Conference on Systems Biology of Mammalian Cells, Dresden, Germany


Heike Hameister, Oliver Ebenhöh
A mathematical model of the proliferating cell nuclear antigen (PCNA)

The proliferating cell nuclear antigen (PCNA) is a central element for DNA replication and repair. It works as a "sliding clamp" and encircles double-stranded DNA and ensures the processivity of the DNA polymerases &delta and ε. The modification of PCNA by ubiquitin and SUMO contributes the close coordination of DNA replication, repair and damage tolerance. The monoubiquitination promotes the translesion synthesis (TLS), which ignores failures during DNA synthesis and requires the polymerases &eta and ζ. This procedure prevents a stoppage of the DNA replication machinery. The continuation of ubiquitination causes an error free bypass replication that is believed to use the genetic information of the undamaged sister chromatid. The functions of SUMO appear to be more diverse. During S phase SUMO binds to PCNA at the conserved lysine residues K164 and K127. The SUMO-modified PCNA cooperates with the helicase Srs2 and inhibits the recombinational repair by disrupting the attendant Rad51 nucleoprotein filaments. This reaction prevents unrequested recombination events and an unregulated sequence substitution. Several mutations of these residues (SUMOylation or Ubiquitination) cause sensitivity towards DNA-damages. A complete inhibition of these PCNA modifications results in an increased survival rate after UV irradiation. Basis of this observation is the SUMOylation of the recombination enzyme Rad52 and consequential homologous recombination.

We develop a mathematical model simulating the interaction between these different modes of DNA replication and repair. The model is based on sets of ordinary differential equations in which the variables describe the states of the central participating proteins. In a first approach we focus on the stage of replication in which synthesis of the new DNA proceeds with maximal velocity. After a qualitative model has been established, we incorporate available experimental data. The goal of our model is to reproduce the different UV sensitivities of various mutant strains and to assess how damage tolerance depends on key parameters such as total protein concentrations, binding affinities, repair rates and amount of damaged DNA. We expect that our model is helpful in developing hypotheses how mutants, which have so far not yet been studied, behave under the influence of damaging agents.

Whereas our knowledge about the detailed processes involved in DNA replication has rapidly increased by experimental research in the last years, only few theoretical approaches exist. We present for the first time a kinetic model encompassing central features of the replication pathway and its interaction with the most important repair mechanisms.

© 2009 · Heike Hameister ·