Wanders, R. J. A. | Search bioRxiv

bioRxiv2021

Peroxisomal ATP uptake is managed by the ABC transporters and two adenine nucleotide transporters

Peroxisomes are essential organelles involved in various metabolic processes, including fatty acid {beta}-oxidation. Their metabolic functions require a controlled exchange of metabolites and co-factors, including ATP across the peroxisomal membrane. We investigated which proteins are involved in the peroxisomal uptake of ATP in the yeast Saccharomyces cerevisiae. Using wild-type and targeted deletion strains, we measured ATP-dependent peroxisomal octanoate {beta}-oxidation, intra-peroxisomal ATP levels employing peroxisome-targeted ATP-sensing reporter proteins, and ATP uptake in proteoliposomes prepared from purified peroxisomes. We show that intra-peroxisomal ATP levels are maintained by different peroxisomal membrane proteins each with different modes of action: (1) the previously reported Ant1p protein, which catalyzes ATP/AMP exchange (2) the ABC transporter protein complex Pxa1p/Pxa2p, which mediates both acyl-CoA and ATP uptake; and; (3) the mitochondrial Aac2p protein, which catalyzes ATP/ADP exchange and was shown to have a dual localization in both mitochondria and peroxisomes. Our results provide compelling evidence for an ingenious complementary system for the uptake of ATP in peroxisomes.

cell biology↗

bioRxiv2019

Fibroblast-specific genome-scale modelling predicts an imbalance in amino acid metabolism in Refsum disease

Refsum disease is an inborn error of metabolism that is characterised by a defect in peroxisomal -oxidation of the branched-chain fatty acid phytanic acid. The disorder presents with late-onset progressive retinitis pigmentosa and polyneuropathy and can be diagnosed biochemically by elevated levels of phytanic acid in plasma and tissues of patients. To date, no cure exists for Refsum disease, but phytanic acid levels in patients can be reduced by plasmapheresis and a strict diet.\n\nIn this study, we reconstructed a fibroblast-specific genome-scale model based on the recently published, FAD-curated model, based on Recon3D reconstruction. We used transcriptomics (available via GEO database with identifier GSE138379), metabolomics, and proteomics data (available via ProteomeXchange with identifier PXD015518), which we obtained from healthy controls and Refsum disease patient fibroblasts incubated with phytol, a precursor of phytanic acid.\n\nOur model correctly represents the metabolism of phytanic acid and displays fibroblast-specific metabolic functions. Using this model, we investigated the metabolic phenotype of Refsum disease at the genome-scale, and we studied the effect of phytanic acid on cell metabolism. We identified 53 metabolites that were predicted to discriminate between Healthy and Refsum disease patients, several of which with a link to amino acid metabolism. Ultimately, these insights in metabolic changes may provide leads for pathophysiology and therapy.

systems biology↗