>Magister Scientiae - MSc / Retinoblastoma binding protein 6 (RBBP6) is a 250 kDa RING finger-containing protein whose function is known to be mediated through interaction with other proteins. RBBP6 plays a role in the regulation of the tumour suppressor protein p53 and is also thought to be involved in mRNA splicing although its role has yet to be characterised. A recent study utilising a yeast 2-hybrid screen identified the cancer-associated protein known as YB-l as an interacting partner of RBBP6, and showed that RBBP6 ubiquitinates YB-I, leading to its degradation in the proteasome.Human Y-box binding protein 1 (YB-I) is member of the cold-shock domain family of proteins, which regulates a number of growth related genes through both transcriptional and translational mechanisms. YB-l is a cell-survival factor whose expression is increased in proliferating normal and cancer cells. It also protects cells against p53-mediated apoptosis by repressing the p53- promoter and down-regulating endogenous p53. The interaction between RBBP6 and YB-l involves the RING finger-like domain ofRBBP6 and the C-terminal62 amino acids ofYB-l. As a means of further localising the interaction, truncated fragments derived from the C-terminal region of YB-I, were tested for their interaction with the RING finger domain of RBBP6 using three different assays: a directed yeast 2-hybrid assay, co-immunoprecipitation and NMR chemical shift perturbation analysis. Our results suggest that the entire 62 amino acid region at the C-terminal domain ofYB-l may be involved in the interaction with RBBP6. Using chemical shift perturbation analysis, this study provides an indication of where YB-l binds to the RING fmger. This represents the first step towards the design of therapeutics aimed at modulating the interaction between RBBP6 and YB-l as a means of targeting the oncogenic effects ofYB-l. In order to identify E2 enzymes involved in the ubiquitination of YB-I, we examined the efficiencies of selected E2s in an in vitro ubiquitination assay. UbcH5c and UbcH7 were both found to catalyse the ubiquitination of YB-l in conjuction with RBBP6, whereas Ubc 13 was not. Finally, we show using NMR that two single-point mutations of the RING finger-like domain are sufficient to abolish homodimerisation of the domain. These will be used in future studies to investigate the requirement for homodimerisation on the ubiquitination activity of RBBP6. www.etd.

Philosophiae Doctor - PhD / Retinoblastoma binding protein 6 (RBBP6) is a 250 kDa protein that is implicated in mRNA processing and ubiquitination functions and has been shown to be highly up-regulated in a number of cancers. In humans and mice,RBBP6 interacts with both tumour suppressors p53 and pRb, suggesting that it is involved in regulation of transcription, induction of apoptosis and cell cycle control. Knock-out of an RBBP6 homologue PACT resulted in p53 dependent cell cycle arrest and apoptosis. Although the biological functions of RBBP6 remain largely unclear, it is possible that its functions are mediated through interaction with other cellular proteins. Since it is possible to unveil novel functions of a target protein through identifying its interacting protein partners,this study aims to further characterize the functions of RBBP6 through identifying novel protein interacting partners using a yeast 2-hybrid screen.In order to identify interaction partners of RBBP6, two well characterized domains of RBBP6, the N-terminal ubiquitin-like DWNN domain and RING finger domain, were used as baits in a yeast 2-hybrid screen of a human testis cDNA library. Putative interactors were verified using in vitro and in vivo immunoprecipitation assays. The RING finger domain was shown to interact with transcriptional factors Y-Box binding protein 1 (YB-1) and zinc finger and BTB containing protein 38 (zBTB38), resulting in their ubiquitination. In the case of YB-1 ubiquitination was correlated with a decrease in the intra-cellular levels of YB-1, suggesting that ubiquitination leads to degradation in the proteosome. The DWNN domain was shown to interact with a splicing associated small nuclear ribonucleoprotein polypeptide G (snRPG) and heat shock protein 70 (Hsp70).The results of this work suggest that, at least in the case of YB-1 and zBTB38,RBBP6 plays a role in the regulation of gene expression by ubiquitination of transcription factors, causing them to be degraded in the proteosome. The study provides further evidence of RBBP6’s involvement in mRNA splicing through its interaction with snRPG. The interaction with Hsp70 suggests a possible role in protein quality control similar to that played by other E3 ligases such as Parkin and CHIP.

Philosophiae Doctor - PhD / Retinoblastoma binding protein 6 (RBBP6) is a 250 kDa protein that is implicated in mRNA processing and ubiquitination functions and has been shown to be highly up-regulated in a number of cancers. In humans and mice, RBBP6 interacts with both tumour suppressors p53 and pRb, suggesting that it is involved in regulation of transcription, induction of apoptosis and cell cycle control. Knock-out of an RBBP6 homologue PACT resulted in p53 dependent cell cycle arrest and apoptosis. Although the biological functions of RBBP6 remain largely unclear, it is possible that its functions are mediated through interaction with other cellular proteins. Since it is possible to unveil novel functions of a target protein through identifying its interacting protein partners, this study aims to further characterize the functions of RBBP6 through identifying novel protein interacting partners using a yeast 2-hybrid screen. In order to identify interaction partners of RBBP6, two well characterized domains of RBBP6, the N-terminal ubiquitin-like DWNN domain and RING finger domain, were used as baits in a yeast 2-hybrid screen of a human testis cDNA library. Putative interactors were verified using in vitro and in vivo immunoprecipitation assays. The RING finger domain was shown to interact with transcriptional factors V-Box binding protein 1 (YB-1) and zinc finger and BTB containing protein 38 (zBTB38), resulting in their ubiquitination. In the case of YB-1 ubiquitination was correlated with a decrease in the intra-cellular levels of YB-1, suggesting that ubiquitination leads to degradation in the proteosome. The DWNN domain was shown to interact with a splicing associated small nuclear ribonucleoprotein polypeptide G (snRPG) and heat shock protein 70 (Hsp70). The results of this work suggest that, at least in the case of YB-1 and zBTB38, RBBP6 plays a role in the regulation of gene expression by ubiquitination of transcription factors, causing them to be degraded in the proteosome. The study provides further evidence of RBBP6's involvement in mRNA splicing through its interaction with snRPG. The interaction with Hsp70 suggests a possible role in protein quality control similar to that played by other E3 ligases such as Parkin and CHIP.

A protein, B0238.11, was identified in a yeast one-hybrid screen to bind to the ribosomal intergenic spacer region (IGS) of Caenorhabditis elegans. Proteins interacting with this region of the DNA have been implicated in ribosome biogenesis in other model organisms, so it is also possible that B0238.11 plays a role in RNA transcription by interacting with RNA polymerase I or other transcription machinery. Thus, the goal of this study was to further characterize the structure and function of B0238.11. I used yeast two-hybrid experiments to identify proteins that interact with B0238.11 within the nucleus. RPS-0, K04G2.2, DPY-4, EFT-3, PAL-1, and B0238.11, itself, were found to bind to B0238.11. Additionally, I analysed the amino acid sequence of B0238.11 using in silico bioinformatics methods to determine its structure and putative function and also to identify and characterize the other interacting proteins. I found that B0238.11 contains a high-mobility group box domain, which is also found in HMO1P in yeast and UBF in vertebrates. These other proteins also bind to the IGS, are known to form homodimers and have been implicated in the initiation of ribosomal RNA transcription. Here I scrutinize the validity of the interaction between each protein and B0238.11. I conclude that B0238.11 is likely to be a C. elegans homolog of UBF and present an updated interactome map for B0238.11. / Synopsis: I carried out yeast two-hybrid assay to find proteins interacting with B0238.11 (O16487_CAEEL). I found that this protein's DNA-binding profile and protein interaction profile mimic other HMG-box containing proteins UBF and HMO1P which are involved in ribosomal RNA transcription initiation. Acknowledgements: I would like to thank my supervisor, Dr. Teresa J. Crease, for not only giving me the opportunity to investigate an interesting topic in Molecular Biology, but also for her patient guidance, encouragement and sound advice. I feel extremely lucky to have a supervisor who cared so much about my work, who responded to my questions and queries so promptly, and was always available to discuss project and career related matters. I would also like to thank Dr. Todd Gillis and Dr. Terry Van Raay for their careful consideration of this project and timely constructive criticisms that helped shape my project. I would like to thank all the members of my committee for helping me see things from different perspectives and helping me develop and critical and mature understanding of the scientific process. I must also express my gratitude to Dr. Robin Floyd for allowing me to build upon his work and Dr. Marian Walhout, at the University of Massachusetts, for providing the Caenorhabditis elegans complimentary DNA library. A large part of this project would not have been possible without the people at the genomics facility in the Department of Integrative Biology, I commend their professionalism and punctuality in delivering results. Completing this work would have been all the more difficult were it not for the support and friendship provided by my peers Shannon Eagle, Tyler Elliott, Nick Jeffery, Joao Lima, Sabina Stanescu, Fatima Mitterboeck and Paola Pierossi. And finally, I would like to thank my parents and siblings Sara Omar and Ali Omar for their continued support through good times and bad, and letting me use their laptops when mine broke down.