Kinetic modelling of DNA replication initiation in budding yeast.

DNA replication is restricted to a specific time window of the cell cycle, called S phase. Successful progression through S phase requires replication to be properly regulated to ensure that the entire genome is duplicated exactly once, without errors, in a timely fashion. As a result, DNA replication has evolved into a tightly regulated process involving the coordinated action of numerous factors that function in all phases of the cell cycle. Biochemical mechanisms driving the eukaryotic cell division cycle have been the subject of a number of mathematical models. However, cell cycle networks reported in literature so far have not addressed the steps of DNA replication events. In particular, the assembly of the replication machinery is crucial for the timing of S phase. This event, called "initiation", which occurs in late M / early G1 of the cell cycle, starts with the assembly of the pre-replicative complex (pre-RC) at the origins of replication on the DNA. Its activation depends on the availability of different kinase complexes, cyclin-dependent kinases (CDKs) and Dbf-dependent kinase (DDK), which phosphorylate specific components of the pre-RC to convert it into the pre-initiation complex (pre-IC). We have developed an ODE-based model of the network responsible for this process in budding yeast by using mass-action kinetics. We considered all steps from the assembly of the first components at the DNA replication origin up to the active replisome that recruits the polymerases and verified the computational dynamics with the available literature data. Our results highlighted the link between activation of CDK and DDK and the step-by-step formation of both pre-RC and pre-IC, suggesting S-CDK (Cdk1-Clb5,6) to be the main regulator of the process.