嗜热泉生古细菌密码子使用偏向性的研究

嗜热泉生古细菌密码子使用偏向性的研究

在最重要的情况下，非正统的非正统的资源分配是不可能的。第一阶段的数据不是很可可执行的。这是一个确保治疗的异常迹象[15,16,17,18,19,20]。努力工作的发展报告了这一阶段的异常迹象[15、16、17、18、19、20]。AeropyrumpernixK1,asasubtypeofCrenarchaeotamicroorganism,wasisolatedfromacoastalsolfataric(volcanichydrothermalareathatemitssulfuricgases)thermalventatKodakara-JimaIsland,Japanin1993.Thisorganismishighlymotile.CellsofA.pernixK1arecoccoidandareoftensurroundedbypili-likeappendages.A.pernixK1growsbetween70and100℃withoptimalgrowthat90-95℃.AlthoughthegenomicsequenceofA.pernixK1hasbeenpublished,littlegenomicanalysisisavailableonthismicroorganism.Inthisstudy,thesynonymouscodonusageofthismicroorganismisanalyzedandacomparisonismadewiththeothertwophylogeneticallyrelatedCrenarchaeotamicroorganisms(i.e.,Pyrobaculumaerophilumstr.IM2andSulfolobusacidocaldariusDSM639).1杏仁杏仁1.1invi结构ThecompletegenomesandthecodingsequencesofA.pernixK1andtwootherCrenarchaeotamicroorganisms,includingP.aerophilumstr.IM2andS.acidocaldariusDSM639,wereextractedfromtheNCBIRefseqproject(AccessionNo.NC_000854,NC_003364,NC_007181,respectively).Thesequencesimilarityisnotenoughtoseparatetheorthologousgenesfromparalogousgenes.So,onlyfivegeneswiththesimilarnameswereselectedfromamongthemicroorganisms,asorthologousgenes,toinvestigatewhethertherewasacorrelationbetweenthegenefunctionandthecodonusagebias.ThefiveorthologousgenesareshowninTable1.1.2我1.2.1quequetrafteriecidiciding、gc3codons,trpToexaminesynonymouscodonusagewithouttheconfoundinginfluenceofaminoacidcompositionofdifferentgenesamples,thevaluesofrelativesynonymouscodonusage(RSCU)ofdifferentcodonsineachsequencewerecalculated.TheRSCUvalueofthejthcodonfortheithaminoacidwascalculatedbywhereobsijistheobservednumberofthejthcodonfortheithaminoacid,whichhasnitypeofsynonymouscodons.ItisobviousthatRSCUvaluescloseto1.0indicatealackofbiasforthecorrespondingcodon.GC3Scontent:GC3SisthefrequencyofthenucleotideG+Catthesynonymousthirdpositionofthecodons,excludingMet,Trp,andtheterminationcodons.Itisagoodindicatoroftheextentofbasecompositionbias.1.2.2接枝外域清cur-soincipara部sigrectorizactizationf3TheENCofageneisgenerallyusedtoquantifythecodonusagebiasofagene,whichisessentiallyindependentofgenelength.TheENCvalueiscalculatedas:Informula2,F2istheprobability,wheretworandomlychosencodonsforanaminoacidwithtwocodonsareidentical.ItissimilarforF3,F4,andF6Recentcomparativesimulationstudyhasshownthatitisthebestoverallmeanstoestimatetheabsolutesynonymouscodonusagebias.ValuesofENCrangefrom20(whenonlyonecodonisusedperaminoacid)to61(whenallsynonymouscodonsareequallyusedforeachaminoacid).TheexpectedENCvalueunderrandomcodonusagecanbecalculatedforanyvalueofGC3sas:Where,srepresentsthegivenGC3Svalue.ThevaluesofENCwouldfallonthecontinuouscurvedescribedinformula3,iftheG+Ccompositionatthesynonymousthirdpositionistheonlydeterminantfactorshapingthecodonusage.1.2.3ge三维建模方法PCAwasusedtoinvestigatethemajortrendincodonusagevariationamongthegenes.TheRSCUvaluesofgeneswereplottedinamultidimensionalspaceof59axes(excludingMet,Trp,andstopcodons)andPCAidentifiedaseriesofneworthogonalaxesaccountingforthegreatestvariationamonggenes.1.2.4规训codonspTheprincipleofhierarchicalclusteringisasfollows.First,eachsequenceisconsideredasaseparateclass.Then,accordingtothedistancebetweenthesesequences,thetwosequencesthathavetheminimumdistanceareamalgamatedintooneclass.ThedistancesbetweenselectedsequenceswerecalculatedusingtheEuclideandistancemethod.Thecalculatingformulais:Aftertheamalgamation,distancesbetweentheamalgamatedclassandotherclassesarecalculatedagain.Thisprocessiscontinueduntilallthesequencesareamalgamatedtooneclass.Duringthisprocess,theRSCUvaluesofallthecodonsRSCUijareconsideredtobedifferentvariablecomponentsforacertainsequenceandalsoasasinglespotinthemultidimensionalspace.Tryptophan(Trp,W)andMethionine(Met,M)arenotconsideredbecauseeachcontainedonlyonecodonandtheirRSCUvalueswerealwaysequalto1.Threestopcodonswereexcluded,sothedimensionnumberofthisspaceisunso领域的选择TheprogramCodonW1.4(http://codonw/)wasusedforcalculatingtheindicesofcodonusage.ThestatisticalanalysiswasimplementedusingSPSS11.0.1.forWindows(2001.Chicago:SPSSInc.)2产品系统2.1理论依据TheoverallRSCUvaluesof59sensecodonsinA.pernixK1isshowninTable2.MostpreferentiallyusedareC-endedorG-endedcodons,amongwhich12C-endedcodonsand5G-endedcodonswereagainst1A-endedcodonandnilU-endedcodons.ApernixK1isaGC-richgenomewiththeGCcontenover56%.Duetocompositionalconstraints,itisexpectedthatC-endedand/orG-endedcodonsarepreferentiallyusedinthisgenome.AlthoughtheoverallRSCUvaluesinagenomecouldunveilthecodonusagepatternofawholegenome,itmayhidecertaincodonusagevariationamongdifferentgenesinagenome.Twoimportancodonusageindices,ENCandGC3S,havebeenwidelyusedtostudythecodonusagevariationamongdifferentgenes.ThedistributionsofENCandGC3SvaluesinA.pernixK1areshowninFig.1,respectively.TheENCvaluesofdifferentA.pernixK1genesvariedfrom26.71to61.00,withameanvalueof44.70andstandarddeviation(S.D.)of6.30.Sincetheapproximate77.2%ENCvalueofA.pernixK1genesaregreaterthan40,thecodonusageinA.pernixK1genomeislessbiased.TheGC3SvalueofA.pernixK1genesrangedfrom0.27to0.92withameanof0.65andS.D.0.11.ItwasreportedthataplotofENCagainstGC3Scanbeeffectivelyusedtoexploretheheterogeneityofcodonusageamonggenes.IfthecodonusagepatternofthegeneshascertaininfluenceotherthantheGCcontent,thecomparisonoftheactualdistributionofgeneswiththeexpecteddistributionundernoselectioncouldbeindicative.Inotherwords,ifGC3Sistheonlydeterminantfactorshapingthecodonusagepattern,thevaluesofENCwouldfallonacontinuouscurve,whichrepresentsrandomcodonusageFig.2showsthedistributionplotofENCagainstGC3SforA.pernixK1.Thepointsintheplotwerequitespreadoutandthebulkofgenesdidnotappeartofollowthetheoreticalcurve,whichsuggeststhatthereareotherfactorsthatcontributedtothecodonusagepatterninA.pernixK1besidesthegenomiccomposition.Tofurtherinvestigatethecorrelationbetweensynonymouscodonusagebiasandnucleotidecomposition,thelinearregressionanalysiswasimplemented.TheR2valueandthesignificancelevelofthesere-gressionanalysesarelistedinTable3.TherewasasignificantcorrelationbetweenGC3ScontentandthefirsttwomainPCAaxesofRSCUinA.pernixK1andothertwoCrenarchaeotamicroorganisms.Therefore,itisunquestionablethatbasecompositionalconstraintsarethemajorsourcedeterminingthecodonusageinthewholegenomeofthesemicroorganisms.2.2eachgene.案例ToinvestigatethesynonymouscodonusagevariationamongA.pernixK1andothertwophylogeneticallyrelatedCrenarchaeotamicroorganismsthecodonusagedataofgenesinthreemicroorganismswasalsocalculated.PrincipalcomponentanalysiswasimplementedforallidentifiedORFsfromthethreegenomesaccordingtotheRSCUvalueofeachgene.Tominimizetheeffectofaminoacidcompositiononcodonusage,eachgeneisrepresentedasa59-dimensionalvector.EachdimensioncorrespondstotheRSCUvalueofonesensecodon(excludingMetTrp,andthestopcodons).AplotofthefirstandthesecondaxisofeachgeneisshowninFig.3.AllgenesintheA.pernixK1wereplottedinred,allgenesinP.aerophilumstrIM2wereplottedingreen,andthegenesinS.acidocaldariusDSM639wereplottedinblue.Althoughthisgraphisalittlecomplexwithcertainoverlapsamongthegenesfromdifferentgenomes,itisclearthatA.pernixK1genesaremainlylocatedonthetoprightcorneroftheplot,whilemostoftheP.aerophilumstr.IM2genesarelocatedonthedownrightcorneroftheplotandS.acidocaldariusDSM639genesarelocatedontheleftsideoftheplot.Hence,synonymouscodonusageappearstobeconservedbetweenphylogeneticallyrelatedCrenarchaeotamicroorganisms.2.3整体拟石结构分子vicdiactip水质特点表3Toshowwhetherthereisacorrelationbetweenthecodonusageofthethreemicroorganismsandtheirstrains,thegenesfromeachmicroorganismweredividedintotwogroupsaccordingtothestrain.Principalcomponentanalysiswasimplementedforeachgenomeofthethreemicroorganisms.Thet-testwasusedtotestwhethertheseparationofgroupswassignificant.TheP-valuesweregreaterthan0.05bothonthefirstaxisandthesecondaxisinA.pernixK1,P.aerophilumstr.IM2,andS.acidocaldariusDSM639.ThissuggeststhatthecodonusagepatterninCrenarchaeotamicroorganismsisnotstrainspecific.2.4while联合非价值学—ThecorrelationbetweengeneexpressionlevelandtheextentofcodonusagebiasIftranslationalselectionalsocontributedtothecodonusagebiasingenes,theextentofcodonusagebiasinstructuralgenes,suchastranslationelongationfactorsandribosomalproteins,shouldbelargerthanthatinnonstructuralgenes.ThereisaninclinationthatthehighlyexpressedgenesseemtohavemorebiasamongA.pernixK1andP.aerophilumstr.IM2.InA.pernixK1,theENCvaluesofstructuralgenesvariedfrom26.71to52.99,withamedianof40.69,ameanvalueof40.61,andS.D.of6.00.Whilethenonstructuralgenesvariedfrom27.99to61.00,withamedianof44.67,ameanvalueof44.81andS.D.of6.27.InS.acidocaldariusDSM639,themeanENCvaluesofthestructuralgenesisapproximately8.8%lowerthatofthenonstructuralgenes.However,inP.aerophilumstr.IM2,theENCvaluesofthestructuralandthenonstructuralgenesareroughlythesamewithdifferencessmallerthan0.4%(Fig.4).Tofurtheranalyzetherelationshipbetweenthegeneexpressionlevelandtheextentofthecodonbias,thet-testwasperformed.TheresultsindicatedthattheextentofcodonbiasofthestructuralgeneswassignificantlydifferentfromthatofthenonstructuralgenesinA.pernixK1andS.vacidocaldariusDSM639withP-valuesbelow0.0001.ButinP.aerophilumstr.IM2,thetranslationalselectionpressureseemedtohavenoeffectonthecodonusagebiaswithP-valueof0.67.ItcanbeconcludedthatthetranslationalselectionpressureplaysanimportantroleinformingthecodonusagebiasinA.pernixK1andS.acidocaldariusDSMbutnotinP.aerophilumstr.IM2.2.5国际习惯法第15ge,关于Sinceallthethreemicroorganismscontaingenecodingforgamma-glutamyltranspeptidase,replicationfactorCsmallsubunit,replicationfactorClargesubunit,acyl-CoAsynthase,andDNApolymeraseⅡ,thesegenegroupswereselectedtoinvestigatewhetheracorrelationexistedbetweencodonusageandgenefunction.Thehierarchicalclusterresultofthe15genes,asshowninFig.5,indicatedthatthegeneswithinthesamemicroorganismsareclusteredtogetherwithonlyoneexceptionmarkedbytheellipse.Thus,itwasconcludedthatitisthespeciesratherthanthegenefunctionthatdeterminesthegenecodonamongtheCrenarchaeotamicroorganisms.3u3000药品pincipactors,现实Amongmicroorganisms,themostacceptedhypothesisfortheunequalusageofsynonymouscodonsstatesthatitistheresultofthemutationalbiasesandnaturalselectionactingattheleveloftranslation.TheanalysisrevealedthatthesynonymouscodonusagebiasinA.pernixK1wasles