Bioinformatical Approaches to the Discovery and Classification of Novel Deubiquitinases

Deubiquitinating enzymes (DUBs) are active at multiple levels of the eukaryotic ubiquitin system. DUBs are important for ubiquitin activation and maintaining cellular ubiquitin levels but can also edit or dissolve ubiquitin chains or deconjugate ubiquitin from substrates. Eukaryotic DUBs can be grouped into seven molecular classes, most of which enzymes are cysteine proteases assuming the papain fold. In recent years, an ever-increasing number of pathogen-encoded DUBs have been characterized, which are active inside the host cell and help the pathogens to evade the defense response. At first sight, bacterial and viral DUBs appear to be very different from their eukaryotic counterparts, making them hard to identify by bioinformatic methods. However, apart from very few exceptions, bacterial and viral DUBs are distantly related to eukaryotic DUB classes and possess several hallmarks that can be used to identify high-confidence DUB candidates from pathogen genomes - even in the complete absence of biochemical or functional annotation. This chapter addresses bioinformatical DUB discovery approaches based on a previously published analysis of DUB evolution. The core set of bioinformatical tools required for this endeavor are freely accessible and do not require a particular bioinformatics infrastructure.