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Domains are the building blo cks of proteins. Exon shuf- fling is an important mechanism accounting for combi- nation of a limited repertoire of protein domains in the evolution of multicellular species. A relative excess of domains encoded by symmetric exons in metazoan phyla has been presented as evidence of exon shuffling, and symmetric domains can be divided into old and new domains by determining the ages of the domains. In this report, we compare the spread, versatility, and subcellular localization of old and new domains by ana- lyzing eight metazoan genomes and their respective an- notated proteomes. We found that new domains have been expanding as multicellular organisms evolved, and this expansion was principally because of increases in class 1-1 domains amongst several classes of domain families. We also found that younger domains have been expanding in membranes and secreted proteins along with multi-cellular orga nism evolution. In contrast, old domains are located mainly in nuclear and cytoplas- mic proteins. We conclude that the increasing mobility and versatility of new domains, in contrast to old do- mains, plays a significant role in metazoan evolution, fa- cilitating the creation of secreted and transmembrane multidomain proteins unique to metazoa.

Comparison of Exon-boundary Old and Young Domains during Metazoan Evolution