Abstract
BackgroundProtein structural domains are evolutionary units whose relationships can be detected over long evolutionary distances. The evolutionary history of protein domains, including the origin of protein domains, the identification of domain loss, transfer, duplication and combination with other domains to form new proteins, and the formation of the entire protein domain repertoire, are of great interest.Methodology/Principal FindingsA methodology is presented for providing a parsimonious domain history based on gain, loss, vertical and horizontal transfer derived from the complete genomic domain assignments of 1015 organisms across the tree of life. When mapped to species trees the evolutionary history of domains and domain combinations is revealed, and the general evolutionary trend of domain and combination is analyzed.Conclusions/SignificanceWe show that this approach provides a powerful tool to study how new proteins and functions emerged and to study such processes as horizontal gene transfer among more distant species.
Highlights
Discovered as spatially distinct regions of proteins, protein domains are considered discrete evolutionary units
Phylogenetic Tree of Protein Domains and Combinations In previous studies, a Venn diagram analysis has often been used to show the distribution of protein domains in the three superkingdoms, archaea, bacteria and eukaryotes, depicting the number and types of protein domains in the last universal common ancestor of life (LUCA) and their early evolution [4,5,22]
The Venn diagram reflects the evolution of protein domains at the root of the tree, where each superkingdom is considered as one single clade
Summary
Discovered as spatially distinct regions of proteins, protein domains are considered discrete evolutionary units. Add to that features of domain arrangements [1] and a limited number relative to the immense possibilities of sequence space [2] and we have the makings of a powerful method of analysis Given these properties, protein domains have been used recently in the study of evolution on genome-wide and specieswide scales [3,4,5]. Protein domain content (PDC), the mere presence or absence of domains in completely sequenced genomes, has been shown to define the major evolutionary changes that lead to the genome content of contemporary organisms Stated another way, the phylogenetic tree of life reconstructed based on PDC is comparable to standard phylogenetic methods based on molecular markers (such as rRNA) and other phylogenomic approaches such as gene content and gene order [5]. The evolutionary history of protein domains, including the origin of protein domains, the identification of domain loss, transfer, duplication and combination with other domains to form new proteins, and the formation of the entire protein domain repertoire, are of great interest
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