In silico evidence 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/dS(avg)=0.44) that is higher than the slow-evolving genes' ratio (dN/dS(avg)=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.

Fig. 2

Sulfate-binding site. (a) The sulfate-binding site is shown for the mouse GSK-3β (1gng). Dotted green lines show hydrogen bonding to sulfate. (b) The residues corresponding to the GSK3 sulfate-binding site in YGK3 (see Fig. 1a) were introduced into the 1gng structure in Swiss-PdbViewer (1gng numbering). The side chains of Gln at position 205 (Gln197 in YGK3) and Asn-213 (Asn205 in YGK3) were rotated at some degree to form hydrogen bonds to the sulfate oxygens. Phosphorylated tyrosine (Tyr216 in GSK-3β) is also shown. Pictures were created using Swiss-PdbViewer.

Fig. 1

Examples of functional sites, in which the fast-evolving yeast protein has diverged significantly. (a) Sulfate binding site in the mouse GSK-3β and yeast proteins. (b) Phosphate anchor motif GXGXXG in MAP kinases. (c) Binding site (bold and underlined) of Rattus norvegicus ARFGAP1 for ADP ribosylation factor ARF1 and the corresponding sites in yeast proteins (Rattus sites are from crystal structure; Goldberg, 1999). (d) Conserved iron ligand binding site in diiron center of RNR proteins. (e) Key residues reported to be important for UDP-glucose pyrophosphorylase activity (Geisler et al., 2004). Differing sites in fast-evolving genes are shown in bold and underlined (a–b and d–e).

Fig. 3

Example of a highly conserved active site in a highly diverged protein. CTL1 is an extremely truncated version of yeast RNA triphosphatase (CET1), which displays only 21% identity in the remaining region. Out of 15 catalytically important residues (shown in bold), only one, histidine (bold and underlined) is different in CTL1 indicating a strong purifying selection in these positions (Lehman et al., 2001). Sites important for dimerization in CET1 are shown underlined (Lehman et al., 2001). Binding site for CEG1 protein (WAQKW) in CET1 is shown in italics and underlined (Ho et al., 1999).

Fig. 4

Schematic presentation of possible divergence modes. The ancestral protein with subfunctions A and B was duplicated in the WGD, and this figure shows schematically how the functional divergence has led to many types of changes in the diverging gene pair. Reduction of functions is common among the fast-evolving genes in the group of 15 gene pairs. Fast-evolving genes have also adopted new roles in the yeast cell. A′B′ minor changes in the subfunctions; A^*, B^*, novel functional properties (e.g. changes in location, interaction with substrate, or protein–protein interactions); (with strikethrough), A′B′ deletion of subfunctions; and C, completely new (sub)function.