A Class of Reactive Acyl-CoA Species Reveals the Non-enzymatic Origins of Protein Acylation

Abstract

SUMMARY The mechanisms underlying the formation of acyl protein modifications remain poorly understood. By investigating the reactivity of endogenous acyl-CoA metabolites, we found a class of acyl-CoAs that undergoes intramolecular catalysis to form reactive intermediates which non-enzymatically modify proteins. Based on this mechanism, we predicted, validated, and characterized a protein modification: 3-hydroxy-3-methylglutaryl(HMG)-lysine. In a model of altered HMG-CoA metabolism, we found evidence of two additional protein modifications: 3-methylglutaconyl(MGc)-lysine and 3-methylglutaryl(MG)-lysine. Using quantitative proteomics, we compared the ‘acylomes’ of two reactive acyl-CoA species, namely HMG-CoA and glutaryl-CoA, which are generated in different pathways. We found proteins that are uniquely modified by each reactive metabolite, as well as common proteins and pathways. We identified the tricarboxylic acid cycle as a pathway commonly regulated by acylation, and validated malate dehydrogenase as a key target. These data uncover a fundamental relationship between reactive acyl-CoA species and proteins, and define a new regulatory paradigm in metabolism.

SHMT2 Desuccinylation by SIRT5 Drives Cancer Cell Proliferation

“…3A). The in vitro succinylation of protein is a nonenzymatic reaction (41) and succinyl-CoA is a reactive agent for protein modification (42). In addition, SHMT2 succinylation levels were increased in cells treated with nicotinamide but not with sodium butyrate, suggesting that SHMT2 succinylation levels were regulated by class III not the class I or II HDACs (Fig.…”

“…Succinyl-CoA is an active mitochondrial tricarboxylic acid cycle intermediate, and the nonenzymatic reaction by succinyl-CoA is tightly controlled by its concentration in the mitochondria matrix (42). Published proteome shows that SHMT1 is succinylated as well (30), and SHMT1 shares conserved amino acid sequence with SHMT2.…”

Nicotinamide mononucleotide requires SIRT3 to improve cardiac function and bioenergetics in a Friedreich’s ataxia cardiomyopathy model

“…In summary, our findings provide mechanistic insight into SIRT3-dependent therapeutic effects of NMN treatment, potentially via deacetylation at key SIRT3 targets in the FXN-KO heart. Recent work from our lab characterized the chemistry of nonenzymatic acylation of common marks like acetylation, as well as novel acyl marks (62). Additionally, recent literature describes high reactivity of lysine residues to nonenzymatic acetylation at strong SIRT3 targets sites, indicating an important role for SIRT3 in suppressing acetylation at these sites rather than at all sites of acetylation (30,63).…”

News and views

“…As a consequence, the proteome of liver mitochondria isolated from HMG-CoA lyase knockout (KO) mice is heavily HMGylated and that of glutaryl-CoA dehydrogenase KO mice is heavily glutarylated. Wagner et al further demonstrate that many protein sites are uniquely modified by either HMG-CoA or glutaryl-CoA, but some pathways, such as the tricarboxylic acid cycle, are commonly modified (Wagner et al 2017). Given that these modifications affect the activity of many enzymes, protein acylation has been proposed as a biological regulatory mechanism that controls metabolism.…”

“…In inborn errors of acylCoA metabolism, aberrant protein acylation is a frequent observation, but it is currently unknown whether it plays a role in pathophysiology (Pougovkina et al 2014;Tan et al 2014). Wagner et al now show that short-chain dicarboxylateCoAs, such as succinyl-, glutaryl-and 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA), are inherently unstable and form a highly reactive anhydride after ring closure (Wagner et al 2017). As a consequence, the proteome of liver mitochondria isolated from HMG-CoA lyase knockout (KO) mice is heavily HMGylated and that of glutaryl-CoA dehydrogenase KO mice is heavily glutarylated.…”