A Potential Mechanism for Targeting Aggregates With Proteasomes and Disaggregases in Liquid Droplets

Abstract

Insoluble protein deposits are hallmarks of neurodegenerative disorders and common forms of dementia. The aberrant aggregation of misfolded proteins involves a complex cascade of events that occur over time, from the cellular to the clinical phase of neurodegeneration. Declining neuronal health through increased cell stress and loss of protein homeostasis (proteostasis) functions correlate with the accumulation of aggregates. On the cellular level, increasing evidence supports that misfolded proteins may undergo liquid-liquid phase separation (LLPS), which is emerging as an important process to drive protein aggregation. Studying, the reverse process of aggregate disassembly and degradation has only recently gained momentum, following reports of enzymes with distinct aggregate-disassembly activities. In this review, we will discuss how the ubiquitin-proteasome system and disaggregation machineries such as VCP/p97 and HSP70 system may disassemble and/or degrade protein aggregates. In addition to their canonically associated functions, these enzymes appear to share a common feature: reversibly assembling into liquid droplets in an LLPS-driven manner. We review the role of LLPS in enhancing the disassembly of aggregates through locally increasing the concentration of these enzymes and their co-proteins together within droplet structures. We propose that such activity may be achieved through the concerted actions of disaggregase machineries, the ubiquitin-proteasome system and their co-proteins, all of which are condensed within transient aggregate-associated droplets (TAADs), ultimately resulting in aggregate clearance. We further speculate that sustained engagement of these enzymatic activities within TAADs will be detrimental to normal cellular functions, where these activities are required. The possibility of facilitating endogenous disaggregation and degradation activities within TAADs potentially represents a novel target for therapeutic intervention to restore protein homeostasis at the early stages of neurodegeneration.

Crosstalk between Biomolecular Condensates and Proteostasis

“…In an elegant autoregulation mechanism, the binding of ubiquitinated substrates causes UBQLN2 to dissociate from SGs back into the cytoplasm, directing its bound substrates to degradation [ 20 , 32 , 78 ]. It is interesting to hypothesize that SGs’ liquid-like environment is a niche that is biochemically favorable for handling UPS and also HSP70-DNAJ client proteins [ 79 ]. Furthermore, ubiquitin conjugation and an autophagic flux are required for degradation of misfolded proteins.…”

Quantitative super-resolution imaging of pathological aggregates reveals distinct toxicity profiles in different synucleinopathies

“…Using HEK293A cells, these invasive aggregates can be distinguished from fibrils, which are prevented from entering the cell by the plasma membrane. We further provide evidence that membrane-permeabilizing aggregates are targeted inside the cell by proteasomes, which concentrate locally into foci, probably as part of wider mechanisms to remove harmful agents ( 74 ). Given their size, it is possible that aggregate 450nm may be fragments of amyloid fibrils.…”

“…We recently proposed a putative cellular ability to reversibly increase local proteasome concentration and thereby degradation activity through assembly of “transient aggregate-associated droplets (TAADs)” ( 74 ). The observed colocalization between aggregates and proteasome foci is largely in agreement with the description of TAADs.…”

Reversible protein assemblies in the proteostasis network in health and disease

“…Aggregates consist of proteins at least in part in non-native states and involve stable intramolecular molecular interactions ( Figure 2B ). These non-native conformations are often toxic to a cell and are usually recognized by the cellular PQC system ( Emma Mee Hayes et al, 2022 ). Practically all protein species are susceptible to aggregation, yet in the cell the process appears to affect proteins differentially.…”