A trio of ubiquitin ligases sequentially drives ubiquitylation and autophagic degradation of dysfunctional yeast proteasomes

As central effectors of ubiquitin (Ub)-mediated proteolysis, proteasomes are regulated at multiple levels, including degradation of unwanted or dysfunctional particles via autophagy (termed proteaphagy). In yeast, inactive proteasomes are exported from the nucleus, sequestered into cytoplasmic aggresomes via the Hsp42 chaperone, extensively ubiquitylated, and then tethered to the expanding phagophore by the autophagy receptor Cue5. Here, we demonstrate the need for ubiquitylation driven by the trio of Ub ligases (E3s), San1, Rsp5, and Hul5, which together with their corresponding E2s work sequentially to promote nuclear export and Cue5 recognition. Whereas San1 functions prior to nuclear export, Rsp5 and Hul5 likely decorate aggresome-localized proteasomes in concert. Ultimately, topologically complex Ub chain(s) containing both K48 and K63 Ub-Ub linkages are assembled, mainly on the regulatory particle, to generate autophagy-competent substrates. Because San1, Rsp5, Hul5, Hsp42, and Cue5 also participate in general proteostasis, proteaphagy likely engages a fundamental mechanism for eliminating inactive/misfolded proteins.

Automated summary

Proteasomes, as central effectors of ubiquitin-mediated proteolysis, are regulated by multiple levels including proteaphagy, a mechanism that degrades unwanted or dysfunctional particles via autophagy. This study demonstrated the importance of ubiquitylation driven by the trio of Ub ligases (E3s), San1, Rsp5, and Hul5, in promoting nuclear export and recognition by the autophagy receptor Cue5. The study also highlighted the assembly of topologically complex Ub chains on the regulatory particle, allowing for the generation of autophagy-competent substrates. Overall, proteaphagy appears to be a fundamental mechanism for eliminating inactive or misfolded proteins.