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Branching and Mixing: New Signals of the Ubiquitin Signaling System

Posttranslational modifications allow cells and organisms to adapt to their environment without the need to synthesize new proteins. The ubiquitin system is one of the most versatile modification systems as it does not only allow a simple on–off modification but, by forming a chain of ubiquitin molecules, allows conveying multiple signals. The structure of the chains is dependent on the linkage to the previous ubiquitin molecule as every lysine can serve as an acceptor point for this modification. Different chain types code for specific signals ranging from protein degradation to protein targeting different cellular compartments. Recently the code of ubiquitin signals has been further expanded as branching and mixing of different chain types has been detected. As an additional layer of complexity, modifications of the ubiquitin chain by ubiquitin-like modifiers, like NEDD8, SUMO, or ISG15, have been found. Here we will discuss the different chain types and the technical challenges which are associated with analyzing ubiquitin topology-based signaling.