MBE Advance Access published online on February 20, 2009
Molecular Biology and Evolution, doi:10.1093/molbev/msp028
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Research Article |
Molecular evolution of the β
lens crystallin superfamily: evidence for a retained ancestral function in N crystallins?
Institution: University of Toronto
Department of Ecology and Evolution (CJW, BSWC), Department of Cell & Systems Biology (BSWC), and Centre for the Analysis of Genome Evolution and Function (BSWC), University of Toronto
Corresponding Author Address: Belinda S. W. Chang, University of Toronto, 25 Harbord Ave., Toronto, Ontario, Canada. M5S 3G5. E-mail: belinda.chang{at}utoronto.ca
Received for publication October 22, 2008. Revision received January 9, 2009. Accepted for publication February 11, 2009.
Within the vertebrate eye, β
crystallins are extremely stable lens proteins that are uniquely adapted to increase refractory power while maintaining transparency. Unlike 
crystallins, which are well-characterized, multifunctional proteins that have important functions both in and out of the lens, β lens crystallins are a diverse group of proteins with no clear ancestral or contemporary non-lens role. We carried out phylogenetic and molecular evolutionary analyses of the β-crystallin superfamily in order to study the evolutionary history of the N crystallins, a recently discovered, biochemically atypical family suggested to possess a divergent or ancestral function. By including non-lens, β-motif-containing sequences in our analysis as outgroups, we confirmed the phylogenetic position of the N family as sister to other crystallins. Using maximum likelihood codon models to estimate lineage specific nonsynonymous to synonymous rate ratios revealed strong positive selection in all of the early lineages within the β family, with the striking exception of the lineage leading to the N crystallins which was characterized by strong purifying selection. Branch-site analysis, used to identify candidate sites involved in functional divergence between N crystallins and its sister clade containing all other crystallins, identified several positively selected changes at sites of known functional importance in the β crystallin protein structure. Further analyses of a fish-specific N crystallin gene duplication revealed a more recent episode of positive selection in only one of the two descendant lineages (N2). Finally, from the guppy, Poecilia reticulata, we isolated complete N1 and N2 coding sequence data from cDNA and partial coding sequence data from genomic DNA in order to confirm the presence of a novel N2 intron, discovered through data mining of two pufferfish genomes. We conclude that the function of the N family likely resembles the ancestral vertebrate β crystallin more than other β families. Furthermore, owing to the presence of an additional intron in some fish N2 crystallins, and the inferred action of positive selection following the fish-specific N duplication, we suggest that further study of fish N crystallins will be critical in further elucidating possible ancestral functions of N crystallins, and any non-structural role they may have.
Key Words: βcrystallins • N crystallins • gene duplication • protein structure-function • novel intron • calcium binding