SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways
Open accessAbstract
SUMMARY Protein function is regulated by diverse posttranslational modifications. The mitochondrial sirtuin SIRT5 removes malonyl and succinyl moieties from target lysines. The spectrum of protein substrates subject to these modifications is unknown. We report systematic profiling of the mammalian succinylome, identifying 2,565 succinylation sites on 779 proteins. Most of these do not overlap with acetylation sites, suggesting differential regulation of succinylation and acetylation. Our analysis reveals potential impacts of lysine succinylation on enzymes involved in mitochondrial metabolism; e.g., amino acid degradation, the tricarboxylic acid cycle (TCA) cycle, and fatty acid metabolism. Lysine succinylation is also present on cytosolic and nuclear proteins; indeed, we show that a substantial fraction of SIRT5 is extra-mitochondrial. SIRT5 represses biochemical activity of, and cellular respiration through, two protein complexes identified in our analysis, pyruvate dehydrogenase complex and succinate dehydrogenase. Our data reveal widespread roles for lysine succinylation in regulating metabolism and potentially other cellular functions.
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- Findingown data
Systematic profiling identified 2,565 succinylation sites on 779 proteins in mouse cells.
“We report systematic profiling of the mammalian succinylome, identifying 2,565 succinylation sites on 779 proteins.”
- Also stated in: § Lysine Succinylation Proteome in Mouse Cells · plain
“After removing overlapping sites, we identified a total of 2,565 Lys succinylation sites from 779 proteins in mouse cells”
Quote in the paperSubstantial claim - Also stated in: § Lysine Succinylation Proteome in Mouse Cells · plain
- Findingown data
For RAN K23, succinylation stoichiometry rose from 15% to 45% upon Sirt5 knockout.
“the K23 site on RAN, located within one of the GTP-binding regions, is Lys succinylated, and its stoichiometry increased from 15% to 45% in Sirt5 KO cells.”
Quote in the paperNot a substantial claim - Findingown data
Ninety-two Ksucc sites lie within five residues of other PTM types.
“we identified 92 Ksucc sites located within five residues in flanking distance to various types of PTMs”
Quote in the paperNot a substantial claim - Findingown data
Succinylated proteins also show enrichment for translation, driven by modified ribosomal proteins.
“Lys-succinylated proteins were enriched for translational processes (adjusted p = 3.4 × 10−30) because of the identification of succinylated ribosome proteins.”
Quote in the paperNot a substantial claim - Findingown data
Most succinylation sites do not overlap with acetylation sites.
“Most of these do not overlap with acetylation sites”
- Also stated in: § Lysine Succinylation Proteome in Mouse Cells · plain
“We found that only 282 sites overlapped between Ksucc and Kac sites identified in MEFs”
Quote in the paperSubstantial claim - Also stated in: § Lysine Succinylation Proteome in Mouse Cells · plain
- Findingown data
Cluster analysis of labeling ratios yielded four main Ksucc turnover groups.
“We performed fuzzy c-means clustering analysis of the labeling ratios from all 15 peptides and identified four core clusters (Figure S6A).”
Quote in the paperNot a substantial claim - Findingown data
18 Ksucc sites overlapped with other modifications.
“we identified 18 Ksucc sites overlapped with other modifications (Table S2)”
Quote in the paperNot a substantial claim - Findingown data
More than 12% of Ksucc sites had at least a fourfold rise in SIRT5-deficient cells.
“over 12% of the sites showed over 4-fold increase in abundance in SIRT5-deficient cells”
Quote in the paperSubstantial claim - Findingown data
Fifteen Ksucc peptides appeared in both light and heavy forms at each of the three time points.
“we were able to identify 15 Ksucc peptides in both light and heavy form from all three time points (Table S4).”
Quote in the paperSubstantial claim - Findingown data
Acetyl-CoA acetyltransferase K265 succinylation increased more than 120-fold in Sirt5 KO cells (about 104-fold after normalization).
“Succinylation at K265, located near a CoA-binding site (K260) increased in abundance by more than 120-fold in Sirt5 KO cells (about 104-fold after normalization with protein abundance changes).”
Quote in the paperSubstantial claim - Findingown data
A substantial fraction of SIRT5 is extra-mitochondrial.
“we show that a substantial fraction of SIRT5 is extra-mitochondrial.”
- Also stated in: § SIRT5 Is Present Extramitochondrially · plain
“Subcellular fractionation revealed that a significant fraction of endogenous SIRT5 was present cytosolically both in human cells (Figure 5A) and mouse liver (Figure 5B).”
Quote in the paperSubstantial claim - Also stated in: § SIRT5 Is Present Extramitochondrially · plain
- Findingown data
SIRT5 represses biochemical activity of pyruvate dehydrogenase complex.
“SIRT5 represses biochemical activity of, and cellular respiration through, two protein complexes identified in our analysis, pyruvate dehydrogenase complex and succinate dehydrogenase.”
Quote in the paperSubstantial claim - Findingown data
Most protein networks showed higher lysine succinylation when SIRT5 was absent.
“Quantitative analysis showed an increase in Lys succinylation among most protein networks in SIRT5 deficiency”
Quote in the paperSubstantial claim - Findingown data
Many cytosolic Ksucc proteins are found exclusively or partly in mitochondria.
“a significant portion of cytosolic Ksucc proteins localized exclusively or partially to mitochondria (p = 2.3 × 10−112, Fisher’s exact test)”
Quote in the paperSubstantial claim - Findingown data
The protein interaction network of Lys-succinylated proteins is vast and highly connected with clusters.
“Our data set showed a vast, highly connected network with clusters of nodes extending out to form protein complex patterns”
Quote in the paperNot a substantial claim - Findingown data
For Cluster 2 Ksucc sites, the mean D4-succinylation gain or H4 loss was roughly 0.92% each hour.
“the average rate of Lys D4 succinylation incorporation (or the average rate of the Lys H4 succinylation loss) is about 0.92% per hr for the Ksucc sites in Cluster 2”
Quote in the paperSubstantial claim - Findingown data
Lysine succinylation occurs on cytosolic and nuclear proteins.
“Lysine succinylation is also present on cytosolic and nuclear proteins”
- Also stated in: § Cellular Localization of the Lys Succinylation Proteome · plain
“we identified similar numbers of proteins that were not annotated as mitochondrial (Figure 4B), including ribosomes and histone proteins H2A, H2B, H3, and H1”
Quote in the paperSubstantial claim - Also stated in: § Cellular Localization of the Lys Succinylation Proteome · plain
- Findingown data
SIRT5 deficiency significantly impacts Ksucc levels.
“These data showed that SIRT5 deficiency significantly impacted Ksucc levels”
Quote in the paperSubstantial claim - Findingown data
More than 20 protein complexes were enriched for lysine succinylation.
“Our analysis showed over 20 enriched protein complexes from Lys-succinylated proteins (adjusted p < 0.01).”
Quote in the paperSubstantial claim- The authors state this as an assumption: Core protein complexes are evolutionarily conserved among mammalian species.
- Findingown data
SIRT5 represses biochemical activity of succinate dehydrogenase.
“SIRT5 represses biochemical activity of, and cellular respiration through, two protein complexes identified in our analysis, pyruvate dehydrogenase complex and succinate dehydrogenase.”
Quote in the paperSubstantial claim - Findingown data
For PKM K498, succinylation stoichiometry rose from 12% to 31% in Sirt5 KO MEFs.
“the stoichiometry of K498 site increased from 12% to 31% in Sirt5 KO MEFs”
Quote in the paperSubstantial claim - Findingown data
In Sirt5 KO MEFs, roughly 85% of measured proteins changed less than onefold in abundance.
“about 85% of the proteins (3,348 out of 3,944) showed less than 1-fold change in abundance in Sirt5 KO MEFs (SILAC Sirt5 KO/WT ratio between 0.5 and 2)”
Quote in the paperNot a substantial claim - Findingown data
No nuclear complexes showed enrichment for Ksucc proteins.
“we were not able to identify any nuclear protein complexes that were enriched among Ksucc proteins.”
Quote in the paperNot a substantial claim- The authors state this as an assumption: Core protein complexes are evolutionarily conserved among mammalian species.
- Findingown data
Molecular functions enriched among succinylated proteins include cofactor binding and oxidoreductase activity.
“the molecular functions carried out by Lys succinylated proteins included cofactor binding (adjusted p = 1.2 × 10−65) and oxidoreductase activity (adjusted p = 4.2 × 10−71)”
Quote in the paperNot a substantial claim - Findingown data
Loss of SIRT5 has no significant effect on global lysine acetylation.
“our data showed that SIRT5 deficiency does not significantly impact global Lys acetylation and has an average KO/WT SILAC ratio of 1.04”
Quote in the paperSubstantial claim - Findingown data
Just 38 of the succinylated proteins had prior annotation as exclusively nuclear.
“only 38 Lys-succinylated proteins identified in this study were previously annotated as exclusively nuclear.”
Quote in the paperNot a substantial claim - Findingown data
The sequence motifs AK, GK, KF, and KA occur more often than expected at Ksucc sites.
“motif analysis identified AK, GK, KF, and KA motifs as significantly overrepresented for Lys succinylation sites (Bonferroni corrected p < 0.05)”
Quote in the paperNot a substantial claim - Findingown data
Adjusting for protein abundance ratios left the Ksucc ratio distribution essentially unchanged.
“normalization by protein quantification ratios did not significantly alter the quantification ratio distribution of Lys succinylation sites”
Quote in the paperNot a substantial claim - Findingown data
Almost every mouse pathway annotated with succinyl-CoA involvement was enriched for succinylated proteins.
“nearly all annotated pathways involving succinyl-CoA in mice were enriched with Lys-succinylated proteins”
Quote in the paperSubstantial claim - Findingown data
Domain enrichment among succinylated proteins includes acyl-CoA dehydrogenase, isomerase, and aldehyde dehydrogenase.
“Lys-succinylated proteins were enriched for acyl-CoA dehydrogenase (adjusted p = 5.3 × 10−17), isomerase (adjusted p = 9.2 × 10−12), and aldehyde dehydrogenase (adjusted p = 2.9 × 10−9)”
Quote in the paperNot a substantial claim - Findingown data
SIRT5 represses cellular respiration through PDC and SDH.
“SIRT5 represses biochemical activity of, and cellular respiration through, two protein complexes identified in our analysis, pyruvate dehydrogenase complex and succinate dehydrogenase.”
Quote in the paperSubstantial claim - Findingown data
Of Ksucc sites that overlap phosphorylation, 18% are close to known or predicted phosphotyrosine sites.
“Among all Ksucc sites colocalized with phosphorylation sites, a surprisingly high percentage (18%) colocalized near known or predicted phosphotyrosine residues.”
Quote in the paperNot a substantial claim - Findingown data
HADH K81 succinylation increased more than 200-fold in Sirt5 KO fibroblasts (about 74-fold after normalization).
“Our data indicate that the HADH amino acid residue K81, which is adjacent to a CoA binding site at K80, is succinylated, and its modification increased by more than 200-fold in Sirt5 KO fibroblasts (about 74-fold after normalization with protein abundance changes).”
Quote in the paperSubstantial claim - Findingown data
Succinylated proteins show enrichment for cellular metabolism, especially oxoacid metabolism, redox processes, and coenzyme metabolism.
“Lys-succinylated proteins are significantly enriched in cellular metabolic process with specific enrichment in oxoacid metabolism (adjusted p = 1.6 × 10−110), oxidation reduction process (adjusted p = 8.2 × 10−86), and coenzyme metabolism (adjusted p = 5.4 × 10−57)”
Quote in the paperSubstantial claim - Findingown data
Only a trace of SIRT5 appeared in the nuclear fraction, most clearly in liver.
“A very small amount of SIRT5 was also detected in the nuclear fraction, which was particularly evident in the liver samples (Figure 5B).”
Quote in the paperNot a substantial claim - Findingown data
Similar trends were apparent for acetylation.
“Similar trends were apparent for acetylation.”
Quote in the paperNot a substantial claim - Findingown data
28 Ksucc sites showed more than 10-fold increase in SIRT5-deficient MEFs.
“In SIRT5-deficient MEFs, 28 Ksucc sites showed a more than 10-fold increase in abundance”
Quote in the paperSubstantial claim - Findingown data
SIRT5 knockdown produced about a 3.5-fold increase in cellular respiration when succinate was supplied to permeabilized cells.
“This was associated with a large (roughly 3.5-fold) elevation in cellular respiration in the presence of the SDH substrate succinate (cells were permeabilized to allow compounds access to mitochondria) (Figures 7H and 7I).”
Quote in the paperSubstantial claim - Findingown data
A substantial portion of SIRT5 protein is located in the cytosol.
“Consistent with a role for SIRT5 in regulating Ksucc levels extra-mitochondrially, we find that a substantial fraction of SIRT5 protein is cytosolic.”
Quote in the paperSubstantial claim - Findingcitation
Histone lysine succinylation sites are mainly in C-terminal globular domains, with histone H2B K5 as an exception.
“Similar to previous findings, Lys succinylation sites on histones primarily localize to the C-terminal globular domains, the exception being the histone H2B K5.”
Quote in the paperNot a substantial claim - Findingown data
Respiration with ascorbate did not differ significantly between wild-type and Sirt5 knockout mitochondria.
“In contrast, no significant differences in respiration between WT and Sirt5 KO were observed with ascorbate.”
Quote in the paperSubstantial claim - Findingown data
Mitochondria from Sirt5 knockout livers showed significantly higher respiration with succinate and pyruvate.
“SIRT5-deficient mitochondria showed significantly increased respiration in the presence of succinate and pyruvate.”
Quote in the paperSubstantial claim - Findingown data
Incubating purified PDC with SIRT5 lowered its holoenzyme activity in vitro.
“Treatment of purified PDC with SIRT5 decreased holoenzyme activity in vitro (Figure 7C).”
Quote in the paperSubstantial claim - Findingown data
SIRT5 knockdown did not change respiration when ascorbate was supplied.
“Sirt5 KD did not impact respiration in the presence of the complex IV substrate ascorbate.”
Quote in the paperSubstantial claim - Findingown data
SIRT5 knockdown markedly increased SDH activity.
“Sirt5 KD led to a substantial increase in SDH activity (Figure 7G).”
Quote in the paperSubstantial claim - Findingown data
Immunoblotting of commercial PDC detected succinylation on multiple PDC subunits.
“We immunoblotted commercially available PDC and confirmed that we could detect succinylation on multiple PDC subunits (Figure 7B).”
Quote in the paperNot a substantial claim - Findingown data
SIRT5 knockdown also increased respiration when pyruvate was supplied.
“Increased respiration was also observed in Sirt5 KD cells in the presence of the PDC substrate pyruvate (Figures 7H and 7I).”
Quote in the paperSubstantial claim - Findingown data
Mass spectrometry of Sirt5 knockout liver identified further succinylation sites on PDC.
“Additional succinylation sites on PDC were identified in MS/MS analysis of Sirt5 KO livers (Tables S1B and S5).”
Quote in the paperNot a substantial claim - Findingown data
In Sirt5 knockout mouse embryonic fibroblasts, SILAC analysis showed that several PDC subunits had increased succinylation.
“Using SILAC analysis, we identified multiple subunits of PDC as hypersuccinylated in Sirt5 KO MEFs (Figure 7A, Tables S1A and S5).”
Quote in the paperSubstantial claim - Findingown data
Knocking down SIRT5 in HEK293T cells raised PDC activity.
“Sirt5 KD resulted in elevated PDC activity (Figure 7E).”
Quote in the paperSubstantial claim - Findingown data
Wild-type SIRT5 removed succinyl groups from PDC in vitro.
“Consistent with our SILAC data, WT SIRT5 robustly desuccinylated PDC in vitro (Figure 7B);”
Quote in the paperSubstantial claim - Findingown data
In Sirt5 wild-type and knockout cells, lysine succinylation and acetylation show limited overlap.
“Our analysis of Lys succinylation and acetylation in Sirt5 WT and KO cells suggests that there is a limited overlap between the two modifications, implying different regulatory mechanisms.”
Quote in the paperSubstantial claim - Findingown data
SILAC identified four lysine succinylation sites on the SDHA subunit of SDH.
“SILAC studies identified four Lys succinylation sites on the SDHA subunit of SDH (Figure 7F).”
Quote in the paperSubstantial claim - Findingown data
The rise in PDC activity after SIRT5 knockdown was synergistic with dichloroacetate treatment.
“This increase was synergistic with treatment with dichloroacetate (DCA)”
Quote in the paperNot a substantial claim - Findingown data
Histone lysine succinylation rises significantly in SIRT5 deficiency, with an average SILAC knockout/wild-type ratio of 5.09.
“Lys succinylation on histones increases significantly in SIRT5 deficiency with an average SILAC KO/WT ratio of 5.09.”
Quote in the paperSubstantial claim - Premisecitation
SIRT5 removes malonyl and succinyl groups from target lysines.
“The mitochondrial sirtuin SIRT5 removes malonyl and succinyl moieties from target lysines.”
Quote in the paperSubstantial claim0 of 3 sources checked - Premisecitation
SIRT5 promotes purine metabolism via urate oxidase.
“and purine metabolism via urate oxidase (Nakamura et al., 2012).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Nakamura et al., 2012 source
Not checked in the free run.
- Interpretationown data
Lys succinylation might contribute to the fasting response.
“Thus, Lys succinylation might contribute to the fasting response.”
Quote in the paperSubstantial claim - Premisereasoning
Earlier work did not conclusively determine the chemical structure of the lysine modification.
“However, these studies were not sufficient to fully establish the chemical structure of the modification.”
Quote in the paperSubstantial claim0 of 3 sources checked - Premisecitation
SIRT5 is the sole enzyme known to remove succinyl and malonyl groups from lysine.
“Our work, as well as that of others, has identified SIRT5 as the only known enzyme to date catalyzing Lys desuccinylation and demalonylation (Du et al., 2011; Peng et al., 2011; Zhang et al., 2011).”
Quote in the paperNot a substantial claim0 of 3 sources checked - Interpretationown data
Succinylation might control its targets over hours to days.
“Thus, Lys succinylation may regulate functions of its targets on a relatively slow time frame (hr to days).”
Quote in the paperNot a substantial claim - Interpretationown data
SIRT5 acts as a main regulator of lysine succinylation in mammalian cells.
“suggesting that SIRT5 is a central regulator of Lys succinylation in mammalian cells”
Quote in the paperSubstantial claim - Premisecitation
SIRT5 promotes urea cycle function via regulation of CPS1.
“SIRT5 promotes urea cycle function via the regulation of carbamoyl phosphate synthase (CPS1) (Nakagawa et al., 2009; Ogura et al., 2010)”
Quote in the paperSubstantial claim0 of 2 sources checked - Interpretationown data
Lysine succinylation and acetylation are differentially regulated.
“suggesting differential regulation of succinylation and acetylation.”
Quote in the paperSubstantial claim - Interpretationown data
Lysine succinylation potentially impacts enzymes in mitochondrial metabolism, including amino-acid breakdown, the TCA cycle, and fat metabolism.
“Our analysis reveals potential impacts of lysine succinylation on enzymes involved in mitochondrial metabolism; e.g., amino acid degradation, the tricarboxylic acid cycle (TCA) cycle, and fatty acid metabolism.”
Quote in the paperSubstantial claim - Interpretationown data
The limited overlap between lysine succinylation and acetylation indicates that the two modifications have different regulatory mechanisms.
“Our analysis of Lys succinylation and acetylation in Sirt5 WT and KO cells suggests that there is a limited overlap between the two modifications, implying different regulatory mechanisms.”
Quote in the paperSubstantial claim - Premisecitation
Elevated succinate levels can cause epigenetic dysregulation.
“Elevated succinate levels can lead to epigenetic dysregulation (Cervera et al., 2009; Smith et al., 2007).”
Quote in the paperSubstantial claim0 of 2 sources checked - Interpretationown data
SIRT5 acts as a negative regulator of PDC activity.
“These data suggested that SIRT5 negatively regulates PDC activity.”
Quote in the paperSubstantial claim - Interpretationown data
SIRT5 regulates lysine succinylation outside mitochondria.
“Consistent with a role for SIRT5 in regulating Ksucc levels extra-mitochondrially, we find that a substantial fraction of SIRT5 protein is cytosolic.”
Quote in the paperSubstantial claim - Premisecitation
The SIRT5H158Y mutant has reduced desuccinylase activity.
“a SIRT5H158Y mutant showed hypomorphic desuccinylase activity (Nakagawa et al., 2009).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Nakagawa et al., 2009 source
Not checked in the free run.
- Interpretationreasoning
SIRT5 may influence neoplasia through its regulation of PDC and SDH.
“Thus, SIRT5 could play a role in neoplasia by regulating PDC and SDH.”
Quote in the paperSubstantial claim - Interpretationreasoning
Histone lysine succinylation may have a distinct epigenetic role compared with lysine acetylation.
“This is in contrast to Lys acetylation, which primarily occupies the N-terminal tails of histones, potentially suggesting a distinct epigenetic role of histone Lys succinylation in comparison to Lys acetylation.”
Quote in the paperNot a substantial claim- Rests on an assumption: Lysine acetylation primarily localizes to the N-terminal tails of histones.
- Interpretationreasoning
SIRT5's effects on mitochondrial respiration and metabolism are likely broader than its repression of PDC and SDH.
“However, it is likely that the impact of SIRT5 on mitochondrial respiration and overall metabolism is much broader than repressing PDC and SDH function.”
Quote in the paperNot a substantial claim
- May combine two claims. 26
- Classified as probably not a substantial claim. 15
May combine two claims.
Findingown dataAbsolute stoichiometries of 137 Ksucc sites were calculated; 134 increased in SIRT5 deficiency.
“we were able to calculate absolute stoichiometries of 137 Ksucc sites in both WT and Sirt5 KO MEFs with a dynamic range from 0.02% to 90%, out of which 134 sites showed increased Ksucc stoichiometries in SIRT5 deficiency”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataFasting increased Ksucc levels in both liver and kidney, with a larger effect in liver.
“We found that Ksucc levels rose in response to fasting in both tissues, and this change was more marked in the liver than the kidney.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataAt the -1 position, Ksucc sites favor Gly or Ala; at +1 they favor Ala; Arg is scarce at both.
“The data showed a preference for Gly or Ala at the −1 position and Ala at the +1 position (Figure 4A). Arg is largely depleted at both the −1 and +1 position.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataImmunofluorescence showed SIRT5 partly overlapping mitochondria and also present in the cytosol.
“SIRT5 (green) partially colocalized with MitoTracker Red to produce a yellow signal. However, a detectable fraction of SIRT5 was present cytosolically”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataIn Sirt5 KO, succinylation covered 37 of 51 Val-Leu-Ile degradation proteins, more than 80% of TCA cycle proteins, and 60% of fatty acid metabolism proteins.
“in Sirt5 KOs, 37 of 51 proteins in the Val-Leu-Ile degradation pathway, as well as over 80% of all proteins in the tricarboxylic acid (TCA) cycle, and 60% of all proteins in fatty acid metabolism were Lys succinylated”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataSIRT5 is present both mitochondrially and extramitochondrially.
“Thus, SIRT5 is present both mitochondrially and extramitochondrially”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataIn Sirt5 KO MEFs, over 90% of measurable Ksucc sites rose, with mean KO/WT ratio 3.61 and median 1.93.
“more than 90% of these showed increasing abundance in Sirt5 KO cells with an average KO/WT SILAC ratio of 3.61 and a median KO/WT SILAC ratio of 1.93.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataSignificant succinylation enrichment was seen for the frataxin complex, the HMGB1-HMGB2-HSC70-ERP60-GAPDH complex, PDC, and the SDH-mABC1-PIC-ANT-ATPase complex.
“we identified significant enrichment of Lys succinylation in the frataxin complex (Figure 6B, adjusted p = 1.8 × 10−11), the HMGB1-HMGB2-HSC70-ERP60-GAPDH complex (Figure 6C, adjusted p = 3.8 × 10−10), the PDC (Figure 6D, adjusted p = 3.6 × 10−10), and the SDH-mABC1-PIC-ANT-ATPase complex (Figure 6E, adjusted p = 7.7 × 10−7)”
Quote in the paperSubstantial claim- The authors state this as an assumption: Core protein complexes are evolutionarily conserved among mammalian species.
May combine two claims.
Findingown dataSubnetworks found by MCODE include F1F0 ATP synthase, respiratory chain supercomplexes, glutathione S-transferases, ribosomes, and the chaperonin TCP1 complex.
“we identified a number of highly connected subnetworks among Lys-succinylated proteins, including the F1F0 ATP synthetase, respiratory chain supercomplexes (complexes I, III, and IV), glutathione S transferases, ribosomes, and the chaperonin-containing TCP1 complex”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataSuccinylation affected 16% of mitochondrial proteins in MEFs, 23% in liver, and 29% overall.
“Sixteen percent of mitochondrial proteins were Lys succinylated in MEFs, whereas 23% of mitochondrial proteins were Lys succinylated in liver tissue. Altogether, 29% of mitochondrial proteins were Lys succinylated”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataIn WT cells, 32% of Ksucc sites exceeded 10% stoichiometry; in KO cells, this rose to 56%.
“32% of the Ksucc sites had stoichiometries greater than 10% in Sirt5 WT cells, whereas this figure increased to 56% in Sirt5 KO cells”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataSirt5 knockout liver analysis found additional SDHA succinylation sites and one SDHB succinylation site.
“Analysis of Sirt5 KO liver tissue identified several additional sites in SDHA as well as a single Lys succinylation site in SDHB (Tables S1B and S6).”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataThirty-five nonredundant histone lysine succinylation sites were found, six of which overlapped with an earlier mouse-cell report.
“Given the reported mitochondrial localization of SIRT5, it is somewhat surprising that we identified 35 nonredundant histone Lys succinylation sites, six of those sites overlapping with our first report of histone succinylation sites in mouse cells (Xie et al., 2012).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Xie et al., 2012 source
Not checked in the free run.
May combine two claims.
Findingown dataFifteen Ksucc sites were found on IDH2, with K180 and K256 within five residues of the catalytic sites Y179 and K251.
“We identified a total of 15 Ksucc sites on IDH2, 2 Ksucc sites (K180 and K256) being located within five residues in flanking sequence to sites on IDH2 that are critical for catalysis (Y179 and K251, respectively).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataLysine succinylation is widespread in fibroblasts and hepatocytes and occurs on mitochondrial metabolic enzymes and on extramitochondrial proteins including histones and ribosomes.
“This modification is widespread in fibroblasts and hepatocytes, occurring on both mitochondrial metabolic enzymes as well as extramitochondrial proteins such as histones and ribosomes.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataSixteen Ksucc sites overlapped with known cofactor-binding or catalytic sites, and 74 Ksucc sites lay within five residues of enzymatic activity sites.
“Sixteen Ksucc sites overlapped with known cofactor binding or catalytic sites, and 74 Ksucc sites were located within five residues in flanking distance to enzymatic activity sites (Table S7).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown data3-NPA treatment slightly raised Ksucc levels, whereas malonate treatment or SDHC knockdown did not.
“3-NPA treatment, but not malonate treatment or SDHC KD, resulted in a slight increase in Ksucc levels.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing), S4 (based).
Interpretationnone givenSome individual sites could turn over much faster.
“However, the modification of specific sites may occur much more rapidly.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationThe authors' earlier work established lysine succinylation and malonylation as validated posttranslational modification pathways.
“Recently, we identified and fully validated Lys succinylation and malonylation as PTM pathways, implying an ancient conserved function (Peng et al., 2011; Zhang et al., 2011).”
Quote in the paperNot a substantial claim0 of 2 sources checkedMay combine two claims.
Interpretationown dataLysine succinylation is functional and broadly affects metabolism and possibly other cell processes.
“Our data reveal widespread roles for lysine succinylation in regulating metabolism and potentially other cellular functions.”
- Also stated in: § INTRODUCTION · hedged
“Thus, Lys succinylation is a functional modification with the potential to impact mitochondrial metabolism and diverse extramitochondrial processes.”
Quote in the paperSubstantial claim- Also stated in: § INTRODUCTION · hedged
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationSIRT5 is thought to localize primarily to mitochondria.
“SIRT5 is thought to localize primarily to mitochondria (Lombard et al., 2007; Michishita et al., 2005; Nakagawa et al., 2009; Schlicker et al., 2008).”
Quote in the paperNot a substantial claim0 of 3 sources checkedProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationSIRT5 deficiency does not impact bulk mitochondrial protein acetylation.
“Less is known regarding the functions of SIRT4 and SIRT5, which, unlike SIRT3, do not impact bulk mitochondrial protein acetylation (Lombard et al., 2007).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Lombard et al., 2007 source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationEarlier work from the authors identified Ksucc sites on E. coli IDH.
“Our previous studies identified Ksucc sites on E. coli IDH (Zhang et al., 2011).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Zhang et al., 2011 source
Not checked in the free run.
May combine two claims.
Interpretationown dataSIRT5 has a major role in controlling lysine succinylation, similar to SIRT3's principal role in mitochondrial lysine acetylation.
“Our data are consistent with a major role for SIRT5 in regulating Ksucc levels, which is analogous to the principal role of SIRT3 in regulating mitochondrial Lys acetylation (Hebert et al., 2013; Lombard et al., 2007; Smith et al., 2011).”
Quote in the paperSubstantial claim0 of 3 sources checkedProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationDichloroacetate increases PDC activity by decreasing E1α phosphorylation and turnover.
“which stimulates PDC activity by reducing the phosphorylation and turnover of E1α (Morten et al., 1999; Stacpoole et al., 2008).”
Quote in the paperNot a substantial claim0 of 2 sources checkedProbably not a substantial claim: may not pass S3 (load-bearing).
Interpretationown dataThe mechanisms by which proteins become lysine-succinylated remain unclear.
“Thus, mechanisms of Lys succinylation remain unclear.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationMutations in IDH2 cause D-2 hydroxyglutaric aciduria type 2.
“Mutations in the IDH2 gene, a mammalian IDH homolog, causes D-2 hydroxyglutaric aciduria type 2 (D2HGA2) (Kranendijk et al., 2010)”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Kranendijk et al., 2010 source
Not checked in the free run.
May combine two claims.
Interpretationown dataSIRT5 acts outside mitochondria and may affect chromatin functions.
“These data imply that SIRT5 functions outside mitochondria, potentially impacting chromatin functions.”
Quote in the paperSubstantial claimClassified as probably not a substantial claim.
PremisecitationGermline SDH mutations in SDHA-SDHD and in SDH assembly factor 2 occur in tumor predisposition syndromes.
“Germline SDH mutations have been identified in the SDH subunits SDHA–SDHD and also in SDH assembly factor 2 in tumor predisposition syndromes (Hao et al., 2009; Korpershoek et al., 2011; Neumann et al., 2004; Niemann and Müller, 2000; Oudijk et al., 2013; Pollard et al., 2005; Ricketts et al., 2008; Ricketts et al., 2010).”
Quote in the paperSubstantial claim0 of 3 sources checkedMay combine two claims.
PremisecitationDysregulated SDH activity in these mutations increases succinate and mitochondrial reactive oxygen species, activates HIF1α, and induces angiogenesis.
“Dysregulated SDH activity in the setting of these mutations promotes the accumulation of succinate and mitochondrial reactive oxygen species, activating HIF1α and inducing angiogenesis (Selak et al., 2005).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Selak et al., 2005 source
Not checked in the free run.
May combine two claims.
InterpretationreasoningSIRT5 and E1α phosphorylation reduce PDC activity by separate mechanisms.
“Thus, SIRT5 and E1α phosphorylation attenuate PDC activity through distinct mechanisms.”
Quote in the paperSubstantial claimMay combine two claims.
Interpretationown dataLysine succinylation may affect IDH2 activity, with possible consequences for epigenetic regulation and neoplasia.
“These data suggest a potential impact of Lys succinylation on the activity of IDH2, which may impact epigenetic regulation and neoplasia.”
Quote in the paperSubstantial claimMay combine two claims.
Interpretationown dataSIRT5 targets PDC and SDH and suppresses their enzymatic activities and the mitochondrial respiration they drive.
“We conclude that SIRT5 targets PDC and SDH to suppress their biochemical activities and mitochondrial respiration driven by these complexes.”
- Also stated in: § DISCUSSION · plain
“SIRT5 suppresses activities of PDC and SDH.”
Quote in the paperSubstantial claim- Also stated in: § DISCUSSION · plain
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationReduced IDH2 expression causes epigenetic dysfunction through loss of 5-hydroxymethyl-cytosine in melanoma.
“whereas its downregulation leads to epigenetic dysfunction via the loss of 5-hydroxymethyl-cytosine in melanoma (Lian et al., 2012).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Lian et al., 2012 source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationIDH1 or IDH2 mutations produce the oncometabolite D-2-hydroxyglutarate.
“IDH1 or IDH2 mutations lead to production of the oncometabolite D2-hydroxyglutarate (D-2HG) (Yen et al., 2010).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Yen et al., 2010 source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationGermline mutations in every Sdh subunit gene can cause mitochondrial disease and tumor susceptibility syndromes.
“Germ-line mutations in all Sdh subunit genes can cause mitochondrial disease and tumor susceptibility syndromes (Gill, 2012).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Gill, 2012 source
Not checked in the free run.
May combine two claims.
Interpretationown dataSIRT5 desuccinylates PDC subunits to inhibit PDC activity, revealing a previously unrecognized aspect of PDC regulation.
“Our finding that SIRT5 desuccinylates PDC subunits to inhibit PDC activity reveals a previously unappreciated aspect of PDC regulation and raises the eventual possibility of inhibiting SIRT5 activity as an adjunct treatment in T2D.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationAbout half of daily caloric intake passes through PDC.
“About 50% of overall daily caloric intake passes through PDC, highlighting the central importance of this holoenzyme in glucose metabolism (Patel and Korotchkina, 2006).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Patel and Korotchkina, 2006
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationPDC dysfunction is associated with type 2 diabetes and other conditions including neoplasia and cardiac ischemia.
“PDC dysfunction is linked to type 2 diabetes (T2D) and a diverse spectrum of other human pathologies, such as neoplasia and cardiac ischemia (Patel and Korotchkina, 2006).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Patel and Korotchkina, 2006
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationPDC activity regulation is the main mechanism controlling glucose oxidation in mammals in vivo.
“The regulation of PDC activity is the major mechanism regulating glucose oxidation in mammals in vivo (Wieland et al., 1972).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Wieland et al., 1972 source
Not checked in the free run.
The authors state this as an assumption.
Core protein complexes are evolutionarily conserved among mammalian species.
“on the basis of the assumption of evolutionary conservation of core protein complexes among mammalian species.”
The paper relies on this without support.
Lysine acetylation primarily localizes to the N-terminal tails of histones.
“This is in contrast to Lys acetylation, which primarily occupies the N-terminal tails of histones”
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?
All four enzymes involved in hepatic ketogenesis are heavily modified by lysine acylations including acetylation, succinylation, glutarylation, and malonylation.
“Interestingly, all the four enzymes involved in this process (Thiolase, HMG-CoA synthase, HMG-CoA lyase, and βOHB dehydrogenase) are heavily modified by lysine acylations including acetylation, succinylation, glutarylation and malonylation ((Rardin, Newman, et al. 2013))((Rardin, He, et al. 2013))((Park et al. 2013))((Tan et al. 2014))((Nishida et al. 2015)).”
From The Mitochondrial Acylome Emerges: Proteomics, Regulation by Sirtuins, and Metabolic and Disease Implications (2018) · cites this paper as Park et al. 2013
SIRT5 is present in the nucleus and cytoplasm in addition to mitochondria.
“Given that SIRT5 is present in the nucleus and cytoplasm in addition to mitochondria ((Matsushita et al. 2011))((Park et al. 2013))((Nishida et al. 2015)), it will be interesting to test whether SIRT5 modulates the activity of the urea cycle via targeting of both mitochondrial and cytosolic enzymes, or whether one compartment’s effects dominate.”
From The Mitochondrial Acylome Emerges: Proteomics, Regulation by Sirtuins, and Metabolic and Disease Implications (2018) · cites this paper as Park et al. 2013
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Self-citationSirt3 promotes the urea cycle and fatty acid oxidation during dietary restriction
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Calorie restriction alters mitochondrial protein acetylation
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“Our work, as well as that of others, has extensively characterized the cellular acetylome (Chen et al., 2012; Choudhary et al., 2009; Hebert et al., 2013; Kendrick et al., 2011; Kim et al., 2006; Schwer et al., 2009; Zhao et al., 2010).”
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- Authors
- Park, J., Chen, Y., Tishkoff, D. X., Peng, C., Tan, M., Dai, L., Xie, Z., Zhang, Y., Zwaans, B. M. M., Skinner, M. E., Lombard, D. B., & Zhao, Y.
- Affiliations
- University of Chicago (US)
- University of Michigan (US)
- Chinese Academy of Sciences (CN)
- Corresponding author
- Lombard, David B.
- Zhao, Yingming
- ORCID
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2013-06
- Volume
- 50
- Issue
- 6
- Pages
- 919-930
- ISSN
- 1097-2765 (ISSN-L)
- PMC
- PMC3769971
- OpenAlex
- W1984658022
- Semantic Scholar
- 47c40fa699d766e0ebccc68356e6ef46b90364b9
- Cited by
- 1,000
- References
- 81
- Citations by year
- 2026: 60 · 2025: 88 · 2024: 83 · 2023: 85 · 2022: 93 · 2021: 106 · 2020: 66 · 2019: 87 · 2018: 82 · 2017: 60 · 2016: 73 · 2015: 63 · 2014: 37 · 2013: 15
- FWCI
- 29.16
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Molecular Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health (1dp3dk094292-01)
- National Institute on Aging (P30AG013283, T32AG000114, P30AG024824)
- National Cancer Institute (R21CA177925)
- National Institute of General Medical Sciences (U54GM103520, R01GM101171)
- National Institute of Diabetes and Digestive and Kidney Diseases (P60DK020572, DP3-DK-094292, P30DK020572, P30DK089503)
- Topics
- Health Sciences › Medicine › Geriatrics and Gerontology › Sirtuins and Resveratrol in Medicine
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Cancer-related gene regulation
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Keywords
- SIRT5, lysine succinylation, succinylome, post-translational modification, mitochondrial metabolism, TCA cycle, amino acid catabolism, fatty acid metabolism, pyruvate dehydrogenase complex, succinate dehydrogenase, cellular respiration, acetylation
- MeSH terms
- Acetylation, Amino Acid Sequence, Animals, Cells, Cultured, Glycosylation, Kinetics, Lysine, Mitochondria, Protein Processing, Post-Translational, Pyruvate Dehydrogenase Complex, Succinate Dehydrogenase, Consensus Sequence, Mice, Knockout, Cell Respiration, Proteome, Protein Transport, Sirtuins, Mice, Metabolic Networks and Pathways, Molecular Sequence Annotation, Protein Interaction Maps
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