Detecting Functional Divergence after Gene Duplication through Evolutionary Changes in Posttranslational Regulatory Sequences
Figure 4
Examples of known regulatory motifs with changes in constraints.
Alignment of the short linear motifs with known function (indicated with arrows) and significant changes in constraints (red boxes) after gene duplication from representative species. A) The Rck2 protein is known to bind and be phosphorylated by Hog1 kinase at two motifs that have significant changes in constraints after gene duplication. Numbers indicate residue position within the S. cerevisiae Rck2 protein. The two identified motifs occur at aa519-538 and aa577-591 for Rck2, and changed constraints within the aligned region aa439-456 and aa492-506 in Rck1. These overlap with the known phosphorylation site in Rck2 (aa520) and the MAP kinase binding site (aa492-506) in Rck2. Both Rck2 and Rck1 retain kinase function. B) The Fkh2 protein is known to be phosphorylated by Cdk1 at two phosphorylation sites on a region shown to have significant changes in constraints after gene duplication. Numbers indicate residue position within the S. cerevisiae Fkh2 protein. The identified motif occurs at region aa692-702 in Fkh2 and has changed constraint in the aligned region aa459-469 in Fkh1. One of the known phosphorylation site in Fkh2 occurs within this region at aa697. Fkh2 and Fkh1 retain their forkhead-associated domain (FHA) and DNA binding domain (DBD). C) The Ace2 protein is known to bind and be phosphorylated by Cbk1 kinase at two motifs that have significant changes in constraints after gene duplication. Numbers indicate residue position within the S. cerevisiae Ace2 protein. The two identified motifs occur at aa121-134 and aa283-287 in Ace2, and changed constraints within the aligned region aa115-128 and aa247-248 (it is a gap) in Swi5. These overlap with the known phosphorylation site in Ace2 (aa122) and the Cbk1 binding site (aa283-286) in Ace2. Both Ace2 and Swi5 retain their DNA binding domain (DBD). Stars represent significant changes in constraints along the lineage. Red double arrow illustrates the duplication event. aa: amino acid position. Scer: S. cerevisiae, Ncas: N. castellii, Zrou: Z. rouxii, Calb: C. albicans.