Genetic and metabolomic architecture of variation in diet restriction-mediated lifespan extension inDrosophila

In most organisms, dietary restriction (DR) increases lifespan. However, several studies have found that genotypes within the same species vary widely in how they respond to DR. To explore the mechanisms underlying this variation, we exposed 178 inbredDrosophila melanogasterlines to a DR orad libitum(AL) diet, and measured a panel of 105 metabolites under both diets. Twenty four out of 105 metabolites were associated with the magnitude of the lifespan response. These included proteinogenic amino acids and metabolites involved in alpha-ketoglutarate (alpha-KG)/glutamine metabolism. We confirm the role of alpha-KG/glutamine synthesis pathways in the DR response through genetic manipulations. We used covariance network analysis to investigate diet-dependent interactions between metabolites, identifying the essential amino acids threonine and arginine as hub metabolites in the DR response. Finally, we employ a novel metabolic and genetic bipartite network analysis to reveal multiple genes that influence DR lifespan response, some of which have not previously been implicated in DR regulation. One of these isCCHa2R, a gene that encodes a neuropeptide receptor that influences satiety response and insulin signaling. Across the lines, variation in an intronic single nucleotide variant ofCCHa2Rcorrelated with variation in levels of five metabolites, all of which in turn were correlated with DR lifespan response. Inhibition of adultCCHa2Rexpression extended DR lifespan of flies, confirming the role ofCCHa2Rin lifespan response. These results provide support for the power of combined genomic and metabolomic analysis to identify key pathways underlying variation in this complex quantitative trait. Author summary Dietary restriction extends lifespan across most organisms in which it has been tested. However, several studies have now demonstrated that this effect can vary dramatically across different genotypes within a population. Within a population, dietary restriction might be beneficial for some, yet detrimental for others. Here, we measure the metabolome of 178 genetically characterized fly strains on fully fed and restricted diets. The fly strains vary widely in their lifespan response to dietary restriction. We then use information about each strain's genome and metabolome (a measure of small molecules circulating in flies) to pinpoint cellular pathways that govern this variation in response. We identify a novel pathway involving the geneCCHa2R, which encodes a neuropeptide receptor that has not previously been implicated in dietary restriction or age-related signaling pathways. This study demonstrates the power of leveraging systems biology and network biology methods to understand how and why different individuals vary in their response to health and lifespan-extending interventions.