Mechanism, functions and conservation of SHRED, a novel pathway regulating protein quality control

蛋白质需要正确折叠以实现其功能。各种应激条件导致错误折叠蛋白质的积累，这对正常细胞功能构成严重威胁。质量控制机制确保错误折叠的蛋白质被识别和消除。我们最近在芽殖酵母中发现了一种新的调节途径，通过重新编程泛素连接酶Ubr 1的底物特异性来促进有效的蛋白质质量控制。我们将这一途径称为应激诱导的稳态调节蛋白降解（SHRED）。当压力增强ROQ 1基因的转录时，SHRED被激活。Roq 1蛋白被蛋白酶Ynm 3切割，导致Roq 1的新N-末端暴露带正电荷的精氨酸残基。通过这个精氨酸残基，裂解Roq 1与Ubr 1中的底物结合位点相互作用，该位点通常识别带正电荷的N-末端残基的底物，作为N-末端规则途径的一部分。Roq 1结合的Ubr 1加速蛋白酶体对错误折叠蛋白的降解，并增加细胞对蛋白错误折叠的抵抗力。此外，Ubr 1重编程的SHRED促进某些天然的，折叠良好的蛋白质的降解，这表明SHRED在生理适应过程中的蛋白质组重塑中有额外的作用。这些发现提出了许多新的问题，包括Roq 1是作为一种变构调节剂还是作为一种底物适配器，SHRED对其他细胞过程的影响以及SHRED是否存在于高等真核生物中。具体而言，我们的目标是（1）阐明通过体外重建和结构研究的途径的精确分子机制，（2）获得一个广泛的认识SHRED在芽殖酵母中的功能，（3）确定一个假定的SHRED途径在哺乳动物。这些调查承诺一般新的见解，泛素连接酶的调节和质量控制。此外，它们可能最终实现用于治疗目的的蛋白质质量控制的药理学操作。

Proteins need to fold properly in order to fulfill their functions. Various stress conditions result in an accumulation of misfolded proteins, which pose a serious threat to normal cell function. Quality control mechanisms ensure that misfolded proteins are recognized and eliminated. Failure to clear misfolded proteins leads to disease, including neurodegenerative disorders.We have recently discovered a novel regulatory pathway in budding yeast that promotes efficient protein quality control by reprograming the substrate specificity of the ubiquitin ligase Ubr1. We have termed this pathway stress-induced homeostatically regulated protein degradation (SHRED). SHRED is activated when stress enhances transcription of the ROQ1 gene. The Roq1 protein is cleaved by the protease Ynm3, leading to exposure of a positively charged arginine residue at the new N-terminus of Roq1. By means of this arginine residue, cleaved Roq1 interacts with a substrate binding site in Ubr1 that normally recognizes substrates with positively charged N-terminal residues as part of the N-end rule pathway. Roq1-bound Ubr1 accelerates degradation of misfolded proteins by the proteasome and increases cellular resistance to protein misfolding. Furthermore, Ubr1 reprogramming by SHRED promotes the degradation of certain native, well-folded proteins, suggesting that SHRED has additional roles in proteome remodelling during physiological adaptation. These findings raise many new questions, including whether Roq1 acts as an allosteric regulator or as a substrate adaptor, which other cellular processes are influenced by SHRED and whether SHRED exists in higher eukaryotes.The goal of our proposed research is a comprehensive understanding of the mechanism, functions and evolutionary conservation of SHRED. Specifically, we aim to (1) elucidate the precise molecular mechanism of the pathway through in vitro reconstitution and structural studies, (2) gain a broad appreciation of the functions of SHRED in budding yeast, and (3) identify a putative SHRED pathway in mammals. These investigations promise general new insights into the regulation of ubiquitin ligases and quality control. Furthermore, they may ultimately enable pharmacological manipulation of protein quality control for therapeutic purposes.