Amit Kumar Sahu (PhD):Comprehensive Landscape of Age-induced alterations in protein Ubiquitination and Deubiquitination
The ability to maintain a functional proteome declines during the aging process, which results in dysregulated protein homeostasis and the accumulation of damaged, misfolded, and partially ubiquitinated proteins and constitutes a major hallmark of the aging process. Protein degradation via the ubiquitin-proteasome system requires post-translational modification of the substrate with ubiquitin and subsequent formation of polyubiquitin chains via linkage type specific lysine residues within ubiquitin. We have previously shown that a subset of enzymes involved in the ubiquitin cycle are perturbed in their abundance with aging, this includes deubiquitinases (DUBs) like UCHL1 being more abundant in the brain of old killifish and mice. In this proposal, we aim (I) to understand the function of linkage type specific polyubiquitin chains in the context of aging, and (II) to systematically assess the activity and specificity of DUBs in the aging brain.
The homeostasis of the proteome of cells is required to maintain the function of organs and it was shown to decline during ageing. Advanced glycation end products (AGEs) are a family of non-enzymatic posttranslational modifications that have been shown to accumulate in ageing tissues. Although a handful of specific AGE-modified proteins have been identified, a detailed characterisation of the targets of AGEs is still missing. Previously, we have devised a mass spectrometry based approach to identify specific sites of carboxymethyllysine (CML, one of the most abundant AGEs) modifications in proteins. Using this approach, we identified over 1000 CML sites in cells treated with glycating agents and over 200 sites in primary tissues. In addition, we have established targeted proteomic assays based on isotopically labeled peptide standards for a subset of identified CML sites. In this project, we would like to investigate the functional role of these modifications and their relationships to the ageing process.