Distinct consequences of posttranslational modification by linear versus K63-linked polyubiquitin chains

Polyubiquitin chains mediate a variety of biological processes,ranging from proteasomal targeting to inflammatory signalingand DNA repair. Their functional diversity is in part due to theirability to adopt distinct conformations, depending on how theubiquitin moieties within the chain are linked. We have usedthe eukaryotic replication clamp PCNA, a natural target of lysine(K)63-linked polyubiquitylation, as a model substrate to directlycompare the consequences of modification by different types ofpolyubiquitin chains. We show here that K63-polyubiquitylatedPCNA is not subject to proteasomal degradation. In contrast, linear,noncleavable ubiquitin chains do not promote DNA damage tolerance,but function as general degradation signals. We find that alinear tetraubiquitin chain is sufficient to afford proteasomaltargeting through the Cdc48-Npl4-Ufd1 complex without furthermodification. Although a minimum chain length of four is requiredfor degradation, a longer chain does not further reduce the half-lifeof the respective substrate protein. Our results suggest that thecellular machinery responsible for recognition of ubiquitylatedsubstrates can make subtle distinctions between highly similarforms of the polyubiquitin signal.