A versatile new ubiquitin detection and purification tool derived from a bacterial deubiquitylase

Protein ubiquitylation is an important post-translational modification affecting an wide range of cellular processes. Due to the low abundance of ubiquitylated species in biological samples, considerable effort has been spent on developing methods to purify and detect ubiquitylated proteins. We have developed and characterized a novel tool for ubiquitin detection and purification based on OtUBD, a high-affinity ubiquitin-binding domain derived from an Orientia tsutsugamushi deubiquitylase. We demonstrate that OtUBD can be used to purify both monoubiquitylated and polyubiquitylated substrates from yeast and human tissue culture samples and compare their performance with existing methods. Importantly, we found conditions for either selective purification of covalently ubiquitylated proteins or co-isolation of both ubiquitylated proteins and their interacting proteins. As a proof-of-principle for these newly developed methods, we profiled the ubiquitylome and ubiquitin-associated proteome of the yeast Saccharomyces cerevisiae. Combining OtUBD affinity purification with quantitative proteomics, we identified potential substrates for E3 ligases Bre1 and Pib1. OtUBD provides a versatile, efficient, and economical tool for ubiquitin researchers with specific advantages over other methods, such as in detecting monoubiquitylation or ubiquitin linkages to noncanonical sites.