Cited by 83Metabolism and Genetic DisordersMitochondrial Function and PathologySirtuins and Resveratrol in Medicine

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

Open access
Gut, Philipp, Matilainen, Sanna, Meyer, Jesse G., Pällijeff, Pieti, Richard, Joy, Carroll, Christopher J., Euro, Liliya, Jackson, Christopher B. +18 more·2020·Nature Communications

Abstract

Mitochondrial acyl-coenzyme A species are emerging as important sources of protein modification and damage. Succinyl-CoA ligase (SCL) deficiency causes a mitochondrial encephalomyopathy of unknown pathomechanism. Here, we show that succinyl-CoA accumulates in cells derived from patients with recessive mutations in the tricarboxylic acid cycle (TCA) gene succinyl-CoA ligase subunit-β (SUCLA2), causing global protein hyper-succinylation. Using mass spectrometry, we quantify nearly 1,000 protein succinylation sites on 366 proteins from patient-derived fibroblasts and myotubes. Interestingly, hyper-succinylated proteins are distributed across cellular compartments, and many are known targets of the (NAD+)-dependent desuccinylase SIRT5. To test the contribution of hyper-succinylation to disease progression, we develop a zebrafish model of the SCL deficiency and find that SIRT5 gain-of-function reduces global protein succinylation and improves survival. Thus, increased succinyl-CoA levels contribute to the pathology of SCL deficiency through post-translational modifications.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/s41467-020-19743-4

Cites

7 of 7 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

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?

Self-check

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

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 52

  1. [1]Verdin E Ott M 50 years of protein acetylation: from gene regulation to epigenetics, metabolism and beyond Nat. Rev. Mol. Cell Biol. 2015 16 258 264 10.1038/nrm3931 25549891 · DOI
  2. [2]Strahl BD Allis CD The language of covalent histone modifications Nature 2000 403 41 45 10.1038/47412 10638745 · DOI · Paper page
  3. [3]Newman JC He W Verdin E Mitochondrial protein acylation and intermediary metabolism: regulation by sirtuins and implications for metabolic disease J. Biol. Chem. 2012 287 42436 42443 10.1074/jbc.R112.404863 23086951 PMC3522244 · DOI
  4. [5]Weinert BT Moustafa T Iesmantavicius V Zechner R Choudhary C Analysis of acetylation stoichiometry suggests that SIRT3 repairs nonenzymatic acetylation lesions EMBO J. 2015 34 2620 2632 10.15252/embj.201591271 26358839 PMC4641529 · DOI
  5. [6]Wagner GR Hirschey MD Nonenzymatic protein acylation as a carbon stress regulated by sirtuin deacylases Mol. Cell 2014 54 5 16 10.1016/j.molcel.2014.03.027 24725594 PMC4040445 · DOI
  6. [7]Trub AG Hirschey MD Reactive Acyl-CoA species modify proteins and induce carbon stress Trends Biochem Sci. 2018 43 369 379 10.1016/j.tibs.2018.02.002 29478872 PMC5924595 · DOI
  7. [8]Wagner GR Payne RM Widespread and enzyme-independent Nepsilon-acetylation and Nepsilon-succinylation of proteins in the chemical conditions of the mitochondrial matrix J. Biol. Chem. 2013 288 29036 29045 10.1074/jbc.M113.486753 23946487 PMC3790002 · DOI
  8. [9]Weinert BT Lysine succinylation is a frequently occurring modification in prokaryotes and eukaryotes and extensively overlaps with acetylation Cell Rep. 2013 4 842 851 10.1016/j.celrep.2013.07.024 23954790 · DOI
  9. [10]Lin H Su X He B Protein lysine acylation and cysteine succination by intermediates of energy metabolism ACS Chem. Biol. 2012 7 947 960 10.1021/cb3001793 22571489 PMC3376250 · DOI
  10. [11]Baeza J Smallegan MJ Denu JM Mechanisms and dynamics of protein acetylation in mitochondria Trends Biochem Sci. 2016 41 231 244 10.1016/j.tibs.2015.12.006 26822488 PMC4783225 · DOI
  11. [12]He W Newman JC Wang MZ Ho L Verdin E Mitochondrial sirtuins: regulators of protein acylation and metabolism Trends Endocrinol. Metab. 2012 23 467 476 10.1016/j.tem.2012.07.004 22902903 · DOI · Paper page
  12. [14]Hirschey MD Zhao Y Metabolic regulation by lysine malonylation, succinylation, and glutarylation Mol. Cell Proteom. 2015 14 2308 2315 10.1074/mcp.R114.046664 PMC4563717 25717114 · DOI
  13. [15]Choudhary C Weinert BT Nishida Y Verdin E Mann M The growing landscape of lysine acetylation links metabolism and cell signalling Nat. Rev. Mol. Cell Biol. 2014 15 536 550 10.1038/nrm3841 25053359 · DOI · Paper page
  14. [17]Rardin MJ SIRT5 regulates the mitochondrial lysine succinylome and metabolic networks Cell Metab. 2013 18 920 933 10.1016/j.cmet.2013.11.013 24315375 PMC4105152 · DOI
  15. [18]Nishida Y SIRT5 regulates both cytosolic and mitochondrial protein malonylation with glycolysis as a major target Mol. Cell 2015 59 321 332 10.1016/j.molcel.2015.05.022 26073543 PMC4571487 · DOI · Paper page
  16. [19]Du Y SIRT5 deacylates metabolism-related proteins and attenuates hepatic steatosis in ob/ob mice EBioMedicine 2018 36 347 357 10.1016/j.ebiom.2018.09.037 30279144 PMC6197389 · DOI
  17. [20]Hershberger KA Sirtuin 5 is required for mouse survival in response to cardiac pressure overload J. Biol. Chem. 2017 292 19767 19781 10.1074/jbc.M117.809897 28972174 PMC5712617 · DOI
  18. [21]Sadhukhan S Metabolomics-assisted proteomics identifies succinylation and SIRT5 as important regulators of cardiac function Proc. Natl Acad. Sci. USA 2016 113 4320 4325 10.1073/pnas.1519858113 27051063 PMC4843474 · DOI
  19. [22]Carrozzo R Succinate-CoA ligase deficiency due to mutations in SUCLA2 and SUCLG1: phenotype and genotype correlations in 71 patients J. Inherit. Metab. Dis. 2016 39 243 252 10.1007/s10545-015-9894-9 26475597 · DOI · Paper page
  20. [23]Elpeleg O Deficiency of the ADP-forming succinyl-CoA synthase activity is associated with encephalomyopathy and mitochondrial DNA depletion Am. J. Hum. Genet. 2005 76 1081 1086 10.1086/430843 15877282 PMC1196446 · DOI
  21. [24]Matilainen S Mitochondrial encephalomyopathy and retinoblastoma explained by compound heterozygosity of SUCLA2 point mutation and 13q14 deletion Eur. J. Human Genet. 2015 23 325 330 10.1038/ejhg.2014.128 24986829 PMC4326715 · DOI
  22. [25]Ostergaard E Deficiency of the alpha subunit of succinate-coenzyme A ligase causes fatal infantile lactic acidosis with mitochondrial DNA depletion Am. J. Hum. Genet 2007 81 383 387 10.1086/519222 17668387 PMC1950792 · DOI
  23. [27]Besse A The GABA transaminase, ABAT, is essential for mitochondrial nucleoside metabolism Cell Metab. 2015 21 417 427 10.1016/j.cmet.2015.02.008 25738457 PMC4757431 · DOI
  24. [28]Meyer JG Temporal dynamics of liver mitochondrial protein acetylation and succinylation and metabolites due to high fat diet and/or excess glucose or fructose PLoS One 2018 13 e0208973 10.1371/journal.pone.0208973 30586434 PMC6306174 · DOI
  25. [29]Meyer JG PIQED: automated identification and quantification of protein modifications from DIA-MS data Nat. Methods 2017 14 646 647 10.1038/nmeth.4334 28661500 PMC5663633 · DOI
  26. [30]Scholz C Avoiding abundance bias in the functional annotation of post-translationally modified proteins Nat. Methods 2015 12 1003 1004 10.1038/nmeth.3621 26513550 · DOI
  27. [31]Rardin MJ Label-free quantitative proteomics of the lysine acetylome in mitochondria identifies substrates of SIRT3 in metabolic pathways Proc. Natl Acad. Sci. USA 2013 110 6601 6606 10.1073/pnas.1302961110 23576753 PMC3631688 · DOI
  28. [32]Gut P Reischauer S Stainier DYR Arnaout R Little fish, big data: zebrafish as a model for cardiovascular and metabolic disease Physiol. Rev. 2017 97 889 938 10.1152/physrev.00038.2016 28468832 PMC5817164 · DOI
  29. [33]Pereira TC Zebrafish as a model organism to evaluate drugs potentially able to modulate sirtuin expression Zebrafish 2011 8 9 16 10.1089/zeb.2010.0677 21413868 · DOI
  30. [34]Lambeth DO Tews KN Adkins S Frohlich D Milavetz BI Expression of two succinyl-CoA synthetases with different nucleotide specificities in mammalian tissues J. Biol. Chem. 2004 279 36621 36624 10.1074/jbc.M406884200 15234968 · DOI · Paper page
  31. [35]Carrozzo R SUCLA2 mutations are associated with mild methylmalonic aciduria, Leigh-like encephalomyopathy, dystonia and deafness Brain 2007 130 862 874 10.1093/brain/awl389 17301081 · DOI · Paper page
  32. [37]MacDonald MJ Smith AD 3rd Hasan NM Sabat G Fahien LA Feasibility of pathways for transfer of acyl groups from mitochondria to the cytosol to form short chain acyl-CoAs in the pancreatic beta cell J. Biol. Chem. 2007 282 30596 30606 10.1074/jbc.M702732200 17724028 · DOI
  33. [40]Pirinen E Niacin cures systemic NAD(+) deficiency and improves muscle performance in adult-onset mitochondrial myopathy Cell Metab. 2020 31 1078 1090.e5 10.1016/j.cmet.2020.04.008 32386566 · DOI
  34. [41]Morscher RJ Mitochondrial translation requires folate-dependent tRNA methylation Nature 2018 554 128 132 10.1038/nature25460 29364879 PMC6020024 · DOI
  35. [42]Minton DR Serine catabolism by SHMT2 is required for proper mitochondrial translation initiation and maintenance of formylmethionyl-tRNAs Mol. Cell 2018 69 610 621 10.1016/j.molcel.2018.01.024 29452640 PMC5819360 · DOI
  36. [43]Wei Z Deacetylation of serine hydroxymethyl-transferase 2 by SIRT3 promotes colorectal carcinogenesis Nat. Commun. 2018 9 4468 10.1038/s41467-018-06812-y 30367038 PMC6203763 · DOI
  37. [44]Yang X SHMT2 desuccinylation by SIRT5 drives cancer cell proliferation Cancer Res 2018 78 372 386 10.1158/0008-5472.CAN-17-1912 29180469 · DOI
  38. [45]Ehinger JK Cell-permeable succinate prodrugs bypass mitochondrial complex I deficiency Nat. Commun. 2016 7 12317 10.1038/ncomms12317 27502960 PMC4980488 · DOI
  39. [46]Rappsilber J Ishihama Y Mann M Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics Anal. Chem. 2003 75 663 670 10.1021/ac026117i 12585499 · DOI
  40. [47]Wang G Regulation of UCP1 and mitochondrial metabolism in brown adipose tissue by reversible succinylation Mol. Cell 2019 74 844 857.e7 10.1016/j.molcel.2019.03.021 31000437 PMC6525068 · DOI
  41. [48]Bruderer R Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver microtissues Mol. Cell Proteom. 2015 14 1400 1410 10.1074/mcp.M114.044305 PMC4424408 25724911 · DOI · Paper page
  42. [49]Rosenberger G A repository of assays to quantify 10,000 human proteins by SWATH-MS Sci. Data 2014 1 140031 10.1038/sdata.2014.31 25977788 PMC4322573 · DOI · Paper page
  43. [50]Cox J Andromeda: a peptide search engine integrated into the MaxQuant environment J. Proteome Res. 2011 10 1794 1805 10.1021/pr101065j 21254760 · DOI
  44. [51]MacLean B Skyline: an open source document editor for creating and analyzing targeted proteomics experiments Bioinformatics 2010 26 966 968 10.1093/bioinformatics/btq054 20147306 PMC2844992 · DOI · Paper page
  45. [52]Teo G mapDIA: Preprocessing and statistical analysis of quantitative proteomics data from data independent acquisition mass spectrometry J. Proteom. 2015 129 108 120 10.1016/j.jprot.2015.09.013 PMC4630088 26381204 · DOI
  46. [53]Huang da W Sherman BT Lempicki RA Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources Nat. Protoc. 2009 4 44 57 10.1038/nprot.2008.211 19131956 · DOI · Paper page
  47. [54]Liu X High-resolution metabolomics with Acyl-CoA profiling reveals widespread remodeling in response to diet Mol. Cell Proteom. 2015 14 1489 1500 10.1074/mcp.M114.044859 PMC4458715 25795660 · DOI
  48. [55]Liu X Ser Z Locasale JW Development and quantitative evaluation of a high-resolution metabolomics technology Anal. Chem. 2014 86 2175 2184 10.1021/ac403845u 24410464 PMC3983012 · DOI
  49. [56]Liu X Ser Z Cluntun AA Mentch SJ Locasale JW A strategy for sensitive, large scale quantitative metabolomics J. Vis. Exp. 2014 87 e51358 PMC4109060 24894601
  50. [57]Liu X Acetate production from glucose and coupling to mitochondrial metabolism in mammals Cell 2018 175 502 513.e13 10.1016/j.cell.2018.08.040 30245009 PMC6173642 · DOI
  51. [58]Elia I Proline metabolism supports metastasis formation and could be inhibited to selectively target metastasizing cancer cells Nat. Commun. 2017 8 15267 10.1038/ncomms15267 28492237 PMC5437289 · DOI
  52. [59]Ostergaard E Mitochondrial encephalomyopathy with elevated methylmalonic acid is caused by SUCLA2 mutations Brain 2007 130 853 861 10.1093/brain/awl383 17287286 · DOI · Paper page

Cited by

Sorted by citations

Authors
Gut, P., Matilainen, S., Meyer, J. G., Pällijeff, P., Richard, J., Carroll, C. J., Euro, L., Jackson, C. B., Isohanni, P., Minassian, B. A., Alkhater, R. A., Østergaard, E., Civiletto, G., Parisi, A., Thevenet, J., Rardin, M. J., He, W., Nishida, Y., Newman, J. C., Liu, X., Christen, S., Moco, S., Locasale, J. W., Schilling, B., Suomalainen, A., & Verdin, E.
Affiliations
  • Gladstone Institutes (US)
  • University of Helsinki (FI)
  • Buck Institute for Research on Aging (US)
  • École Polytechnique Fédérale de Lausanne (CH)
  • University of London (GB)
  • University of Toronto (CA)
  • Saudi Aramco Medical Services Organization (SA)
  • Copenhagen University Hospital (DK)
  • Amgen (United States) (US)
  • North Carolina State University (US)
  • Duke University (US)
Corresponding author
  • Gut, Philipp
  • Schilling, Birgit
  • Suomalainen, Anu
  • Verdin, Eric
Venue
Nature Communications
Published
2020-11-23
Volume
11
Issue
1
Pages
5927-5927
ISSN
2041-1723 (ISSN-L)
OpenAlex
W3110110283
Cited by
83
References
7
Citations by year
2026: 15 · 2025: 25 · 2024: 14 · 2023: 11 · 2022: 14 · 2021: 4
FWCI
4.80
Type
journal article
Language
en
Open access
Locations
  • Nature Communications (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by)
  • St George's Online Research Archive (St George's University of London) (acceptedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Työväentutkimus Vuosikirja (submittedVersion)
Funders
  • Helsingin Yliopisto
  • Buck Institute for Research on Aging
  • Academy of Finland
  • Sigrid Juséliuksen Säätiö
  • National Institutes of Health (1s10od016281-01)
  • National Institute of Diabetes and Digestive and Kidney Diseases (R24DK085610, DK085610)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Clinical Biochemistry › Metabolism and Genetic Disorders
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Mitochondrial Function and Pathology
  • Health Sciences › Medicine › Geriatrics and Gerontology › Sirtuins and Resveratrol in Medicine
Keywords
SUCLA2, succinylation, SIRT5, mitochondrial encephalomyopathy, TCA cycle, post-translational modification, zebrafish model, fibroblasts, myotubes
MeSH terms
Acyl Coenzyme A, Animals, Cells, Cultured, Female, Humans, Infant, Lysine, Male, Mitochondria, Mutation, Succinate-CoA Ligases, Zebrafish, Survival Analysis, Mice, Knockout, Mitochondrial Diseases, Sirtuins, Proteomics, Mice

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.

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.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review