Expression Profiles Reveal Parallel Evolution of Epistatic Interactions Involving the CRP Regulon in Escherichia coli 英文参考文献.docVIP

ExpressionProfilesRevealParallelEvolution ofEpistaticInteractionsInvolvingtheCRP ReguloninEscherichiacoli Tim F.Cooper1*,Susanna K.Remold2,Richard E.Lenski3,Dominique Schneider4,5 1DepartmentofBiologyandBiochemistry,UniversityofHouston,Houston,Texas,UnitedStatesofAmerica,2DepartmentofBiology,UniversityofLouisville,Louisville, Kentucky,UnitedStatesofAmerica,3DepartmentofMicrobiologyandMolecularGenetics,MichiganStateUniversity,EastLansing,Michigan,UnitedStatesofAmerica,4 LaboratoireAdaptationetPathoge′niedesMicro-organismes,Universite′ JosephFourierGrenoble1,Grenoble,France, 5CNRSUMR5163,Grenoble,France The extent and nature of epistatic interactions between mutations are issues of fundamental importance in evolutionary biology. However, they are difficult to study and their influence on adaptation remains poorly understood.Here,weuseasystems-levelapproachtoexamineepistaticinteractionsthataroseduringtheevolutionof Escherichiacoliinadefinedenvironment.Weusedexpressionarraystocomparetheeffectonglobalpatternsofgene expressionofdeletingacentralregulatorygene,crp.Effectsweremeasuredintwolineagesthathadindependently evolvedfor20,000generationsandintheircommonancestor.Wefoundthatdeletingcrphadamuchmoredramatic effectontheexpressionprofileofthetwoevolvedlinesthanontheancestor.Becausethesequenceofthecrpgene wasunchangedduringevolution,thesedifferencesindicateepistaticinteractionsbetweencrpandmutationsatother loci that accumulated during evolution. Moreover, a striking degree of parallelism was observed between the two independentlyevolvedlines;115genesthatwerenotcrp-dependentintheancestorbecamedependentoncrpinboth evolved lines. An analysis of changes in crp dependence of well-characterized regulons identified a number of regulatory genes as candidates for harboring beneficial mutations that could account for these parallel expression changes. Mutations within three of these genes have previously been found and shown to contribute to fitness. Overall,thesefindings