Experimental evolution of metabolism under nutrient restriction: enhanced amino acid catabolism and a key role of branched-chain amino acids

Abstract

Periodic food shortage is a common ecological stressor for animals, likely to drive physiological and metabolic adaptations to alleviate its consequences, particularly for juveniles that have no option but to continue to grow and develop despite undernutrition. Here we study changes in metabolism associated with adaptation to nutrient shortage, evolved by replicate Drosophila melanogaster populations maintained on a nutrient-poor larval diet for over 240 generations. In a factorial metabolomics experiment we showed that both phenotypic plasticity and genetically-based adaptation to the poor diet involved wide-ranging changes in metabolite abundance; however, the plastic response did not predict the evolutionary change. Compared to nonadapted larvae exposed to the poor diet for the first time, the adapted larvae showed lower levels of multiple free amino acids in their tissues—and yet they grew faster. By quantifying accumulation of the nitrogen stable isotope 15N we show that adaptation to the poor diet led to an increased use of amino acids for energy generation. This apparent “waste” of scarce amino acids likely results from the trade-off between acquisition of dietary amino acids and carbohydrates observed in these populations. The three branched-chain amino acids (leucine, isoleucine, and valine) showed a unique pattern of depletion in adapted larvae raised on the poor diet. A diet supplementation experiment demonstrated that these amino acids are limiting for growth on the poor diet, suggesting that their low levels resulted from their expeditious use for protein synthesis. These results demonstrate that selection driven by nutrient shortage not only promotes improved acquisition of limiting nutrients, but also has wide-ranging effects on how the nutrients are used. They also show that the abundance of free amino acids in the tissues does not, in general, reflect the nutritional condition and growth potential of an animal.

Cis-regulatory polymorphism at fiz ecdysone oxidase contributes to polygenic evolutionary response to malnutrition in Drosophila

“…The adaptation of Selected populations to poor diet is manifested in both faster larval growth and higher egg-to-adult survival compared to Control populations [ 11 , 12 , 14 ]. In contrast, even though fiz knockdown resulted in substantially enhanced larval growth on the poor diet (thus recapitulating one aspect of adaptation in Selected populations), this occurred at a great cost to survival.…”

“…Given that fiz acts as growth inhibitor, one may speculate that downregulation in the Selected larvae allowed them to better realize their growth potential despite nutrient shortage. This potential may have been enhanced by improved assimilation of dietary amino acids [ 13 ] or changes in metabolism [ 14 ]. In contrast, downregulation of fiz in otherwise non-adapted larvae appears to cause them to overextend themselves trying to grow at a rate that their metabolism cannot sustain.…”

“…Metabolome analysis indicated divergence in ways in which the acquired nutrients are used by the Selected and Control larvae. Notably, in spite of their faster acquisition from the diet, the concentrations of multiple free amino acids, including seven essential, are lower in Selected than Control larvae raised on poor diet [ 14 ]. This is consistent with a more expeditious use of amino acids for protein synthesis underpinning the faster growth of Selected larvae.…”

“…This is consistent with a more expeditious use of amino acids for protein synthesis underpinning the faster growth of Selected larvae. However, we have also shown that Selected larvae use a greater fraction of acquired amino acids for energy generation [ 14 ]. The Selected populations also evolved a smaller critical size at which metamorphosis is initiated, allowing them to complete development with a lower total accumulated biomass [ 15 ]; hence, in spite of their faster larval growth they emerge as smaller adults than Controls [ 14 ].…”

“…However, we have also shown that Selected larvae use a greater fraction of acquired amino acids for energy generation [ 14 ]. The Selected populations also evolved a smaller critical size at which metamorphosis is initiated, allowing them to complete development with a lower total accumulated biomass [ 15 ]; hence, in spite of their faster larval growth they emerge as smaller adults than Controls [ 14 ]. Furthermore, the Selected larvae move less while foraging [ 16 ] and show increased cannibalistic tendencies [ 17 ].…”