Genetic Analysis Uncovers Functions of Atypical Polyubiquitin Chains

Polyubiquitination, the covalent attachment of a chain of ubiquitin to lysine (K) residues on proteins, is a highly conserved and abundant post-translational modification. It most commonly targets proteins for degradation but also has non-proteolytic functions. Polyubiquitin chains linked by each of the seven lysines on ubiquitin adopt distinct conformations. This structural variation is thought to explain the functional diversity of polyubiquitination. Although the functions of K48 and K63-linked chains are well understood, the functions of chains linked by the remaining ubiquitin lysine residues remain to be discovered. The aim of the dissertation work described here was to elucidate the functions of atypical polyubiquitin chains in Saccharomyces cerevisiae. In Chapters 1 and 2, a high-throughput genetic screen that served to uncover the genetic interactions of six of the seven ubiquitin-chain types is described. This genetic screen led to the discovery of two novel functions in amino acid homeostasis and cell cycle regulation by polyubiquitin chains linked through lysine 11 of ubiquitin. Chapter 3 details a novel method that is currently being developed to comprehensively identify substrates of specific polyubiquitin chain types using top-down proteomics. Altogether, the present work has advanced our understanding of the functions of polyubiquitin and provided novel methodologies to study the ubiquitin-proteasome system