Proteins are molecular machines that perform the majority of cellular functions that characterize living organisms. Protein levels within cells are the result of a delicate balance between protein synthesis and protein degradation. Eukaryotic cells are able to shift this balance to one or the other side to regulate the steady state level of each protein within a cell. If a protein or a functional group of proteins is needed to fulfill a certain duty, cells have evolved a number of pathways to

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... crease the levels of these proteins rapidly. On the other hand, if a protein or functional group of proteins is no longer required, eukaryotes are able to rapidly decrease the concentrations of these proteins. While historically much attention and research has been devoted to how proteins are synthesized, the reverse process, i.e. how and when proteins are degraded, is not understood as well. This thesis is structured into three parts, addressing regulation of protein turnover on a molecular as well as on a system-wide level. In part one, to gain deeper insight into how eukaryotes regulate targeted protein degradation, the molecular mechanisms of regulation of Cullin-RING ubiquitin ligases (CRLs) by the COP9 signalosome (CSN), the deubiquitylating enzyme Ubp12p, and the cullin-associated protein Can1p were investigated in the fission yeast Schizosaccharomyces pombe. In a survey of eight F-box proteins, which confer target specificity to CRLs, the study uncovered the existence of variant F-box proteins lacking a critical proline residue required for efficient regulation by the CSN. The results suggest that distinctive features of the F-box motif specify the assembly of F-box proteins into CRL complexes thus destining them for regulation by the CSN through a mechanism, which can principally function independently of Can1p and Ubp12p. In part two, a large-scale biochemical approach was used to investigate whether E2 ubiquitin conjugating enzymes contribute to substrate selection. Because of the lack of a reliable method for t [...]