biostudies-literatureUnknown11(7)Ossareh-Nazari BUbiquitin-dependent processes can be antagonized by substrate-specific deubiquitination enzymes involved in many cellular functions. In this study, we show that the yeast Ubp3-Bre5 deubiquitination complex interacts with both the chaperone-like Cdc48, a major actor of the ubiquitin and proteasome system, and Ufd3, a ubiquitin-binding cofactor of Cdc48. We observed that these partners are required for the Ubp3-Bre5-dependent and starvation-induced selective degradation of yeast mature ribosomes, also called ribophagy. By contrast, proteasome-dependent degradation does not participate in this process. Our data favour the idea that these factors cooperate to recognize and deubiquitinate specific substrates of ribophagy before their vacuolar degradation.EMBO reports548-54https://www.ebi.ac.uk/biostudies/studies/S-EPMC2897114biostudies-literatureCdc48 and Ufd3, new partners of the ubiquitin protease Ubp3, are required for ribophagy.PMC2897114Schaeffer CDelalande FVan Dorsselaer ADargemont CCohen MDokudovskaya SBonizec MOssareh-Nazari BfalseCdc48 and Ufd3, new partners of the ubiquitin protease Ubp3, are required for ribophagy.Ubiquitin-dependent processes can be antagonized by substrate-specific deubiquitination enzymes involved in many cellular functions. In this study, we show that the yeast Ubp3-Bre5 deubiquitination complex interacts with both the chaperone-like Cdc48, a major actor of the ubiquitin and proteasome system, and Ufd3, a ubiquitin-binding cofactor of Cdc48. We observed that these partners are required for the Ubp3-Bre5-dependent and starvation-induced selective degradation of yeast mature ribosomes, also called ribophagy. By contrast, proteasome-dependent degradation does not participate in this process. Our data favour the idea that these factors cooperate to recognize and deubiquitinate specific substrates of ribophagy before their vacuolar degradation.2010-01-01T00:00:00Z2010 Jul2025-04-05T12:23:21.949Z2019-03-27T00:32:07ZS-EPMC28971142050864310.1038/embor.2010.74