The Mitochondrial Acylome Emerges: Proteomics, Regulation by Sirtuins, and Metabolic and Disease Implications

Abstract

Post-translational modification of lysine residues via reversible acylation occurs on proteins from diverse pathways, functions, and organisms. While nuclear protein acylation reflects the competing activities of enzymatic acyltransferases and deacylases, mitochondrial acylation appears to be driven mostly via a non-enzymatic mechanism. Three protein deacylases, SIRT3, SIRT4, and SIRT5, reside in the mitochondria and remove these modifications from targeted proteins in an NAD⁺-dependent manner. Recent proteomic surveys of mitochondrial protein acylation have identified the sites of protein acetylation, succinylation, glutarylation, and malonylation and their regulation by SIRT3 and SIRT5. Here, we review recent advances in this rapidly moving field, their biological significance, and their implications for mitochondrial function, metabolic regulation, and disease pathogenesis.

Keywords: SIRT3; SIRT4; SIRT5; mitochondrial acylation; sirtuin biology.

Figure 1. Mass Spectrometry Methods for Relative Quantification of Site-Specific Protein Acylation

Workflows pictured here reflect the respective studies from the text, and are representative of the most common strategy although slight variations are used. The number of arrows along each workflow indicates where sample mixing occurs, if at all. A, Workflow for Label-Free Quantification (LFQ). B, Workflow for metabolic labeling of MEFs from mutant mice using SILAC. C, Workflow for in vitro isobaric labeling of peptides using TMT reagent. D, Comparison of relative strengths and weaknesses among the methods in (A–C). All strategies use protein isolation, trypsin digestion, immuno-affinity enrichment of the low-abundance peptides containing acetyl-lysine, and LC-MS/MS for identification and quantification. All strategies can be combined with fractionation before LC-MSMS to increase the number of identified acetylation sites, but this greatly complicates LFQ data analysis.

Figure 2. Mitochondrial Acylations are Regulated by SIRT3-5 by Structural Class

Any unmodified lysine residue can react non-enzymatically with the acyl-CoAs found in the mitochondrial matrix. Which sirtuin reverses the resulting acyllysine is determined by structural features of the product. SIRT3 reverses short-chain modifications such as acetylation. SIRT5 reverses divalent modifications including succinylation, malonylation, and glutarylation. SIRT4 reverses branched-chain modifications such as methylglutarylation. Each sirtuin thus regulates the side products of acyl-CoAs corresponding to different facets of mitochondrial metabolism.

Figure 3. Mitochondrial Acylation and Sirtuin-Mediated Deacylation Affect The Urea Cycle At Multiple Points

The urea cycle allows cellular disposal of nitrogen from mitochondrially catabolized glutamate via mitochondrial conversion to carbamoyl phosphate, citrulline shuttling to the cytosol, and loss of urea from arginine. Each enzyme in the pathway is depicted with the number of known sirtuin-regulated sites of each acyl-lysine type shown. SIRT5 desuccinylates and deglutarylates CPS1 to allow efficient clearance of mitochondrial ammonia; and SIRT3 deacetylates Ornithine Carbamoyltransfrase (OTC) to maintain its function. Furthermore, SIRT5 expression in the cytosol maintains the conversion of citrulline to argininosuccinate by demalonylating ASSY.

Figure 4. Acyl-CoA Thioesters Are Common Intermediates In Mitochondrial Metabolism

All major nutrient classes - carbohydrates, fats, proteins, and ketone bodies - are catabolized in part through mitochondrial pathway mediated by acyl-CoAs. Acetylation and succinylation by acetyl-CoA and succinyl-CoA respectively are associated with TCA cycle through all nutrient types, and have been characterized at the proteomic level by mass spectrometry. Similar studies have identified glutarylated, malonylated, and propionylated proteins in mitochondria. Whether the wide variety of lower-abundance acyl-CoA species are in turn transduced into mitochondrial lysine acylation remains to be seen.