Evolution of the p53-MDM2 pathway

Abstract

Background: The p53 signalling pathway, which controls cell fate, has been extensively studied due to its prominent role in tumor development. The pathway includes the tumor supressor protein p53, its vertebrate paralogs p63 and p73, and their negative regulators MDM2 and MDM4. The p53/p63/p73-MDM system is ancient and can be traced in all extant animal phyla. Despite this, correct phylogenetic trees including both vertebrate and invertebrate species of the p53/p63/p73 and MDM families have not been published.

Results: Here, we have examined the evolution of the p53/p63/p73 protein family with particular focus on the p53/p63/p73 transactivation domain (TAD) and its co-evolution with the p53/p63/p73-binding domain (p53/p63/p73BD) of MDM2. We found that the TAD and p53/p63/p73BD share a strong evolutionary connection. If one of the domains of the protein is lost in a phylum, then it seems very likely to be followed by loss of function by the other domain as well, and due to the loss of function it is likely to eventually disappear. By focusing our phylogenetic analysis to p53/p63/p73 and MDM proteins from phyla that retain the interaction domains TAD and p53/p63/p73BD, we built phylogenetic trees of p53/p63/p73 and MDM based on both vertebrate and invertebrate species. The trees follow species evolution and contain a total number of 183 and 98 species for p53/p63/p73 and MDM, respectively. We also demonstrate that the p53/p63/p73 and MDM families result from whole genome duplications.

Conclusions: The signaling pathway of the TAD and p53/p63/p73BD in p53/p63/p73 and MDM, respectively, dates back to early metazoan time and has since then tightly co-evolved, or disappeared in distinct lineages.

Keywords: Co-evolution; MDM; Phylogeny; p53.

Fig. 1

Domain organization of (a) the p53/p63/p73 protein family comprising the transactivation domain (TAD), DNA binding domain (DNA BD), oligomerisation domain (OD) and the sterile alpha-motif (SAM) domain. b the MDM protein family containing the p53/p63/p73-binding domain (p53/p63/p73BD), the Acidic domain, a zinc binding domain (Zinc BD) and a RING domain. c Species tree displaying the existence of p53/p63/p73 TAD (in red) and MDM p53/p63/p73BD (in blue) along with the presence of the other domains in the respective protein. Grey branches in the tree illustrate that p53/p63/p73BD and TAD is not present. The domains displayed in white indicate that the domains are present in a few organisms in that specific lineage, but in the majority of the examined species the domain could not be found. The SAM domain was lost in p53 after the whole genome duplication, denoted 1R in the tree, but is retained in vertebrate p63 and p73. This variability is illustrated with absence of lines connecting the OD and SAM domain. The second whole genome duplication is denoted 2R

Fig. 2

a Phylogenetic tree based on multiple sequence alignment of the p53/p63/p73 protein family only including species with the TAD. The evolutionary relations are the same as what is generally accepted regarding species evolution and whole genome duplications. The Placozoa sequence is most distantly related to all the other genes in the tree and was therefore used as an outgroup. b Phylogenetic tree based on multiple sequence alignment of the MDM protein family only including species with the p53/p63/p73BD. The evolutionary relations are the same as what is generally accepted regarding species evolution and whole genome duplications. The Placozoa sequence is most distantly related to all the other genes in the tree and was therefore used as an outgroup

Fig. 3

Paralogous blocks descended from the two whole genome duplication events that happened prior to the emergence of bony vertebrates. The localization of the genes is illustrated with a grey line and the paralogons have the same color. a A region on an ancestral chromosome was duplicated and can in humans be found in chromosome 3, 1 and 17 in which p63, p73 and p53 are localized, respectively. b A region on an ancestral chromosome was duplicated and can in humans be found in chromosome 1 and 12 where MDM2 and MDM4 are localized, respectively [18]

Fig. 4

a Crystal structure of the complex between mouse p53 TAD (red) and the p53/p63/p73BD of MDM2 (blue) (PDB entry: 1YCR) [37]. The residues in p53 TAD shown as sticks are the three conserved residues in the FxxxWxxL motif. b Alignment of the TAD of selected species. Amino acid numbering and phosphorylation sites are according to human p53. Agadir prediction [39] of the helical propensity in percent is shown beside the alignment for the different species. The color-coding is according to eBioX alignment tool