EvoProDom: Evolutionary model of protein families by means of translocations of protein domains

Abstract

Here, we developed a novel evolution of protein domains (EvoProDom) model for evolution of proteins, which was based on mix and merge of protein domains. We collected and integrated genomic and proteome data for 109 organisms. These data include protein domain content and orthologous protein families. In EvoProDom, we defined evolutionary events, such as translocations, as reciprocal exchanges of protein domains between orthologous proteins of different organisms. We found that protein domains, which frequently appear in translocation events, were enriched in trans-splicing events, i.e., producing novel transcripts fused from two distinct genes. We presented in EvoProDom, a general method to obtain protein domain content and orthologous protein annotation, by predicting these data from protein sequences using the Pfam search tool and KoFamKOALA, respectively. This method can be implemented in other research such as proteomics, protein design and host-virus interactions.