Functional Applications of Systems Biology Tools: Identification of Novel DNA Repair Factors and Peptide Design

The highly annotated budding yeast Saccharomyces cerevisiae has emerged as the primary model for systems biology, the study of how individual cellular components function within the context of a dynamic cellular system.Several genome/proteomescale tools developed using the S. cerevisiae model have produced extensive information on gene function and interaction networks that is stored in publicly accessible databases.Bioinformatic tools can exploit these databases to infer novel biological activity but these predictions must be tested in functioning cellular systems to assess the effectiveness of any method.The work herein uses systems-based computational tools to make predictions on novel protein/gene function that are tested using yeast functional genomic approaches.This thesis describes the development and validation of a new tool to design synthetic binding proteins that bind to and inhibit targeted yeast proteins Psk1 and Pin4 as well as the identification and functional analysis of three yeast DNA repair genes, PSK1, ARP6, and DEF1.The in-silico protein synthesizer, InSiPS successfully engineered two synthetic proteins known as anti-Psk1 and anti-Pin4.This demonstrated the ability of our approach to translate from computational prediction, to a specific biological interaction and importantly, a functionally significant phenotype.Chemical-genetic interaction analysis showed that cells expressing α-Psk1 and α-Pin4 phenocopy Δpsk1 and Δpin4 mutants and yeast-twohybrid confirmed binary interactions in vivo while in vitro assays verify that binding is iii occurring at predicted loci.Further analysis of the anti-Psk1/Psk1 interaction motif showed strong, specific binding.Psk1 was inferred to participate in yeast nonhomologous end-joining (NHEJ) repair of double-strand breaks (DSB), an essential DNA repair pathway.Our functional genetic analysis showed that PSK1 is an important novel NHEJ gene that contributes to repair fidelity while appearing to function through RAD27 activity.We also report that ARP6, affects NHEJ through the RSC chromatin remodeling complex.Lastly, we identify new properties of the Def1 DNA repair protein in yeast NHEJ and a physical and genetic interaction between Yku80 and Def1.Together, these findings demonstrate the ability to predict novel gene/protein function using computational tools and expand our understanding of eukaryotic DSB repair.

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