Evolution utilizes 3D topologically associated domains to build new proteins by means of chromosomal translocations

We developed and applied a novel "evolution of protein domains" (EvoProDom) model for evolution of proteins which is based on "mix and merge" of protein domains. In EvoProDom we defined evolutionary events, translocation, as reciprocal exchange of protein domains between two groups of orthologous proteins in the studied organisms. EvoProDom is implemented on an assembled comprehensive collection of 76 organisms, with complete genomes and annotated proteomes, from diverse taxa. EvoProDom includes a detailed comparison between subterranean, fossorial and above-ground species. We found translocations of key protein domains that are involved in pathways for sensing and regulating responses to environmental cues such as light and oxygen. Proteins containing these domains were found to be essential hubs in their PPI sub-networks. Hubs are the major contributors to the over-all shape of PPI network. A measure of the topology was used for the clustering analysis. Therefore, the distribution of hubs in ecology-specific of these PPI sub-networks accounts for the sub-clustering by ecology. Moreover, we found a significant association between the domains exchange and 3D topological association using HiC experimental data. We organized our data for the subterranean, fossorial and aboveground animals in a user-friendly accessible database, PASTORAL, which contains organisms from diverse taxa confined to specific ecologies. This feature enables evolutionary biologists to study convergent evolution related to stress response and other ecology related features.