SHRED Is a Regulatory Cascade that Reprograms Ubr1 Substrate Specificity for Enhanced Protein Quality Control during Stress

Abstract

When faced with proteotoxic stress, cells mount adaptive responses to eliminate aberrant proteins. Adaptive responses increase the expression of protein folding and degradation factors to enhance the cellular quality control machinery. However, it is unclear whether and how this augmented machinery acquires new activities during stress. Here, we uncover a regulatory cascade in budding yeast that consists of the hydrophilin protein Roq1/Yjl144w, the HtrA-type protease Ynm3/Nma111, and the ubiquitin ligase Ubr1. Various stresses stimulate ROQ1 transcription. The Roq1 protein is cleaved by Ynm3. Cleaved Roq1 interacts with Ubr1, transforming its substrate specificity. Altered substrate recognition by Ubr1 accelerates proteasomal degradation of misfolded as well as native proteins at the endoplasmic reticulum membrane and in the cytosol. We term this pathway stress-induced homeostatically regulated protein degradation (SHRED) and propose that it promotes physiological adaptation by reprogramming a key component of the quality control machinery.

N-degron and C-degron pathways of protein degradation

“…1 and 2 and SI Appendix, Fig. S2A) (22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35)(36)(37)(38)(39)(40)(41). Other studies, in the 1990s and afterward, have also identified many internal degrons, defined as degradation signals whose functionally essential elements do not include either Nt-residues or C-terminal (Ct) residues.…”

“…Pathway. A natural Ct-fragment of S. cerevisiae Roq1 acts as both a substrate and regulator of the Arg/N-degron pathway (41). Tunicamycin, a drug that causes protein misfolding in the endoplasmic reticulum (ER), increases the level of ROQ1 mRNA.…”

“…This cleavage of Roq1 is required for the accelerated degradation of the above reporter. Arg-Roq1 is destroyed, in part, by the Arg/N-degron pathway (41). Remarkably, interactions between Arg-Roq1 and Ubr1 can alter the targeting efficacy of Ubr1 toward its other substrates, such as, for example, Cup9, which bears an internal degron.…”

“…Remarkably, interactions between Arg-Roq1 and Ubr1 can alter the targeting efficacy of Ubr1 toward its other substrates, such as, for example, Cup9, which bears an internal degron. One possibility is that Arg-Roq1 modulates the specificity and efficacy of Ubr1 under conditions of stress (41).…”

Interconversion between Anticipatory and Active GID E3 Ubiquitin Ligase Conformations via Metabolically Driven Substrate Receptor Assembly

“…N-degron (formerly termed "N-end rule") and C-degron (collectively referred to as "terminal degron") E3s recognize substrate N-or C-termini and regulate vast biology (Varshavsky, 2019). Nonetheless, beyond knowledge of pathways creating, exposing, or cloaking substrate N-or C-degrons, and structures showing their recognition by E3 ligases, there is limited structural information explaining regulation of terminal degron E3s (Brower et al, 2013;Choi et al, 2010;Dong et al, 2018;Hu et al, 2005;Koren et al, 2018;Lin et al, 2018;Matta-Camacho et al, 2010;Rao et al, 2001;Rusnac et al, 2018;Shemorry et al, 2013;Szoradi et al, 2018;Timms et al, 2019;Varshavsky, 2011;Wang et al, 2008). Moreover, Fbp1, Mdh2, and Icl1 each harbor natively exposed GID E3-targeting N-terminal prolines essential for their degradation (Hammerle et al, 1998).…”