Metabolic pathway profiling of mitochondrial respiratory chain mutants in C. elegans

Abstract

C. elegans affords a model of primary mitochondrial dysfunction that provides insight into cellular adaptations which accompany mutations in nuclear gene that encode mitochondrial proteins. To this end, we characterized genome-wide expression profiles of C. elegans strains with mutations in nuclear-encoded subunits of respiratory chain complexes. Our goal was to detect concordant changes among clusters of genes that comprise defined metabolic pathways. Results indicate that respiratory chain mutants significantly upregulate a variety of basic cellular metabolic pathways involved in carbohydrate, amino acid, and fatty acid metabolism, as well as cellular defense pathways such as the metabolism of P450 and glutathione. To further confirm and extend expression analysis findings, quantitation of whole worm free amino acid levels was performed in C. elegans mitochondrial mutants for subunits of complexes I, II, and III. Significant differences were seen for 13 of 16 amino acid levels in complex I mutants compared with controls, as well as overarching similarities among profiles of complex I, II, and III mutants compared with controls. The specific pattern of amino acid alterations observed provides novel evidence to suggest that an increase in glutamate-linked transamination reactions caused by the failure of NAD + dependent oxidation of ketoacids occurs in primary mitochondrial respiratory chain mutants. Recognition of consistent alterations among patterns of nuclear gene expression for multiple biochemical pathways and in quantitative amino acid profiles in a translational genetic model of mitochondrial dysfunction allows insight into the complex pathogenesis underlying primary mitochondrial disease. Such knowledge may enable the development of a metabolomic profiling diagnostic tool applicable to human mitochondrial disease.

A plasma signature of human mitochondrial disease revealed through metabolic profiling of spent media from cultured muscle cells

“…Characterizing the spectrum of metabolic alterations in RC dysfunction could reveal the pathways contingent on RC activity and holds potential for better understanding the pathogenesis of human RCD. A number of recent studies have each evaluated a single family of metabolites, such as amino acids or TCA-cycle intermediates, in biological fluids of individuals with RCD (7,19) or in animal models of the disease (20). In the current study we targeted multiple biochemical groups, enabling the discovery of a rich metabolic signature spanning amino acids and other nitrogenous compounds, glycolysis, the TCA cycle, purines, and pyrimidines (Fig.…”

Environmental metabolomics: a critical review and future perspectives

“…Extensive metabolomics studies have been conducted on S. cerevisiae and A. thaliana, but it is perhaps surprising that few have yet been published on the other common model organisms. For example, the first metabolomics experiments on C. elegans (Atherton et al 2008;Blaise et al 2007;Falk et al 2008), A. l. petraea (Davey et al 2008) and D. magna (Taylor et al in press) have only just been reported. We recommend that resources within environmental metabolomics are focused on these and a few other ecologically important species (for instance, insects are not included in the above list by Snape et al (2004); and the earthworm L. rubellus has some advantages as a model in addition to E. fetida).…”

Collaboration between mitochondria and the nucleus is key to long life in Caenorhabditis elegans

“…These mitochondrial ETC mutants share some similar characteristics but each has their own unique properties. To date, three genome-wide studies have surveyed the transcriptional changes in response to nuo-6, isp-1 , clk-1 , gas-1 , and mev-1 mutations [20,35,36]. These investigations revealed that a compensatory transcriptional response likely plays an important role in the longevity of these mutants.…”