Abstract
Ageing is driven by a loss of cellular integrity1. Given the major role of ubiquitin modifications in cell function2, here we assess the link between ubiquitination and ageing by quantifying whole-proteome ubiquitin signatures in Caenorhabditis elegans. We find a remodelling of the ubiquitinated proteome during ageing, which is ameliorated by longevity paradigms such as dietary restriction and reduced insulin signalling. Notably, ageing causes a global loss of ubiquitination that is triggered by increased deubiquitinase activity. Because ubiquitination can tag proteins for recognition by the proteasome3, a fundamental question is whether deficits in targeted degradation influence longevity. By integrating data from worms with a defective proteasome, we identify proteasomal targets that accumulate with age owing to decreased ubiquitination and subsequent degradation. Lowering the levels of age-dysregulated proteasome targets prolongs longevity, whereas preventing their degradation shortens lifespan. Among the proteasomal targets, we find the IFB-2 intermediate filament4 and the EPS-8 modulator of RAC signalling5. While increased levels of IFB-2 promote the loss of intestinal integrity and bacterial colonization, upregulation of EPS-8 hyperactivates RAC in muscle and neurons, and leads to alterations in the actin cytoskeleton and protein kinase JNK. In summary, age-related changes in targeted degradation of structural and regulatory proteins across tissues determine longevity.
Highlights
The ubiquitination cascade links additional molecules to the internal lysine sites of the primary ubiquitin
The other differentially abundant Ub-peptides were inversely correlated with protein levels or corresponded to proteins that did not change in abundance with age (Fig. 1e, Extended Data Fig. 1e, f, Supplementary Table 5)
In C. elegans, there are more than 170 E3 ligases[14] but we only found significant changes in the expression of 12 E3s with age
Summary
Because we detected a higher number of ubiquitination changes after day 5, we directly compared day-5 and day-15 wild-type worms. We found that 192 proteins were less ubiquitinated in at least one of their lysine sites during ageing, whereas the total levels of the protein increased (Fig. 2a, Extended Data Fig. 1e) If these proteins are age-dysregulated proteasomal targets, defects in proteasome activity could diminish their degradation in young worms. Several age-dysregulated proteasome targets such as EPS-8 contained Lys48-linked polyUb chains for proteasomal recognition By contrast, they did not have Lys63-linked polyUb, with the exception of LEC-1 and IFB-2 that contained both Lys[63] and Lys[48] ubiquitin linkages (Fig. 2b, Extended Data Fig. 4d, Supplementary Table 9). We hypothesized that if age-dysregulated proteasome targets are not essential for adult viability, lowering their levels after development could prolong longevity Both the chaperone hsp-43 and usp-5 are essential for cell viability[24,25] and their knockdown in adult worms shortened lifespan (Extended Data Fig. 4e).
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