General Rules for Optimal Codon Choice 英文参考文献.docVIP

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General Rules for Optimal Codon Choice 英文参考文献.doc

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General Rules for Optimal Codon Choice 英文参考文献

GeneralRulesforOptimalCodonChoice RuthHershberg*,DmitriA.Petrov DepartmentofBiology,StanfordUniversity,Stanford,California,UnitedStatesofAmerica Abstract Differentsynonymouscodonsarefavoredbynaturalselectionfortranslationefficiencyandaccuracyindifferentorganisms. Therulesgoverningtheidentitiesoffavoredcodonsindifferentorganismsremainobscure.Infact,itisnotknownwhether such rules exist or whether favored codons are chosen randomly in evolution in a process akin to a series of frozen accidents.Here,westudythisquestionbyidentifyingforthefirsttimethefavoredcodonsin675bacteria,52archea,and10 fungi.Weuseanumberofteststoshowthattheidentifiedcodonsareindeedlikelytobefavoredandfindthatacrossall studiedorganismstheidentityoffavoredcodonstrackstheGCcontentofthegenomes.OncetheeffectofthegenomicGC contentonselectivelyfavoredcodonchoiceistakenintoaccount,additionaluniversalaminoacidspecificrulesgoverning theidentityoffavoredcodonsbecomeapparent.Ourresultsprovideforthefirsttimeaclearsetofrulesgoverningthe evolutionofselectivelyfavoredcodonusage.Basedontheseresults,wedescribeaputativescenarioforhowevolutionary shiftsintheidentityofselectivelyfavoredcodonscanoccurwithouteventemporaryweakeningofnaturalselectionfor codonbias. Citation:HershbergR,PetrovDA(2009)GeneralRulesforOptimalCodonChoice.PLoSGenet5(7):e1000556.doi:10.1371/journal.pgen.1000556 Editor:MichaelW.Nachman,UniversityofArizona,UnitedStatesofAmerica ReceivedJanuary27,2009;AcceptedJune10,2009;PublishedJuly10,2009 Copyright:?2009Hershberg,Petrov.Thisisanopen-accessarticledistributedunderthetermsoftheCreativeCommonsAttributionLicense,whichpermits unrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited. Funding:RHwassupportedbyfellowshipfromtheStanfordGenomeTrainingprogram(SGTP).TheworkwasalsosupportedbytheNIHgrantsGM077368and HG002568-07toDAP.Thefundershadnoroleinstudydesign,datacollectionandanalysis,decisiontopublish,orpreparationofthemanuscript. CompetingInterests:Theauthorsha