In silicoevidence for functional specialization after genome duplication in yeast

Abstract

A fairly recent whole-genome duplication (WGD) event in yeast enables the effects of gene duplication and subsequent functional divergence to be characterized. We examined 15 ohnolog pairs (i.e. paralogs from a WGD) out of c. 500 Saccharomyces cerevisiae ohnolog pairs that have persisted over an estimated 100 million years of evolution. These 15 pairs were chosen for their high levels of asymmetry, i.e. within the pair, one ohnolog had evolved much faster than the other. Sequence comparisons of the 15 pairs revealed that the faster evolving duplicated genes typically appear to have experienced partially – but not fully – relaxed negative selection as evidenced by an average nonsynonymous/synonymous substitution ratio (dN/dSavg=0.44) that is higher than the slow-evolving genes' ratio (dN/dSavg=0.14) but still <1. Increased number of insertions and deletions in the fast-evolving genes also indicated loosened structural constraints. Sequence and structural comparisons indicated that a subset of these pairs had significant differences in their catalytically important residues and active or cofactor-binding sites. A literature survey revealed that several of the fast-evolving genes have gained a specialized function. Our results indicate that subfunctionalization and even neofunctionalization has occurred along with degenerative evolution, in which unneeded functions were destroyed by mutations.

Codon models applied to the study of fungal genomes

“…Interestingly, a burst of protein evolution followed gene duplication even for slowly evolving genes and the asymmetric rate accelerations persist even after prolonged periods of time. A similar study reached the same conclusions using codon models to compare paralogs derived from a WGD event (Turunen et al, 2009). …”

Detection and Analysis of Functional Specialization in Duplicated Genes

“…tissue localization) or coding sequence. Claims of neofunctionalization tend to focus on the generation of new functions, though it should be noted that these developments may also result in the loss of ancestral function(s) (Turunen et al, 2009). A specific example of neofunctionalization can be found in a recent study of the MADS-box gene family in angiosperms.…”

“…orthologous) duplicates -that is to say, WGD duplicates that becomes fixed in one lineage, were also often fixed in the other (Semon & Wolfe, 2008). Pairs of duplicate genes that arose through WGD are sometimes referred to as Ohnologs (Turunen et al, 2009). WGD events are relatively common in plant lineages, which may have interesting implications for the evolution of gene regulation (Lockton & Gaut, 2005).…”

“…While not necessarily illustrative of the nature of the difference, this method can provide evidence for asymmetrical selection, suggesting one duplicate is acquiring amino acid altering mutations faster than the other (Ganko et al, 2007). Working from a list of 15 of the most asymmetrically diverged WGD-derived protein sequences in S. cerevisiae, Turunen et al (2009) noted substantial indels in addition to changes in important catalytic residues and Fig. 3.…”

“…Gene products, on the other hand, primarily dictate the "how" in a gene's function (along with some regulatory and subcellular localization information present in the 5' and 3' untranslated regions (UTRs)). Studies of duplicated genes have focused on changes to various coding sequence properties, such as binding sites, eligible cofactors, indels, and catalytic residues (Turunen et al, 2009). It's theoretically possible for a duplicate gene to become functionally specialized without any change to its regulation (Des Marais & Rausher, 2008).…”