Regulation of proteasome activation by a ubiquitin-independent feedback mechanism

Abstract

The ubiquitin-proteasome system is the major pathway for selective protein degradation in eukaryotic cells. Some proteins are degraded by the proteasome without ubiquitination, but the prevalence and underlying mechanisms remain poorly understood. Here, we use pulsed-SILAC proteomics to systematically identify proteins undergoing ubiquitin-independent proteasomal degradation (UbInPD). We identify the paralogous proteasome activation factors ZFAND5 and ZFAND6 (ZFAND5/6) and show that ZFAND5 contains a ubiquitin-independent degron that can both promote its rapid turnover and allosterically activate the proteasome. These findings support a model in which proteasome activation and activator degradation are coupled through a ubiquitin-independent feedback mechanism. We further show that ZFAND5/6, together with the scaffold protein p62, restrain NF-{kappa}B activation in the TLR4 pathway. We link this regulation to the degradation of UBCH5c, an abundant E2 ubiquitin-conjugating enzyme that can initiate or prime ubiquitin chain synthesis. Our findings expand the known landscape of UbInPD and reveal unexpected links between proteasome activation, E2 enzyme regulation, and inflammatory signalling.