The ubiquitin-proteasome system (UPS) controls the stability, activity and localisation of most of the proteome and regulates virtually all cellular processes through modification of proteins with ubiquitin. Ubiquitin conjugation is mediated by a conserved enzymatic cascade composed of E1, E2 and E3 enzymes, which cooperate to activate and transfer ubiquitin to substrate proteins. Dysfunction of the UPS is implicated in many disease states, including cancer, neurodegeneration, immune and cardiovascular disorders. Despite the central role of the UPS in cellular regulation, our understanding of the function, interactions and specificity of proteins that comprise the UPS is still limited. One approach to dissect and to study the UPS is to identify molecular probes, which can be used to specifically interrogate catalytic mechanisms and can be potentially considered as entry points for drug discovery. This work focuses on developing novel high-throughput screening methods for inhibitors of the ubiquitin-conjugating enzymes (E2s), using a unicellular organism Saccharomyces cerevisiae and in vitro technologies. S. cerevisiae is a model organism, commonly used in research as a valuable tool for genetic investigations and other high-throughput studies. In this work, we evaluated the toxicity of exogenously expressed human E2s on yeast cells and discovered that one of the E2s, Ube2U, significantly inhibited yeast growth. This inhibition was dependent on the Ube2U ubiquitin-conjugation activity, as demonstrated with a catalytically inactive Ube2U C89A control, which did not affect yeast growth. The growth defect induced by Ube2U allowed us to develop a screening setup for inhibitors of Ube2U, where the enzyme activity was coupled to cell growth readout. Potential Ube2U inhibitors would be identified as rescuers of the slow growing Ube2U-expressing yeast phenotype. Although screening methods in yeast are relatively straightforward to set up and run, the advantages of this system, namely simplicity of the detection signal and high-throughput, are limited by the fact that yeast is not a recognised large scale screening system in pharmaceutical industry, and that it is difficult to identify the target in a complex pathway such as the UPS. In vitro technologies are needed to provide the necessary structure-activity relationship for chemical optimisation. Therefore, we developed a novel, fluorescence-based, miniaturised assay technology, suitable for biochemical investigations and screening for inhibitors of a wide range of specific ubiquitination reactions within the UPS.

In Saccharomyces cerevisiae nimmt die membrangebundene RING-Ub-Ligase Doa10 eine bedeutende Rolle in der Proteinqualitätskontrolle (PQC) des Endoplasmatischen Retikulums (ER) und des Nukleus ein. Doa10 katalysiert dabei die Verknüpfung K48- verbundener Ub-Ketten auf Proteine, die entweder in der ER-Membran oder löslich im Cytosol oder dem Nukleoplasma vorliegen. Diese Markierung leitet die Degradation dieser Proteine ein. Interessanterweise kooperiert Doa10, im Gegensatz zu anderen RING-Ub-Ligasen, mit zwei Ub-konjugierenden Enzymen (E2), um ihre Substrate zu prozessieren. In dieser Arbeit wird veranschaulicht, wie die beiden hochspezialisierten E2 Enzyme Ubc6 und Ubc7 sequentiell agieren, um Doa10 Substrate zu modifizieren. Zuerst wird ein einzelnes Ub-Molekül Ubc6-abhängig an ein Substrat konjugiert (Initiation). Von diesem Rest ausgehen katalysiert Ubc7 die Ausbildung einer K48-verbundenen Ub-Kette (Elongation). Die Fähigkeit von Ubc6 nicht nur Lysine, sondern auch hydroxylierten Aminosäuren wie Serin und Threonin mit Ub-Molekülen zu verknüpfen, erweitert das Substratspektrum von Doa10 und ermöglicht die Prozessieren von Proteinen, die keine zugänglichen Lysinreste exponieren. Weiterhin wird gezeigt, dass ein Überangebot von Ubc6 den Doa10-abhängigen Substratabbau beeinträchtigt. Dies weist darauf hin, dass die Generierung eines effizienten Poly-Ub-Signals einer streng kontrollierten Koordination beider E2 Enzyme am Doa10-Ligase-Komplex unterliegt. / In Saccharomyces cerevisiae, the membrane-bound RING-type Ub ligase Doa10 is a key player of Protein Quality Control (PQC) in the endoplasmic reticulum (ER) and the nucleus. Doa10 promotes lysine 48-linked poly-ubiquitylation of proteins that either reside in the ER membrane or are soluble in the cytosol or the nucleus and thereby labels them for degradation. Strikingly, in contrast to other RING Ub ligases, which typically employ a single Ub conjugating enzyme (E2) for substrate ubiquitylation, the Doa10 ligase requires two of such enzymes for client processing. This study demonstrates that the highly specialized E2 enzymes Ubc6 and Ubc7 act in a sequential manner on Doa10 client proteins. In a first step Ubc6 attaches a single Ub molecule to a substrate (priming), which is followed by the elongation of this moiety with K48-linked Ub chains by Ubc7 (elongation). The ability of Ubc6 to conjugate Ub not only to lysine but also to hydroxylated amino acids like serine and threonine broadens the substrate range of Doa10 and allows processing of proteins, which do not expose accessible lysine residues. Overproduction of Ubc6 was shown to impair Doa10 dependent substrate degradation. Apparently, the generation of a productive K48-linked poly-Ub signal requires a tightly coordinated activity of the individual E2 enzymes at the Doa10 ligase complex.