G×G×E for lifespan in Drosophila: mitochondrial, nuclear, and dietary interactions that modify longevity

Abstract

Dietary restriction (DR) is the most consistent means of extending longevity in a wide range of organisms. A growing body of literature indicates that mitochondria play an important role in longevity extension by DR, but the impact of mitochondrial genotypes on the DR process have received little attention. Mitochondrial function requires proper integration of gene products from their own genomes (mtDNA) and the nuclear genome as well as the metabolic state of the cell, which is heavily influenced by diet. These three-way mitochondrial-nuclear-dietary interactions influence cellular and organismal functions that affect fitness, aging, and disease in nature. To examine these interactions in the context of longevity, we generated 18 "mito-nuclear" genotypes by placing mtDNA from strains of Drosophila melanogaster and D. simulans onto controlled nuclear backgrounds of D. melanogaster (Oregon-R, w1118, SIR2 overexpression and control) and quantified the lifespan of each mitonuclear genotype on five different sugar:yeast diets spanning a range of caloric and dietary restriction (CR and DR). Using mixed effect models to quantify main and interaction effects, we uncovered strong mitochondrial-diet, mitochondrial-nuclear, and nuclear-diet interaction effects, in addition to three-way interactions. Survival analyses demonstrate that interaction effects can be more important than individual genetic or dietary effects on longevity. Overexpression of SIR2 reduces lifespan variation among different mitochondrial genotypes and further dampens the response of lifespan to CR but not to DR, suggesting that response to these two diets involve different underlying mechanisms. Overall the results reveal that mitochondrial-nuclear genetic interactions play important roles in modulating Drosophila lifespan and these epistatic interactions are further modified by diet. More generally, these findings illustrate that gene-by-gene and gene-by-environment interactions are not simply modifiers of key factors affecting longevity, but these interactions themselves are the very factors that underlie important variation in this trait.

Figure 1. Diagram of diets used in this study.

The horizontal axis shows the sugar concentration and the vertical axis shows yeast concentration, both as weight/volume. The Roman numerals are the short-hand used in the text and figures, and the numbers in parentheses show the ratios of sugar/yeast. The diets I-II-III span a diet concentration axis reflecting caloric restriction(CR); the diets IV-II-V span a diet composition axis reflecting diet restriction (DR).

Figure 2. Mean lifespan response to diet alterations of different mitotypes in OreR (A and B panels) and w ¹¹¹⁸ (C and D panels) nuclear backgrounds.

Food concentration gradient is presented in the left panels (A and C) and food composition gradients in the right panels (B and D). Error bars represent the standard error of the mean. Mitotypes are presented with different markers and line styles. D. simulans mtDNAs have open symbols: siI, square marker with dot line; sm21, triangle marker with dot-dash line; w501, circle marker with double-dot-dash line; D. melanogaster mtDNAs have filled symbols: Zim, filled triangle with dash line; and OreR, filled square with solid line. Different genetic backgrounds, OreR and w ¹¹¹⁸, are shown in lower and upper panels respectively.

Figure 3. sm21 and w501 mitotypes effects on mtDNA/nDNA copy number ratio in OreR and w ¹¹¹⁸ nuclear background.

Error bars represent the standard error of the mean.

Figure 4. Mean lifespan and standard error of SIR2 overexpression (A and B panels) and control (C and D panels) genotypes in different mitotype background.

Mitotypes are presented with different markers and linestyles following the same scheme of figure 2. Food concentration gradient is presented in the left panels (A and C) and food composition gradients in the right panels (B and D).

Figure 5. SIR2 overexpression level in both sexes of mitotype si1 and OreR.

Error bars represent the standard error of the mean of log(fold change); the differences are not significant in either sex (P>0.05 for both).