text:
Evolution of the p53-MDM2 pathway
Emma Åberg1,
Fulvio Saccoccia1,
Manfred Grabherr1,
Wai Ying Josefin Ore1,
Per Jemth1 &
Greta Hultqvist ORCID: orcid.org/0000-0002-4136-67921,2
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.
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.
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.
Cancer has been observed in virtually all vertebrates, regardless of body size and lifespan, while cancer-like growths have been reported in protostome invertebrates [1]. In mammals, such as humans and mice, there are protective systems in place. As part of this system, p53, often referred to as the "guardian of the genome", plays the important role as an anti-cancer protein. p53 is a transcription factor responsible for regulating the fate of the cell, for example during stress and DNA damage [2]. MDM2 is the primary negative regulator of p53, keeping p53 at appropriate levels by ubiquitination in normal functioning cells [3]. Upon stress, p53 is activated and fulfils its role as a tumor suppressor protein, for example by inducing apoptosis. p53, or the p53 pathway, is disabled in roughly half of all human cancers [4]. Consequently, the prominent role of p53 and MDM2 in tumor suppression makes them outstanding targets for drug design [5], as well as highly interesting for detailed evolutionary studies [6, 7].
p53 shares ancestry with two other transcription factors, p63 and p73, which are paralogs of p53 [8]: p63 is responsible for skin and epithelial development, while p73 plays a role in neuronal development and differentiation [9]. In vertebrates, MDM2 belongs to a family with two members, MDM2 and MDM4. To date, members of the p53/p63/p73 and MDM families have been reported in chordates, but also in non-chordate species, such as Mytilus trossulus (bay mussel) [10], Ixodes scapularis (deer tick) [11] and Trichoplax adhaerens, a small (<1 mm) animal that is the only known living representative of the phylum Placozoa [12]. Thus, the ubiquitous presence of both proteins suggests that they were present in the common ancestor of all present-day animals, and we thus refer to these proteins as p53/p63/p73ancestor and MDMancestor, respectively.
Interestingly, the evolutionary history of the p53/p63/p73 family has proven difficult to fully understand, and there is no published phylogenetic tree that agrees with the generally accepted tree of life for animal evolution [13,14,15]. For the MDM family no comprehensive phylogenetic tree has been published. To investigate the interaction between p53/p63/p73 and MDM, we have re-examined their evolutionary history. We found a strong correlation in the conservation of the interacting domains, p53/p63/p73 TAD and MDM p53/p63/p73BD. Loss of one of the domains is associated with the lack of the other domain, with few exceptions, demonstrating their functional dependence. By utilizing conserved amino acid sequences in domains with retained function, we could infer a phylogenetic relationship of metazoan genes containing p53/p63/p73 TAD and p53/p63/p73BD, respectively. These trees include both vertebrate and invertebrate species, and are consistent with the species evolution for both p53/p63/p73 and MDM. Finally, we have examined the evolution of the p53/p63/p73 TAD domain on a molecular level with regard to protein disorder and regulatory properties. We observed similarities in the phosphorylation pattern of vertebrate p53 and mollusk and annelid p53/p63/p73, which imply that the functional properties of regulation through phosphorylation were present already in the ancestor of deuterostomes (e.g. Chordata) and protostomes (e.g. Mollusca and Arthropoda).
Emergence and loss of domains within the p53/p63/p73 family
Four distinct domains: the transactivation domain (TAD), the DNA binding domain (DNA BD), the oligomerisation domain (OD) and the sterile alpha motif (SAM) (Fig. 1a) are common in proteins from the p53/p63/p73 family. By extensive BLAST searches in metazoan genome databases, we found 342 unique p53/p63/p73 family genes belonging to 183 species. We could confirm the presence of two p53/p63/p73-like genes in the unicellular choanoflagellate Monosiga brevicollis [16]. The two Monosiga brevicollis p53/p63/p73 genes do not contain the TAD but only the DNA BD and the OD, whereas the SAM domain is present in one of the genes but is missing in the other. As compared to vertebrates, the most distantly related p53/p63/p73 gene comprising TAD is that of Trichoplax adhaerens (a multicellular eukaryote, the only member of the phylum Placozoa) [12] (Fig. 1c). Partial or complete gene loss has resulted in complete lack of p53/p63/p73 in Porifera (sponges), and in a truncated version of p53/p63/p73 in Cnidarian species (including e.g., corals and jellyfish), in which the TAD and SAM domains have been lost. The loss of TAD and SAM appears to be a restricted event in these branches since the domains can be identified in sister groups (Fig. 1c). The gene is present in both deuterostome and protostome species suggesting that it appeared early in metazoan (animal) evolution and was present in the common ancestor of animals [17].
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
Protostomes can be divided into four phyla, where closer ancestry is shared between Annelida (ringed worms) and Mollusca, and between Arthropoda and Nematoda (roundworms), respectively. In species from Annelida and Mollusca, all four p53/p63/p73 domains are conserved, but within the Arthropoda phylum, certain domains have been lost (Fig. 1c). Species in the Arthropoda subphyla Chelicerata (including e.g., scorpions and spiders) and Myriapoda (e.g., millipeds) have a p53/p63/p73 gene that contains all four domains while species from subphyla Hexapoda (e.g., insects), and Crustacea (e.g., crayfish and crabs) contain a truncated p53/p63/p73 gene with the DNA BD and OD. Similarly, in p53/p63/p73 from Nematoda, the TAD and SAM domains have been lost, and only the DNA BD and OD are present (Fig. 1c). All extant phyla of deuterostomes (including Chordata, Hemichordata and Echinodermata) have p53/p63/p73 genes comprising all four domains, which implies that the ancestor of deuterostome species also contained a p53/p63/p73 gene with all domains. Following two whole genome duplications early in the vertebrate lineage [18], the three paralogs p53, p63, and p73 emerged. p63 and p73 have retained all four domains, while the SAM domain was lost in the p53 lineage and replaced with a C-terminal disordered domain involved in protein-protein interactions [19].
Duplications within the p53/p63/p73 family
There are several papers that have analyzed the number of p53/p63/p73 genes and which domains these contain in different species in order to understand the p53/p63/p73 evolution [6, 20, 21]. These papers often refer to the genes with the SAM domain in invertebrates as p63/p73 or p63/p73-like and to the ones lacking the SAM domain to p53 or p53-like. To infer such a relationship is however not straightforward since domains are frequently lost during evolution and hence lack of a particular domain in a protein does not confirm close relationship with another protein lacking the same domain. The SAM domain has indeed been lost at multiple occasions during the evolution of the p53/p63/p73 family. A recent study by dos Santos et al. where they published a phylogenetic tree and included duplicates of invertebrates shows that there has been multiple duplications in the evolution of the p53/p63/p73 family [13]. For instance, the choanoflagellate Monosiga brevicollis have one copy of p53/p63/p73 with the SAM domain and one without and these are more similar to each other than to the vertebrate p53, p63 and p73 genes according to the results in dos Santos et al. Furthermore, in several hexapod species in the arthropod lineage the p53/p63/p73 gene has been duplicated at different time points: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus p53/p63/p73 gene seem to have been duplicated in the ancestor of these species as they cluster together while the p53/p63/p73 gene in Nasonia vitripennis and Tribolium castaneum have been duplicated in two separate events. In another genus of non-vertebrate chordates, Branchiostoma floridae, one of the p53/p63/p73 genes variants has lost the SAM domain while the other has retained it, they do not cluster in the phylogenetic tree, however they are neither located in a way that implies closer relationship to any of the vertebrate p53, p63 or p73 [13]. A more recent duplication of the p53/p63/p73 gene can be found in the chordate but non-vertebrate tunicate Ciona intestinalis. In conclusion, the p53/p63/p73 genes have been duplicated multiple times during the evolution. Furthermore, after the whole genome duplications in the vertebrate lineage leading to fishes, reptiles and mammals the three distinct p53, p63 and p73 genes were retained in the majority of species. However, gene duplications in vertebrates can also be observed, for example, there are 20 copies of p53 in the African elephant Loxodonta africana [22].
Emergence and loss of domains within the MDM family
Similarly to p53/p63/p73, we performed BLAST searches in metazoan genome databases for MDM, and found 166 unique MDM family genes belonging to 98 species. The MDM protein family consists of four domains, the p53/p63/p73-binding domain (p53/p63/p73BD), the Acidic domain, the zinc binding domain (Zinc BD), and the RING domain (Fig. 1b). An MDM protein comprising all four domains was previously identified in the multicellular Placozoan, Trichoplax adhaerens [12]. The MDM gene is not present in Porifera (sponges), but it can be found within the Cnidaria phylum. However, Cnidaria MDM (i.e., from the species Nematostella vectensis, Hydra vulgaris and Acropora digitifera) lacks the p53/p63/p73BD (Fig. 1c). Since the MDM gene is present in deuterostomes and protostomes, it was consequently present in the common ancestor of extant multicellular animal species. Certain domains of MDM have been lost in the protostome lineage similarly to what we observe for p53/p63/p73 (Fig. 1c). In the Mollusca, Annelida and Arthropoda subphyla Myriapoda and Chelicerata, an MDM gene comprising all four domains was identified. However, in Nematoda, the whole gene has disappeared. In the Arthropoda subphyla Hexapoda and Crustacea, the acidic domain, zinc binding domain and the RING finger domain can be identified in a few species, but not the p53/p63/p73BD. In deuterostome species, all four domains are present in both paralogs, MDM2 and MDM4.
Loss of the TAD domain in p53/p63/p73 correlates with the loss of the p53/p63/p73BD in MDM
The interaction between p53 TAD and MDM2 p53/p63/p73BD is important in mammals, since it is involved in tumor suppression. The origin of the interaction between the domains dates back to the time of early metazoan species [12]. Similar to p53/p63/p73, the MDM gene is not present in Porifera (sponges), but can be found within the Cnidaria phylum. However, the interaction domains in MDM and p53/p63/p73 in Cnidaria are both missing (Fig. 1c). A similar correlation between loss of p53/p63/p73BD in MDM and loss of TAD in p53/p63/p73 was observed in protostomes. For example, species belonging to the Mollusca and Annelida phyla and the Arthropoda subphyla Chelicerata and Myriapoda all contain four p53/p63/p73 domains, as well as the p53/p63/p73BD of MDM. Interestingly, the p53/p63/p73BD in MDM in the Arthropoda subphyla Chelicerata and Myriapoda species Stegodyphus mimosarum (african social velvet spider), Ixodes ricius (castor bean tick), Ixodes scapularis (deer tick), Metaseiulus occidentalis (western predatory mite) and the Strigamia maritima (centipede), is less conserved in length compared to the p53/p63/p73BD in vertebrate, annelid and mollusk species. Likewise, the p53/p63/p73 TAD from these species contains a less conserved MDM binding motif. On the other hand, in the Arthropoda subphyla Hexapoda and Crustacea, we could only find truncated versions of p53/p63/p73 and MDM where the interaction domains is not present. Likewise, all species in the Nematoda phylum lack the whole MDM protein and p53/p63/p73 TAD. By contrast, all deuterostome species contain all MDM domains, as well as the p53/p63/p73 TAD. Thus, we find a clear correlation between presence of p53/p63/p73 TAD and the p53/p63/p73BD in MDM. This suggests a strong and ancient, yet dynamic co-evolution of the interaction domains TAD and p53/p63/p73BD in the p53/p63/p73-MDM regulatory pathway. However, there are a few cases that are not clear, which are detailed below.
Species that might not conform to the co-evolution hypothesis
While the co-evolution of p53/p63/p73 and MDM appears strong, some of our data are inconclusive. Among invertebrates, we found species in the Mollusca phylum having p53/p63/p73 with the TAD but not MDM, for example Haliotis tuberculat (a sea snail), Euprymna scolopes (bobtail squid), Spisula solidissima (Atlantic sea clam) and Loligo forbesii (long-finned squid). By contrast, in Biomphalaria glabrata (ram's horn snail), an MDM with a p53/p63/p73BD was found, while its p53/p63/p73 lack the TAD. However, since all these genomes have relatively poor sequence coverage, and since there are related species, for example Mytilus trossulus (bay mussel), Crassostrea gigas (Pacific oyster) and Lottia gigantea (owl limpet), where both interaction domains are present, it is likely that all Mollusca species contain the gene with the interaction domain (Fig. 2a, b). In the majority of deuterostome species, the same paralogs are present: in the p53/p63/p73 family, the three distinct proteins p53, p63 and p73 and in the MDM family, the two proteins MDM2 and MDM4. Species belonging to the Chondrichthyes phylum (cartilaginous fish), such as Scyliorhinus canicula (small-spotted catshark) and Leucoraja erinacea (little skate) appear to not have a p53, p63 or p73 protein, but contain MDM2 and MDM4. On the other hand, Callorhinchus milli (Australian ghostshark), which also belongs to the Chondrichthyes phylum, contains p53, p63, p73, MDM2 and MDM4 (including the p53/p63/p73BD), which leads us to believe that the missing sequences among Chondrichthyes might be due to poor sequencing coverage. In Osteichthyes (bony fish), Reptilia, and Mammalia, there are certain species in which we cannot identify all p53, p63, p73, MDM2 and MDM4 and/or their respective interaction domain; however, the majority of the species in a phylum contains the genes. We also further investigated the previous notion that p53 is missing from the genome assemblies in the majority of species in the phylum Aves (birds) [13]. While not present in any avian genome assembly, p53 mRNA has been found in the published transcriptomes of two birds, Gallus gallus (Chicken) and Pseudopodoces humilis (ground tit). The Gallus gallus p53 gene has all four-domains, whereas the Pseudopodoces humilis p53 gene only contains the DNA-BD and OD. The high GC content of about 65% indicates that p53 is located in one of the GC rich microchromosomes, which are difficult to assemble due to sequencing bias and low complexity. Fragments of the p53 mRNA could also be found in the transcriptomes of two other bird species from different clades, Columba livia (pigeon) and Erythrura gouldiae (gouldian finch, personal communication with Malgorzata Anna Gazda), suggesting that p53 is present in all bird species, albeit difficult to detect due to its high GC content.
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
Phylogeny of proteins containing the interacting domains produces phylogenetic trees that follow the species evolution
There have been several attempts to solve the evolutionary history of the p53/p63/p73 protein family [6, 13,14,15, 20], but so far no phylogenetic tree, including both vertebrate and invertebrate species, has been published that agrees with the evolution of species. The phylogeny of MDM has been sparsely investigated, and the best published tree comprises only five vertebrates and three invertebrates species [23]. Due to less structural constraints, intrinsically disordered regions, like the p53/p63/p73 TAD, are allowed to substitute at a faster rate compared to structured regions [24, 25]. Since we observe a strong co-evolution of the two interacting domains, p53/p63/p73 TAD and MDM p53/p63/p73BD, the species that contain these two domains are very likely to have retained their interaction and function limiting the amino acid substitutions and improving the likelihood of a correct alignment. We were therefore curious to examine the phylogeny of p53/p63/p73 and MDM only including species having the interaction domain to investigate the phylogenetic relationship. Thus, we reconstructed a phylogenetic tree of the p53/p63/p73 family only including species containing the TAD (Fig. 3a) and a tree of the MDM family only including species containing the p53/p63/p73BD (Fig. 3b). Our analysis includes 111 and 84 vertebrate and 15 and 14 invertebrate species for p53/p63/p73 and MDM, respectively, resulting in phylogenetic trees that follow the evolution of species almost perfectly, according to interactive Tree Of Life [26].
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]
Co-localization of genes on paralogons confirms that p53/p63/p73 and MDM2/MDM4 result from whole genome duplications
In local gene duplications, the two duplicated genes are located in the proximity of each other, while after whole genome duplications, the duplicated gene is found on a paralogous block resulting from recombination of chromosomes. The existence of paralogons has been confirmed by comparing the chromosomal location of duplicated human genes with the location of the evolutionary connected genes in invertebrate species as Drosophila melanogaster and Caenorhabditis elegans, which did not undergo whole genome duplications [27]. The duplicated genes were further investigated by phylogenetic and molecular clock analysis to find the time point of the duplication, which was estimated to be around the time of early vertebrate evolution [18]. Present day mammalian p53, p63 and p73, as well as MDM2 and MDM4, have been suggested to result from these two whole genome duplications in the vertebrate lineage, only due to their time point of divergence [13, 28]. That the duplications occur at the time point of the whole genome duplications is supported by our phylogenetic analysis, where the time of duplication happened after the divergence of Vertebrata and Agnatha (Jawless fish). For the p53/p63/p73 family, one copy was subsequently lost, and in case of MDM, two copies were lost. To confirm that the p53/p63/p73 and MDM family genes evolved from whole genome duplication events, we analyzed genes that are co-localized in paralogous chromosomal regions (synteny). p63 is located on chromosome 3, p53 is located on chromosome 17, and p73 is located on chromosome 1. These three regions form a paralogous block [18], hence supporting that the vertebrate p53/p63/p73 family members arose through whole genome duplications (Fig. 3a). Likewise, the location of MDM2 and MDM4 can be traced to a paralogous block in chromosome 12 and 1, respectively (Fig. 3b). These results strongly suggest that the p53/p63/p73 and MDM genes arose from the whole genome duplications in the vertebrate lineage. In teleost fish, an additional whole genome duplication occurred after the divergence from present day tetrapods [29], implying that two copies of p53, p63, p73, MDM2 and MDM4, respectively, can be present in some teleost fish species. However, we did not find any instances where the duplicated genes were preserved suggesting they have been lost, which is a common event.
Evolution of phosphorylation sites in the p53-TAD domain
Studies on mammalian p53 TAD have shown that it is intrinsically disordered in the free state, but adopts a helical structure when binding to MDM2 and other interaction partners (Fig. 4a) [30]. Posttranslational modifications help to regulate the function and affinities for different binding partners, and are common in regions with intrinsic disorder [31]. Human p53 TAD has three possible phosphorylation sites, at Ser15, Thr18 and Ser20 (Fig. 4b). Especially, the phosphorylation of Thr18 in p53 TAD increases the affinity for proteins activating p53, such as CBP [32] and p300 [33]. The affinity is increased in an additive manner for each site that becomes phosphorylated [33]. On the other hand, phosphorylation of Thr18 decreases the affinity for MDM2 [30]. We were interested to see when this phosphorylation pattern appeared, and if it is conserved in evolution. Our result shows that all three putative phosphorylation sites are conserved in the p53 vertebrate linage. However, only Ser15 is conserved in the p63 lineage. Among p73 vertebrates Thr18 is instead conserved, and additional Ser and Thr residues have emerged, but are not confirmed phosphorylation sites according to the PhosphositePlus webpage [34]. The vertebrate p53 phosphorylation sites Ser15 and Thr18 are present in mollusk species, whereas in Capitella teleta (a polychaete worm from the phylum Annelida), only Ser15 is conserved and has a Ser residue at position 18 instead, which is also a putative phosphorylation site. In Chordata species that did not undergo whole genome duplication, such as Ciona intestinalis and Ciona savignyi, the phosphorylation sites in p53/p63/p73 TAD are Ser15, Thr18 and Ser20, while the echinoderm species Patiria miniata and Strongylocentrotus purpuratus contain the putative phosphorylation sites Ser15 and Thr18. Thus, the mollusk and annelid p53/p63/p73 phosphorylation pattern is more similar to the pattern in echinoderm p53/p63/p73 and vertebrate p53 compared to vertebrate p63 and p73, suggesting that the present day vertebrate p53 pattern (and thus possibly the regulation through phosphorylation) was present already in the deuterostome/protostome ancestor (Fig. 4b).
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
Evolution of residual helicity in p53/p63/p73 TAD domain
The molecular evolution of intrinsically disordered proteins (IDPs) is known to have less constraints and is more prone to insertions and deletions compared to structured domains [35]. However, binding motifs, amino acid composition, and the length of IDPs are generally conserved [25]. Computational analysis of the primary structure in disordered regions in different species can provide some insights with regard to important residues that have persisted in the evolutionary process. Prolines are of interest when considering the residual helicity, since they sterically hinder the continuation of helical structures. The human p53 TAD has two N-terminal prolines and one C-terminal proline present at the respective end of the FxxxWxxL binding motif (Fig. 4). In a recent study [36] the prolines of human p53 TAD were mutated to alanine to assess the effect of the helical structure on binding affinity to MDM2 p53/p63/73BD and general function of p53. The study revealed that the N-terminal prolines (position 12 and 13) have no effect on binding, while mutation of the C-terminal proline (position 27) results in higher residual helicity and a higher affinity for the p53/p63/73BD. The C-terminal proline is conserved in the vertebrate lineage for p53. Human p63 and p73 also have a proline C-terminal of the TAD binding motif, at position 65 and 24, respectively, while invertebrate p53/p63/p73 TAD lacks a proline in this position (Fig. 4b). Published structures of p53 TAD [37] (Fig. 4a) and p73 TAD [38] in complex with MDM2 indicate a helical structure between positions 18-26 and 14-21, respectively. Agadir predictions [39] of the helical content of TAD from human p53, p63 and p73, as well as for invertebrate p53/p63/p73, indicate a very low helical content, suggesting that the degree of disorder in the free state is preserved in evolution irrespective of the proline (Fig. 4b). However, the conserved C-terminal proline in the vertebrate lineage of p53, p63 and p73 could provide a means for TAD to modulate helicity upon binding and thus the affinity of the interaction [36].
Explaining the evolution of p53/p63/p73 is challenging since no phylogenetic tree including both vertebrate and invertebrate species, which follows the species evolution, has been published [13]. Phylogenetic trees including deuterostomes [15, 40] present a satisfying evolutionary relationship, while three trees including invertebrates [13, 14, 20] are not consistent with the species evolution. The relationships of species in these three trees are similarly inferred, where deuterostomes, mollusks, and annelids cluster together, while nematodes and arthropods are grouped together in another cluster. This is not in concordance with the evolution of the species, where mollusks, annelids, nematodes and arthropods should cluster together (Fig. 1c), indicating constraints in the gene family. For MDM, a comprehensive phylogenetic study has not been published, however, there are studies involving an evolutionary perspective of the protein family [7, 28]. Here, we present comprehensive phylogenetic trees for both the p53/p63/p73 and MDM family, in which the topology follows the species phylogeny and the whole genome duplications (Fig. 2a, b). We manage to do this by excluding genes that lack the two interacting domains, p53/p63/p73 TAD and MDM p53/p63/p73BD, or essential motifs in these domains.
Our phylogenetic trees of p53/p63/p73 and MDM exclude species belonging to the phylum Nematoda and the Arthropoda subphyla Hexapoda and Crustacea, since these genes lack the complete interaction domains. We believe that this particular limitation of genes is essential for the correct phylogenetic relationship since the species included have an evolutionary conserved p53/p63/p73 TAD: MDM p53/p63/p73BD interaction and hence have more similar constraints. There have been other attempts to create trees of the p53/p63/p73 family with only selected domains in the alignment. For instance dos Santos et al. made an alignment containing only the p53 DNA BD, which is conserved in all p53/p63/p73 family members, but the resulting tree did not follow the species evolution [13]. The TAD domain is intrinsically disordered and has accumulated distinct mutations in different lineages, hence contains valuable evolutionary information. Intrinsically disordered domains can be difficult to align due to the high substitution rates but the conserved FxxxWxxL motif aids in aligning the less conserved regions of the TAD domain. While the TAD domain is only a small part of the whole p53/p63/p73 gene, it is likely that the combination of the TAD and the very conserved folded domains of p53/p63/p73 provides enough information for a correct phylogenetic reconstruction. In the cases where p53/p63/p73 TAD has lost its functional connection to MDM, the substitution rate increased, resulting in sequences that could easily distort a phylogenetic reconstruction.
The human p53/p63/p73BD in MDM2 and MDM4 can both interact with TAD in p53, p63, and p73, respectively [41]. This, together with the interaction between p53/p63/p73 and MDM in bay mussel [10] implies that the interaction was present in the ancestor of deuterostomes and protostomes. The function of invertebrate p53/p63/p73 (and of p53/p63/p73ancestor) is thought to be protection of the germ line from DNA damage in response to stress [6], which is similar to the function of vertebrate p53. There is also evidence of leukemic-like disease in mollusks where p53/p63/p73 is up regulated [10] suggesting that p53/p63/p73 and MDM are involved in cancer in invertebrates as well as in vertebrates. Our data suggests that the TAD domain in mollusk and annelid p53/p63/p73 has a more similar phosphorylation pattern to vertebrate p53 and echinoderm p53/p63/p73 than to the vertebrate p63 and p73 family members. This leads us to propose that at the time of the split of deuterostomes and protostomes, the p53/p63/p73-MDM interaction had p53-like functionality, which has been retained in mollusk and annelid species and in p53 vertebrates. It has been suggested [6] that the ancestral and invertebrate function of p53/p63/p73 mainly resembles the p63 vertebrate function based on the presence of the conserved SAM domain and a greater sequence similarity between vertebrate p63 and invertebrate p53/p63/p73 [14]. Therefore, we also propose that some functions of p53/p63/p73ancestor are more similar to that of p63 (i.e. the SAM domain functions) and others more similar to p53 (TAD domain functions). It is also possible that other functions not yet analyzed are more similar to p73, since all three family members are equally evolutionarily close to the p53/p63/p73ancestor.
Including all genes that have sequence similarity to MDM in the phylogenetic analysis does not produce a correct relationship according to the species tree. However, similarly to p53/p63/p73, when only species that contain the p53/p63/p73BD are included, the tree is in accordance with the whole genome duplications and species evolution. The MDM family shows highest conservation in the RING domain. The functional role of the RING domain in MDM2, which is conserved in all vertebrate species and jawless fish, is to form heterodimers with MDM4 stimulating MDM2 to ubiquitinate p53 [40]. It has been reported [42] that MDM4 has no E3-ligase activity, which raises the question whether invertebrate MDM and MDMancestor possess E3-ligase activity.
In conclusion, the signaling pathway of the TAD and p53/p63/p73BD in p53/p63/p73 and MDM, respectively, dates back to the beginning of multicellular life and has since then tightly co-evolved. We have here, by only including genes containing the interaction domains for the first time constructed phylogenetic trees of both p53/p63/p73 and MDM, displaying a relationship in accordance with the whole genome duplications and species evolution.
Identification of p53/p63/p73 genes
p53/p63/p73 was identified in Ensembl using TBLASTN [43] (www.ensembl.org) and its gene tree (ENSGT00390000015092) was downloaded. In Uniprot (www.uniprot.org) the human p53 sequence was used as query to blast against all metazoan species, all hits were collected. The same search was performed in Ortho DB [44] (http://orthodb.org/) where all the hits were collected. Additional searches were made in NCBI (www.ncbi.nlm.nih.gov) and at the Reptilian transcriptomes webpage (http://www.reptilian-transcriptomes.org). All retrieved sequences were pooled together and duplicates were removed by using the online programme ElimDupes (www.hiv.lanl.gov/content/sequence/ELIMDUPES/elimdupes.html). The p53 TAD has a well-conserved FxxxWxxL binding motif and previous studies have shown that these are the most critical amino acids for the interaction with MDM2 [37, 45]. In the alignment we kept all sequences containing the TAD and a binding motif resembling the FxxxWxxL in amino acid character. The alignment resulted in 342 sequences from 183 species (Additional file 1: Table S1).
Alignment and phylogenetic tree of p53/p63/p73
The amino acid alignment was done in Guidance [46] (http://guidance.tau.ac.il) using the MAFFT algorithm with the advanced option max-iterate set to 1000 and pairwise alignment option set to localpair. Gaps where removed with a gap tolerance of 95% with Gap Strip/Squeeze v2.1.0 (http://www.hiv.lanl.gov/content/sequence/GAPSTREEZE/gap.html) and this alignment was used to generate the phylogenetic tree. Alignment of the TAD is presented in Additional file 2: Figure S1 and Sequence Logos of this alignment is presented in Additional file 3: Figure S2. The best-fit model, according to Bayesian information criterion [47] (BIC) was calculated using MEGA 6 [48] and resulted in the Jones-Taylor-Thornton substitution model (JTT) model with gamma-shaped function (G) (4 categories, fixed alpha to 1.030) together with empirical amino acid equilibrium frequencies (F) and the invariant site model (I). The phylogenetic tree was generated in PhyML 3.0 [49] (http://www.atgc-montpellier.fr/phyml/) using this model with Nearest-Neighbor-Interchange (NNI) improvement and Shimodaira-Hasegawa approximate Likelihood Ratio Test (SH-aLRT) branch support. The tree was rooted against Trichoplax adhaerens (Fig. 2a) (Additional file 4: Figure S3).
Co-localization of p53/p63/p73 genes on the same paralogous block
The human p53 gene (ENSG00000141510) is located at chromosome 17: 7,661,779-7,687,550, the p63 gene (ENSG00000073282) is found at chromosome 3: 189,631,416-189,897,279 and the p73 gene (ENSG00000078900) is located at chromosome 1: 3,652,520-3,736,201 (Fig. 3a). Searching the http://wolfe.ucd.ie/dup/human5.28/ homepage [18] a paralogous block in the human genome comprises chromosome 17 (5,01-8,10) and chromosome 3 (167,0-187,25), chromosome 1 (0,76-11,92) and chromosome 3(144,91-185,57), which means that all genes belonging to the p53/p63/p73 family are located on or in close proximity of the same paralogous block (Fig. 3a). VAMP2 (ENSG00000220205) is located in the proximity (5 Mb) of p53, and it has a paralog gene, VAMP3, in the proximity of p73 (10 Mb) which further confirms that these genes are a result from the whole genome duplications. The multicellular organism Trichoplax adhaerens contains a single gene of p53/63/73 (TriadG64021) located on scaffold 6 and VAMP2 give a TBLASTN hit on scaffold 6 as well.
Identification of MDM genes
MDM2 was identified using a TBLASTN search in Ensembl [43] (www.ensembl.org) and its gene tree (ENSGT00530000063539) was downloaded containing 142 MDM2 and MDM4 protein sequences. Additional sequences were collected using TBLASTN human MDM2 (ENST00000258149) as a query. MDM sequences lacking the p53/p63/p73BD were removed. The databases used for browsing and downloading additional sequences were Ensembl Metazoa (www.metazoa.ensembl.org), Pre Ensembl (http://pre.ensembl.org/index.html), NCBI (www.ncbi.nlm.nih.gov), Skatebase [50] (http://skatebase.org), Elephant Shark Genome project [51] (http://esharkgenome.imcb.a-star.edu.sg/), Japanese lamprey genome project (http://jlampreygenome.imcb.a-star.edu.sg/), EchinoBase [52] (www.echinobase.org), MOSAS amphioxus (http://genome.bucm.edu.cn/lancelet/download_data.php), Uniprot (http://www.uniprot.org/), and Botryllus schlosseri genome project [53] (http://botryllus.stanford.edu/botryllusgenome/). MDM proteins contain a well-conserved RING domain responsible for binding zinc, this RING domain differ from other RING domains in the binding motif. The common motif of zinc binding is Cys3HisCys4, while MDM has a unique motif, Cys2His2Cys4 [28]. Presence of the MDM specific motif in the RING domain was a criterion for keeping the sequence in the alignment. The sequences lacking the p53/p63/p73BD were also removed from the final alignment. The alignment resulted in a total number of 166 MDM sequences from 98 species (Additional file 5: Table S2).
Alignment and phylogenetic tree of MDM
The amino acid alignment was generated in Guidance [46] (http://guidance.tau.ac.il) using MAFFT algorithm with the advanced option max-iterate set to 1000 and pairwise alignment option set to localpair. The alignment was lightly masked [54] (0.050) so that 98,9% of the amino acids remained. Gaps where removed with a gap tolerance of 95% with Gap Strip/Squeeze v2.1.0 (http://www.hiv.lanl.gov/content/sequence/GAPSTREEZE/gap.html) and this alignment was used to generate the phylogenetic tree. The alignment of the p53/p63/p73BD is presented in Additional file 6: Figure S4 and Sequence Logos of this alignment is presented in Additional file 7: Figure S5. The best-fit model, according to Bayesian information criterion [47] (BIC) was calculated using MEGA 6 [48] and resulted in the Jones-Taylor-Thornton substitution (JTT) model with gamma-shaped function (4 categories, fixed alpha to 1.367) (G) together with the invariant site model (I). The phylogenetic tree was calculated using this model in PhyML 3.0 [49] (http://www.atgc-montpellier.fr/phyml/) with Nearest-Neighbor-Interchange (NNI) improvement and Shimodaira-Hasegawa approximate Likelihood Ratio Test (SH-aLRT) branch support. The tree was rooted against Trichoplax adhaerens (Fig. 2b)(Additional file 8: Figure S6).
Co-localization of MDM genes on the same paralogous block
The human MDM2 gene (ENSG00000135679) is located at chromosome 12: 68,808,172-68,850,686 and the MDM4 gene (ENSG00000198625) is located at chromosome 1: 204,516,379-204,558,120 (Fig. 3b). Searching the http://wolfe.ucd.ie/dup/human5.28/ homepage [18] there is a paralogous block located on chromosome 1 (205,69-211,23) and 12 (70,14-98,25), which is in the proximity where MDM2 and MDM4 genes are located (Fig. 3b). Two other genes called PPP1R12A (ENSG00000058272) and MYF5 (ENSG00000111049) are located in the proximity (12 Mb) of MDM2 and have paralog genes, PPP1R12B (ENSG00000077157) and MYOG (ENSG000001221809) in the proximity of MDM4 (3 Mb). Thus, the genes are all located in the proximity of the same paralogous block, which is a result of whole genome duplications (Fig. 3b). The multicellular organism Trichoplax adhaerens contains an MDM ancestor (TriadG54791) located on scaffold 3:7,103,976-7,107,199. MYOG and PPP1R12A give a TBLAST hit on scaffold 3 as well, TriadG54311 and TriadG54295 respectively.
Aktipis CA, Boddy AM, Jansen G, Hibner U, Hochberg ME, Maley CC, et al. Cancer across the tree of life: cooperation and cheating in multicellularity. Philos Trans R Soc Lond B Biol Sci. 2015;370(1673).
Chen J. The cell-cycle arrest and apoptotic functions of p53 in tumor initiation and progression. Cold Spring Harb Perspect Med. 2016;6:a026104.
Pei D, Zhang Y, Zheng J. Regulation of p53: a collaboration between Mdm2 and MdmX. Oncotarget. 2012;3:228–35.
Lane D, Levine A. p53 research : the past thirty years and the next thirty years p53 research : the past thirty years and. Cold Spring Harb Perspect Biol. 2010;2:1–11.
Khoo KH, Hoe KK, Verma CS, Lane DP. Drugging the p53 pathway: understanding the route to clinical efficacy. Nat Rev Drug Discov. 2014;13:217–36.
Belyi VA, Ak P, Markert E, Wang H, Hu W, Puzio-Kuter A, et al. The origins and evolution of the p53 family of genes. Cold Spring Harb Perspect Biol. 2010;2:a001198.
Momand J, Villegas A, Belyi VA. The evolution of MDM2 family genes. Gene. 2011;486:23–30.
Harms KL, Chen X. The functional domains in p53 family proteins exhibit both common and distinct properties. Cell Death Differ. 2006;13:890–7.
Dötsch V, Bernassola F, Coutandin D, Candi E, Melino G. P63 and P73, the ancestors of P53. Cold Spring Harb Perspect Biol. 2010;2:1–15.
Muttray AF, O'Toole TF, Morrill W, Van Beneden RJ, Baldwin SA. An invertebrate mdm homolog interacts with p53 and is differentially expressed together with p53 and ras in neoplastic Mytilus Trossulus haemocytes. Comp Biochem Physiol B Biochem Mol Biol. 2010;156:298–308.
Lane DP, Cheok CF, Brown CJ, Madhumalar A, Ghadessy FJ, Verma C. The Mdm2 and p53 genes are conserved in the arachnids. Cell Cycle. 2010;9:748–54.
Lane DP, Cheok CF, Brown C, Madhumalar A, Ghadessy FJ, Verma C. Mdm2 and p53 are highly conserved from placozoans to man. Cell Cycle. 2010;9:540–7.
Gomes Dos Santos H, Nunez-Castilla J, Siltberg-Liberles J. Functional Diversification after Gene Duplication: Paralog Specific Regions of Structural Disorder and Phosphorylation in p53, p63, and p73. PLoS One. 2016;11(3):1–27.
Rutkowski R, Hofmann K, Gartner A. Phylogeny and function of the invertebrate p53 superfamily. Cold Spring Harb Perspect Biol. 2010;2:a001131.
Pintus SS, Fomin ES, Oshurkov IS, Ivanisenko VA. Phylogenetic analysis of the p53 and p63/p73 gene families. In Silico Biol. 2007;7:319–32.
King N, Westbrook MJ, Young SL, Kuo A, Abedin M, Chapman J, et al. The genome of the choanoflagellate Monosiga Brevicollis and the origin of metazoans. Nature. 2008;451:783–8.
Belyi VA, Levine AJ. One billion years of p53/p63/p73 evolution. Proc Natl Acad Sci U S A. 2009;106:17609–10.
McLysaght A, Hokamp K, Wolfe KH. Extensive genomic duplication during early chordate evolution. Nat Genet. 2002;31:200–4.
Oldfield CJ, Meng J, Yang JY, Yang MQ, Uversky VN, Dunker a K. Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners. BMC Genomics. 2008;9 Suppl 1:S1.
Nedelcu AM, Tan C. Early diversification and complex evolutionary history of the p53 tumor suppressor gene family. Dev Genes Evol. 2007;217:801–6.
Lu W-J, Amatruda JF, Abrams JM. p53 ancestry: gazing through an evolutionary lens. Nat Rev Cancer. 2009;9:758–62.
Sulak M, Fong L, Mika K, Chigurupati S, Yon L, Mongan NP, et al. TP53 copy number expansion is associated with the evolution of increased body size and an enhanced DNA damage response in elephants. elife. 2016;5:e11994.
Karakostis K, Ponnuswamy A, Fusée LTS, Bailly X, Laguerre L, Worall E, Vojtesek B, Nylander K, Fåhraeus R. p53 mRNA and p53 protein structures have evolved independently to interact with MDM2; 2015. p. 1–32.
Brown CJ, Johnson AK, Dunker AK, Daughdrill GW. Evolution and disorder. Curr Opin Struct Biol. 2011;21:441–6.
Forman-Kay JD, Mittag T. From sequence and forces to structure, function, and evolution of intrinsically disordered proteins. Structure Elsevier Ltd. 2013;21:1492–9.
Letunic I, Bork P. Interactive tree of life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res. 2011;39:W475–8.
Dehal P, Boore JL. Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol. 2005;3:e314.
Mendoza M, Mandani G, Momand J. The MDM2 gene family. Biomol Concepts. 2014;5:9–19.
Meyer A, Van De Peer Y. From 2R to 3R: evidence for a fish-specific genome duplication (FSGD). BioEssays. 2005;27:937–45.
Schon O, Friedler A, Bycroft M, Freund SM, Fersht AR. Molecular mechanism of the interaction between MDM2 and p53. J Mol Biol. 2002;323:491–501.
Iakoucheva LM, Radivojac P, Brown CJ, O'Connor TR, Sikes JG, Obradovic Z, et al. The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res. 2004;32:1037–49.
Teufel DP, Bycroft M, Fersht AR. Regulation by phosphorylation of the relative affinities of the N-terminal transactivation domains of p53 for p300 domains and Mdm2. Oncogene. 2009;28:2112–8.
Lee CW, Ferreon JC, Ferreon ACM, Arai M, Wright PE. Graded enhancement of p53 binding to CREB-binding protein (CBP) by multisite phosphorylation. Proc Natl Acad Sci U S A. 2010;107:19290–5.
Hornbeck PV, Zhang B, Murray B, Kornhauser JM, Latham V, Skrzypek E. PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Nucleic Acids Res. 2015;43:D512–20.
Light S, Sagit R, Sachenkova O, Ekman D, Elofsson A. Protein expansion is primarily due to indels in intrinsically disordered regions. Mol Biol Evol. 2013;30:2645–53.
Borcherds W, Theillet F, Katzer A, Finzel A, Mishall KM, Powell AT, et al. Disorder and residual helicity alter p53-Mdm2 binding affinity and signaling in cells. Nat Chem Biol. 2014;10(12):1000–2.
Kussie PH, Gorina S, Marechal V, Elenbaas B, Moreau J, Levine AJ, et al. Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain. Science. 1996;274:948–53.
Shin J-S, Ha J-H, Lee D-H, Ryu K-S, Bae K-H, Park BC, et al. Structural convergence of unstructured p53 family transactivation domains in MDM2 recognition. Cell Cycle. 2015;14(4):533–43.
Muñoz V, Serrano L. Elucidating the folding problem of helical peptides using empirical parameters. Nat Struct Biol. 1994;1:399–409.
Coffill CR, Lee AP, Siau JW, Chee SM, Joseph TL, Tan YS, et al. The p53 – Mdm2 interaction and the E3 ligase activity of Mdm2 / Mdm4 are conserved from lampreys to humans. Genes Dev. 2016;30(3):281–92.
Zdzalik M, Pustelny K, Kedracka-Krok S, Huben K, Pecak A, Wladyka B, et al. Interaction of regulators Mdm2 and Mdmx with transcription factors p53, p63 and p73. Cell Cycle. 2010;9:4584–91.
Tanimura S, Ohtsuka S, Mitsui K, Shirouzu K, Yoshimura A, Ohtsubo M. MDM2 interacts with MDMX through their RING finger domains. FEBS Lett. 1999;447:5–9.
Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, et al. Ensembl 2013. Nucleic Acids Res. 2013;41:D48–55.
Waterhouse RM, Tegenfeldt F, Li J, Zdobnov EM, Kriventseva EV. OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs. Nucleic Acids Res. 2013;41:D358–65.
Li C, Pazgier M, Li C, Yuan W, Liu M, Wei G, et al. Systematic mutational analysis of peptide inhibition of the p53-MDM2/MDMX interactions. J Mol Biol. 2010;398:200–13.
Penn O, Privman E, Ashkenazy H, Landan G, Graur D, Pupko T. GUIDANCE: a web server for assessing alignment confidence scores. Nucleic Acids Res. 2010;38:W23–8.
Schwarz G. Estimating the dimension of a model. Ann Stat Institute of Mathematical Statistics. 1978;6:461–4.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30:2725–9.
Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59:307–21.
Wang Q, Arighi CN, King BL, Polson SW, Vincent J, Chen C, et al. Community annotation and bioinformatics workforce development in concert--Little Skate Genome Annotation Workshops and Jamborees. Database (Oxford). 2012;0:bar064.
Venkatesh B, Lee AP, Ravi V, Maurya AK, Lian MM, Swann JB, et al. Elephant shark genome provides unique insights into gnathostome evolution. Nature. 2014;505:174–9.
Cameron RA, Samanta M, Yuan A, He D, Davidson E. SpBase: the sea urchin genome database and web site. Nucleic Acids Res. 2009;37:D750–4.
Voskoboynik A, Neff NF, Sahoo D, Newman AM, Pushkarev D, Koh W, et al. The genome sequence of the colonial chordate, Botryllus Schlosseri. elife. 2013;2:e00569.
Privman E, Penn O, Pupko T. Improving the performance of positive selection inference by filtering unreliable alignment regions. Mol Biol Evol. 2012;29(1):1–5.
This work was supported by the Swedish Research Council.
Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123, Uppsala, Sweden
Emma Åberg, Fulvio Saccoccia, Manfred Grabherr, Wai Ying Josefin Ore, Per Jemth & Greta Hultqvist
Department of Pharmaceutical Biosciences, Uppsala University, BMC, Box 591, SE-75124, Uppsala, Sweden
Greta Hultqvist
Emma Åberg
Fulvio Saccoccia
Manfred Grabherr
Wai Ying Josefin Ore
Per Jemth
Conceptualizon EÅ, PJ and GH. Methodology EÅ, FS, WO, MG and GH. Analysis EÅ, FS, MG, PJ and GH. Writing EÅ, PJ and GH. All authors read and approved the final manuscript.
Correspondence to Per Jemth or Greta Hultqvist.
Identification list of all p53/p63/p73 sequences that are in the phylogenetic tree in Fig. 2a. The species included are itemized according to phyla and paralog where the Latin name, sequence ID and database is listed. (PDF 81 kb)
Alignment of the TAD in the p53/p63/p73 protein family. This alignment together with the alignment of the rest of the protein (not shown) was used to generate the phylogenetic tree. The color-coding is according to the eBioX alignment tool. (PDF 106 kb)
Sequences Logos based on the multiple sequence alignment of p53/p63/p73 TAD. The color-coding is according to the eBioX alignment tool. (PDF 13 kb)
Phylogenetic tree with support values based on multiple sequence alignment of the p53/p63/p73 protein family only including species with the TAD. Support values are presented as numbers between 0 and 1 in a color gradient between red and blue. (PDF 94 kb)
Identification list of all MDM sequences that are in the phylogenetic tree in Fig. 2B. The species included are itemized according to phyla and paralog where the Latin name, sequence ID and database are listed. (PDF 74 kb)
Alignment of the p53/p63/p73BD in the MDM protein family. This alignment together with the alignment of the rest of the protein (not shown) was used to generate the phylogenetic tree. The color-coding is according to the eBioX alignment tool. (PDF 3715 kb)
Sequence Logos based on the multiple sequence alignment of MDM p53/p63/p73BD. The color-coding is according to the eBioX alignment tool. (PDF 25 kb)
Phylogenetic tree with support values based on multiple sequence alignment of the MDM protein family only including species with the p53/p63/p73 BD. Support values are presented as numbers between 0 and 1 in a color gradient between red and blue. (PDF 21 kb)
Åberg, E., Saccoccia, F., Grabherr, M. et al. Evolution of the p53-MDM2 pathway. BMC Evol Biol 17, 177 (2017). https://doi.org/10.1186/s12862-017-1023-y
DOI: https://doi.org/10.1186/s12862-017-1023-y


text:
Danish Motor merchant
Photo courtesy of Danish Maritime Museum, Elsinore
Name Argentina
Completed 1921 - Kjobenhavns Flydedok & Skibsværft A/S, Copenhagen
Owner Det Forenede D/S (DFDS), Copenhagen
Homeport Copenhagen
Date of attack 17 Mar 1940 Nationality: Danish
Fate Sunk by U-38 (Heinrich Liebe)
Position 60° 47'N, 0° 30'W - Grid AN 2125
Complement 33 (33 dead - no survivors)
Route Copenhagen (13 Mar) - Las Palmas - South America
Cargo General cargo
History Completed in December 1921 as Danish Polarhavet for O.J. Eskildsen, Copenhagen. 1924 renamed Argentina for Det Forenede D/S (DFDS), Copenhagen.
On 13 March 1940 the neutral Argentina left Copenhagen and was reported missing in the North Sea, after sending her last radio messsage on 17 March.
At 23.25 hours on 17 March 1940 U-38 fired a spread of two torpedoes at an illuminated steamer of about 5000 grt east of Unst, Shetlands. The ship sank 10 minutes after being hit by one torpedo. The victim must have been the Argentina.
On board We have details of 32 people who were on board.

redpajama_set_name: RedPajamaCommonCrawl


Join us for another free BCSEA Webinar.
Our Earth stores an enormous source of renewable energy right beneath our feet: geothermal power.
Geothermal energy is delivering clean, base-load and low cost electricity in 25 countries as well as commercial heating in 70 countries.
In Canada, the geothermal industry has yet to gain traction despite having world class resources. It has great promise... but what will it take to turn the promise into reality?Our guest presenter Alison Thompson has dedicated a substantial part of her career to investigating and demonstrating the technical and commercial viability of high enthalpy geothermal energy. Since 2007, she has been the Managing Director and Executive Director of the Canadian Geothermal Energy Association.
With over 15 years of experience in project management, business and technology development in the North American energy sector, Ms. Thompson has successfully sought changes in federal tax regulations that now include geothermal energy. She has also been influential in creating eligibility for geothermal projects and reports for provincial and federal government funding. She was the inaugural recipient of the Belle Mulligan Award for Leadership from the Canadian Investor Relations Institute, and is a frequent contributor to published geothermal papers.
She is Chair of Borealis GeoPower, and a board member of Deep Earth Energy Production; a past Officer of Alterra Power (formerly Magma Energy); and an external evaluator for the Canada Foundation for Innovation. Globally, she has a seat on the Executive Committee of IEA-GIA; is a board member of the IGA; and was Geothermal Energy Forum Chair at the 20th World Petroleum Congress. She has also served on the European Union's Enhanced Geothermal Innovative Network for Europe's (ENGINE) Stakeholders Committee.
Ms. Thompson holds Bachelor and Master of Chemical Engineering degrees from McGill University, a Professional Engineering designation from the Association of Professional Engineers and Geoscientists of Alberta, a U.S. Engineer Intern designation, and a Master of Business Administration degree from Queen's University. She lives in Calgary, Alberta, with her husband and son.


text:
Rob Jamieson
Rob brings an impressive 49-years of real estate experience to RE/MAX having worked as an agent in New Zealand for 5 years, Canada for 17 years and most recently in the Cayman Islands for 27 years. Rob specializes in all aspects of real estate including residential, commercial and investment. In Canada, he also worked in the inflationary and deflationary markets in British Columbia.
Rob made the move to the Cayman Islands in early 1994. He was hired to run a tall ship operation because of his background in business and sailing.
"Besides the weather, the diversity of its population with 130 different nationalities is what I truly love about the Cayman Islands and real estate is primarily a people business," added Rob Jamieson
Rob has completed numerous courses over the years through BCREA and UBC on ICI and real estate management. He completed and passed all courses of CCIM. Rob has also been honored by CIREBA for his 25 years of dedicated service in the real estate industry.
$5,699,000 KYD
Le Blanc - Britannia Estates
5 beds | 6 bath | 5,000 sqft
Le Bleu - Britannia Estates
RE/MAX Cayman Islands
Seven Mile Shops, West Bay Road
P.O. Box 30189, KY1-1201
2023 © RE/MAX Cayman Islands. All rights reserved. Proud member of CIREBA. | Privacy Policy | Cookies Policy | Back office


Whatever you want, Southern California has got it. With dive bars, designer boutiques, and divine beaches, there is truly something for everyone here. San Diego, Santa Barbara, and beyond—there is so much to see in So Cal.
From luxe city escapes to ultra chill beaches, you really can live the dream here. If you haven't been to the Golden State yet, it is time to get over here!
Spend a week or a year exploring my favorite things to do in Southern California!
San Diego's urban cultural park is home to renowned museums, theaters, and, of course, the world-famous San Diego Zoo. It's easy to see why the San Diego Zoo was voted the number one zoo on the planet—it has more than 3,700 different animals and 650 unique species!
This is the ultimate California beauty activity. Swim, fish, surf, and camp at one of So Cal's great beaches—Crystal Cove State Park and El Capitan State Beach!
You need to spend at least one day wandering the powdery sand beach, exploring the caves and beachside cliffs, and appreciating the natural wonders of the Crystal Cove State Park.
While El Capitan State Beach is an amazing place 365 days a year, you absolutely have to visit the beach during fall when Monarch butterflies come here to breed. After a long day out, watching the sunset over the crystal clear water is the best past time!
Indulge in fresh California cuisine, browse the indie boutiques, admire the stunning architecture of State Street in Santa Barbara. It's the perfect place for a leisure stroll–find out why everyone adores this city at the heart of the American Riviera!
There is no better place than Hollywood to admire the stars! Head to the Griffith Observatory to check out the Samuel Oschin Planetarium, get an up close and personal view of the Hollywood Sign, and look beyond this world to see some of the universe's brightest stars.
Anyone who follows my Instagram, knows I'm a frequent visitor to this heavenly place. Founded in So Cal in 1948, In-N-Out gave us the world's first drive-through hamburger restaurant, and they have been giving back to the world ever since.
Seriously, the best burgers ever.
Be sure to check out the "secret" menu, featuring greats like the grilled cheese sandwich or the famous animal-style burger.
One of San Diego's best spots for diving, snorkeling, and kayaking, this calm oasis is the perfect place to splash around all day. There are secret sea caves around the cove that you can only access from the water, so kayaking is a must!
When you're done, grab an ice cream cone and people watch or enjoy browsing the shops around the cove.
Home to amazing hikes ranging from easy to advanced difficulties, Southern California has something for everyone. Some of my favorites hikes are The Slot in Anza Borrego, Bridge to Nowhere and of course, the Hollywood Sign.
If you want something a bit easier, take a stroll through Torrey Pines Reserve in San Diego—ocean views and sea breezes!
Welcome to my hometown of Temecula! Did you know that the illustrious Temecula Valley grows grapes for more than 50 different types of wine?
I didn't appreciate my hometown much growing up, but now I'd highly recommend that you come thirsty, book a bed and breakfast, and see why American wine really is something to rave about.
The Californian desert city of Palm Springs has been one of the hottest getaway destinations for those looking for a little break from the big cities for over half a century.
The city is within easy reach of Los Angeles, San Diego, and San Bernardino, and is surrounded by beautiful mountain scenery. The desert climate makes Palm Springs an ideal vacation destination year-round and is the perfect spot for a weekend escape with your girlfriends.
As a girl born and raised in So Cal, I believe that Disneyland really is worth the hype. The newer park, California Adventure, shows off the Golden State's style and combines the magic of Disney with the best that California has to offer.
A Park-Hopper ticket will get you into both parks, and you'll get the best of both worlds!
The Santa Monica Pier is probably one of the busiest piers on the West coast, but you'll find restaurants, food carts, specialty shops, and amusements galore!
Hit the boardwalk, enjoy an ice cream cone and take a spin on the roller coaster.
Carved into the Hollywood Hills, this iconic amphiteather hosts hundreds of concert each year. It is the ideal outdoor venue, perfect for the warm summer nights!
Take Route 1 starting in the sleepy beach town of Dana Point, through the luxe Laguna Beach, the glittering lights of Los Angeles, and up through glam Santa Barbara and into the lush wine country. The more time you have to appreciate the Pacific Coast Highway, the better.
My tip: Keep going up toward San Francisco for the ultimate Californian road trip.
Ever wonder what So Cal looked like when the first settlers came? You can explore the lush 2,000 acres of Torrey Pines and see exactly what the first Californians saw. I highly suggest planning some time for tandem paragliding at Torrey Pines. It's one of the coolest things you can do in San Diego!
Joshua Tree National Park straddles the cactus-dotted Colorado Desert and the Mojave Desert and overlooks the Coachella Valley. It is home to a handful of eclectic towns in the middle of a vast wilderness.
Named after the native yucca brevifolia, the beautiful desert will amaze you with its serene beauty!
Los Angeles County Museum of Art is the largest art museum in the western US and attracts nearly a million visitors annually. It holds more than 150,000 works spanning the history of art from ancient times to the present–it's the perfect spot to hit to feel the creative vibes of Los Angeles.
In addition to art exhibits, the museum features film and concert series.
My Favorite SoCal Travel Styles!
I really enjoyed reading your thorough breakdown of things to do in SoCal. I've been up to CA before but never been to this area. Going up in June and I can't wait.
Keep up the great write-ups. Does your Instagram also have more pictures and such?


I have a major woman-crush on Rosie Huntington-Whiteley.
Not only is she gorgeous...her style is flawless!
How is it possible to always look so stylish and put-together, while also looking like "I didn't try too hard"?? Oh, NBD, I just roll out of bed this good looking...pssh! I wish.
Who is your style crush??
Total girl crush too! Her and Blake Lively-- can I have their wardrobe please?!


Oxford dons are challenging their new vice-chancellor over his plans to reform the way the ancient university is run.
New Zealander John Hood has published proposals to streamline decision-making, including setting up a small board of trustees composed of alumni business people, which are due to be discussed by Congregation, the "dons' parliament" of 3,552 academics.
Before the consultation period on Professor Hood's green paper has elapsed, a group of academics is mounting a challenge in Congregation to delay discussion of the reforms. It is also seeking to stop reviews of research and teaching performance and challenge the current reorganisation of the historic Bodleian library.
Congregation is the university's governing body but rarely exercises its powers to call the management to account. The last time it flexed its muscles was in 1996, when millionaire Wafic Said offered £20m for a business school. Congregation overruled his planned site and the business school was built on a site near Oxford railway station - where it has helped transform a rundown area of the city.
At Cambridge University there have been frequent clashes between members of the equivalent body, Regent House, and the former vice-chancellor Sir Alec Broers, over his attempts to modernise the university's structure and increase the powers of the executive.
But in Oxford reform was agreed more amicably in 2000. However the 20-member council responsible for academic governance which was introduced then has been mirrored by a body for the colleges which felt sidelined by that reform. This dual system has led to delays and confusion.
Professor Hood's proposal for a 150-strong academic council would comprise all 39 heads of colleges and so bring them into a single structure. It would also contain members elected by Congregation, heads of the 40 largest departments and individuals from the museums, and the chief executive of Oxford University Press, among others.
But his plan for a board of trustees, putting the affairs of Oxford in the hands of business people for the first time in its 800 years, has stirred opposition among the dons, who also claim the proposal is being rushed through in the middle of the examination season without proper opportunity for full consideration.
A delaying motion put down today, which gathered more than 80 signatures, seeks to postpone discussion until November. A second motion warns of a threat of academic freedom in a second green paper on academic strategy and seeks to ban joint college/university reviews of individuals' performances.
A third motion calls on the management of Oxford libraries to present a full report to Congregation on plans for reorganisation. Some academics fear the reorganisation of the Bodleian will empty books from the iconic Radcliffe Camera building.
However Ronald Milne, the acting director of the university library services, has sought to reassure them with a statement that although consultation was taking place on a different use for the building, no decision had been taken and "one does not despoil an icon".


text:
Winnipeggers on Ukrainian flight that crashed in Iran
Megan Benedictson Supervising Digital News Producer
@CTVMDB Contact
Published Wednesday, January 8, 2020 12:15PM CST Last Updated Friday, January 10, 2020 10:51AM CST
WINNIPEG -- A scientist who was an alumna of the University of Manitoba, a family of three, and a graduate student in biomedical engineering were among a number of victims from Winnipeg who were on the plane that crashed shortly after taking off from Tehran Wednesday morning.
A solemn gathering for students was held at the University of Manitoba campus Wednesday afternoon, involving members of the university's Iranian Student Association, which told CTV News it was aware of eight people with connections to Winnipeg who were on board the plane.
(Source: Touria Izri)
The students put up a memorial with photos of victims of the crash, including Amirhossein Ghorbani Bahabadi, who was studying at the International College of Manitoba, was on board the flight.
His friends told CTV News Winnipeg he had recently travelled from Winnipeg to Iran. Ghorbani Bahabadi was studying science and was planning to become a medical doctor. His friend, Arman Ahmadi said he's sad his friend will no longer be able to pursue his passion.
Amirhossein Ghorbani Bahabadi, who was studying at the International College of Manitoba, was on board the plane.
GRADUATE STUDENT AMONG VICTIMS
A member of the board with the student association told the Canadian Press his friend Amirhossien Ghasemi, a graduate student in biomedical engineering, was among those on the plane.
"I saw him before he left the country," said Amir Shirzadi.
(Submitted photo).
Shirzadi said Ghasemi was visiting family in Iran and heading back to Winnipeg at the time of the crash.
"I can't use past tense. I think he's coming back. We play again. We talk again. It's too difficult to use past tense, too difficult. No one can believe it."
(Touria Izri/CTV News)
FAMILY RETURNING FROM HOLIDAY IN CRASH
A family of three, Mehdi Sadeghi, his wife Bahareh Hajesfandiari and their daughter Anisa Sadeghi, was also among the victims from Winnipeg.
A neighbour of the family, Behnam Soltani, told CTV News the three had travelled to Iran for the first time in four years, to visit their family over the holidays.
"They were a really nice family, a caring family," Soltani told CTV News. "Not just me, everybody who know them – they are in shock. We can't even believe it."
He said the saddest part was that the trio had said goodbye to family members less than 20 minutes before the plane went down.
Soltani said he had lived next to the family for around four or five years, and was close with them. He described them as active members of the Iranian community in Winnipeg.
He said Mehdi Sadeghi had worked for Habitat for Humanity. He was working at Fresh Projects Builders at the time of the crash.
In a statement to CTV News, Janice Froese, president of Fresh Projects Builders, said Mahdi was "an amazing co-worker and friend" that had worked there since 2017.
"We at FRESH Projects will be forever grateful for the opportunity to have known him and his family. It is with heavy hearts that we will remember his warm smile and genuine caring personality."
Froese said Bahareh has also worked there for a time and will "truly be missed," extending condolences for all who died in the crash.
"We hold all the family and friends of the victims close in our thoughts as we go through this difficult time together," Froese said.
Soltani said a memorial for the family is in the works for this weekend.
Bahareh is being remembered by her co-workers as an excellent and accomplished engineer and a very kind person. Bahareh was working as a project administrator at a development and construction company called Marwest Group of Companies.
"She was very, very sweet, one of the kindest people you will ever meet," said Armin W. Martens, a principal at the company. "She made connections to everybody that she met, even though she was quiet."
He said her death has hit her co-workers, many of whom had become friends with her, very hard.
"She's an amazing human being," said Martens. "This is a sad event, but people should know how great she is."
MIDDLE SCHOOL STUDENTS OFFERED SUPPORT
A spokesperson for the Pembina Trails School Division said two of its students, who attended different schools within the division, were also listed as being on board.
A letter was sent home to parents of students at Henry G. Izatt Middle School, indicating the name of a grade 5 student was on the passenger list.
"Relatives of the student have shared that they have begun the mourning process," said the letter, adding the division's student services team would be offering support.
SCIENTIST REMEMBERED AS 'ONE OF THE BEST'
Scientist Forough Khadem, who graduated from the U of M with a PhD in 2016, was a passenger on the flight.
Khadem worked in Winnipeg for Mitacs, a non-profit research organization that collaborates with academic institutions.
Forough Khadem, who graduated from the U of M with a PhD in 2016, was a passenger on the flight. (Source: lindau-nobel.org, with courtesy to Forough Khadem)
A statement from Eric Bosco, chief business development officer for Mitacs, said the organization is "deeply saddened" by the news.
He said Khadem had worked as a business development specialist with Mitacs since May of 2016 and she was "a passionate supporter of innovation in Manitoba."
"We will remember Forough's passion for Mitacs, enthusiasm for innovation in Manitoba, and her positive outlook on life. We will miss her humour, her kindness, and her warm spirit," said Bosco.
An immunologist who knew her described her on Twitter as "one of the best human beings" he knew.
Seemed like yesterday we celebrated your Ph.D. defense. You were one of my best trainees. So difficult to believe you are gone. Died in #Tehran crash. My heart is broken. ���������� @UM_Immu @umanitoba @UM_RadyFHS @um_research @umanitoba pic.twitter.com/JDKvJ70KGR
— Jude (@drleish) January 8, 2020
Gone so soon!! You were one of the best human beings I ever know. You will forever remain a gem. I will miss you and humanity will miss you dearly. Rest in Peace, Dear Forough. @UM_RadyFHS @umanitoba @UM_Immu @um_research @Research_MB pic.twitter.com/Rwd6CCerMD
She will be missed dearly! Our humanity lost a beautiful soul ... Rest in Peace my dearest friend and sister! My deepest condolences to the families and friends of all the victims of this tragic plane crash. May God grant us strength as we all go through this difficult time
— Hana Klassen Vakili (@HanaVakili) January 8, 2020
The University of Manitoba is deeply saddened by the tragic news coming out of Tehran. It is our understanding that there were UM students and an alumna on board the flight.
— University of Manitoba (@umanitoba) January 8, 2020
Another two graduates of the University of Manitoba, who were most recently living in Alberta, have been confirmed as being among the crash victims.
Pedram Mousavi and Mojgan Daneshmand, who were with the University of Alberta's Faculty of Engineering, both graduated with PhDs from the U of M in 2001. They were on the flight with their daughters, Darya and Darina Mousavi.
A MOTHER AND SON
CTV News Winnipeg confirmed that mother and son Farzaneh Naderi and Noojan Sadr were on the plane.
Naderi worked as a full-time staff at St. Amant, a resource for Manitobans with developmental disabilities and autism. In a statement, St. Amant described Naderi as a "dedicated autism tutor" who had a "big heart" and "genuinely cared about the children she supported, their families and her colleagues."
Mother and son Farzaneh Naderi and Noojan Sadr, who are pictured in this image, were on the flight. (Source: Amir Shirzadi)
Crash leaves U of M shocked
President of the University of Manitoba, David Barnard, said it has been hard having this tragedy hit so close to home and it has rocked the school.
"For many of us, it's a feeling of something that was formerly at a distance, not a good thing, a bad thing for sure, but distant from us, all of a sudden it's now part of us. I think the shock of that is a difficult thing for each of us to cope with," said Barnard.
"These are, as you say, students and some folks who have worked at the university in various capacities and it's just difficult to reconcile where we were yesterday with where we are today, as we think of those members of our community."
Barnard said in the coming days the school will be looking at ways to help those at the university deal with this tragedy and move forward from the incident.
Sixty-three Canadians were on board Ukrainian International Airlines flight PS752, which was destined for Kyiv when it went down minutes after take-off.
READ MORE: Flight PS752 crash: What we know about the Canadians killed in airliner tragedy
Winnipeg's mayor and Manitoba's premier have both shared condolences for victims of the crash.
Saddened to hear of the tragic plane crash in Tehran. We mourn the loss of those on board, including the 63 Canadians and those with ties to Manitoba.
Our thoughts and prayers go out to the family and friends of the victims during this difficult time.
— Brian Pallister (@BrianPallister) January 8, 2020
63 Canadians are among reported dead after Ukraine International Airlines plane crashed near Iran's capital, killing all on board. The #WinnipegSign is dimmed in respect to the tragic loss of all life incl Iranian, Canadian, Ukrainian, Swedish, Afghan, German & British citizens. pic.twitter.com/go8KqWmHUv
— Mayor Brian Bowman (@Mayor_Bowman) January 8, 2020
-With files from CTV's Touria Izri, CTV's Danton Unger and The Canadian Press
Vigil for victims of plane crash in Iran to take place Friday at University of Manitoba


Similar to the Solstice frame, the Helix frame was designed without the cat eye flare to appeal to all adventurers. This frame is made from Zebrawood, a tropical hardwood found in West Africa. These bold frames are distinguished by their cream colored grain streaked with dark brown stripes.


text:
All Living Organisms in a Habitat
When you look around and observe nature, have you ever wondered how do animals and plants live according to the region and atmosphere? How they are dependent on each other for survival?
Scientists have categorized these regions into habitats and ecosystems in which living organisms either live independently or are interdependent.
A habitat is different from an ecosystem in that
Different environments around the world
Polar Habitats
Aquatic Habitats
Coastal Habitat
Desert Habitat
Deep-Ocean
The living organisms in a habitat are called
The place where a community of plants and animals lives
What needs of an organism are provided by its habitat
Where do most of the worlds living things live
Which of the following is not a component of the physical habitat in which organisms live?
A habitat is different from an ecosystem in that of size, where living and non-living organisms interact and thus consist of many habitats. A single ecosystem will include humans and numerous communities of all living organisms.
All living organisms in a habitat are composed of living matter. This includes oxygen, hydrogen, carbon and nitrogen.
Carbon is the most important matter contained in living organisms. The natural environment and the area where an organism lives is called a habitat.
Living organisms in a habitat
Different environments around the world give rise to different types of habitats. Each area is unique and specific for supporting biological life.
Polar habitats include the North and South poles, which are highest in latitude and receive the lowest sun energy, resulting in extremely low temperatures. These habitats are inhabited by polar bears, seals, whales, fish, and penguins at the South Pole only.
Aquatic habitats include freshwater (lakes, rivers, ponds), and coastal and marine habitats (seas, oceans).
Coastal habitats are the juncture where aquatic habitat congregates with terrestrial habitat, including rock pools, beaches, and dunes.
Desert habitats cover 35% of the world's land with extreme dryness, heat, arid conditions, and water scarcity. Cacti and sidewinder snakes are examples of adaptation to the environment by a population in a desert habitat.
Forests are a natural habitat covering 31% of the world's land, dominated by lush green trees and categorized according to the world's environment, including coastal, coniferous, tropical rain, and boreal forests.
Grassland habitats have warm to moderate weather conditions, consisting of open plains ideal for grazing animals. The soil surface protects the grass stems from extreme weather. Wild horses in Asia and bison in the US are examples of grassland habitat animals.
Tundra habitats are also known as ice deserts with shallow temperatures and are dominated by wolves, reindeers, and penguins, located in Alaska and Canada.
Wetlands are waterlogged habitats covering 7% of the world's land and act as a natural filtration system for cleaning freshwater habitats. In addition, they act as a protective barrier for the surrounding natural habitats.
Microhabitats are small-sized habitats found in minute areas, including leaves' underside, which has the perfect environment for bacterial growth.
Deep-Ocean habitats are found in an extreme depth of aquatic environment and still has undiscovered areas due to high water pressure conditions.
The living organisms in a habitat are called biotic components. For example, plants and animals are all living organisms that inhabit an environment.
All non-living things are called abiotic components, including soil and water. An organisms environment consists of biotic and abiotic components.
The place where a community of plants and animals lives is called an ecosystem. It is affected by geographical conditions including climate and water availability.
These conditions play a role in determining the types of organisms and its size. As a result, the ecosystem size can vary; from a microscopic cell to a gigantic continent.
The dynamics of any ecosystem include the following major processes:
· Flow of energy from sun
· Cycling of nutrients
Pond ecosystems are an example of animal ecosystem which includes snakes, ducks, swans, turtles, fish, insects and microorganism. It is a perfect example of a community of living organisms and their nonliving environment. The dynamics of pond ecosystem can be explained as:
Producers: photosynthetic algae and floating microorganisms are called producers and produce food by absorbing sunlight
Primary Consumers: Floating insects and eat producers
Secondary Consumers: Small fish, and frogs that eat primary consumers
Tertiary Consumers: Prawns and animals that eat secondary consumers
Decomposers: Fungi and bacteria that live at the bottom of the pond or in floating water and help the decaying process and form the reusable chemical substances for producers
These terms can be categorized by their interrelationships as follows:
Habitat: The physical location where an organism lives is termed its habitat
Population: All members of the habitat are collectively called a population
Community: All populations of organisms that live in a habitat
Ecosystem: A community and habitat where all organisms live and coordinate
Biosphere: Earths landscape and all of its life is known as the bioshpere
The needs of an organism provided by its habitat are food, water, and shelter. A habitat contains all sufficient items for an organism to survive.
Most of the world's living things live on land.
· Land (80%)
· Ocean (15%)
· Freshwater (5%)
Environmental differences within ecosystems are generally caused by natural or human interventions. These include flooding, droughts, seasonal changes, earthquake, tornados, deforestation, land conversions/developments, and pollution.
With this change, animals and plants adapt themselves to survive and search for food, water, and shelter. One species' abandoned habitat is home for some other species.
For example, grassland forestation can lead to a habitat for squirrels and birds when grazing animals exit their habitats.
150 to 200 species of living organisms become extinct within a day due to the loss of their habitat. Therefore, worldwide organizations seek to conserve natural land and ocean habitats due to environmental changes.
Every species cannot survive human intervention in natural habitats.
The research found that the earth's terrestrial surface has changed due to massive human activities.
The only solution for stopping human intervention and maintaining sustainability is to apply strict laws and regulations and regular monitoring to concerned authorities for protecting all living animals in a habitat.
In addition, scientists are also trying to discover new ecosystems for preserving nature. Jaich Maa is the new ecosystem discovered in 2018 underwater in the Gulf of California by research institutions of Mexico and US.
The study of the patterns in the distribution of plants and animals around the world is called Biogeography. It should be encouraged by every government for protecting our safe environment.
Bacteria is not a component of the physical habitat in which organisms live.
Sunlight, wind, sand and water are examples of the non living environment and components of the physical habitat.
What is a Primary Consumer in Ecology? Examples in a Food Chain
What are Secondary Consumers in Ecology? Examples in Food Chain
What is a Tertiary Consumer in Ecology? Examples and Definition
The variety of organisms able to adapt to various environments on earth
Study of the distribution of animals and plants around the world