HSP70-binding motifs function as protein quality control degrons

Abstract

Protein quality control (PQC) degrons are short protein segments that target misfolded proteins for proteasomal degradation, and thus protect cells against the accumulation of potentially toxic non-native proteins. Studies have shown that PQC degrons are hydrophobic and rarely contain negatively charged residues, features which are shared with chaperone-binding regions. Here we explore the notion that chaperone-binding regions may function as PQC degrons. When directly tested, we found that a canonical Hsp70-binding motif (the APPY peptide) functioned as a dose-dependent PQC degron both in yeast and in human cells. In yeast, Hsp70, Hsp110, Fes1, and the E3 Ubr1 target the APPY degron. Screening revealed that the sequence space within the chaperone-binding region of APPY that is compatible with degron function is vast. We find that the number of exposed Hsp70-binding sites in the yeast proteome correlates with a reduced protein abundance and half-life. Our results suggest that when protein folding fails, chaperone-binding sites may operate as PQC degrons, and PQC-linked degradation therefore overlaps in specificity with chaperone binding. This sheds new light on how the PQC system has evolved to exploit the intrinsic capacity of chaperones to recognize misfolded proteins, thereby placing them at the nexus of protein folding and degradation. Significance StatementIt is broadly accepted that misfolded proteins are often rapidly degraded by the ubiquitin-proteasome system, but how cells specifically recognize this immensely diverse group of proteins is largely unknown. Here we show that upon uncoupling of protein folding from protein degradation, a canonical chaperone-binding motif doubles as a degradation signal (degron), and that within the context of a Hsp70-binding region, many sequences are compatible with degron function. We find that degradation is correlated with the number of Hsp70-binding sites within a protein, and that the number of exposed Hsp70-binding sites in the yeast proteome correlates with more rapid degradation.