Disorder Targets Misorder in Nuclear Quality Control Degradation: A Disordered Ubiquitin Ligase Directly Recognizes Its Misfolded Substrates

Abstract

Summary Protein quality control (PQC) degradation systems protect the cell from the toxic accumulation of misfolded proteins. Because any protein can become misfolded, these systems must be able to distinguish abnormal proteins from normal ones, yet be capable of recognizing the wide variety of distinctly shaped misfolded proteins they are likely to encounter. How individual PQC degradation systems accomplish this remains an open question. Here we show that the yeast nuclear PQC ubiquitin ligase San1 directly recognizes its misfolded substrates via intrinsically disordered N- and C-terminal domains. These disordered domains are punctuated with small segments of order and high sequence conservation that serve as substrate-recognition sites San1 uses to target its different substrates. We propose that these substrate-recognition sites, interspersed among flexible, disordered regions, provide San1 an inherent plasticity that allows it to bind its many, differently shaped misfolded substrates.

Two functionally distinct E2/E3 pairs coordinate sequential ubiquitination of a common substrate in Caenorhabditis elegans development

“…Final plasmids were sequenced to verify that the fusion constructs were correct. Y2H assays were performed as described previously (45). Serial dilutions of yeast cells expressing fusions with GAD and GBD fusions were spotted onto selective media (-His, -Leu, -Trp) to assess interactions and onto nonselective media (-Leu, -Trp) with histidine to control for spotting efficiency.…”

Proteostasis impairment in protein-misfolding and -aggregation diseases

“…Besides specific roles in histone remodeling, the nuclear chaperone machinery is therefore mainly involved in conformational protein maintenance and in the degradation of misfolded proteins. The nucleus is highly enriched in proteasome complexes [111] and contains specific ubiquitin ligases dedicated to quality control [112,113]. During stress, import of most proteins into the nucleus is reduced but additional chaperones and proteasome complexes enter using specific import factors [114].…”

Ubiquitin-Dependent Sorting in Endocytosis

“…These include Ubr1/2, UBE3A, and Cul5; however, their contribution to plasma membrane quality control has not been addressed (Okiyoneda et al 2011). There are also precedents for chaperone-independent recognition of non-native client protein as exemplified by CHIP, Hrd1, and San1 activity in the cytoplasm, ER, and nucleus, respectively (Rosser et al 2007;Kanehara et al 2010;Rosenbaum et al 2011). Substrate recognition by San1 is catalyzed by intrinsically disordered amino-and carboxy-terminal domains with embedded conserved recognition motifs (Rosenbaum et al 2011).…”

“…There are also precedents for chaperone-independent recognition of non-native client protein as exemplified by CHIP, Hrd1, and San1 activity in the cytoplasm, ER, and nucleus, respectively (Rosser et al 2007;Kanehara et al 2010;Rosenbaum et al 2011). Substrate recognition by San1 is catalyzed by intrinsically disordered amino-and carboxy-terminal domains with embedded conserved recognition motifs (Rosenbaum et al 2011). It is conceivable that multiple ligases are involved in plasma membrane quality control, each with an overlapping set of possible substrates.…”