_0565andZPR_1126)thataresimilartoWbaPfromSalmonellaenterica.
WbaPisresponsiblefortheinitia-tionofpolysaccharidesynthesis,transferringthefirstsugartoundecaprenylphosphate(Und-P)[34].
SimilartoWbaP,ZPR_1126has462aminoacidresiduesandfivepredictedtransmembraneregions.
Thetopologicalorga-nizationofthetransmembraneregionsofthesetwoenzymesissimilar:therearefourtransmembraneregionsattheN-terminusandonetransmembranedomainwithsugar-phosphatetransferaseactivityattheC-terminus.
ZPR_0565consistsof339aminoacidresiduesandhasonlyonetransmembranedomain.
Amultiplesequencealignment[seeAdditionalfile2]showsthatZPR_0565correspondstotheC-terminusofWbaPandotherinitialglycosyltransferases;inaddition,theyallcontainthehighlyconservedaminoacidmotifsKFRSM,DELPQ,andPGITG[35].
ThisimpliesthatZPR_0565containsonlyTable2:ComparisonofthenumbersofselectedproteinsbetweenSM-A87andotherfourmarinebacteria.
SM-A87P.
profundumSS9S.
piezotoleransWP3G.
forsetiiKT0803F.
psychrophilumSensingcomponentsHistidinekinase4720463713RagB/susDfamilyprotein2200140EnzymesfordegradationPeptidase1130(60)74(18)129(50)94(47)59(42)Glucosidase110550Xylanase60000Xylosidase30010Beta-galactosidase53240Amylase32430Chitinase23200Otherglycosidase5046212Lipase1411793Esterase462032227TransportorsABC-typetransporter40155642840TonB-dependentreceptor4003340221Inparenthesesisthenumberofproteinswithsignalpeptides.
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com/1471-2164/11/247Page5of10theglycosyltransferasecatalyticdomain.
Genesencodingotherglycosyltransferasesandpolysaccharideexportpro-teinsarefoundclosetoZPR_0565andZPR_1126;together,thesegenesformtwogeneclustersforpolysac-charidesynthesisandexport[seeAdditionalfile3].
ZPR_1123,whichisupstreamofZPR_1126,ispredictedtoencodeanO-antigenpolymerase,implyingthatpoly-saccharidesaresynthesizedthroughtheWzy-dependentpathwayinSM-A87[36].
SM-A87harborstwopredictedcapsularpolysaccharidebiosynthesisproteinsthatareprobablyinvolvedinthesynthesisofcapsularpolysaccha-rides.
TheproductionofcapsularpolysaccharideisadvantageousforSM-A87tothriveinthemarineenvi-ronment.
HydrolysisabilitySignalpeptideanalysissuggeststhatSM-A87cansecretealargenumberofhydrolysisenzymes,andithasmoreexportedpeptidasesthantheothercomparedstrains(Table2),reflectingitsunusualabilitytodegradeorganicnitrogen.
SM-A87contains130predictedpeptidases,61ofwhichhavesignalpeptides.
Thepeptidaseswithsignalpeptideshavemoreasparticacidsandahigherratioofacidicresiduestobasicresidues.
Additionally,theyhavealowerpredictedisoelectricpoint(pI)thanthepeptidaseswithoutsignalpeptides(Table3),adifferencethatissta-tisticallysignificant(p<0.
05).
Thus,theextracellularpeptidasesaremorehalophilicthantheintracellularpep-tidases,ashighnumbersofacidicresiduesandlowpIsarekeyfeaturesofhalophilicproteins[37].
Thehalophi-licityoftheextracellularpeptidaseshelpsthemfunctioninsalineenvironmentsanddecomposeextracellularorganicnitrogenmatterinthemarinesaltycondition.
Fifty-twooftheSM-A87peptidaseswithsignalpep-tidescanbeassignedtodifferentfamiliesintheMEROPSpeptidasedatabase[38].
AsshowninFigure2,thepepti-dasesmainlybelongtofamiliesofmetallopeptidasesandserinepeptidases,consistentwithourpreviousstudythattheextracellularpeptidasesofmarinesedimentarybacte-riaaremainlyserineproteasesandmetalloproteases[9].
ComparedtoG.
forsetiiKT0803,deep-seabacteriaSM-A87andS.
piezotoleransWP3havemorepeptidasesinfamiliesS09andS41,butfewerinfamilyM14(Figure2).
ThevarietyofextracellularpeptidasessuggeststhatSM-A87hasthecapacitytodecomposediversepeptidesandproteinsfromitssurroundings.
Forinstance,SM-A87hassixexportedfamilyM01peptidases,whichareamino-peptidases.
Ithasbeenreportedthatwhenmarinebacte-riagrowonHMWdissolvedorganicnitrogen(DON)asthesolenitrogensource,aminopeptidaseactivityisgreatlyenhanced[39].
Aminopeptidaseactivityinthedeep-seasedimentishigherthanthatinthesurfacesea-water;however,thisisnotthecaseforotherhydrolysisenzymes[40].
ThelargenumberofaminopeptidasessecretedbySM-A87maycontributetothehighamino-peptidaseactivityinthedeep-seasediment,andsuggeststhatSM-A87maybeabletorespondtoHMWDONanddecomposeit.
SM-A87secretessevenS09peptidases,whichareprolyloligopeptidasesthatcannotdegradepeptidesofmorethan30residuesinlength[41].
There-fore,theS09peptidasesspecificallyhydrolyzeoligopep-tides.
Notably,therearesixexportedpeptidasesthatcontainaPDZdomain,whichisknowntobeinvolvedinpeptidebinding[42].
ThelargenumberofPDZdomain-containingpeptidasessecretedbySM-A87suggestsastrategyforbindinganddegradingproteins,similartothePKDdomainsofexportedproteinsinG.
forsetiiKT0803[19].
Inthedeep-seasedimentarynitrogencycle,thepro-cessbywhichparticulateorganicnitrogenisconvertedtoNH4+isknowntobedominatedbybacteriabutispoorlycharacterized[1,14].
ThesecretedpeptidasesofSM-A87mayplayanimportantroleinthisprocess.
Amongthecomparedstrains,SM-A87hasthelargestproportionofproteinsbelongingtocarbohydratetrans-portandmetabolismCOGs(Figure1).
Accordingly,ithasmanygenesencodingenzymesthatdegradeoligo-andpolysaccharides(Table2)[Additionalfile4].
SM-A87hasTable3:Propertiesofpeptidaseswithandwithoutsignalpeptides.
WithsignalpeptidesWithoutsignalpeptidesNumber6169G+Ccontent(%)37.
536.
8Asp(percentage)6.
66.
0Glu(percentage)7.
27.
2Lys(percentage)8.
08.
1Arg(percentage)3.
63.
5(Asp+Glu)/(Lys+Arg)1.
21.
1pI16.
0±1.
76.
7±2.
01pI,predictedisoelectricpoint.
Thedataareaverageswithstandarddeviation.
Qinetal.
BMCGenomics2010,11:247http://www.
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com/1471-2164/11/247Page6of1050annotatedglycosidases,17ofwhichhavesignalpep-tides,suggestingthatSM-A87canhydrolyzeextracellularcarbohydrates.
Itdoesnotcontainanypredictedcellu-lases,agreeingwiththeexperimentalresultthatitcannothydrolyzecellulose.
AlthoughSM-A87hasageneforexportedchitinase(ZPR_1703),experimentssuggestthatitdoesnotdegradechitin.
SM-A87harborssixxylanasegenesandthreexylosidasegenes,ofwhichthreexyla-nasesandtwoxylosidaseshavesignalpeptides,indicatingthatthestrainshouldhavetheabilitytodegradexylan.
Thegenomealsohasfourgenesencodingexportedbeta-galactosidases;correspondingly,beta-galactosidaseactiv-ityhasbeendetectedinthisstrain[22].
SM-A87contains11predictedglucosidases,ofwhichsevenhavesignalpeptides.
Glucosidaseproductioncanbeinducedbydissolvedpolymericglucose[43].
ThelargenumberofglucosidasesinSM-A87indicatesthatitisabletodecomposetheeasilyusedpolymericsugarintheenvi-ronment.
Thecarbohydrate-hydrolyzingenzymesmen-tionedaboveimplythatSM-A87isabletouseavarietyofcarbohydratesintheenvironmentascarbonandenergysources.
SM-A87harborssevengenesencodingextracellularlipases,includingonephospholipaseA1(ZPR_0295)andtwoGDSLfamilylipases.
Thestraincontains20genesencodingesteraseswithsignalpeptides,ofwhichfivearecarboxylesterasesandsixarephosphoesterases.
TheseenzymesmayallowSM-A87todegradevariousphospho-lipidsandcarboxylestersintheenvironmentascarbonandphosphorussources.
DNAisabundantinthedeep-seasediment,andmostofitisextracellular.
Morethanhalfofthetotalextracellu-larDNAcanberapidlydegradedbyenzymes[44].
DNAcanbeutilizedbybacteriaasasourceofcarbon,nitrogen,andphosphorous,contributingtophosphaterecycling[44].
SM-A87harborstwopredictedextracellularendo-nucleases(ZPR_0199,ZPR_1186),implyingthatitcanobtainnutrientelementsbydegradingextracellularDNA.
Ithasbeenreportedthatsedimentarycarbohydrateishydrolyzedmoreeasilywhenitistreatedwithfourenzymes,α-amylase,β-glucosidase,proteaseandlipase,thanwhenitistreatedwithonlyoneenzyme[45].
SM-A87containsthesefourkindsofextracellularenzymes,implyingthatthestraincanhydrolyzesedimentarycar-bohydrateseasily.
ThevarietyofexportedpeptidasesandotherhydrolysisenzymesintheSM-A87genomewouldallowthebacteriumtodegradesedimentarybiopoly-mericmaterialsintosmallmoleculesthatcanbeabsorbedbythecell.
ApreviousgenomeanalysisrevealedthatG.
forsetiiKT0803fromsurfaceseawaterisgoodatdegradingpolymericorganicmaterials[19].
OuranalysisoftheSM-A87genomeindicatesthatthisdeep-seasedi-mentBacteroidetesspeciesalsohastheunusualabilitytodecomposepolymericorganicmaterials,whichcouldcontributeconsiderablytodeep-seasedimentarybiogeo-chemistrycycles.
NitrogenandsulfurmetabolismAccordingtotheKEGGpathwaymap,nitritereductasecancatalyzetheconversionofnitritetoammonia[46].
Twonitritereductases(ZPR_3631,ZPR_4195)couldberesponsiblefortheconversionofnitritetoammoniainSM-A87.
Oneformate/nitritetransporter(ZPR_2292)andthreeputativenitrate/nitriteDNA-bindingresponseregulatorsinthegenomeindicatethatSM-A87canabsorbnitritefromtheenvironment.
Alloftheaboveevi-dencesuggeststhatthestraincanuseinorganicnitrogen.
TheSM-A87genomeencodesonesulfatetransporter(ZPR_0777)andtwosodium:sulfatesymporters(ZPR_0364,ZPR_4168)thatcantransportsulfateionsintothecell.
Italsohascorrespondingenzymestoutilizesulfate.
TherearethreeadjacentORFsthatencodeadeny-lylsulfatekinase(ZPR_0539)andtwosubunitsofsulfateadenylyltransferase(ZPR_0540,ZPR_0541),whichcon-vertsulfatetoadenylylsulfate(APS)andsubsequentlyto3'-phosphoadenylylsulfate(PAPS).
Phosphoadenosinephosphosulfatereductase(ZPR_3632)canconvertPAPSintosulfite,andthenhydrogensulfide(H2S)couldbeproducedfromsulfitebythesulfitereductases(ZPR_0424,ZPR_4048).
However,ourpreviousexperi-mentsshowedthatSM-A87doesnotsecreteH2S(22).
Thus,H2Sisprobablyusedtoproduceacetateviacysteinesynthase(ZPR_2076),whichconverts3-O-acetyl-L-serine(fromserine)andH2Stoacetate.
SubstratetransportsystemsSinceSM-A87hasmanyextracellularhydrolyticenzymes,theremustberelatedsystemstotransportthenutrientproductsintothecell.
TheATP-bindingcassetteFigure2TheMEROPScategoryoftheextracellularpeptidasesfromZ.
profundaSM-A87,G.
forsetiiKT0803andS.
piezotoleransWP3.
Qinetal.
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com/1471-2164/11/247Page7of10(ABC)transporters,whicharewidespreadamongbacte-ria,cancoupleATPhydrolysistothetransportofavari-etyofsubstratesintoandoutofthecell[47].
AnexaminationofSM-A87genomeidentifiedmanygenesencodingpossibleABCtransporters(Table2),whichisconsistentwiththereportthatthereisanenrichmentofABCtransportergenesinthegenomesofdeep-seamicroorganisms[48].
SM-A87hasthreepredictedaminoacidpermeasesandthreeaminoacidtransporters,whichmakeitpossibleforthestraintoabsorbaminoacidsandoligopeptides.
AccordingtotheKEGGpathwaymap,thestrainmaybeabletotransportmolybdate,ironcom-plexes,lipopolysaccharidesandlipoproteins.
Inaddition,thepresenceofgenesencodingxylosepermease(ZPR_0446),fucosepermease(ZPR_4359)andglucose/galactosetransporter(ZPR_0518)maycorrespondtothecarbohydratetransportabilityofSM-A87.
TheTonB-dependenttransportsystemcantakeuplargesubstratemolecules,suchassiderophoresandvita-mins,intothecellfromtheenvironment[49].
Thegenomeanalysisshowedthat40TonB-dependentrecep-torgenesand5TonBproteingenesarepresentinSM-A87.
Consistentwithpreviousreports,therearefewerTonBproteinsthanTonBreceptors[50].
ThepredictedTonB-dependentsiderophorereceptors(ZPR_0148,ZPR_2532)arelikelytobeinvolvedintheenrichmentandtransportofironintothecell.
MobileelementsSM-A87ispredictedtocarrymanytransposases,sup-portingtheideathattransposasesareabundantinthedeep-seaenvironment[5,48].
TwopredictedputativetransposonswereidentifiedintheSM-A87genome.
OneiscomposedofZPR_3981,ZPR_3982andZPR_3983,ofwhichZPR_3981andZPR_3983belongtotheIS66fam-ilyoftransposases.
Surprisingly,ZPR_3982ispredictedtobeanRNA-directedDNApolymerase(reversetran-scriptase),implyingthattheDNAsegmentofZPR_3982mayhavecomefromanRNAvirus.
Thesecondtranspo-soniscomposedofZPR_1509,ZPR_1511andZPR_1512,ofwhichZPR_1509isanIS3familytransposaseandZPR_1512isaIS116/IS110/IS902familytransposase.
ZPR_1511encodesaglyoxalasefamilyproteinwiththehighestaminoacidsimilarity(63%)toaglyoxalasefromMyxococcusxanthus.
CRISPRClusteredregularlyinterspacedshortpalindromicrepeat(CRISPR)elementsarecommoninbacteriaandarchaea.
ACRISPRischaracterizedbydirectrepeats(DR)thatareseparatedbysimilarlysizednon-repetitivespacers.
TherearealsoCRISPR-associated(CAS)genesandaleadersequencebeforetherepeatarea.
CRISPRelementscanbedescribedasfollows:CASgenes-leader-DR1-spacer1-DR2-spacer2.
.
.
DRn-1-spacern-1-DRn,wherenisthenum-berofrepeats[51,52].
AsingleCRISPRlocushasbeendetectedinmanybacterialgenomes[52].
However,therearetwopredictedCRISPRlociintheSM-A87genome.
Thefirstlocusis5594bpinlength(bp1642261tobp1647855).
Inthefirstlocus,theDRsequenceis37bpinlengthwith76spacers.
SixCASgenesofthecas1,cas2,cas3andcas5familiesweredetectedupstreamofthefirstlocus.
Thesecondlocusis2114bpinlength(bp4768893tobp4771007),witha47-bpDRsequenceand26spacers.
ThereareonlytwoCASgenesupstreamofthesecondlocus,onebelongingtothecas1familyandonetothecas2family.
ThetwoCASsystemsareclassifiedasdifferenttypesaccordingtothefamilyandarrangementoftheCASgenes.
CRISPRisthoughttofunctionasananti-phagedefensesystemviaanRNA-silencing-likemechanism,andthespacersareoftenfoundtosharehighsequencesimilari-tieswithphagesequences[52].
However,ourBLASTsearchesresultedinnohitsinthepublicdatabases,prob-ablybecauseonlyasmallfractionofphagesequencesaredepositedinthedatabases.
Intheocean,thequantityofphagesisabout5-10timesmorethanthatofbacteria[53].
SM-A87'sCRISPRsmayhelpdefendagainstinfec-tionbyunknownphagesinthedeepsea.
AdaptationtosaltandcoldHalophileshavetwodifferentwaystomaintaintheircel-lularosmoticbalanceinsaltyenvironments:byaccumu-latingorganiccompatiblesolutesorbymaintainingahighconcentrationofionssuchaspotassiuminthecell[54,55].
SM-A87isamoderatehalophileandcantolerate0-12%NaCl[22].
ToanalyzethemechanismofSM-A87'sadaptationtothemarinesaltyenvironment,wepredictedandcomparedthepIsofintracellularandextracellularproteinsfromSM-A87,G.
forsetiiKT0803,hyperhalo-philicbacteriumSalinibacterruber,nonhalophilicbacte-riumEscherichiacoliandBacteroidetessoilbacteriumCytophagahutchinsonii(Table4).
HalophilicproteinscontainmoreacidicresiduesandhavelowerpIsthannonhalophilicproteins[55].
E.
coliisnothalophilic,andthereisnostatisticallysignificantdifferencebetweenthepIsofitsintracellularandextracellularproteins.
S.
ruberisahyperhalophilicbacteriumthathasahighintracellu-larpotassiumconcentrationtomaintainitscellularosmoticbalance[55];thus,theionconcentrationsinsideandoutsideofthecellarebothhigh.
ThepIsofboththeintracellularandextracellularproteinsofS.
ruberaremuchlowerthanthoseofE.
coliandC.
hutchinsonii(Table4),suggestingthattheS.
ruberproteinsareallhalophilic.
ForthemarinebacteriaSM-A87andG.
forsetiiKT0803,theintracellularproteinpIsarehigherthanthoseoftheextracellularproteins,withastatisticallysignificantdifference(p<0.
01forallproteins,p<0.
05forQinetal.
BMCGenomics2010,11:247http://www.
biomedcentral.
com/1471-2164/11/247Page8of10peptidases).
ThisindicatesthattheintracellularproteinsofSM-A87havepoorsalt-tolerance,anditisthereforeimpossibleforSM-A87tomaintainhighionconcentra-tionsinthecellforosmoticbalance.
Instead,SM-A87hasaglycinebetainetransporter(ZPR_3842).
Glycinebetaineisawell-knownosmoregulator,implyingthatSM-A87mayuseorganiccompatiblesolutesratherthanionstomaintainitscellularosmoticbalance.
Thus,theintracellularproteinsofSM-A87arenothalophilicandhavehigherpIs.
Incontrast,theextracellularproteinsofSM-A87mustfacethemoderatelyhighionconcentration(~3%)ofthesea,sotheseproteinsarehalophilicandhavelowpIs.
ThisisalsothecaseforG.
forsetiiKT0803,whichalsocontainsglycinebetainetransporter.
Thesalt-toler-anceoftheextracellularproteinsofSM-A87andtheirlowerpIsareindicativeoftheiradaptationtothesaltymarineenvironment.
Unsaturatedfattyacidscanincreasethefluidityofthemembrane,whichisacommonstrategyusedbybacteriatoadapttoacoldenvironment.
Themembranesofdeep-seabacteriacontainahighproportionofmonounsatu-ratedfattyacids,whichareveryimportantformaintain-ingbacterialmembranefluidity[56].
SM-A87hasfivefattyaciddesaturasegenes,whichmaycontributetohighmembranefluidity,andthuscoldadaptation.
InadditiontothechaperonesGroELandDnaJ,SM-A87hasfourcoldshockproteingenesandoneheatshockproteingene,whichmayhelpthestrainsurviveinthecolddeep-seaenvironment.
SM-A87alsohasgenesencodingthepyruvatedehydrogenasecomplexandtrehalosephos-phatesynthase(ZPR_2459),whicharebothassociatedwithcoldadaptation[57].
ConclusionThisworkpresentsthefirstcompletedeep-seabacterialgenomeofamemberofthephylumBacteroidetes.
SM-A87hassomefeaturesthatarecommonindeep-seabac-teria,suchasnumeroustransposasesandABC-typetransporters.
Ourgenomesurveyalsorevealsitsmeta-bolicversatilityandextensivehydrolyticcapabilities.
Additionally,basedonthecontentsofitsgenome,SM-A87cansensenutrientpulses,synthesizeexopolysaccha-ridestoabsorbnutrients,exportavarietyofenzymestodegradematerials,transportsubstratesintothecelleffi-cientlyandutilizeresourcesviaversatilemetabolicpath-ways.
Withthesefeatures,SM-A87canthriveinthedeep-seaenvironment.
MethodsStrainSM-A87,originallyisolatedfromdeep-seasedi-mentinthesouthernOkinawaTrough,wasculturedaspreviouslydescribed[22].
Thecellswereharvestedbycentrifugationat12000gat10°Cfor30min.
GenomicDNAwaspreparedbyusingagenomicDNAextractionkit(BioTeke,China)accordingtothemanufacturer'sinstructions.
ThegenomesequenceofstrainSM-A87wasdeter-minedusingacombinedstrategyofSangersequencingand454pyrosequencing.
About100megabasesofdatawereobtainedfromone454(GS-FLX)sequencingrun.
Thesequenceswereassembledinto144largecontigsthatwereorientedbySangersequencingreadsfrompairedendsofplasmidandfosmidlibrarieswithinsertsizesvaryingfrom3kband5kbto40kb.
ThegapswereclosedbyprimerwalkingandPCRsegmentsequencing.
Thephred-phrap-consedpackagewasusedfortheassemblyandfinishing[58],andthefinishedgenomewasvalidatedfurtherby10-kblongPCR.
ThetRNAgeneswerepredictedbytRNAscan-SE[59].
TherRNAgeneswereidentifiedbyBLASTsearchagainstRfam[60].
Theopenreadingframes(ORFs)werefoundbyusingGLIMMER3.
0[61].
ThepredictedORFswereannotatedbysimilaritysearchesagainstdatabasesofnonredundantproteinsequencesfromNCBI,SWIS-SPROT,Pfam[62],COG[63],KEGGandInterPro[64].
TheannotationofORFswasmanuallycuratedwithArtemis[65].
TransmembraneregionsofthepredictedproteinswerepredictedwithTMHMM2.
0http://www.
cbs.
dtu.
dk/services/TMHMM/.
Signalpeptidepre-dictionwasdonewithSignalP3.
0[66].
Clusteredregu-larlyinterspacedshortpalindromicrepeats(CRISPR)werefoundwithCRISPR-finderhttp://crispr.
u-psud.
fr/Server/CRISPRfinder.
php.
ThesequencealignmentwasdonewithClustalX[67].
Table4:PredictedisoelectricpointsoftheproteinsofSM-A87andcomparedstrains1.
SM-A87G.
forsetiiKT0803E.
coliC.
hutchinsoniiS.
rubberWithsignalpeptidesWithoutsignalpeptidesWithsignalpeptidesWithoutsignalpeptidesWithsignalpeptidesWithoutsignalpeptidesWithsignalpeptidesWithoutsignalpeptidesWithsignalpeptidesWithoutsignalpeptidesAllproteins6.
29±2.
087.
28±2.
215.
73±1.
907.
07±2.
207.
22±2.
177.
20±2.
117.
45±1.
506.
47±1.
426.
58±2.
525.
79±2.
15Peptidases5.
96±1.
656.
65±2.
025.
29±1.
435.
93±1.
667.
54±2.
387.
33±2.
137.
65±1.
957.
35±1.
935.
76±1.
905.
91±2.
171Thedataareaverageswithstandarddeviation.
Qinetal.
BMCGenomics2010,11:247http://www.
biomedcentral.
com/1471-2164/11/247Page9of10ThecomparedgenomesequenceswereobtainedfromtheNCBIdatabaseFTPsite:ftp://ftp.
ncbi.
nih.
gov/genomes/Bacteria/.
AminoacidcompositionandproteinisoelectricpointswerepredictedbytheEMBOSSPep-statsprogram.
Thecomparedproteinnumberswerecountedbysearchingthegenomeannotationfileusingtheproteinnamewithnofurtherrefinementoftheanno-tation.
COGfunctionalcategorieswereassignedbyusingablastpprogramtosearchtheCOGdatabasewithallSM-A87proteins,andthefinalresultswerecompiledusingcustom-madePerlscripts.
ThecompletegenomesequenceofstrainSM-A87wasdepositedinGenBankundertheaccessionno.
CP001650.
AdditionalmaterialAuthors'contributionsXZcoordinatedthestudy.
YZ,BZandJYdesignedtheproject;HDproviedthestrain;QQpreparedtheDNA;XWandGLcarriedoutthesequencingandassembly;QQandXZfinishedthegenome;QQ,GL,BXandXZanalyzedthedata;QQwrotethepaper;YZandXCcriticallyreviewedthepaper.
Allauthorsapprovedthefinalmanuscript.
AcknowledgementsWethankHaiboSunforhishelpinsequenceassembly.
Theworkwassup-portedbyNationalNaturalScienceFoundationofChina(30770040,40706001),Hi-TechResearchandDevelopmentprogramofChina(2007AA091903,2007AA021306),andCOMRAProgram(DYXM-115-02-2-6).
AuthorDetails1StateKeyLabofMicrobialTechnology,MarineBiotechnologyResearchCenter,ShandongUniversity,Jinan250100,PRChina,2CASKeyLaboratoryofGenomeSciencesandInformation,BeijingInstituteofGenomics,ChineseAcademyofSciences,Beijing,100029,PRChinaand3CentreforBioengineeringandBiotechnology,ChinaUniversityofPetroleum(EastChina),Qingdao266555,PRChinaReferences1.
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Additionalfile2SequencealignmentofZPR_0565andZPR_1126withotherinitialglycosyltransferases.
CpsE(CAC18355),EpsE(AAC44012),EpsT(EF362569),ExoY(Q02731),GumD(AAA86372),RfbP(P26406),WbaP(AAD21565),WchA(AAK20699).
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Additionalfile4Summaryofthecarbohydrate-degradingenzymesfromZ.
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Received:26September2009Accepted:17April2010Published:17April2010Thisarticleisavailablefrom:http://www.
biomedcentral.
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org/licenses/by/2.
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