Genotype to phenotype: Diet-by-mitochondrial DNA haplotype interactions drive metabolic flexibility and organismal fitness.

Wen C Aw,Samuel G Towarnicki,J William O Ballard,Richard G Melvin,Michael R Garvin,Shaun Nielsen,Russell Pickford,Gordon K Smyth,Antón Vila-Sanjurjo,Torsten Thomas,Neil A Youngson,Sonia Bustamante,Yifang Hu

doi:10.1371/journal.pgen.1007735

Abstract

Diet may be modified seasonally or by biogeographic, demographic or cultural shifts. It can differentially influence mitochondrial bioenergetics, retrograde signalling to the nuclear genome, and anterograde signalling to mitochondria. All these interactions have the potential to alter the frequencies of mtDNA haplotypes (mitotypes) in nature and may impact human health. In a model laboratory system, we fed four diets varying in Protein: Carbohydrate (P:C) ratio (1:2, 1:4, 1:8 and 1:16 P:C) to four homoplasmic Drosophila melanogaster mitotypes (nuclear genome standardised) and assayed their frequency in population cages. When fed a high protein 1:2 P:C diet, the frequency of flies harbouring Alstonville mtDNA increased. In contrast, when fed the high carbohydrate 1:16 P:C food the incidence of flies harbouring Dahomey mtDNA increased. This result, driven by differences in larval development, was generalisable to the replacement of the laboratory diet with fruits having high and low P:C ratios, perturbation of the nuclear genome and changes to the microbiome. Structural modelling and cellular assays suggested a V161L mutation in the ND4 subunit of complex I of Dahomey mtDNA was mildly deleterious, reduced mitochondrial functions, increased oxidative stress and resulted in an increase in larval development time on the 1:2 P:C diet. The 1:16 P:C diet triggered a cascade of changes in both mitotypes. In Dahomey larvae, increased feeding fuelled increased β-oxidation and the partial bypass of the complex I mutation. Conversely, Alstonville larvae upregulated genes involved with oxidative phosphorylation, increased glycogen metabolism and they were more physically active. We hypothesise that the increased physical activity diverted energy from growth and cell division and thereby slowed development. These data further question the use of mtDNA as an assumed neutral marker in evolutionary and population genetic studies. Moreover, if humans respond similarly, we posit that individuals with specific mtDNA variations may differentially metabolise carbohydrates, which has implications for a variety of diseases including cardiovascular disease, obesity, and perhaps Parkinson’s Disease.

Highlights

We concluded that differential provisioning of macronutrients to mitochondria harbouring distinct mitotypes led to phenotypic changes in food consumption, starvation resistance, and movement, as oxidative phosphorylation and β-oxidation of fatty acids were differentially regulated
The nuclear genome was standardised to w1118 and the microbiome controlled each generation by adding a ground homogenate of laboratory males
When fed the 1:2 P:C diet, Alstonville larvae had a relative advantage as the V161L ND4 mutation in Dahomey caused an increase in reactive oxygen species (ROS) production, which resulted in oxidative stress and

Summary

Author summary

The detection and quantitation of mtDNA polymorphisms in populations and across whole habitats continues to be used as a central investigatory tool in evolutionary genetics. When flies were fed the high carbohydrate diet, energy metabolism was extensively remodelled in both mitotypes causing increased physical activity in Alstonville flies. These data invite an extensive experimental re-evaluation of the assumption that mtDNA inescapably evolves in a manner consistent with a strictly neutral equilibrium model. It motivates investigation of genotype-specific dietary manipulation as an integrative treatment of human disorders involving mitochondrial metabolism and offers the potential for future therapeutic strategies

Introduction

Results and discussion

Conclusion

Materials and methods