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

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.

Defective Function of α-Ketoglutarate Dehydrogenase Exacerbates Mitochondrial ATP Deficits during Complex I Deficiency

“…We demonstrate a profound decrease in global mitochondrial succinylation. Alterations in succinylation had not been documented in mitochondrial encephalomyopathies until a recent report demonstrating hypersuccinylation in SUCLA2 deficiency, a mtDNA depletion syndrome (Gut et al 2020). Hypersuccinylation contrasts with the deficient succinylation that we report, but these striking differences may underlie the heterogeneity of the molecular and clinical phenotype of these Leigh-like encephalopathies.…”

The Mystery of Extramitochondrial Proteins Lysine Succinylation

“…This was recently demonstrated in erythropoiesis [ 16 ] and is likely to be the case during most other pathophysiological conditions [ 17 , 18 , 19 ]. Indeed, succinate-CoA ligase deficiency leads to hyper-succinylation of proteins [ 20 ]. Nonetheless, it is firmly established that lysine succinylation also occurs outside mitochondria [ 2 , 20 , 21 , 22 , 23 ].…”

“…Indeed, succinate-CoA ligase deficiency leads to hyper-succinylation of proteins [ 20 ]. Nonetheless, it is firmly established that lysine succinylation also occurs outside mitochondria [ 2 , 20 , 21 , 22 , 23 ]. Furthermore, carnitine palmitoyltransferase (CPT), an enzyme attached to the outer mitochondrial membrane facing the cytosol, exhibits lysine succinyltransferase activity [ 5 ].…”

“…However, in that study, they specifically examined the succinylation of lysines in mitochondrial proteins. On the other hand, in [ 20 ], the authors showed that mutations in the gene coding of a critical subunit of succinate-CoA ligase causes global protein succinylation, not just those found in mitochondria. The authors postulated that this could be due to secondary deficiency of sirtuin SIRT5 attributed to the depletion of NAD + levels, similarly described in other diseases encompassing mitochondrial dysfunction [ 72 , 73 , 74 ].…”

The promises of lysine polyphosphorylation as a regulatory modification in mammals are tempered by conceptual and technical challenges

“…Many large‐scale analyses of other lysine‐based modifications (e.g., ubiquitylation, [ 34 ] acetylation, [ 35 ] and succinylation [ 36 ] ) have employed mass spectrometry. A mass spectrometry approach to identifying lysine polyphosphorylations would go a long way to speed the discovery of new targets.…”