title: Proteins with Highly Evolvable Domain Architectures Are Nonessential but Highly Retained.
abstract: 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.
authors.affiliation: Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan, ROC Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan, ROC Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC.
authors.forename: Chia-Hsin
authors.initials: CH
authors.lastname: Hsu
authors.affiliation: Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan, ROC Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan, ROC Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC.
authors.forename: Austin W T
authors.initials: AW
authors.lastname: Chiang
authors.affiliation: Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan, ROC Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan, ROC Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC mjhwang@ibms.sinica.edu.tw liaoby@nhri.org.tw.
authors.forename: Ming-Jing
authors.initials: MJ
authors.lastname: Hwang
authors.affiliation: Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Miaoli County, Taiwan, ROC mjhwang@ibms.sinica.edu.tw liaoby@nhri.org.tw.
authors.forename: Ben-Yang
authors.initials: BY
authors.lastname: Liao
mesh_terms: D000818:Animals; D003198:Computer Simulation; D019143:Evolution, Molecular; D016678:Genome; D006801:Humans; D010802:Phylogeny; D000072417:Protein Domains; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000235:genetics*; D013329:Structure-Activity Relationship
chemical_list: D011506:Proteins
keywords: essentiality; evolutionarily inferred network; evolvability; protein domain architecture; protein evolution