Several neurodegenerative diseases including Alzheim er’s Disease
(AD) are characterized by ubiquitin-positive pathological protein aggregates.
Here, an immunoaffinity approach is utilized to enrich ubiquitylated isopeptides
after trypsin digestion from five AD and five age-matched control postmortem
brain tissues. Label-free MS-based proteomic analysis identified 4,291 unique
ubiquitylation sites mapping to 1,682 unique proteins. Differential enrichment
analysis showed that over 800 ubiquitylation sites were significantly altered
between AD and control cases. Of these, approximately 80% were increased in AD,
including seven polyubiquitin linkages, which is consistent with proteolytic
stress and high burden of ubiquitylated pathological aggregates in AD. The
microtubule associated protein Tau, the core component of neurofibrillary
tangles, had the highest number of increased sites of ubiquitylation per any
protein in AD. Tau polyubiquitylation from AD brain homogenates was confirmed by
reciprocal co-immunoprecipitation and by affinity capture using tandem ubiquitin
binding entities (TUBEs). Co-modified peptides, with both ubiquitylation and
phosphorylation sites, were also enriched in AD. Notably, many of the
co-modified peptides mapped to Tau within KXGS motifs in the microtubule binding
repeat suggesting that cross-talk between phosphorylation and ubiquitylation
occurs on Tau in AD. Overall, these findings highlight the utility of MS to map
ubiquitylated substrates in human brain and provides insight into mechanisms
underlying pathological protein posttranslational modification in AD.