Protein and DNA Sequence Determinants of Thermophilic Adaptation 英文参考文献.docVIP

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Protein and DNA Sequence Determinants of Thermophilic Adaptation 英文参考文献.doc

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Protein and DNA Sequence Determinants of Thermophilic Adaptation 英文参考文献

ProteinandDNASequenceDeterminants ofThermophilicAdaptation Konstantin B.Zeldovich, Igor N.Berezovsky, Eugene I.Shakhnovich* DepartmentofChemistryandChemicalBiology,HarvardUniversity,Cambridge,Massachusetts,UnitedStatesofAmerica Therehavebeenconsiderableattemptsinthepasttorelatephenotypictrait—habitattemperatureoforganisms—to theirgenotypes,mostimportantlycompositionsoftheirgenomesandproteomes.However,despiteaccumulationof anecdotal evidence, an exact and conclusive relationship between the former and the latter has been elusive. We present an exhaustive study of the relationship between amino acid composition of proteomes, nucleotide composition of DNA, and optimal growth temperature (OGT) of prokaryotes. Based on 204 complete proteomes of archaeaandbacteriaspanningthetemperaturerangefromà108Cto1108C,weperformedanexhaustiveenumeration ofallpossiblesetsofaminoacidsandfoundasetofaminoacidswhosetotalfractioninaproteomeiscorrelated,toa remarkableextent,withtheOGT.TheuniversalsetisIle,Val,Tyr,Trp,Arg,Glu,Leu(IVYWREL),andthecorrelation coefficient is as high as 0.93. We also found that the GtC content in 204 complete genomes does not exhibit a significantcorrelationwithOGT(R?à0.10).Ontheotherhand,thefractionofAtGincodingDNAiscorrelatedwith temperature,toaconsiderableextent,duetocodonpatternsofIVYWRELaminoacids.Further,wefoundstrongand independentcorrelationbetweenOGTandthefrequencywithwhichpairsofAandGnucleotidesappearasnearest neighbors in genome sequences. This adaptation is achieved via codon bias. These findings present a direct link betweenprinciplesofproteinsstructureandstabilityandevolutionarymechanismsofthermophylicadaptation.On thenucleotidelevel,theanalysisprovidesanexampleofhownatureutilizescodonbiasforevolutionaryadaptationto extreme conditions. Together these results provide a complete picture of how compositions of proteomes and genomesinprokaryotesadjusttotheextremeconditionsoftheenvironment. Citation:ZeldovichKB,BerezovskyIN,ShakhnovichEI(2007)Proteinan