Mechanism of APC catalyzed ubiquitination of cyclin B1, and, Analysis of degradative role of ubiquitin linkage

Postranslational modification of proteins with ubiquitin is a fundamental method of cellular regulation. Ubiquitination can lead to many diverse cellular fates depending on the topology of the ubiquitin linkage. In this dissertation we describe the method by which the anaphase promoting complex or cyclosome (APC) ubiquitinates cyclin B1, which is then recognized and destroyed by the 26S proteasome, marking a critical step in the exit from mitosis. In chapter II, we reconstitute the ubiquitination of cyclin B1 by the APC in vitro and utilize a novel mass spectroscopy technique to detail this mechanism. We found that the APC ubiquitinates cyclin B1 in two distinct steps: first it pre-dominantly multiply mono-ubiquitinates cyclin B1, then after the addition of the fifth or sixth ubiquitin to cyclin B1 the APC begins forming poly-ubiquitin chain extensions while still modifying new lysines in cyclin B1. These short multi-ubiquitin chains contain a heterogeneous mixture of ubiquitin-ubiquitin linkages predominantly through three different lysines of ubiquitin-Lys11, Lys48, Lys63. These species readily bind ubiquitin binding domain (UBD)-containing proteasome associated receptors and are good substrates for purified proteasomes. In chapter III, we present data on the auto-regulation of the APC by the ubiquitination of an unknown component that is associated with the APC and illustrate how small molecule inhibitors modulate the in vitro ubiquitination of cyclin B1. Intrigued by our results from chapter II, we wondered what comprises a sufficient degradation signal. To address this question, in chapter IV, we systematically analyzed the requirement of ubiquitin linkage through a variety of different biochemical methods. Surprisingly, we found that cyclin B1 modified by multiple mono-ubiquitin additions alone can support binding to UBD-containing proteasome associated receptors, degradation by purified proteasomes and rapid degradation in Xenopus egg extracts. However, the nature of the ubiquitin-ubiquitin linkage does change the rate of substrate degradation, as cyclin B1 modified by mono-ubiquitin additions was degraded more slowly in Xenopus egg extracts than cyclin B1 containing multiple poly-ubiquitin linked chains. These results suggest that the manner in which ubiquitin is linked to the substrate and itself plays an intricate role in the temporal control of substrate turnover.