The Interaction of Natural Selection and GC Skew May Drive the Fast Evolution of a Sand Rat Homeobox Gene

Several processes can lead to strong GC skew in localized genomic regions. In most cases, GC skew should not affect conserved amino acids because natural selection will purge deleterious alleles. However, in the gerbil subfamily of rodents, several conserved genes have undergone radical alteration in association with strong GC skew. An extreme example concerns the highly conserved homeobox gene Pdx1, which is uniquely divergent and GC rich in the sand rat Psammomys obesus and close relatives. Here, we investigate the antagonistic interplay between very rare amino acid changes driven by GC skew and the force of natural selection. Using ectopic protein expression in cell culture, pulse-chase labeling, in vitro mutagenesis, and drug treatment, we compare properties of mouse and sand rat Pdx1 proteins. We find that amino acid change driven by GC skew resulted in altered protein stability, with a significantly longer protein half-life for sand rat Pdx1. Using a reversible inhibitor of the 26S proteasome, MG132, we find that sand rat and mouse Pdx1 are both degraded through the ubiquitin proteasome pathway. However, in vitro mutagenesis reveals this pathway operates through different amino acid residues. We propose that GC skew caused loss of a key ubiquitination site, conserved through vertebrate evolution, and that sand rat Pdx1 evolved or fixed a new ubiquitination site to compensate. Our results give molecular insight into the power of natural selection in the face of maladaptive changes driven by strong GC skew.