Positive selection of yeast nonhomologous end-joining genes and a retrotransposon conflict hypothesis

Abstract

Transposable elements have clearly played a major role in shaping both the size and organization of eukaryotic genomes. However, the evolution of essential genes in core biological processes may also have been shaped by coevolution with these elements. This would be predicted to occur in instances where host proteins are either hijacked for use by mobile elements or recruited to defend against them. To detect such cases, we have used the Saccharomyces cerevisiae-Saccharomyces paradoxus sibling species pair to identify genes that have evolved under positive selection. We identify 72 such genes, which participate in a variety of biological processes but are enriched for genes involved in meiosis and DNA repair by nonhomologous end-joining (NHEJ). We confirm the signature of positive selection acting on NHEJ genes using orthologous sequences from all seven Saccharomyces sensu stricto species. Previous studies have found altered rates of Ty retrotransposition when these NHEJ genes are disrupted. We propose that the evolution of these repair proteins is likely to have been shaped by their interactions with Ty elements. Antagonistic pleiotropy, where critical genes like those involved in DNA repair are also subject to selective pressures imposed by mobile elements, could favor alleles that might be otherwise deleterious for their normal roles related to genome stability.

Fig. 1.

A dN/dS sliding-window strategy identifies yeast genes evolving under positive selection. (A) As an example, a window in the NUP53 gene rejects the neutral expectation of dN/dS = 1 with high significance (P = 0.004). This 100-bp window has 13 nonsynonymous (or replacement, R) changes and 2 synonymous (S) changes. (B) The GO Slim Mapping tool (Saccharomyces Genome Database web site) was used to assign 72 yeast genes found to have at least one significant window of positive selection to major, high-level categories in the “biological process” GO. Many of the 72 genes are listed in more than one major process category, as would be expected. (C) The incidence of significant windows of positive selection is plotted versus whole-gene dN/dS values (as determined in ref. 4). Upon reanalysis, several genes had whole-gene dN/dS values lower than previously reported, probably because of additional sequence information that is now available, so the 0.10–0.19 bin represents only 33 genes.

Fig. 2.

NHEJ genes are subject to positive selection. (A) The process of DSB repair via NHEJ is schematized in three steps: end-binding, bridging, and DNA synthesis/ligation. Proteins that play key roles in each of these steps are indicated. Those in bold (Xrs2, Sae2, Nej1, and Pol4) were found to be positively selected in the sliding-window dN/dS analysis. (B) The sliding-window analyses of all S. cerevisiae–S. paradoxus NHEJ genes are shown. Regions where dN/dS is >1 are potential sites of positive selection. Windows that significantly reject neutrality are indicated under the gene name in base pairs, labeled with a P value and the actual number of replacement (R) and synonymous (S) DNA changes. (C) All 10 NHEJ genes from the genomes of seven Saccharomyces sensu stricto species (S. cerevisiae, S. cariocanus, S. paradoxus, S. mikatae, S. kudriavzevii, S. bayanus, and S. pastorianus) were analyzed. S. cariocanus is denoted with a dashed line in the cladogram above the table. The second through fourth columns list results from sliding-window analyses (100-bp window, 20-bp step size) on orthologous gene sets. +, presence of a significant window in cer-par comparison from B; −, no statistically significant (P < 0.05) window of dN/dS >1 was detected. All other cells indicate the presence of a significant window and indicate the dN/dS value of that 100-bp window followed by the P value in parentheses. The final two columns report results of PAML analysis, where we compared the likelihoods obtained by modeling codon evolution under neutral evolution (M7) versus positive selection (M8) using a multiple alignment of all seven sensu stricto orthologs for each gene (see Materials and Methods). By evaluating twice the difference of the log-likelihoods (2*ΔlnL) between M7 and M8, under a χ² distribution with 2 df, P values for positive selection were obtained. ns, not significant (P > 0.05). S. cariocanus sequence was not included in the PAML analysis of YKU70 and YKU80.

Fig. 3.

Two hypothetical models for genetic conflict between Ty retrotransposons and host NHEJ proteins. Ty elements are transcribed, and this RNA is exported to the cytoplasm where it is translated. Genomic RNA also serves as a template for reverse transcription, after which a double-stranded DNA intermediate protected by integrase (IN) proteins is formed in the cytoplasm (together known as the preintegration complex, PIC). The formation of virus-like particles and their disassembly in the cytoplasm is not shown. After entry of the PIC into the nucleus, the Ty elements may (upper arrow) seek out DSBs by virtue of recognizing NHEJ proteins. In this “defensive” model, NHEJ proteins would be predicted to evolve “away” from Ty PIC recognition to maximize host fitness. Under an alternative “offensive” model (lower arrow), entering PICs encounter NHEJ proteins, which circularize PICs into 2-LTR circles that are dead-end products. In this model, the NHEJ proteins are evolving “toward” recognition of Ty PICs.