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外文翻译-- Nucleotide fluctuation analysis of dim-light visionrhodopsin gene and mRNA sequences in vertebrates.PDF

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外文翻译-- Nucleotide fluctuation analysis of dim-light visionrhodopsin gene and mRNA sequences in vertebrates.PDF

NucleotidefluctuationanalysisofdimlightvisionrhodopsingeneandmRNAsequencesinvertebratesToddHolden,N.Gadura,E.Cheung,J.Rada,P.Schneider,G.Tremberger,Jr,D.Sunil,D.Lieberman,andT.CheungPhysicsandBiologyDepartmentsCUNYQueensboroghCommunityCollegeBayside,NY11364USAContactemailtholdenqcc.cuny.eduAbstractFractaldimensionandShannonentropywereusedtoanalyzethenucleotidefluctuationofdimlightvisionrhodopsingene.Themaximalabsorptionwavelengthsofthestudiedgenesequencesspanarangeof480nmto526nm.ThedinucleotideShannonentropycorrelateswithathemononucleotideShannonentropywithR2of0.99btheCGGCcontentwithR2of0.86N6.TheabsorptionmaximalwavelengthcorrelationwiththeCGGCcontentwasfoundtohaveanR2of0.82forthegenesequenceand0.91forthemRNAsequence.ThefractaldimensionsofthegenesequencesandmRNAsequenceswerefoundtobecorrelatedwithR2of0.78.SelectionpressureontheCGGCcontentatthegeneandmRNAlevelswouldbeaconsistentobservationforphenotypedimlightfunctionality.KeywordscomponentDimlightvisionrhodopsingenerhodopsinmRNAShannondinucleotideentropyfractaldimensioncorrelationI.INTRODUCTIONCloselyrelatedspeciescanbeclassifiedbyacollectionofbioinformaticsmarkerswithnumbersdeterminedfrommathematicaloperationsonDNAsequence.Incaseswheresuchmarkersaresignificantlydifferentfromwhatwouldbeexpectedforrandommutations,wecangetanideaofhowmuchnaturalselectionhasinfluencedtheevolutionofaparticulargene.Itwasreportedrecentlythattherhodopsinswithvariablemaximalabsorptionwavelengthbetween480–525nmhadevolvedatleast18separateoccasions1.RhodopsinisamemberoftheGproteincoupledreceptorGPCRfamilywiththecharacteristicseventransmembranedomainreceptorsandisverysensitivetolight.CrystalstructureandsequencecomparisonofGPCRmembersincludingrhodopsinwasreportedrecently2.Forexample,Reference2reportedthatwatermoleculesinthevicinityofhighlyconservedaminoacidsarebeingusedforstructurestabilization.Conservedregionwouldimplylessrandomnucleotidefluctuationacrossspecies.Here,weanalyzethereporteddimlightvisionrhodopsingeneanditsmRNAsequences,usingnucleotidefrequency,monoanddinucleotideentropy,andfractaldimension.Therelationshipsamongtheabovementionedbioinformaticsmarkersshowssomeevidencethatthereisselectionpressureresultinginasystematicnucleotidefluctuationtrendanditscorrelationwithdimlightfunctionality.Thenucleotidebasepairchangesoveragenesequencecanbeviewedasafluctuationand,consequently,canbeinvestigatedwithstandardtoolsthatincludecorrelationandfractaldimensionanalysis.Forthisstudy,thenumericalsequencerepresentingthefluctuationofnucleotidesinagenesequencewasgeneratedusingtheprotonnumberofeachnucleotide.Nucleotidefluctuationhasbeenstudiedusingotherassignmentschemes3,4,5.TheuseofprotonnumberwasmotivatedpartlybytheobservationofmassfractaldimensionintheXraydataofproteinsandribosomes6,andusingaprotonassignmentschememayrevealprotonsensitivityintheunderlyinggeneticsequencetothefoldinginducedmassfractal.Thisnumericalseriescanthenbeprocessedfurtherusingnumericalmethodssuchasamovingaverage,whichisoftenusedinstockmarkettimeseriesanalysis.Thefractaldimensionofsucharandomseriesorrandomseriesderivedfromtheoriginalatomicnumberbasedsequencecanbecomputed.Arecentcomparisonofhumanandchimpanzeegenomesrevealedthatitispossibletomeasuretheaccelerationrateoftheacceleratedregionsofthehumangenome7.Themostacceleratedregion,HAR1,wasshownbyageneexpressionexperimentinthehumanembryotobetranscriptionactiveandcoexpressedwithreelin,whichisanessentialproteininvolvedinthedevelopmentofthesixlayercortexofthehumanbrain.FractalanalysiswasappliedtotheHAR1nucleotidesequenceandthehomologoussequenceinthechimpanzeegenome8.Analysisshowsthatthedifferencesinfractaldimensioncanbeusedasamarkerofevolution.The118bpinHAR1contains18pointsubstitutionsoveranevolutionaryspanof5millionyearswhencomparingthehumantothechimpanzee.However,thesame118bpregiononlycontainstwopointsubstitutionsoveraspanof300millionyearswhencomparingthechickentothechimpanzee.Theimplicationsofevolutionandpositiveselectionhavebeendiscussedinrecentliterature9.II.METHODSA.GeneticSequenceTheDNAsequencesweredownloadedfromGenbankusingtheaccessionnos.EU407248–EU407253listedinReference1.ThecorrespondingspeciesareAristostomiasscintillansrhodopsinRH1gene1569bp,IdiacanthusantrostomusrhodopsinRH1gene1547bp,ChauliodusmacounirhodopsinRH1gene1608bp,StenobrachiusleucopsarusrhodopsinRH1gene1213bp,LepidopusfitchirhodopsinRH1Agene1438bp,andLepidopusfitchirhodopsinRH1Bgene1286bp.B.HiguchiFractalMethodTheprojectwaspartiallysupportedbyseveralCUNYgrantsandNIHBridgetoBaccalaureateGrantPISchneider9781424447138/10/25.00©2010IEEETheATCGsequencewasconvertedtoanumericalsequencebyassigningtheatomicnumber,thetotalnumberofprotons,ineachnucleotideA70,T66,C58,G78.Theassignednumberisproportionaltothenucleotidemassignoringisotopes.TheATandCGpairsindoublestrandedDNAhavethesamevalueof136.Amongthevariousfractaldimensionmethods,theHiguchifractalmethodiswellsuitedforstudyingsignalfluctuationandhasbeenappliedtonucleotidesequencesasfollows10.ThenumericalsequenceIisusedtogenerateadifferenceseriesIjIifordifferentlags.ThenonnormalizedapparentlengthoftheseriescurveissimplyLkΣ|IjIi|foralljipairsthatequalk.Thenumberoftermsinakseriesvariesandnormalizationmustbeused.Thenormalizationvaluesareinopenliterature11.IftheIiisafractalfunction,thenthelogLkversuslog1/kwillbeastraightlinewiththeslopeequaltothefractaldimension.Higuchiincorporatedacalibrationdivisionstepdivisionbyksuchthatthetheoreticalvalueofthefractaldimension,FD,iscalibratedtotherange1≤FD≤2.Whencomparingthedimensionoftwofractalforms,thepopularmethodoftakingthedifferenceofthetwoHiguchifractaldimensionvaluesisvalidtowithinaconstantregardlessofthecalibrationdivisionstep.TheHiguchifractalalgorithmusedinthisprojectwascalibratedwiththeWeierstrassfunction.ThisfunctionhastheformWxΣanhcos2πanxforallthenvalues0,1,2,3ThefractaldimensionoftheWeierstrassfunctionwasgivenby2hwherehtakesonanarbitraryvaluebetweenzeroandone.TheShannonentropyofasequencecanbeusedtomonitortheleveloffunctionalconstraintsactingonthegene12.AsequencewitharelativelylownucleotidevarietywouldhavelowShannonentropymoreconstraintintermsofthesetof16possibledinucleotidepairs.Asequencesentropycanbecomputedasthesumofpilogpioverallstatesiandtheprobabilitypicanbeobtainedfromtheempiricalhistogramofthe16dinucleotidepairs.Themaximumentropyis4binarybitsperpairfor16possibilities24.Themaximumentropyistwobitspermononucleotidewithfourpossibilities22.III.RESULTSANDDISCUSSIONA.CGdinucleotidefluctationTheCGGCdinucleotidepairpercentagewascalculatedandthecorrelationwiththeShannondinucleotideentropyisdisplayedinFigure1.TheCGGCdinucleotidepairpercentagecorrelationwiththeShannondinucleotideentropywasnotobservedatthemRNAlevel,ascanbeseenfromthelowR2inFigure2.y0.6108x2.534R20.855600.050.10.150.23.93.923.943.963.98dinucleotideentropybitsCGGCFigure1TheCGGCdinucleotidepairpercentageversustheShannondinucleotideentropyforthegenesequences.y599.1x2482.1R20.524400.050.10.150.23.863.883.93.923.943.96dinucleotideentropybitsCGGCFigure2TheCGGCdinucleotidepairpercentageversustheShannondinucleotideentropyforthemRNAsequences.ThevanishingofthecorrelationofentropywithCGGCcontentatthetranscriptionmRNAlevelwouldbeconsistentwiththerequirementofrelativelymorestablebondbetweenCandGtobelesspracticalinamRNA,atemporaryproduct.TherelativelyshortermRNAlengthsforthecorrespondingspeciesareAristostomiasscintillansrhodopsin1041bpbp,Idiacanthusantrostomusrhodopsin1059bpbp,Chauliodusmacounirhodopsin1059bp,Stenobrachiusleucopsarus1038bp,Lepidopusfitchirhodopsin1053bp,andLepidopusfitchi1053bp.y0.4753x0.1064R20.98671.961.971.981.9923.93.923.943.963.98dinucleotideentropybitsmonoentropFigure3TheShannonmonoentropyversusthedinucleotideentropyforthegenesequences.TheShannonmonoentropycorrelationwiththeShannondinucleotideentropywasobservedforboththeentiregenesequencesandatthemRNAlevelwithR20.95Figures3and4.dinucleotidevsmonoentropyy0.5073x0.0164R20.9541.951.961.971.981.993.863.883.93.923.943.96Figure4TheShannonmonoentropyversusthedinucleotideentropyforthemRNAsequences.y0.0009x0.5772R20.82100.050.10.150.2460480500520540wavelengthnmCGGCFigure5ThemaximalabsorptionwavelengthofthegeneversustheCGGCcontentpercentageN5.y0.0009x0.5721R20.905400.050.10.150.2460480500520540wavelengthnmCGGCFigure6ThemaximalabsorptionwavelengthofthemRNAsequenceversustheCGGCcontentpercentage.TheCGGCcontentpercentagecorrelateswellwithdimlightfunctionalityconductedbythemRNAproducts.TheblackdragonfishIdiacanthusantrostomusmaximalabsorptionwavelengthwasnotreportedinReference1andwasomittedintheregressionsuchthatN5.ItappearsthatthereisasystematictrendforincludingtheappropriateCGGCcontentthatspanthe480525nmrange.Reference1reportedthatonly12aminoacidsitesintheopsinproteincanaccountforthevariabilityofwavelengthsensitivityforthesespecies.However,thesechangeshavealmostnoeffectontheCGGCcontentaccountingforlessthan2oftheobservedtrend.Thisindicatesthatsecondaryeffects,suchasgeneexpressionorproteinstability,aretheevolutionaryforcedrivingsmallgradualadaptationsfromtheCGGCviewpoint.B.FractaldimensionfluctationThefractaldimensionFDwascomputedusingtheHiguchimethod.Theslopewastakenusing7datapoints,consistentwithourpreviousreportofnucleotidefluctuation7.ThefractalanalysisresultisshowninFigure7.y1.9792x9.4164R20.999102468103210Ln1/kLnLkFigure7FractaldimensionoftheAristostomiasscintillansrhodopsinRH1genesequenceusingthesevendatapoints.Thesequencehas1569bp.TheyaxiisLnkandthexaxisisLn1/k.ThefractaldimensionofthegenesequenceandmRNAsequenceswerecomputed.FDgenevsFDmRNAy0.6544x0.6878R20.78121.971.9751.981.9851.991.99521.961.971.981.992Figure8FractaldimensionofmRNAsequencexaxisversusfractaldimensionofgenesequenceyaxis.ThefractaldimensionincreaseforfiveofthestudiedmRNAsequenceexceptblackdragonfishIdiacanthusantrostomuswouldbeconsistentwithpreviousobservationthatanexonregiongenerallywouldhavehigherfractaldimensionascomparedtoanoncodingregion13.ThemoderatecorrelationwithRsquareof0.78suggeststhatFDisafairlyrobustparameter.Onthecontrary,thereisverylittlecorrelationintheentropyparameterbetweengeneandmRNAFigure9geneentropyvsmRNAentropyy0.4393x2.169R20.26663.873.883.893.93.913.923.933.943.953.93.923.943.963.98Figure9EntropyofmRNAsequenceyaxisversusentropyofgenesequencexaxis.ThetranscriptionprocesslosesinformationwithlowerentropyforallthestudiedsequenceshoweverthereisnosystematicpatternforentropycorrelationofgenewithmRNA.Thisfurtherreinforcedthatthefractaldimensionwhichmeasuresinformationcapacityisamorerobustparameter.Itwasreportedthatthespectraltuningsitesmaynotbethesameasthefunctionallyconservedsitesimportantfortheproperfunctioningoftheopsin14,15.Thefractaldimensionmaybeameasurerelatedtothefunctionallyconservedsites.IV.CONCLUSIONThefractaldimensionandShannonentropywereusedtoanalyzethenucleotidefluctuationofdimlightvisionrhodopsingene.TranscriptionfromgenetomRNApreservesthefractaldimensioninsuchawaythatthereisamoderatecorrelation.TheabsorptionmaximalwavelengthcorrelationwiththeCGGCcontentwasfoundtohaveanRsquareof0.82forthegenesequenceand0.91forthemRNAsequence.SelectionpressureontheCGGCcontentatthegeneandmRNAlevelswouldbeaconsistentobservationfordimlightphenotypefunctionalityevolutionintherangeof480525nm.FuturestudiesmayincludetheRhodopsinlikegenesintheGproteincoupledreceptorfamily.REFERENCES1ShozoYokoyama,TakashiTada,HuanZhang,andLyleBritt,ElucidationofphenotypicadaptationsMolecularanalysesofdimlightvisionproteinsinvertebrates,PNAS,Vol105,13480–13485,2008.2WorthCL,KleinauG,KrauseG,ComparativeSequenceandStructuralAnalysesofGProteinCoupledReceptorCrystalStructuresandImplicationsforMolecularModels.PLoSONE49e7011.doi10.1371/journal.pone.0007011,20093N.N.OiwaandJ.A.Glazier,Thefractalstructureofthemitochondrialgenomes,PhysicaA,vol311,pp221–230,20024Z.G.Yu,A.Vo,Z.M.GongandS.C.Long,FractalsinDNAsequenceanalysis,ChinesePhysics,vol11,pp13131318,2002.5H.D.Liu,Z.H.Liu,X.Sun,StudiesofHurstIndexforDifferentRegionsofGenes,ICBBE2007,pp238240,20076C.Y.Lee,MassFractalDimensionoftheRibosomeandImplicationofitsDynamicCharacteristics,PhysicalReviewE,vol73,0429013pages,2006.7K.S.Pollard,S.R.Salama,N.Lambert,S.Coppens,J.S.Pedersen,etal.AnRNAgeneexpressedduringcorticaldevelopmentevolvedrapidlyinhumans.Nature,vol443,pp167172,2006.8T.Holden,R.Subramaniam,R.Sullivan,E.Cheung,C.Schneider,G.Tremberger,Jr.,A.Flamholz,D.H.Lieberman,andT.D.Cheung,ATCGnucleotidefluctuationofDeinococcusradioduransradiationgenes,Proc.SPIE,vol6694,669417,10pages,20079PollardKS,SalamaSR,KingB,KernAD,DreszerT,etal.Forcesshapingthefastestevolvingregionsinthehumangenome,PLoSGenet210e168.DOI10.1371/journal.pgen.0020168,200610M.J.Berryman,A.Allison,andD.Abbott,MutualInformationforexaminingcorrelationsinDNA,FluctuationNoiseLetters,vol4,ppL237L246,200411T.Higuchi,Approachtoanirregulartimeseriesonthebasisoffractaltheory,PhysicaD,vol31,277283,199812Parkhomchuk,DV,DinucleotideEntropyasaMeasureofGenomicSequenceFunctionality,arXivqbio/0611059,200613Holden,T.,G.Tremberger,Jr.,P.Marchese,E.Cheung,R.Subramaniam,R.Sullivan,P.Schneider,A.Flamholz,D.Lieberman,T.Cheung,DNAsequencebasedcomparativestudiesofbetweennonextremophileandextremophileorganismswithimplicationsinexobiology,SPIEAstrobiologyConferenceProceedings,Instruments,Methods,andMissionsforAstrobiologyXI,EditorsRichardB.HooverGilbertV.LevinAlexeiY.RozanovPaulC.Davies,70970Q,12pagesinvited,200814YokoyamaS2000.Molecularevolutionofvertebratevisualpigments.ProgressinRetinalandEyeResearch194385–419.15DeebSS,Themolecularbasisofvariationinhumancolorvision.Clinicalgenetics675369–77,2005.

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