Analyzing the Saccharomyces cerevisiae post replication repair pathway through a systems biology approach

Genomic DNA is constantly damaged. If not repaired, DNA damage can lead to mutations or interferes with processes such as DNA replication, transcription and chromosome segregation. All Saccharomyces cerevisiae rad mutants, collected during the seventies, can be grouped into three phenotypic groups: one group of mutants predominantly sensitive to UV light (RAD3 epistasis) and involved in Nucleotide Excision Repair (NER), another group of mutants predominantly sensitive to γ-irradiation (RAD52 epistasis), and a third group of mutants sensitive to both agents (RAD6 epistasis) and showing defects in Post Replication Repair (PRR). In this work we will focus on the S.cerevisiae PRR pathway. The current model of PRR pathway consist of three sub-pathways: the Translesion synthesis (TLS) error-prone, the TLS ± error-free and a totally error-free branch. The choice among these three sub- pathways seems to depend on the covalent modification (mono/poly-ubiquitination) of a key protein: the Proliferating Cell Nuclear Antigen (PCNA). To elucidate the spatio-temporal control mechanism involved in PRR, we will combine laboratory results with computational modelling and analysis. In particular, we plan to adopt a stochastic modelling approach, in order to account for the dynamical effects of biological noise, due to the relatively low amounts of molecular species interacting inside the nucleus. Thereby, the dynamics of the PRR pathway will be investigated by means of the tau-leaping simulation algorithm, that has been recently proved to be a fast and reliable procedure for the simulation of biological systems. We have already started to devise the topology of molecular interactions concerning the error-free sub-pathway, providing a mechanistic and detailed description of the corresponding biochemical reactions. After the modelling and validation of the error-free sub-pathway, we will then proceed with its integration with the other two branches of the PRR pathway, as well as with the DNA damage checkpoint.