Rapid Changes in Gene Expression Dynamics in Response to Superoxide Reveal SoxRS-Dependent and Independent Transcriptional Networks 英文参考文献.docVIP

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Rapid Changes in Gene Expression Dynamics in Response to Superoxide Reveal SoxRS-Dependent and Independent Transcriptional Networks 英文参考文献.doc

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Rapid Changes in Gene Expression Dynamics in Response to Superoxide Reveal SoxRS-Dependent and Independent Transcriptional Networks 英文参考文献

RapidChangesinGeneExpressionDynamicsin ResponsetoSuperoxideRevealSoxRS-Dependentand IndependentTranscriptionalNetworks JeffreyL.Blanchard1*,Wei-YunWholey1¤,ErinM.Conlon2,PabloJ.Pomposiello1 1DepartmentofMicrobiology,UniversityofMassachusetts,Amherst,Massachusetts,UnitedStatesofAmerica,2DepartmentofMathematicsand Statistics,UniversityofMassachusetts,Amherst,Massachusetts,UnitedStatesofAmerica Background. SoxR and SoxS constitute an intracellular signal response system that rapidly detects changes in superoxide levels and modulates gene expression in E. coli. A time series microarray design was used to identify co-regulated SoxRS- dependent and independent genes modulated by superoxide minutes after exposure to stress. Methodology/Principal Findings.soxSmRNAlevelssurgedtonearmaximallevelswithinthefirstfewminutesofexposuretoparaquat,asuperoxide- producing compound, followed by a rise in mRNA levels of known SoxS-regulated genes. Based on a new method for determiningthebiologicalsignificanceofclusteringresults,atotalof138genicregions,includingseveraltranscriptionfactors andputativesRNAswereidentifiedasbeingregulatedthroughtheSoxRSsignalingpathwaywithin10minutesofparaquat treatment. A statistically significant two-block SoxS motif was identified through analysis ofthe SoxS-regulated genes. The SoxRS-independentresponseincludedmembersoftheOxyR,CysB,IscR,BirAandFurregulons.Finally,therelativesensitivity to superoxide was measured in 94 strains carrying deletions in individual, superoxide-regulated genes. Conclusions/ Significance.Byintegratingourmicroarraytimeseriesresultswithothermicroarraydata,E.colidatabasesandtheprimary literature,weproposeamodeloftheprimarytranscriptionalresponsecontaining226protein-codingandsRNAsequences. FromtheSoxSdependentnetworkthefirststatisticallysignificantSoxS-relatedmotifwasidentified. Citation: Blanchard JL, Wholey W-Y, Conlon EM, Pomposiello PJ (2007) Rapid Changes in Gene Expression Dynamics in Response to Superoxide RevealSoxRS-Depen