Alternative systems for misfolded protein clearance: life beyond the proteasome

Protein misfolding is a major driver of ageing‐associated frailty and disease pathology. Although all cells possess multiple, well‐characterised protein quality control systems to mitigate the toxicity of misfolded proteins, how they are integrated to maintain protein homeostasis (‘proteostasis’) in health—and how their disintegration contributes to disease—is still an exciting and fast‐paced area of research. Under physiological conditions, the predominant route for misfolded protein clearance involves ubiquitylation and proteasome‐mediated degradation. When the capacity of this route is overwhelmed—as happens during conditions of acute environmental stress, or chronic ageing‐related decline—alternative routes for protein quality control are activated. In this review, we summarise our current understanding of how proteasome‐targeted misfolded proteins are retrafficked to alternative protein quality control routes such as juxta‐nuclear sequestration and selective autophagy when the ubiquitin–proteasome system is compromised. We also discuss the molecular determinants of these alternative protein quality control systems, attempt to clarify distinctions between various cytoplasmic spatial quality control inclusion bodies (e.g., Q‐bodies, p62 bodies, JUNQ, aggresomes, and aggresome‐like induced structures ‘ALIS’), and speculate on emerging concepts in the field that we hope will spur future research—with the potential to benefit the rational development of healthy ageing strategies.