Mayeen, N. | Search bioRxiv

bioRxiv2025

Loss of the Parkinson's disease-associated protein DJ-1 impacts dopamine metabolism in astrocytes

The selective loss of dopaminergic neurons in the substantia nigra is a hallmark of Parkinsons disease (PD), yet the contribution of glial cells to this vulnerability is not fully understood. Studies in rodent models suggest that astrocytes can take up and metabolize dopamine (DA), potentially protecting neurons by detoxifying reactive DA metabolites via glutathione S-transferase mu 2 (GSTM2) release. However, these mechanisms remain underexplored in human systems, particularly in the context of PD. Here, we used CRISPR-engineered iPSC-derived human astrocytes with a PD-linked DJ-1 mutation and isogenic controls to investigate astrocytic DA metabolism. Upon DA exposure, control astrocytes upregulated quinone-reducing enzymes NAD(P)H quinone dehydrogenase 1 (NQO1) and GSTM2, whereas DJ-1 mutant astrocytes failed to adaptively respond. In addition, only control astrocytes presented with increased DA quinone products upon DA exposure, not DJ-1 mutants. These results demonstrate astrocytic DA handling being disrupted in DJ-1-linked PD, implicating astroglial dysfunction as an important contributor to PD pathogenesis and potential target for therapeutic intervention.

neuroscience↗

bioRxiv2025

Structural proteomics of the human ubiquitinome

The proteasome maintains the integrity of eukaryotic proteomes by selectively degrading ubiquitinated protein substrates. Ubiquitination targets a wide range of substrates for degradation, including translationally stalled nascent chains, misfolded proteins, and properly folded but short-lived proteins destined for regulatory degradation. Distinct structural features and ubiquitination patterns across these classes of substrates remain largely undefined. In this study, we combine structural proteomics and time-resolved isotopic labeling to profile the modification sites, dynamics, and conformational properties of the human ubiquitinome. We show that proteins undergoing rapid proteasomal degradation are ubiquitinated at lysine residues that are normally buried within structured regions of their native conformations. We provide proteome-wide evidence that this high-flux subset of the ubiquitinome is enriched in newly synthesized proteins that have non-native conformations. Together, our findings demonstrate how the lack of structural integrity of misfolded nascent proteins influences their ubiquitination patterns and ensures proper proteasomal degradation. Significance StatementProtein degradation by the ubiquitin-proteasome system (UPS) is central to maintaining cellular protein quality control, yet the structural and kinetic determinants that govern which proteins are targeted for degradation remain poorly defined. Using deep-coverage structural proteomics combined with metabolic labeling, we show that ubiquitination events can be categorized into two broad classes with distinct properties: those at buried lysines within nascent misfolded proteins that lead to rapid proteasomal degradation, and those at exposed lysines in mature proteins that are associated with slower turnover or regulatory functions. This proteome-wide partitioning provides structural insights into how the UPS targets defective nascent and mature proteins for proteasomal clearance.

molecular biology↗