A comparative analysis of the G1/S transition control in kinetic models of the eukaryotic cell cycle

[摘要] ENGLISH ABSTRACT: The multiplication of cells proceeds through consecutive phases of growth and division(G1, S, G2 and M phases), in a process known as the cell cycle. The transition betweenthese phases is regulated by so-called checkpoints, which are important to ensure properfunctioning of the cell cycle. For instance, mutations leading to faulty regulation of theG1/S transition point are seen as one of the main causes of cancer.Traditionally, models for biological systems that show rich dynamic behavior, suchas the cell cycle, are studied using dynamical systems analysis. However, using thisanalysis method one cannot quantify the extent of control of an individual process inthe system. To understand system properties at the process level, one needs to employmethods such as metabolic control analysis (MCA). MCA was, however, developedfor steady-state systems, and is thus limited to the analysis of such systems, unless thenecessary extensions would be made to the framework. The central question of this thesis focuses on quantifying the control in mathematicalmodels of the G1/S transition by the individual cell cycle processes. Since MCA wasnever applied to the cell cycle, several new methods needed to be added to the framework.The most important extension made it possible to follow and quantify, during asingle cell cycle, the control properties of the individual system processes.Subsequently, these newly developed methods were used to determine the controlby the individual processes of an important checkpoint in mammalian cells, the restrictionpoint. The positioning of the restriction point in the cell cycle was distributed overnumerous system processes, but the following processes carried most of the control:reactions involved in the interplay between retinoblastoma protein (Rb) and E2F transcriptionfactor, reactions responsible for the synthesis of Delayed Response Genes andCyclin D/Cdk4 in response to growth signals, the E2F dependent Cyclin E/Cdk2 synthesisreaction, as well as the reactions involved in p27 formation. In addition it wasshown that these reactions exhibited their control on the restriction point via the CyclinE/Cdk2/p27 complex. Any perturbation of the system leading to a change in therestriction point could be explained via its e ect on the Cyclin E/Cdk2/p27 complex,showing a causal relation between restriction point positioning and the concentration ofthe Cyclin E/Cdk2/p27 complex.Finally, we applied the new methods, with a modular approach, to compare a numberof cell cycle models for Saccharomyces cerevisiae (budding yeast) and mammalian cellswith respect to the existence of a mass checkpoint. Such a checkpoint ensures that cellswould have a critical mass at the G1/S transition point. Indeed, in budding yeast, acorrection mechanism was observed in the G1 phase, which stabilizes the size of cellsat the G1/S transition point, irrespective of changes in the specific growth rate. This incontrast to the mammalian cell cycle models in which no such mass checkpoint couldbe observed in the G1 phase.In this thesis it is shown that by casting specific questions on the regulation andcontrol of cell cycle transition points in the here extended framework of MCA, it ispossible to derive consensus answers for subsets of mathematical models.

[发布机构] Stellenbosch University