p53 (CDK-dependent phosphorylation pathway)

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  • Created by Atsushi Doi.

Description

A gene p53 is called a tumor suppressor gene since p53 regulates cell cycle arrest and induces apoptosis. A modification of the protein p53 complicates the relationship between the concentration of p53 and its transcriptional activity. The protein p53 is stablized by the protein ARF and phosphorylated by kinases [2]. The pathway databases store these information of stabilization and phosphorylation in a map. Although the map describes molecular interactions between the proteins p53, ARF and kinases, the synegestic effect of the stabilization and the phosphorylation is still unclear.

We have constructed the ARF-dependent stabilization pathway and attempted the simulation-based validation of the p53 transcriptional activity with hybrid functional Petri net [1]. We represent the CDK-dependent phosphorylation pathway with HFPN (Fig. 1) and combine this phosphorylation pathway with ARF-dependent stabilization pathway, and demonstrate the effect which is not observed in the single, combining two pathways by the simulation-based validation.

CDK-dependent phophorylation pathway

Fig. 1 shows an HFPN model of CDK-dependent phosphorylation pathway which has been constructed by compiling and interpreting the information of complex CDK7-cycH-p36 and the protein p53 interactions in the literature [2].

Figure 1: CDK-dependent phosphorylation pathway with hybrid functional Petri net. The pathway represents the complex CDK7 cycH p36 binds and phosphorylates the protein p53. The phosphorylated protein p53 has the enhanced transcriptional activity which is assiged by the speed of the transitions.

Results of simulation 1

When all genes p53, CDK7, cycH, and p36 are expressed, p21 mRNA is activated by phosphorylated p53 (p53{p}) (Fig. 2 (1)). When the transcription of the gene CDK7 is prohibited, p21 mRNA is activated by complex p36_p53 (Fig. 2 (2)). When the transcriptions of the genes CDK7 and p36 are prohibited, p21 mRNA is activated by p53 itself (p53(N)) (Fig. 2 (3)). Fig. 2 (1) shows that the concentration of p21 mRNA becomes higher compared to its concentration in Fig. 2 (2) and 3 (3). Because we assign the faster speed for transition T19 than transitions T20 and T21. Although the simulation results of CDK-dependent phosphorylation pathway are consistent with the literature [12], we could not obtain other suggestions.

Figure 2: The simulation results of concentration behaviors of p53(N), p36_p53, p53{p}, CDK7(N), p36(N), CDK7_cycH_p36 and p21 mRNA in Fig. 1. +; transactivate the expression of the corresponding genes, -; prohibit the expression of the corresponding genes.

Combined pathway

We have conducted the protein interactions of p53, MDM2, and p19ARF as the ARF-dependent stabilization pathway for the validation of p53 transcriptional activity with hybrid functional Petri net [1]. For the incorporation of quantitative and qualitative alteration of the protein p53, we combine the ARF-dependent stabilization pathway and CDK-dependent phosphorylation pathway.

Fig. 3 shows the combined pathway model which includes whole ARF-dependent stabilization pathway (surrounded with a line) and CDK-dependent phosphorylation pathway (Fig. 1).

Figure 3: A merged pathway that includes the ARF-dependent stabilization pathway (surrounded with a line) and CDK-dependent phosphorylation pathway (Fig. 1).

Results of simulation 2

Fig. 4 is the simulation results of concentration behaviors of p53(N), p36 p53, p53{p}, CDK7(N), p36(N), CDK7 cycH p36, and p21 mRNA on combinations of p19ARF, CDK7, and p36 expressions.

We considered the following cases:

1. All genes including genes p19ARF, CDK7, and p36 are expressed.

2. Only the transcription of the gene p19ARF is prohibited (remove the transition for the transcription of p19ARF ).

3. The transcriptions of genes p19ARF and CDK7 are prohibited (remove the transition for the transcription of p19ARF and the transition T4 ).

4. The transcriptions of three genes ARF, CDK7, and p36 are prohibited (remove the transition for the transcription of p19ARF, the transition T4 , and T10 ).

From Fig. 4 (1) and 5 (2), we observed the effect of ARF-dependent stabilization pathway. In spite of the destabilization of p53(N), phosphorylated p53 still have a efficient transcriptional activity (Fig. 4 (2)). The protein p36 performed like the protein p19ARF and stabilized the concentration of the protein p53 (Fig. 4(3) and (4)).

Figure 4: The simulation results of concentration behaviors of p53(N), p36_p53, p53{p}, CDK7(N), p36(N), CDK7_cycH_p36, MDM2 mRNA and p21 mRNA in Fig. 3. +; transactivate the expression of the corresponding genes, -; prohibit the expression of the corresponding genes.

Publication

  • Doi A, Nagasaki M, Ueno K, Matsuno H, Miyano S, A combined pathway to simulate CDK-dependent phosphorylation and ARF-dependent stabilization for p53 transcriptional activity, Genome Informatics, In Press.

References

  1. Doi A, Nagasaki M, Matsuno H, Miyano S, Simulation-based validation of the p53 transcriptional activity with hybrid functional Petri net, In Silico Biology, 6(1-2): 0001 (2006).(PubMed_16789909)(.html)
  2. Lu H, Fisher R P, Bailey P, Levine A J, The CDK7-cycH-p36 complex of transcription factor IIH phosphorylates p53, enhancing its sequence-specific DNA binding activity in vitro, Mol. Cell. Biol., 17(10):5923--5934, 1997.