Proteins with Highly Evolvable Domain Architectures Are Nonessential but Highly Retained

The functions of proteins are usually determined by domains, and the sequential order in which domains are connected to make up a protein chain is known as the domain architecture. Here, we constructed evolutionary networks of protein domain architectures in species from three major life lineages (bacteria, fungi, and metazoans) by connecting any two architectures between which an evolutionary event could be inferred by a model that assumes maximum parsimony. We found that proteins with domain architectures with a higher level of evolvability, indicated by a greater number of connections in the evolutionary network, are present in a wider range of species. However, these proteins tend to be less essential to the organism, are duplicated more often during evolution, have more isoforms, and, intriguingly, tend to be associated with functional categories important for organismal adaptation. These results reveal the presence, in many genomes, of genes coding for a core set of nonessential proteins that have a highly evolvable domain architecture and thus a repertoire of genetic materials accessible for organismal adaptation.