Cdc48/p97 promotes degradation of aberrant nascent polypeptides bound to the ribosome

Abstract

Ubiquitin-dependent proteolysis can initiate at ribosomes for myriad reasons including misfolding of a nascent chain or stalling of the ribosome during translation of mRNA. Clearance of a stalled complex is required to recycle the ribosome for future use. Here we show that the ubiquitin (Ub) pathway segregase Cdc48/p97 and its adaptors Ufd1-Npl4 participate in ribosome-associated degradation (RAD) by mediating the clearance of ubiquitinated, tRNA-linked nascent peptides from ribosomes. Through characterization of both endogenously-generated and heterologous model substrates for the RAD pathway, we conclude that budding yeast Cdc48 functions downstream of the Ub ligases Ltn1 and Ubr1 to release nascent proteins from the ribosome so that they can be degraded by the proteasome. Defective RAD could contribute to the pathophysiology of human diseases caused by mutations in p97.DOI: http://dx.doi.org/10.7554/eLife.00308.001

Structural basis for translational surveillance by the large ribosomal subunit-associated protein quality control complex

“…5). Subsequently, downstream cofactors would extract and deliver stalled chains to the proteasome for degradation (7)(8)(9). Such a mechanism ensures that stalled nascent chains encoded by defective messages are promptly recognized and dealt with before being released and posing harm to the cell.…”

“…S7). Whereas tRNA would not be expected to be found associated with the P site in free 60S subunits, unhydrolyzed peptidyl-tRNA is a product of defective translation termination (5) and has been shown to accumulate in the absence of Ltn1 function (8), suggesting that it can be targeted by Ltn1-mediated ubiquitylation and degradation. We thus presume the Tae2-bound P-tRNA shown in Fig.…”

“…Mutation of the Ltn1 mouse ortholog, listerin, causes neurodegeneration (6), suggesting an important function for this process. Ltn1 works together with several cofactors as part of the ribosome-associated quality control complex (RQC) (7)(8)(9) and appears to first associate with nascent chain-stalled 60S subunits together with two proteins of unknown function, Tae2 and Rqc1 (7,9). Ltn1-mediated ubiquitylation of the stalled polypeptide then results in the recruitment of the AAA ATPase Cdc48/p97/ VCP.…”

“…Ltn1-mediated ubiquitylation of the stalled polypeptide then results in the recruitment of the AAA ATPase Cdc48/p97/ VCP. This recruitment also requires Rqc1 and Tae2, and is followed by Cdc48-mediated nascent chain extraction and delivery to the proteasome for degradation (7)(8)(9).…”

Profiling human protein degradome delineates cellular responses to proteasomal inhibition and reveals a feedback mechanism in regulating proteasome homeostasis

“…Particularly, the N-end rule, a classic pathway in the ubiquitin-proteasome system (UPS), relates the in vivo half-lives of the proteins to the identities of their N-terminal destabilizing residues (termed as N-degrons) [18][19][20]. The N-degrons are known to mediate degradation of substrates that regulate many fundamental biological processes including cell signaling, apoptosis, embryonic development, neurodegeneration, peptide import and protein quality control [21][22][23][24][25]. The functionality of N-degrons could be severely compromised if repositioned elsewhere in the proteins.…”