Deciphering atypical ubiquitin signals using pathogen‐derived E3 ubiquitin ligases

Abstract

Ubiquitination is a post-translational modification process in eukaryotes that is required for homeostatic cellular functions and for the response to threats such as pathogen invasion. Ubiquitination occurs through the coordinated effort of many ubiquitin-regulating enzymes, with the terminal event occurring when an E3 ubiquitin ligase assembles ubiquitin onto its target. Instead of a single modification, many E3s attach multiple ubiquitin proteins together to form polymeric chains on their targets. Because these ubiquitin chains can be attached together at one of eight different sites, a vast array of distinct poly-ubiquitin signals can be made and each is thought to direct a distinct cellular outcome. Some E3s reproducibly ligate the same ubiquitin signals, a phenomenon that intimately links an E3 to a particular signaling pathway. For example, some E3s in the proteasomal degradation pathway generate lysine (Lys)-48 ubiquitin chains onto targets, and these Lys-48 ubiquitin chains are specifically recognized by proteasome machinery. Other well-described E3s and their ubiquitin chain signals include Lys-63 ubiquitin chains (cellular trafficking) and methionine (Met)-1 ubiquitin chains (the innate immune response). However, the E3s and signaling outcomes for other, so-called ‘atypical’ ubiquitin chains, remain unclear. Interestingly, because of the critical role of ubiquitin signaling for responding to pathogen invasion, several viruses and bacteria have evolved their own ubiquitin regulating enzymes, including E3s and others. A handful of these enzymes have demonstrated the ability to target atypical ubiquitin chains, potentially suggesting a role for those signal types at the host-pathogen interface. In an effort to understand the extent to which pathogens hijack atypical ubiquitin signaling in their hosts, we used bioinformatics and molecular biology techniques to identify new E3s encoded by pathogenic bacteria. Using our identified E3s as well as previously reported E3s from bacteria, we explore the unknown biochemical and structural determinants of atypical ubiquitin chain specificity and its impacts on our immune responses to pathogen invasion.