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Page 187: Here - European Bioinformatics Institute

The6thInternationalBiocurationConference

184Integrationofthetranscriptionalregulationofcarbonsources,inEscherichialcoliK‐12,withtheircentralmetabolismandothercellularsystems

Peralta‐GilM.,Ledezma‐TejeidaD.,Gama‐CastroS.,Santos‐ZavaletaA.andCollado‐VidesJ.

UNAM,Mexico

Presenter:DanielaLedezma‐Tejeida

RegulonDBisadatabasethatintegratesmainlythebiologicalknowledgeofthemechanismsthatregulatetranscriptioninitiationinEscherichiacoliand,eventually,theknowledgeonitscompleteregulatorynetwork.Thus,wehavefolloweddifferentstrategiesinordertobetterdescribethecomplexityofthebiologywithinthedatabase,suchascuratingbypublicationdate,onthebasesofregulonsandsigmulons,byfunctionalclass,bybiologicalsystem,bybindingsitesofaparticulartranscriptionfactor(TF),includingotherregulatorymechanisms,andfinallybyelementarygeneticsensoryresponseunit,orGensorunit(GU).Inthissense,toattainanunderstandingofbacterialmetabolicadaptationstocarbonsourceavailability,currentlywehavecuratedabout40regulonsrelatedtocarbonsourceutilization,andwehavediagrammed15GUsinvolvedintheuptakeanddegradationofdifferentcarbonsources.OurmaingoalofthisspecificintegrationistofacilitateunderstandingofE.colimetabolicadaptationstocarbonsourceavailabilityandthecouplingbetweenthedifferentgeneticregulatorylayerswithinthecentralmetabolism.Weareintegratingandmodelingtheinformationonthemetabolicpathwaysforthedifferentcarbonsourceswiththeavailableinformationatthemolecularlevel,includingtheinterplaybetweentranscriptionalregulationandregulatorymechanisms,suchasallostericinteractionsandtheeffectsofsecondaryproducts.Thus,theseinteractionsatthemolecularlevelleadtoadjustmentsinmetabolismbetweenglycolyticandgluconeogeniccarbonsourcesandtheefficientadaptationbetweentheelectrontransportchain,differenttwo‐componentsystems,andtheacidstressresponse,amongothercellularsystems.Theunifiedviewoftransport,metabolismandgeneregulationhelptobetterunderstandbothmetabolismandtheregulationadaptationtoalternativecarbonsourcesencodedinthegenomeofE.coliK‐12.