Abstract
BackgroundIn individual living cells p53 has been found to be expressed in a series of discrete pulses after DNA damage. Its negative regulator Mdm2 also demonstrates oscillatory behaviour. Attempts have been made recently to explain this behaviour by mathematical models but these have not addressed explicit molecular mechanisms. We describe two stochastic mechanistic models of the p53/Mdm2 circuit and show that sustained oscillations result directly from the key biological features, without assuming complicated mathematical functions or requiring more than one feedback loop. Each model examines a different mechanism for providing a negative feedback loop which results in p53 activation after DNA damage. The first model (ARF model) looks at the mechanism of p14ARF which sequesters Mdm2 and leads to stabilisation of p53. The second model (ATM model) examines the mechanism of ATM activation which leads to phosphorylation of both p53 and Mdm2 and increased degradation of Mdm2, which again results in p53 stabilisation. The models can readily be modified as further information becomes available, and linked to other models of cellular ageing.ResultsThe ARF model is robust to changes in its parameters and predicts undamped oscillations after DNA damage so long as the signal persists. It also predicts that if there is a gradual accumulation of DNA damage, such as may occur in ageing, oscillations break out once a threshold level of damage is acquired. The ATM model requires an additional step for p53 synthesis for sustained oscillations to develop. The ATM model shows much more variability in the oscillatory behaviour and this variability is observed over a wide range of parameter values. This may account for the large variability seen in the experimental data which so far has examined ARF negative cells.ConclusionThe models predict more regular oscillations if ARF is present and suggest the need for further experiments in ARF positive cells to test these predictions. Our work illustrates the importance of systems biology approaches to understanding the complex role of p53 in both ageing and cancer.
Highlights
In individual living cells p53 has been found to be expressed in a series of discrete pulses after DNA damage
(2) ATM Model Variable oscillations after DNA damage Figure 9 shows the part of the ATM model which differs from the ARF model. We found that this model generally produced one large initial peak of p53 after DNA damage, followed by irregular oscillations in which p53 levels remained relatively high (Figure 10)
We considered two different mechanisms for the DNA damage response: ARF activation, followed by sequestering of Mdm2, and ATM activation
Summary
In individual living cells p53 has been found to be expressed in a series of discrete pulses after DNA damage. Each model examines a different mechanism for providing a negative feedback loop which results in p53 activation after DNA damage. The second model (ATM model) examines the mechanism of ATM activation which leads to phosphorylation of both p53 and Mdm and increased degradation of Mdm, which again results in p53 stabilisation. The TP53 gene encodes a transcription factor with target genes that are involved in DNA repair, cell cycle arrest and apoptosis. There is basal transcription of the p53 gene even in unstressed cells but the protein product does not accumulate as it has a short half-life (about 15–30 minutes) [12] and is usually bound to Mdm, an ubiquitin E3 ligase, which targets p53 to the proteasome for degradation [13,14]. The transcription of Mdm is regulated by p53 [19] and so under normal conditions, levels of both p53 and Mdm are kept at low levels
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