In vivo metabolic flux profiling with stable isotopes discriminates sites and quantifies effects of mitochondrial dysfunction in C. elegans

Abstract Mitochondrial respiratory chain (RC) disease diagnosis is complicated both by an absence of biomarkers that sufficiently divulge all cases and limited capacity to quantify adverse effects across intermediary metabolism. We applied high performance liquid chromatography (HPLC) and mass spectrometry (MS) studies of stable-isotope based precursor–product relationships in the nematode, C. elegans , to interrogate in vivo differences in metabolic flux among distinct genetic models of primary RC defects and closely related metabolic disorders. Methods C. elegans strains studied harbor single nuclear gene defects in complex I, II, or III RC subunits ( gas-1 , mev-1 , isp-1 ); enzymes involved in coenzyme Q biosynthesis ( clk-1 ), the tricarboxylic acid cycle (TCA, idh-1 ), or pyruvate metabolism ( pdha-1 ); and central nodes of the nutrient-sensing signaling network that involve insulin response ( daf-2 ) or the sirtuin homologue ( sir-2.1 ). Synchronous populations of 2000 early larval stage worms were fed standard Escherichia coli on nematode growth media plates containing 1,6- 13 C 2 -glucose throughout their developmental period, with samples extracted on the first day of adult life in 4% perchloric acid with an internal standard. Quantitation of whole animal free amino acid concentrations and isotopic incorporation into amino and organic acids throughout development was performed in all strains by HPLC and isotope ratio MS, respectively. GC/MS analysis was also performed to quantify absolute isotopic incorporation in all molecular species of key TCA cycle intermediates in gas-1 and N2 adult worms. Results Genetic mutations within different metabolic pathways displayed distinct metabolic profiles. RC complex I ( gas-1 ) and III ( isp-1 ) subunit mutants, together with the coenzyme Q biosynthetic mutant ( clk-1 ), shared a similar amino acid profile of elevated alanine and decreased glutamate. The metabolic signature of the complex II mutant ( mev-1 ) was distinct from that of the other RC mutants but resembled that of the TCA cycle mutant ( idh-1 ) and both signaling mutants ( daf-2 and sir-2.1 ). All branched chain amino acid levels were significantly increased in the complex I and III mutants but decreased in the PDH mutant ( pdha-1 ). The RC complex I, coenzyme Q, TCA cycle, and PDH mutants shared significantly increased relative enrichment of lactate+1 and absolute concentration of alanine+1, while glutamate+1 enrichment was significantly decreased uniquely in the RC mutants. Relative intermediary flux analyses were suggestive of proximal TCA cycle disruption in idh-1 , completely reduced TCA cycle flux in sir-2.1 , and apparent distal TCA cycle alteration in daf-2 . GC/MS analysis with universally-labeled 13 C-glucose in adult worms further showed significantly increased isotopic enrichment in lactate, citrate, and malate species in the complex I ( gas-1 ) mutant. Conclusions Stable isotopic/mass spectrometric analysis can sensitively discriminate primary RC dysfunction from genetic deficiencies affecting either the TCA cycle or pyruvate metabolism. These data are further suggestive that metabolic flux analysis using stable isotopes may offer a robust means to discriminate and quantify the secondary effects of primary RC dysfunction across intermediary metabolism.