UsingUbiquitinbinderstodeciphertheUbiquitinCodeMichaelMattern1#,JamesSutherland2#,KarteekKadimisetty3,RosaBarrio2,ManuelS.Rodriguez4*1ProgenraInc.,277GreatValleyParkway,Malvern19355,Pennsylvania,USA2CICbioGUNE,TechnologyParkofBizkaia,Bldg.801A,48160Derio,Spain3LifeSensorsInc.,271GreatValleyParkway,Malvern19355,Pennsylvania,USA4ITAV-IPBS-UPSCNRSUSR3505,1placePierrePotier,OncopoleentréeB,31106Toulouse,France#Equalcontribution*Correspondingauthor:Manuel.RODRIGUEZ@itav.frKeywords:Ubiquitin-codeUBDsTUBEsAffimersProteolysisSignalingUPSALSAbstractPost-translationalmodifications(PTMs)byubiquitin(Ub)areversatile,highlydynamic,andinvolvedinnearlyallaspectsofeukaryotebiologicalfunction.ThereversibilityandheterogeneityofUbchainsattachedtoproteinsubstrateshavecomplicatedtheirisolation,quantification,andcharacterization.Strategieshaveemergedtoisolateendogenousubiquitylatedtargets,includingtechnologiesbasedontheuseofUb-bindingpeptides,suchasTUBEs(Tandem-repeatedUbiquitin-BindingEntities).TUBEsallowtheidentificationandcharacterizationofubiquitinchains,novelsubstratesfordeubiquitylases(DUBs)andUbligases(E3s).Herewereviewtheirimpactonpurification,analysisofpanorchain-selectivepolyubiquitylatedproteinsandunderlinethebiologicalrelevanceofthisinformation.TogetherwithpeptideaptamersandotherUbaffinity-basedapproaches,TUBEswillcontributetounravellingthesecretsoftheUb-code.TheComplexityoftheUbiquitinCodeUbiquitinationofproteinsisasignificantregulatoryprocessthataffectsalmostallcellularfunctions.Ubiquitin(Ub)isasmall,compact,andhighlyconserved76aminoacidprotein.TheC-terminusofUbisattachedbyanisopeptidebondtotheƐ-aminogroupoflysineresiduesontargetproteins.AfterUbisattachedtoaprotein,thisproximalUbcanactasasubstrateforadditionalUbs,whichareconjugatedtoanyofitssevenlysineresidues(K6,K11,K27,K29,K33,K48,andK63)ortoitsN-terminalmethionine(M1)[1].Proteinubiquitylationwasfirstdescribedasasignalforproteasomaldegradation.ThesocalledUb-proteasomesystem(UPS)(seeGlossary)usesmainlyK48andK11polyubiq...
