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Cited by 343Sirtuins and Resveratrol in MedicineMitochondrial Function and PathologyAutophagy in Disease and Therapy

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

Open access
Carrico, Chris, Meyer, Jesse G., He, Wenjuan, Gibson, Brad W., Verdin, Eric·2018·Cell Metabolism
DOI 10.1016/j.cmet.2018.01.016PMC PMC5863732
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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.

AI snapshot

Written from the paper’s full text.

TL;DR

This review argues that mitochondrial lysine acylation is largely a non-enzymatic consequence of reactive acyl-CoA species and is reversed by mitochondrial sirtuins SIRT3, SIRT4, and SIRT5. It synthesizes proteomic and biochemical evidence linking these modifications to mitochondrial metabolism, stress responses, and diseases including metabolic syndrome, cancer, neurological disorders, and hearing loss.

Key findings

  • Mitochondrial acylation includes acetylation, succinylation, malonylation, glutarylation, and other acyl marks; SIRT3 is the major mitochondrial deacetylase, SIRT5 removes acidic acyl groups such as succinyl, malonyl, and glutaryl, and SIRT4 remains the least understood but has been linked to lipoyl, biotinyl, and branched-chain acyl modifications.
  • Proteomic surveys mapped thousands of sites: for example, 2,187 acetylation sites in 483 mouse liver mitochondrial proteins, with 283 sites in 136 proteins increased more than twofold in SIRT3-deficient mice; 2,565 succinylation sites in 779 proteins in SIRT5-deficient liver and MEFs; and 1,137 malonylation sites in 430 proteins, with 183 sites increased in SIRT5 knockout liver.
  • Acylation is often inhibitory for mitochondrial enzymes, and sirtuin-mediated removal can activate pathways such as fatty acid oxidation, ketone body synthesis, the urea cycle, and oxidative stress defense; examples include PDH, HMGCS2, CPS1, OTC, MnSOD, and IDH2.
  • Disease connections include SIRT3 loss with metabolic syndrome, pulmonary arterial hypertension, age-related hearing loss, and context-dependent cancer roles; SIRT5 loss with altered ketone body production, ammonia handling, and glycolysis; and SIRT4 with leucine metabolism and insulin secretion.

Methods

  • Narrative review synthesizing published proteomic, biochemical, genetic, and structural studies; no new primary experimental data are reported.
  • The paper compares mass-spectrometry strategies for acylation profiling, including label-free quantification, SILAC, isobaric tagging such as TMT, and newer stoichiometry methods.
  • Evidence discussed comes from mouse knockout models, cell lines, human tissues, and in vitro enzyme assays, with emphasis on SIRT3 and SIRT5 datasets and selected SIRT4 studies.

Limitations

  • Stated: SIRT4’s enzymatic activity and target specificity remain poorly defined; most acylation sites appear to have low stoichiometry, often below 1% for acetylation, raising questions about functional relevance; indirect SILAC-based stoichiometry can overestimate occupancy because lysine carries multiple modifications; and study discrepancies exist, such as the 28% versus 79% overlap reported between succinylation and acetylation sites.
  • Stated: the mechanisms connecting acylation changes to whole-organism disease phenotypes are largely unknown, and many disease effects are likely mediated by multiple low-occupancy modifications rather than a single site.
  • Evident: as a review, the conclusions depend on the cited literature rather than new experiments, and the field lacks comprehensive stoichiometry data for most acyl modifications.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1016/j.cmet.2018.01.016

Cites

103 of 103 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 149 cited sources checked · 0 supported · 0 flagged

  • Premisenone given

    SIRT3, SIRT4, and SIRT5 are mitochondrial NAD+-dependent deacylases that remove acyl modifications from target proteins.

    “Three protein deacylases, SIRT3, SIRT4 and SIRT5 reside in the mitochondria and remove these modifications from targeted proteins in an NAD+-dependent manner.”
    Quote in the paperSubstantial claim
  • Interpretationcitation

    SIRT3 is the major mitochondrial protein deacetylase.

    “Early experiments using western blotting analysis and antisera specific for acetyl-lysine showed globally increased mitochondrial protein acetylation in mice lacking SIRT3 ((Lombard et al. 2007)), indicating that SIRT3 was the major mitochondrial protein deacetylase.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Lombard et al. 2007 source

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  • Premisecitation

    Patients with MCD deficiency exhibit increased protein malonylation.

    “Similarly, and from the same study, human SCAD-deficient fibroblasts show increased lysine butyrylation, patients with malonyl-CoA decarboxylase (MCD) deficiency exhibit increased protein malonylation and finally, propionyl-CoA carboxylase (PCC) deficient patient cells show increased lysine propionylation.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Pougovkina et al. 2014 source

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  • Premisecitation

    Loss of SIRT3 exacerbates hypernutrition-induced impairment of skeletal muscle glucose uptake.

    “However, prolonged hypernutrition leads to type 2 diabetes, and has been shown to impair skeletal muscle glucose uptake in a manner exacerbated by the loss of SIRT3 (Jing et al. 2013),(Lantier et al. 2015).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Jing et al. 2013 source

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    • cites Lantier et al. 2015 source

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  • Premisecitation

    Loss of SIRT3 inhibits fatty acid oxidation.

    “Loss of SIRT3 has been shown to inhibit fatty acid oxidation ((Hirschey et al. 2010)); the same study showed decreased gluconeogenic production of glucose in response to cold challenge and decreased production of the ketone body beta-hydroxybutyrate during fasting.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Hirschey et al. 2010 source

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  • May combine two claims. 60
  • Classified as probably not a substantial claim. 6

  • May combine two claims.

    Premisecitation

    SIRT4 can regulate lipoyl- and biotinyl-lysine modifications and demethylglutarylate branched-chain acyl-lysines.

    “One study has shown that SIRT4 can regulate the levels of both lipoyl- and biotinyl-lysine modifications in pyruvate dehydrogenase and likely other proteins ((Mathias et al. 2014)).”
    • Also stated in: § The Emerging Targets of SIRT4 · plain
      “Recombinant SIRT4 was sufficient to demethylglutarylate lysine residues, and SIRT4-overexpressing cells contained lower levels of these branched-chain acyl-lysines.”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites Mathias et al. 2014 source

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    • cites Anderson 2017 source

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  • May combine two claims.

    Interpretationnone given

    Mitochondrial acylation is mostly non-enzymatic, while nuclear acylation is controlled by competing enzymatic acyltransferases and deacylases.

    “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.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    SIRT5 regulates lysine succinylation, malonylation, and glutarylation.

    “This work resulted in the identification of novel modifications targeted by SIRT5: succinylation, malonylation and glutarylation as described in details below ((Du et al. 2011{Zhang, 2011 #16);(Peng et al. 2011);(Tan et al. 2014)}.”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites Du et al. 2011

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    • cites Peng et al. 2011 source

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    • cites Tan et al. 2014 source

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  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationreasoning

    A semi-enzymatic mechanism may account for increased acetylation of PDP1 and PDHA1.

    “Assuming that ACAT1 is capable of holding a reactive acetyl-CoA molecule in place for long enough, increasing the local concentration of reactive thioester, a semi-enzymatic mechanism may account for increased acetylation to PDP1/PDHA1.”
    Quote in the paperNot a substantial claim
    • The authors state this as an assumption: ACAT1 can hold a reactive acetyl-CoA molecule in place long enough to increase the local concentration of reactive thioester, enabling a semi-enzymatic mechanism for increased acetylation of PDP1 and PDHA1.

  • May combine two claims.

    Premisecitation

    GCN5L1 interacts with and promotes acetylation of respiratory chain proteins and reverses global SIRT3 effects on mitochondrial acetylation, respiration, and bioenergetics.

    “GCN5L1 interacts with and promotes acetylation respiratory chain target proteins and reverses global SIRT3 effects on mitochondrial protein acetylation, respiration and bioenergetics ((Scott et al. 2012)).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Scott et al. 2012 source

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  • May combine two claims.

    Premisenone given

    Proteomic surveys have identified mitochondrial acetylation, succinylation, glutarylation, and malonylation sites and their regulation by SIRT3 and SIRT5.

    “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.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    Denatured proteins are more rapidly acetylated by coincubation with acetyl-CoA, indicating that local structure slows acylation.

    “For example, denatured proteins are more rapidly acetylated by coincubation with acetyl-CoA (Wagner and Payne 2013), indicating that local structure slows acylation; past studies have shown that sirtuins favor either unstructured regions (Khan and Lewis 2005, Smith et al. 2011) or, in the case of SIRT3, beta sheets (Smith et al. 2011).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Wagner and Payne 2013

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    Interpretationnone given

    Dietary inputs and tissue metabolic demands create acyl-CoA concentrations that interact with mitochondrial molecular context to drive acylation at different rates, and sirtuin expression and NAD+ supply reverse this process.

    “Broadly, dietary inputs and the metabolic demands of various tissues create acyl-CoA concentrations with interact with molecular contexts in mitochondria to drive acylation at differing rates for different targets; gene expression of and NAD+ supply to sirtuins then reverses this process.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    VDACs are outer mitochondrial membrane proteins with tissue-dependent expression and are part of the acylcarnitine translocase pathway.

    “Voltage-dependent anion channels (VDACs) are outer mitochondrial membrane proteins with tissue-dependent expression patterns and are part of the acylcarnitine translocase pathway ((Lee, Kerner, and Hoppel 2011)); their partners on the inner membrane, adenine nucleotide translocases (ANTs), are known to be acetylated and some sites are predicted to be functionally important to channel function (Mie”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Lee, Kerner, and Hoppel 2011 source

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    Premisecitation

    Mice with SCAD deficiency accumulate high levels of butyryl-CoA and show increased protein lysine butyrylation.

    “Mice with short-chain acyl-CoA dehydrogenase (SCAD) deficiency accumulate high levels of butyryl-CoA and show increased protein lysine butyrylation ((Pougovkina et al. 2014)).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Pougovkina et al. 2014 source

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  • May combine two claims.

    Premisecitation

    Knockdown of GCN5L1 reduces mitochondrial protein acetylation, and reconstitution in intact mitochondria restores it.

    “Genetic knockdown of GCN5L1 blunts mitochondrial protein acetylation, and its reconstitution in intact mitochondria restores protein acetylation.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Scott et al. 2012 source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Prolonged hypernutrition leads to type 2 diabetes and impairs skeletal muscle glucose uptake.

    “However, prolonged hypernutrition leads to type 2 diabetes, and has been shown to impair skeletal muscle glucose uptake in a manner exacerbated by the loss of SIRT3 (Jing et al. 2013),(Lantier et al. 2015).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Jing et al. 2013 source

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    • cites Lantier et al. 2015 source

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    Premisecitation

    Calorie restriction does not change brain mitochondrial acetylation and decreases skeletal muscle acetylation.

    “Metabolic supplier organs such as the liver and kidney demonstrate mitochondrial hyperacetylation under CR, as does the heart (Schwer et al. 2009); brain mitochondrial acetylation was unchanged, however, and skeletal muscle acetylation decreased.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Schwer et al. 2009 source

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  • May combine two claims.

    Premisecitation

    Loss of SIRT3 decreases gluconeogenic glucose production after cold challenge and decreases beta-hydroxybutyrate production during fasting.

    “Loss of SIRT3 has been shown to inhibit fatty acid oxidation ((Hirschey et al. 2010)); the same study showed decreased gluconeogenic production of glucose in response to cold challenge and decreased production of the ketone body beta-hydroxybutyrate during fasting.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Hirschey et al. 2010 source

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  • May combine two claims.

    Premisecitation

    During calorie restriction, liver mitochondrial proteins show an overall increase in acetylation, while proteins in other cellular compartments do not.

    “Proteomic characterization of the changes in liver reveals a complicated landscape of alterations, but an overall increase in acetylation levels for mitochondrial proteins but not those found in other cellular compartments during CR (Hebert et al. 2013).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Hebert et al. 2013 source

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  • May combine two claims.

    Premisecitation

    ANTs are known to be acetylated, and some acetylation sites are predicted to be functionally important for channel function.

    “their partners on the inner membrane, adenine nucleotide translocases (ANTs), are known to be acetylated and some sites are predicted to be functionally important to channel function (Mielke et al. 2014).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Mielke et al. 2014 source

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  • May combine two claims.

    Premisecitation

    Sirtuins favor unstructured regions, and SIRT3 favors beta sheets.

    “past studies have shown that sirtuins favor either unstructured regions (Khan and Lewis 2005, Smith et al. 2011) or, in the case of SIRT3, beta sheets (Smith et al. 2011).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Khan and Lewis 2005

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    • cites Smith et al. 2011 source

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  • May combine two claims.

    Interpretationreasoning

    Evidence such as the link to MnSOD supports roles for acylation both as a direct effector modulated by NAD+ and in transducing NAD+ into an N-methylnicotinamide signal.

    “As NAD+ supplementation also results in potentially beneficial production of N-methylnicotinamide via sirtuins ((Schmeisser et al. 2013)), evidence such as the link to MnSOD affirms roles for acylation both as a direct effector modulated by NAD+ and in transducing NAD+ into an N-methylnicotinamide signal.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    SIRT3 deacetylates PDP, enhancing its phosphatase activity on PDC and decreasing PDC phosphorylation.

    “First, SIRT3 deacetylates K321 and second, SIRT3 also deacetylates PDP, enhancing its phosphatase activity on PDC and thereby decreasing PDC phosphorylation. ((Fan et al. 2014)).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Fan et al. 2014 source

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  • May combine two claims.

    Premisecitation

    Lipoylation occurs at two sites in the E2 N-terminal region, K132 and K259 in the human sequence, and is enzymatically reversed by SIRT4.

    “Lipoylation occurs at two sites in the E2 N-terminal region (K132 and K259 in the human sequence), and is enzymatically reversed by SIRT4 ((Mathias et al. 2014)).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Mathias et al. 2014 source

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  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based). May combine two claims.

    Interpretationreasoning

    The effect of SIRT5-mediated removal of PDC succinylation is not known but would be expected to activate the enzyme similarly to SIRT3.

    “The effect of SIRT5-mediated removal of PDC succinylation is not known but would be expected to activate the enzyme similar to SIRT3.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    Acetylation of PDHA1 K321 recruits PDK, leading to PDC phosphorylation and inhibition of its enzymatic activity.

    “Acetylation of PDHA1 K321 recruits PDK leading to PDC phosphorylation and inhibition of its enzymatic activity.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Jing et al. 2013 source

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  • May combine two claims.

    Premisecitation

    The protective effects of nicotinamide riboside on noise-induced hearing loss appear to be mediated in mitochondria because SIRT3-overexpressing mice are resistant and SIRT3 deletion abrogates the protection.

    “These effects appear to be mediated in the mitochondria because SIRT3-overexpressing mice are resistant to noise-induced hearing loss and SIRT3 deletion abrogates the protective effects of nicotinamide riboside ((Brown et al. 2014))”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Brown et al. 2014 source

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  • May combine two claims.

    Premisecitation

    Lysine succinylation has been observed on DLAT, DLD, and PDHA1, including multiple succinylations controlled by SIRT5.

    “Lysine succinylation has been observed on DLAT in addition to DLD and PDHA1, including multiple succinylations controlled by SIRT5 ((Rardin, He, et al. 2013)).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Rardin, He, et al. 2013

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  • May combine two claims.

    Interpretationreasoning

    SIRT3 facilitates fatty acid catabolism in the liver and the peripheral use of lipid-derived acetate and ketone bodies during fasting.

    “SIRT3 therefore facilitates the catabolism of fatty acids in the liver and the peripheral use of lipid-derived acetate and ketone bodies during fasting.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationreasoning

    Lysine residues near arginine may have decreased pKa and be more likely to be uncharged, leaving their free electron pair available for acylation.

    “For example, lysine residues near arginine may have decreased pKa and be more likely to have no charge, leaving their free electron pair available for acylation.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    SIRT3 and SIRT4 regulate the PDC in opposing directions: SIRT3 clearance of lysine acetylation allows efficient PDC function, while SIRT4 removal of enzymatically active cofactors from specific lysine residues inhibits the PDC.

    “Thus, SIRT3 and SIRT4 regulate the PDC in opposing directions; SIRT3’s clearance of lysine acetylation allows for efficient PDC function, while SIRT4’s removal of enzymatically active cofactors from specific lysine residues inhibits the PDC.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    Administering the NAD precursor nicotinamide riboside prevents noise-induced hearing loss and degeneration of spiral ganglia neurites.

    “Administering the NAD precursor nicotinamide riboside prevents noise-induced hearing loss and degeneration of spiral ganglia neurite degeneration.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Brown et al. 2014 source

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  • May combine two claims.

    Premisecitation

    SIRT3 and SIRT5 both positively regulate HMGCS2 activity via deacetylation and desuccinylation, respectively.

    “SIRT3 and SIRT5 both positively regulate HMGCS2 activity via respectively deacetylating and desuccinylating it ((Shimazu et al. 2010))((Rardin, He, et al. 2013)).”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites Shimazu et al. 2010 source

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    • cites Rardin, He, et al. 2013

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  • May combine two claims.

    Premisecitation

    Mice lacking SIRT5 fail to upregulate CPS1 activity and show elevated blood ammonia under fasting, calorie restriction, or high protein diet.

    “Mice lacking SIRT5 fail to upregulate CPS1 activity and show elevated blood ammonia under these conditions ((Nakagawa et al. 2009))((Tan et al. 2014)).”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites Nakagawa et al. 2009 source

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    • cites Tan et al. 2014 source

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    Premisecitation

    CPS1 has at least 52 acetylated, 44 succinylated, 33 glutarylated, and 29 malonylated lysine sites.

    “At least 52 lysine sites are found to be acetylated, 44 sites succinylated, 33 sites glutarylated and 29 sites malonylated.”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Nakagawa et al. 2009 source

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    • cites Rardin, Newman, et al. 2013

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    • cites Rardin, He, et al. 2013

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    Interpretationcitation

    CPS1 and OTC carry out the first two steps of the urea cycle and are both regulated by mitochondrial sirtuins.

    “The two mitochondrial enzymes, carbamoyl phosphate synthetase 1 (CPS1) and Ornithine transcarbamylase (OTC), which carry out the first two steps of urea cycle reactions, are both regulated by the activities of mitochondrial sirtuins.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    Calorie restriction stimulates the urea cycle and upregulates OTC activity; this upregulation is lost in the absence of SIRT3, leading to increased orotic acid levels.

    “Calorie restriction stimulates the urea cycle and up-regulates OTC activity; this up-regulation of OTC activity is lost in the absence of SIRT3, leading to increased orotic acid levels, a known outcome of OTC deficiency ((Hallows et al. 2011)).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Hallows et al. 2011 source

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  • May combine two claims.

    Interpretationreasoning

    SIRT5 restores the positively charged microenvironment of HMGCS2 and facilitates enzymatic function by removing succinyl groups.

    “SIRT5, by removing these succinyl groups, restores the positively charged microenvironment and facilitates enzymatic function.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    Beta-hydroxybutyrate is an endogenous inhibitor of HDACs and can affect gene expression via chromatin modifications and regulate the response to oxidative stress.

    “Beta-hydroxybutyrate is an endogenous inhibitor of HDACs and can thereby affect gene expression via chromatin modifications and regulate the response to oxidative stress ((Shimazu et al. 2013)).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Shimazu et al. 2013 source

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  • May combine two claims.

    Premisecitation

    In silico deacetylation of HMGCS2 lysines 310, 447, and 473 causes conformational changes near the catalytic site, suggesting acetylation might interfere with enzymatic activity via changing conformation.

    “Structural simulations show that in silico deacetylation of these three lysines causes conformational changes of HMGCS2 near the catalytic site, suggesting acetylation might interfere with the enzymatic activity via changing its conformation ((Shimazu et al. 2010)).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Shimazu et al. 2010 source

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  • May combine two claims.

    Interpretationreasoning

    Succinylation of HMGCS2 K83 and K310 may disrupt the positively charged microenvironment and reduce enzymatic activity.

    “This highly positive microenvironment might be disrupted when the two lysines are modified by negatively charged succinyl groups leading to a reduction in enzymatic activity.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    Mice lacking SIRT3 or SIRT5 have reduced levels of ketone bodies upon fasting, supporting a positive role for sirtuins in regulating ketone body biosynthesis.

    “Mice lacking SIRT3 or SIRT5 have reduced levels of ketone bodies upon fasting, supporting a positive role for sirtuins in regulating ketone body biosynthesis ((Shimazu et al. 2010))((Rardin, He, et al. 2013)).”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites Shimazu et al. 2010 source

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    • cites Rardin, He, et al. 2013

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  • May combine two claims.

    Premisecitation

    The three cytosolic urea cycle enzymes are malonylated at multiple sites and demalonylated at some sites by SIRT5.

    “The three other enzymes in the urea cycle are located in the cytosol and are also malonylated at multiple sites with demalonylation at some sites by SIRT5 (Nishida et al. 2015).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Nishida et al. 2015 source

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  • May combine two claims.

    Premisereasoning

    CPS1 is the most heavily modified protein in mitochondria, possibly due to its high abundance and relatively large size.

    “CPS1 is the most heavily modified protein in mitochondria, possibly due to its high abundance and relatively large size.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    SIRT3 deacetylates manganese superoxide dismutase and isocitrate dehydrogenase 2.

    “The mitochondrial SIRT3 deacetylates two of these enzymes: manganese superoxide dismutase (MnSOD) (Tao et al. 2010) and isocitrate dehydrogenase 2 (IDH2)(Someya et al. 2010).”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites Tao et al. 2010 source

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    • cites Someya et al. 2010 source

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  • May combine two claims.

    Premisecitation

    SIRT3 attenuates cell death after excitotoxic stress and mediates the protective effect of exercise against such stress, possibly via deacetylation of cyclophilin D.

    “Similarly, SIRT3 function has been shown to attenuate cell death after excitotoxic stress, and mediates the protective effect of exercise against such stress ((Cheng et al. 2016)), possibly via deacetylation of cyclophilin D ((Cheng et al. 2016),(Amigo et al. 2017)).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Cheng et al. 2016 source

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    • cites Amigo et al. 2017 source

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  • May combine two claims.

    Premisecitation

    Both MnSOD and the various mitochondrial superoxide sources are acylated.

    “Both MnSOD and the various mitochondrial superoxide sources are acylated ((Rardin, Newman, et al. 2013), (Rardin, He, et al. 2013);(Tan et al. 2014)); MnSOD also carries glutarylation, succinylation, and acetylation at functionally required lysine residues near its active site, K122 in particular bears all three modifications ((Tao et al. 2010)).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Rardin, Newman, et al. 2013

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    • cites Rardin, He, et al. 2013

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    • cites Tan et al. 2014 source

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  • May combine two claims.

    Interpretationreasoning

    SIRT4 control of tumorigenesis is particularly relevant to c-Myc-driven, mitochondrially active, glutamine-dependent tumors, while SIRT3 prevents less mitochondrially active tumors.

    “SIRT4 control of tumorigenesis is therefore particularly relevant to c-Myc-driven, mitochondrially active, glutamine-dependent tumors, while SIRT3 prevents less mitochondrially active tumors.”
    Quote in the paperSubstantial claim

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    Premisecitation

    GLUD1 is inhibited by SIRT4 and by acetylation that can be reversed by SIRT3.

    “GLUD1 is inhibited by SIRT4 ((Haigis et al. 2006)) and by acetylation which can be reversed by SIRT3 ((Schlicker et al. 2008)).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Haigis et al. 2006 source

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    • cites Schlicker et al. 2008 source

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    Premisecitation

    Oxidized glutathione underpins all mitochondrial H2O2 detoxification and is reduced by NADPH-dependent glutathione reductases.

    “Oxidized glutathione thus underpins all mitochondrial H2O2 detoxification, and is reduced by NADPH-dependent glutathione reductases ((Merksamer et al. 2013)).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Merksamer et al. 2013 source

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  • May combine two claims.

    Interpretationreasoning

    Mitochondrial acylation can modulate neuronal function, and its removal by sirtuins can help improve health.

    “Given the effects already demonstrated of mitochondrial acylation in allowing tumorigenesis and increasing production of reactive oxygen species, it should come as no surprise that mitochondrial acylation can modulate neuronal function - and, more interestingly, that its removal by sirtuins can help improve health.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    IDH2 function is inhibited by acetylation, and its deacetylation by SIRT3 restores function.

    “IDH2 function is inhibited by acetylation, and its deacetylation by SIRT3 restores function ((Schlicker et al. 2008)).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Schlicker et al. 2008 source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    ASSY is demalonylated by SIRT5 at 2 of 11, ARLY at 1 of 6, and ARG1 at 3 of 16 malonyllysine sites.

    “These are argininosuccinate synthase (ASSY), argininosuccinate lyase (ARLY), and arginase (ARGI1); ASSY is demalonylated by SIRT5 at 2 of 11, ARLY at 1 of 6, and ARG1 at 3 of 16 malonyllysine sites.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Nishida et al. 2015 source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    SIRT3 has been reported as pro-apoptotic, and SIRT3 loss is associated with a tumor-permissive environment via inhibition of ROS production.

    “SIRT3 has been reported as pro-apoptotic ((Allison and Milner 2007)) and SIRT3 loss is associated with a tumor-permissive environment via the inhibition of ROS production ((Kim et al. 2010);(Bell et al. 2011);(Finley et al. 2011)).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Allison and Milner 2007

      Not checked in the free run.

    • cites Kim et al. 2010 source

      Not checked in the free run.

    • cites Bell et al. 2011 source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    MnSOD carries glutarylation, succinylation, and acetylation at functionally required lysine residues near its active site, with K122 bearing all three modifications.

    “MnSOD also carries glutarylation, succinylation, and acetylation at functionally required lysine residues near its active site, K122 in particular bears all three modifications ((Tao et al. 2010)).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Tao et al. 2010 source

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    IDH2 competes with NAD+-dependent IDH3 for isocitrate, so tuning IDH2 activity regulates available NADPH for H2O2 detoxification.

    “IDH2 competes with NAD+-dependent IDH3 for isocitrate; tuning the activity of IDH2 thus regulates available NADPH for H2O2 detoxification.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    Thiol groups can mediate nucleophilic attack at least as well as deprotonated amines and are abundant in the mitochondrial matrix.

    “thiol residues are as capable as deprotonated amines of mediating nucleophilic attack, if not more so, and are found in large numbers in the mitochondrial matrix ((Requejo et al. 2010)).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Requejo et al. 2010 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationreasoning

    Since pathway-wide acylation is frequently observed, biological effects might arise from the combined action of many modifications each at low occupancy.

    “Given that studies often find pathway-wide acylation, it may be that the cumulative effect of dozens of low-occupancy modifications mediates biological effects.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    Reduced SIRT3 activity narrows mitochondrial functional capacity in several ways, and the specific failure mode in any disease depends on which linked mitochondrial pathway is most burdened and therefore most vulnerable to hyperacetylation.

    “Loss of SIRT3 activity thus limits the functional envelope of mitochondria in multiple directions, with the precise failure mechanism for a given disease depending on which of many connected mitochondrial pathways is most taxed and thus most sensitive to hyperacetylation.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationreasoning

    SIRT3 opposes aging both by reducing systemic stressors like NAD+ decline and by improving the ability to withstand the damage they cause.

    “SIRT3 thus fights aging by attenuating the development of systemic stressors such as NAD+ loss and by enhancing our ability to survive the resulting insults.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    The V208I mutation increases the KM of SIRT3 for NAD+ and reduces the Vmax toward peptide substrate, reducing catalytic efficiency and creating a ~1.4-fold increase in risk for metabolic syndrome.

    “The V208I mutation caused by this polymorphism both increased the KM of SIRT3 for NAD+ and reduced the Vmax of the enzyme towards peptide substrate, reducing overall catalytic efficiency and mimicking the effects of reduced SIRT3 expression at the whole-body level and creating a ~1.4-fold increase in risk for metabolic syndrome ((Hirschey et al. 2011)).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Hirschey et al. 2011 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Interpretationnone given

    Sirtuins may not alter the overall rate of organismal aging.

    “while sirtuins may not alter the overall rate of organismal aging”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    The protective effects of nicotinamide riboside against noise-induced hearing loss depend on SIRT3, since SIRT3 overexpression confers resistance and SIRT3 deletion abrogates protection.

    “These effects are dependent on SIRT3, since SIRT3-overexpressing mice are resistant to noise-induced hearing loss and SIRT3 deletion abrogates the protective effects of NR.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Brown et al. 2014 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationcitation

    Current research argues both for and against a causative role for mitochondrial protein acylation in metabolic disorders.

    “Current research argues both for and against a causative role for mitochondrial protein acylation in metabolic disorders.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S4 (based).

    Interpretationnone given

    Hypernutrition and its associated disease states are characterized by increased availability of acyl-CoA precursors believed to drive the bulk of mitochondrial acylation.

    “Hypernutrition and its associated disease states, such as obesity and type 2 diabetes, are characterized by an increased availability of the acyl-CoA precursors which are believed to drive the bulk of mitochondrial acylation.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    Cochlear NAD+ levels increased in mice after administering nicotinamide riboside and prevented noise-induced hearing loss.

    “Cochlear NAD(+) levels increased in mice after administering nicotinamide riboside, a precursor to NAD(+) and prevented noise-induced hearing loss.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Brown et al. 2014 source

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    With age, CD38 lowers NAD+, raising inflammatory SASP cytokines that drive proliferation of cells expressing CD38; SIRT3 restrains this cycle by lessening the associated mitochondrial dysfunction.

    “The CD38-induced loss of NAD+ with age thus leads to increases in inflammatory SASP cytokines, which in turn lead to proliferation of CD38-expressing cells; SIRT3 function, by attenuating the resulting loss of mitochondrial function, helps keep this loop in check.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    In diseased smooth muscle, hyperacetylation of mitochondrial proteins drives mitochondrial hyperpolarization, greater proliferation, reduced apoptosis, and eventual arterial wall thickening.

    “Increased acetylation of mitochondrial proteins in the affected smooth muscle leads to mitochondrial hyperpolarization, increased proliferation, suppressed apoptosis, and eventually to progressive arterial thickening.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Paulin et al. 2014 source

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    A single SIRT3 polymorphism may produce harmful overactivity in arterial cells while causing harmful underactivity in metabolic pathways.

    “the same polymorphism can lead to pathological gain of function in arterial cells and pathological loss of function in metabolism.”
    Quote in the paperSubstantial claim
65 of 65

  • The authors state this as an assumption.

    ACAT1 can hold a reactive acetyl-CoA molecule in place long enough to increase the local concentration of reactive thioester, enabling a semi-enzymatic mechanism for increased acetylation of PDP1 and PDHA1.

    “Assuming that ACAT1 is capable of holding a reactive acetyl-CoA molecule in place for long enough, increasing the local concentration of reactive thioester, a semi-enzymatic mechanism may account for increased acetylation to PDP1/PDHA1.”

  • The paper relies on this without support.

    Mitochondrial acylation sites generally have low stoichiometry.

    “Given the generally low stoichiometry of mitochondrial acylation sites, each disease is likely mediated by multiple presently-unidentified acylations, each slightly but cooperatively impairing mitochondrial function.”

  • The paper relies on this without support.

    Both over-nutrition and under-nutrition create abnormal metabolic states with high levels of acyl-CoAs.

    “Both over- and under-nutrition create abnormal metabolic states with high levels of acyl-CoAs.”
3 of 3

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Sirtuins regulate key metabolic processes, stress responses and ageing biology.

    “Since their discovery, the sirtuins have received much attention because they regulate key metabolic processes, stress responses and ageing biology7.”

    From NAD+ metabolism and its roles in cellular processes during ageing (2021) · cites this paper as [7]

  • Nuclear SIRT1, SIRT6 and SIRT7 are critical regulators of DNA repair and genome stability, and mitochondrial SIRT3, SIRT4 and SIRT5 and nuclear SIRT1 regulate mitochondrial homeostasis and metabolism.

    “Specifically, recent evidence has shown that nuclear SIRT1, SIRT6 and SIRT7 are critical regulators of DNA repair and genome stability and that mitochondrial SIRT3, SIRT4 and SIRT5 and nuclear SIRT1 regulate mitochondrial homeostasis and metabolism7.”

    From NAD+ metabolism and its roles in cellular processes during ageing (2021) · cites this paper as [7]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Incorrect percentage of SIRT5-regulated malonylation sites

    Minor

    The reported 183 sites are about 16.1% of the 1,137 sites identified, not 13%.

    Reported 13 · recomputed 16.094987

  • Five-tissue quantification conflicts with the reported overlap

    Minor

    If 80% of the 6,286 sites were quantified in all five tissues, more than 5,000 sites would be shared across them. The passage instead reports only 87 shared sites.

  • Opposite claims about SIRT3 loss and ROS production

    Minor

    The cancer section attributes an effect of SIRT3 loss to inhibited ROS production, but elsewhere says SIRT3 itself attenuates ROS production. These assign opposite directions to the effect of losing SIRT3.

  • Conflicting claims about functional PDHA1 acetylation sites

    Minor

    One passage says acetylation at K336 inhibits pyruvate dehydrogenase activity; another says a functional role has been demonstrated only for acetylation at K321.

4 of 4

Cites

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Related

Authors
Carrico, C., Meyer, J. G., He, W., Gibson, B. W., & Verdin, E.
Affiliations
  • Gladstone Institutes (US)
  • Buck Institute for Research on Aging (US)
Corresponding author
Verdin, Eric
ORCID
Venue
Cell Metabolism
Publisher
Elsevier BV
Published
2018-03
Volume
27
Issue
3
Pages
497-512
ISSN
1550-4131 (ISSN-L)
DOI
10.1016/j.cmet.2018.01.016
PMC
PMC5863732
OpenAlex
W2793563787
Cited by
331
References
103
Citations by year
2026: 26 · 2025: 42 · 2024: 36 · 2023: 46 · 2022: 49 · 2021: 47 · 2020: 38 · 2019: 32 · 2018: 15
FWCI
3.73
Type
journal article
Language
en
Open access
Licence
Locations
  • Cell Metabolism (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • NIDDK (R24 DK085610)
  • NIH (T32 AG000266)
Topics
  • Health Sciences › Medicine › Geriatrics and Gerontology › Sirtuins and Resveratrol in Medicine
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Mitochondrial Function and Pathology
  • Health Sciences › Medicine › Epidemiology › Autophagy in Disease and Therapy
Keywords
protein acetylation, succinylation, SIRT3, SIRT5, mitochondrial function, metabolic regulation, mitochondrial disease
MeSH terms
Acetylation, Acylation, Animals, Humans, Mitochondria, Protein Processing, Post-Translational, Mitochondrial Proteins, Sirtuins, Proteomics

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-06.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-06.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

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