Special evolutionary properties of genes encoding a protein with a simple amino acid repeat

We have examined the evolution of a gene, SM50, encoding a component of the spicule matrix, which plays an integral role in the formation of the echinoderm skeleton. This gene was originally characterized in Strongylocentrotus purpuratus and encodes an imperfect tandem repeat of six or seven amino acids. We have analyzed the sequence of this repeat in a number of sea urchin species and have determined that the repeat regions have undergone concerted evolution. There are differences in the repeat region between species, but the overall repeat structure is conserved, suggesting the repeat forms a structural domain important in biomineralization. The inherent conserved amino acid repeat structure promotes concerted evolution due to the high probability of misreplication and unequal crossing-over in the repeated segment of the gene. While there are constraints on the amino acids allowed in the repeat region, there are also variations, so that the sequences observed illustrate the balance between amino acid substitutions and concerted evolution. We have evidence that substitutions can alter the mechanisms of unequal crossing-over, altering the way concerted evolution occurs. The way in which concerted evolution occurred appears to be determined by the degree of sequence similarity between the repeats in a given gene, which influences how unequal crossing over may occur. We have mapped the differences in repeat regions on existing phylogenetic trees and indicate where concerted evolution has taken place. We also confirm an earlier report that Hemicentrotus pulcherrimus fits into the Strongylocentrotus genus and examine the evolution of the H. pulcherrimus SM50 repeat relative to other members of this genus.