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Explaining oscillations and variability in the p53-Mdm2 system.

Proctor CJ, Gray DA - BMC Syst Biol (2008)

Bottom Line: 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.The 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centre for Integrated Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Newcastle University, Newcastle upon Tyne, UK. c.j.proctor@ncl.ac.uk

ABSTRACT

Background: In 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.

Results: The 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.

Conclusion: The 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.

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Network diagram of the p53 signalling pathway. Adapted from the KEGG signalling pathway [11].
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Figure 1: Network diagram of the p53 signalling pathway. Adapted from the KEGG signalling pathway [11].

Mentions: The p53 tumour suppressor plays a major role in cancer, as evidenced by frequent TP53 gene mutations in human tumours [1] and by the high incidence of cancer in Li-Fraumeni individuals carrying germline mutations in the TP53 gene [2]. There is a growing consensus that p53 plays an important role in ageing and limitations to lifespan (reviewed in Bauer and Helfand (2006) [3] and in Papazoglu and Mills (2007) [4]) but this assertion has been recently challenged on evolutionary grounds [5]. The TP53 gene encodes a transcription factor with target genes that are involved in DNA repair, cell cycle arrest and apoptosis. It has been described as the 'guardian of the genome' [6], blocking cell cycle progression to allow the repair of damaged DNA. It has also been described as a 'gatekeeper' [7-9] that dictates the fate of cells that have suffered stress by directing them into irreversible pathways of senescence or apoptosis [10]. Figure 1 shows part of the p53 signalling pathway which is a simplification of the KEGG pathway [11]. Under normal homeostatic conditions the cellular levels of p53 protein are kept at a low level. 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 Mdm2, an ubiquitin E3 ligase, which targets p53 to the proteasome for degradation [13,14]. Mdm2-binding prevents the transcriptional activity of p53 [15], a phenomenon that is dependent on the catalytic activity of Mdm2 [16]. Mdm2 also has a short half-life and is a substrate of its own E3 ligase activity in vitro [17]. The degradation of a knocked-in RING finger mutant of Mdm2 indicates the presence of an as-yet unidentified cellular E3 ligase that ubiquitinates Mdm2 in vivo [18]. The transcription of Mdm2 is regulated by p53 [19] and so under normal conditions, levels of both p53 and Mdm2 are kept at low levels.


Explaining oscillations and variability in the p53-Mdm2 system.

Proctor CJ, Gray DA - BMC Syst Biol (2008)

Network diagram of the p53 signalling pathway. Adapted from the KEGG signalling pathway [11].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2553322&req=5

Figure 1: Network diagram of the p53 signalling pathway. Adapted from the KEGG signalling pathway [11].
Mentions: The p53 tumour suppressor plays a major role in cancer, as evidenced by frequent TP53 gene mutations in human tumours [1] and by the high incidence of cancer in Li-Fraumeni individuals carrying germline mutations in the TP53 gene [2]. There is a growing consensus that p53 plays an important role in ageing and limitations to lifespan (reviewed in Bauer and Helfand (2006) [3] and in Papazoglu and Mills (2007) [4]) but this assertion has been recently challenged on evolutionary grounds [5]. The TP53 gene encodes a transcription factor with target genes that are involved in DNA repair, cell cycle arrest and apoptosis. It has been described as the 'guardian of the genome' [6], blocking cell cycle progression to allow the repair of damaged DNA. It has also been described as a 'gatekeeper' [7-9] that dictates the fate of cells that have suffered stress by directing them into irreversible pathways of senescence or apoptosis [10]. Figure 1 shows part of the p53 signalling pathway which is a simplification of the KEGG pathway [11]. Under normal homeostatic conditions the cellular levels of p53 protein are kept at a low level. 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 Mdm2, an ubiquitin E3 ligase, which targets p53 to the proteasome for degradation [13,14]. Mdm2-binding prevents the transcriptional activity of p53 [15], a phenomenon that is dependent on the catalytic activity of Mdm2 [16]. Mdm2 also has a short half-life and is a substrate of its own E3 ligase activity in vitro [17]. The degradation of a knocked-in RING finger mutant of Mdm2 indicates the presence of an as-yet unidentified cellular E3 ligase that ubiquitinates Mdm2 in vivo [18]. The transcription of Mdm2 is regulated by p53 [19] and so under normal conditions, levels of both p53 and Mdm2 are kept at low levels.

Bottom Line: 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.The 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centre for Integrated Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Newcastle University, Newcastle upon Tyne, UK. c.j.proctor@ncl.ac.uk

ABSTRACT

Background: In 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.

Results: The 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.

Conclusion: The 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.

Show MeSH
Related in: MedlinePlus