Mitochondrial-nuclear epistasis contributes to phenotypic variation and coadaptation in natural isolates of Saccharomyces cerevisiae

Abstract

Mitochondria are essential multifunctional organelles whose metabolic functions, biogenesis, and maintenance are controlled through genetic interactions between mitochondrial and nuclear genomes. In natural populations, mitochondrial efficiencies may be impacted by epistatic interactions between naturally segregating genome variants. The extent that mitochondrial-nuclear epistasis contributes to the phenotypic variation present in nature is unknown. We have systematically replaced mitochondrial DNAs in a collection of divergent Saccharomyces cerevisiae yeast isolates and quantified the effects on growth rates in a variety of environments. We found that mitochondrial-nuclear interactions significantly affected growth rates and explained a substantial proportion of the phenotypic variances under some environmental conditions. Naturally occurring mitochondrial-nuclear genome combinations were more likely to provide growth advantages, but genetic distance could not predict the effects of epistasis. Interruption of naturally occurring mitochondrial-nuclear genome combinations increased endogenous reactive oxygen species in several strains to levels that were not always proportional to growth rate differences. Our results demonstrate that interactions between mitochondrial and nuclear genomes generate phenotypic diversity in natural populations of yeasts and that coadaptation of intergenomic interactions likely occurs quickly within the specific niches that yeast occupy. This study reveals the importance of considering allelic interactions between mitochondrial and nuclear genomes when investigating evolutionary relationships and mapping the genetic basis underlying complex traits.

Keywords: coadaptation; coevolution; genetic interactions; genotype by environment; reactive oxygen species.

Figure 1

mtDNA polymorphisms in S. cerevisiae. (A) RFLP analysis of purified mtDNA from 10 isolates restricted with EcoRV separated by agarose gel electrophoreses (0.8%). Nine unique banding patterns were observed. Banding patterns of strains C₁ and C₄ are similar. No bands were observed from a ρ⁰ control, demonstrating specificity of mtDNA purification. (B) Neighbor-joining phlogenetic tree based on 6684 bp of available mtDNA sequences (Skelly et al. 2013). (mtDNA sequences not available for C₃, F₁, and F₂). Scale bar indicates frequency of base-pair differences.

Figure 2

Fitness effects of 10 mitotypes on 10 nuclear backgrounds. Changes in fitness are presented as interaction plots, where each colored line follows the changes in fitness (V_max) of a single nuclear genetic background when paired with 10 different mt haplotypes, as indicated on the x-axis, under different media conditions. The ordering of mitotypes does not reflect genetic relatedness. (A) Fermentable glucose media (CSM). (B) Nonfermentable media (EG). (C) CSM at elevated temperature (37°). (D) CSM + paraquat (CSM + PQ). (E) EG + PQ. Note that the scale of the axes are different for each media condition.

Figure 3

Growth rate distributions of nuclear genotypes and mitochondrial haplotypes. (A–E) Box plots showing the distributions of individual nuclear backgrounds with all 10 mitotypes. (F–J) Box plots showing the distributions of each mitotype across all nuclear genotypes. Each box plot shows the combined data for 10 strains and indicates the 25th percentile (lower edge of the box), median (solid line in the box), 75th percentile (upper edge of the box), and 90th percentile (whisker). The fitness scale on the y-axis is the same for each plot. Tukey groupings are shown in blue across the top of each plot. (A and F) CSM. (B and G) EG. (C and H) 37°. (D and I) CSM + PQ. (E and J) EG + PQ.

Figure 4

Phenotypic variance under five environmental conditions. The components of variance due to mitotype (yellow), nuclear genetic background (white), and mt-n epistasis (red) are indicated in each bar graph. The proportion of variance contributed by each component is shown in pie charts, noting significance. ***P < 0.001.

Figure 5

Evidence for coadapted mt-n genomes. (A) Average growth rates of strains with native (red) or non-native (gray) mt-n genome combinations under different media conditions. (B) Strains containing native mt-n genome combinations are shown as circles color-coded by isolation habitat. Circles are connected by bold lines when significant mt-n epistasis was noted following an exchange of mtDNA between the two strains (two-way ANOVA, P < 0.05). mt haplotype exchanges that did not reveal epistasis are shown as gray lines. The percentage of all significant epistasis tests is shown for each condition. Missing data, due to occasional strain flocculation, prevented certain tests from being performed and are indicated by an absence of lines or gray circles: orange (clinical), blue (environmental), green (fermentation). (C) The frequency of observed mito-nuclear epistasis (two-way ANOVA, P < 0.05) when interrupting native (red) or non-native (gray) mt-n genome combinations. (D) The average magnitude of the epistatic response (ΔΔV_max) when interrupting native (red) or non-native (gray) mt-n genome combiantions. ΔΔV_max was measured as the absolute value of the difference in slopes from two-way interaction plots containing four different mt-n combinations. Native tests contain two native mito-nuclear combinations and the corresponding non-natives while non-native tests contain four strains containing two unique mt and n genomes with non-native mito-nuclear combinations. ***P <0.001, **P <0.01, *P <0.05.

Figure 6

Interaction plot showing V_max for native and non-native mt-n genome combinations from different ecotypes grown in EG media. Native combinations outperformed non-native combinations for fermentation and clinical strains (P < 0.001). Native fermentation strains performed the best with a strong interaction between native status and ecotype (P = 0.008).

Figure 7

Coadapted mt-n genome pairs influence ROS production. Interaction plots of (A) growth rates at 37° of C₁ and C₄ nuclear backgrounds paired with C₁ and C₄ mitotypes; (B) endogenous ROS values at 37° for strains in A; (C) growth rates of C₁ and F₂ nuclear backgrounds paired with C₁ and F₂ mitotypes; and (D) ROS values for strains in C. The P-values are provided for the nuclear (P_n), mitochondrial (P_mt), and interaction (P_mtxn) components of two-way ANOVAs, nesting biological replicate within the interaction term. ***P < 0.001, **P < 0.01, *P <0.05.