SUCLA2 mutations cause global protein succinylation contributing to the pathomechanism of a hereditary mitochondrial disease

John C Newman,Pieti W Pallijeff ,Jesse G Meyer,Jason W Locasale,Sofia Moco,Anu Suomalainen,Reem A Alkhater,Pirjo Isohanni,Berge A Minassian,Birgit Schilling,Wenjuan He,Jonathan Thévenet ,Yuya Nishida,Matthew J Rardin,J Wall Richard ,Eric Verdin,Liliya Euro,Elsebet Østergaard,Xiaojing Liu,Sanna Matilainen,Philipp Gut,Gabriele Civiletto,Alice Parisi,Christopher B Jackson,Christopher J Carroll,Stefan Christen

doi:10.1038/s41467-020-19743-4

Abstract

Mitochondrial acyl-coenzyme A species are emerging as important sources of protein modification and damage. Succinyl-CoA ligase (SCL) deficiency causes a mitochondrial encephalomyopathy of unknown pathomechanism. Here, we show that succinyl-CoA accumulates in cells derived from patients with recessive mutations in the tricarboxylic acid cycle (TCA) gene succinyl-CoA ligase subunit-β (SUCLA2), causing global protein hyper-succinylation. Using mass spectrometry, we quantify nearly 1,000 protein succinylation sites on 366 proteins from patient-derived fibroblasts and myotubes. Interestingly, hyper-succinylated proteins are distributed across cellular compartments, and many are known targets of the (NAD+)-dependent desuccinylase SIRT5. To test the contribution of hyper-succinylation to disease progression, we develop a zebrafish model of the SCL deficiency and find that SIRT5 gain-of-function reduces global protein succinylation and improves survival. Thus, increased succinyl-CoA levels contribute to the pathology of SCL deficiency through post-translational modifications.

Highlights

Mitochondrial acyl-coenzyme A species are emerging as important sources of protein modification and damage
Among all reported succinylated proteins, tricarboxylic acid cycle (TCA) cycle enzymes are enriched for succinylation modifications when all cellular proteins are rank-sorted by the number of acylated sites corrected by the abundance of those proteins (Wilcoxon test p-value = 6E-4, Supplementary Fig. 1a)
Most TCA cycle subunits carry several succinylation sites (Supplementary Fig. 1b). This finding is consistent with the concepts that the abundance of succinyl-CoA in the mitochondria drives non-enzymatic acylation and that the TCA cycle is the predominant source of succinyl-CoA4,9

Summary

Introduction

Mitochondrial acyl-coenzyme A species are emerging as important sources of protein modification and damage. We first proposed that acyl-CoA metabolites are highly reactive chemical species that likely modify lysine side chains in the absence of a catalyst, at the basic pH of the mitochondrial matrix[3]. Pathways involved in the generation or utilization of mitochondrial acyl-CoAs include, among others, the tricarboxylic acid (TCA) cycle, fatty acid oxidation, urea detoxification, ketogenesis, and initial steps of cholesterol synthesis. These pathways are extensively modified by acylation and are the main targets of the mitochondrial sirtuins SIRT3, SIRT4 and SIRT5 that function as lysine deacylases (KDAC)[12,13]. Mitochondrial protein succinylation regulates the urea cycle, ketogenesis, fatty acid oxidation and TCA cycle flux by modulating the key enzymes of these processes[16,17]

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