Exploring metazoan evolution through dynamic and
holistic changes in protein families and domains
Proteins convey the majority of biochemical and cellular activities in organisms. Over thecourse of evolution, proteins undergo normal sequence mutations as well as large scalemutations involving domain duplication and/or domain shuffling.
These events result in thegeneration of new proteins and protein families. Processes that affect proteome evolutiondrive species diversity and adaptation.
Herein, change over the course of metazoan evolution,as defined by birth/death and duplication/deletion events within protein families and domains,was examined using the proteomes of 9 metazoan and two outgroup species.
In studying members of the three major metazoan groups, the vertebrates, arthropods, andnematodes, we found that the number of protein families increased at the majority of lineagesover the course of metazoan evolution where the magnitude of these increases was greatest atthe lineages leading to mammals. In contrast, the number of protein domains decreased atmost lineages and at all terminal lineages.
This resulted in a weak correlation between proteinfamily birth and domain birth; however, the correlation between domain birth and domainmember duplication was quite strong. These data suggest that domain birth and proteinfamily birth occur via different mechanisms, and that domain shuffling plays a role in theformation of protein families.
The ratio of protein family birth to protein domain birth(domain shuffling index) suggests that shuffling had a more demonstrable effect on proteinfamilies in nematodes and arthropods than in vertebrates. Through the contrast of high andlow domain shuffling indices at the lineages of Trichinella spiralis and Gallus gallus, wepropose a link between protein redundancy and evolutionary changes controlled by domainshuffling; however, the speed of adaptation among the different lineages was relativelyinvariant.
Evaluating the functions of protein families that appeared or disappeared at the lastcommon ancestors (LCAs) of the three metazoan clades supports a correlation with organismadaptation. Furthermore, bursts of new protein families and domains in the LCAs ofmetazoans and vertebrates are consistent with whole genome duplications.
Metazoan speciation and adaptation were explored by birth/death and duplication/deletionevents among protein families and domains.
Our results provide insights into proteinevolution and its bearing on metazoan evolution.
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