Cell growth and survival depend on a delicate balance between energy production and synthesis of metabolites. Here, we provide evidence that an alternative mitochondrial complex II (CII) assembly, designated as CIIlow, serves as a checkpoint for metabolite biosynthesis under bioenergetic stress, with cells suppressing their energy utilization by modulating DNA synthesis and cell cycle progression. Depletion of CIIlow leads to an imbalance in energy utilization and metabolite synthesis, as evidenced by recovery of the de novo pyrimidine pathway and unlocking cell cycle arrest from the S-phase. In vitro experiments are further corroborated by analysis of paraganglioma tissues from patients with sporadic, SDHA and SDHB mutations. These findings suggest that CIIlow is a core complex inside mitochondria that provides homeostatic control of cellular metabolism depending on the availability of energy.

Australian Proteome Analysis Facility Macquarie University North Ryde 2109 NSW Australia

Clem Jones Centre for Ageing Dementia Research Queensland Brain Institute University of Queensland Brisbane 4072 Qld Australia

College of Pharmacy Natural Product Research Institute Seoul National University Seoul 08826 Korea

Department of Biochemistry and Molecular Biology Shenzhen University School of Medicine Shenzhen 518060 China

Eunice Kennedy Shriver National Institute of Child Health and Human Development National Institutes of Health Bethesda 20892 MD USA

Faculty of Science University of South Bohemia Ceske Budejovice 37005 Czech Republic

Institute of Biotechnology Czech Academy of Sciences Prague West 25250 Czech Republic

Institute of Molecular Genetics Czech Academy of Sciences Prague 14220 Czech Republic

Malaghan Institute of Medical Research Wellington 6242 New Zealand

School of Medical Sciences Griffith University Southport 4222 Qld Australia

TATAA Biocenter Gothenburg 41103 Sweden

See more in PubMed

Jones RG, Thompson CB. Tumor suppressors and cell metabolism: a recipe for cancer growth. Genes Dev. 2009;23:537–548. doi: 10.1101/gad.1756509. PubMed DOI PMC

King A, Selak MA, Gottlieb E. Succinate dehydrogenase and fumarate hydratase: linking mitochondrial dysfunction and cancer. Oncogene. 2006;25:4675–4682. doi: 10.1038/sj.onc.1209594. PubMed DOI

Selak MA, et al. Succinate links TCA cycle dysfunction to oncogenesis by inhibiting HIF-alpha prolyl hydroxylase. Cancer Cell. 2005;7:77–85. doi: 10.1016/j.ccr.2004.11.022. PubMed DOI

Bezawork-Geleta A, Rohlena J, Dong L, Pacak K, Neuzil J. Mitochondrial Complex II: at the Crossroads. Trends Biochem. Sci. 2017;42:312–325. doi: 10.1016/j.tibs.2017.01.003. PubMed DOI PMC

Fendt L, et al. Accumulation of mutations over the entire mitochondrial genome of breast cancer cells obtained by tissue microdissection. Breast Cancer Res. Treat. 2011;128:327–336. doi: 10.1007/s10549-010-1092-8. PubMed DOI

Parrella P, et al. Detection of mitochondrial DNA mutations in primary breast cancer and fine-needle aspirates. Cancer Res. 2001;61:7623–7626. PubMed

Tseng LM, et al. Mitochondrial DNA mutations and mitochondrial DNA depletion in breast cancer. Genes Chromosomes Cancer. 2006;45:629–638. doi: 10.1002/gcc.20326. PubMed DOI

Wallace DC. Mitochondria and cancer. Nat. Rev. Cancer. 2012;12:685–698. doi: 10.1038/nrc3365. PubMed DOI PMC

McKenzie M, Lazarou M, Thorburn DR, Ryan MT. Mitochondrial respiratory chain supercomplexes are destabilized in Barth Syndrome patients. J. Mol. Biol. 2006;361:462–469. doi: 10.1016/j.jmb.2006.06.057. PubMed DOI

Lapuente-Brun E, et al. Supercomplex assembly determines electron flux in the mitochondrial electron transport chain. Science. 2013;340:1567–1570. doi: 10.1126/science.1230381. PubMed DOI

Acin-Perez R, Fernandez-Silva P, Peleato ML, Perez-Martos A, Enriquez JA. Respiratory active mitochondrial supercomplexes. Mol. Cell. 2008;32:529–539. doi: 10.1016/j.molcel.2008.10.021. PubMed DOI

Kovarova N, et al. High molecular weight forms of mammalian respiratory chain complex II. PLoS ONE. 2013;8:e71869. doi: 10.1371/journal.pone.0071869. PubMed DOI PMC

Tan AS, et al. Mitochondrial genome acquisition restores respiratory function and tumorigenic potential of cancer cells without mitochondrial DNA. Cell Metab. 2015;21:81–94. doi: 10.1016/j.cmet.2014.12.003. PubMed DOI

Plass C, et al. Mutations in regulators of the epigenome and their connections to global chromatin patterns in cancer. Nat. Rev. Genet. 2013;14:765–780. doi: 10.1038/nrg3554. PubMed DOI

Maiuri MC, Kroemer G. Essential role for oxidative phosphorylation in cancer progression. Cell Metab. 2015;21:11–12. doi: 10.1016/j.cmet.2014.12.013. PubMed DOI

Leach KL, et al. The site of action of oxazolidinone antibiotics in living bacteria and in human mitochondria. Mol. Cell. 2007;26:393–402. doi: 10.1016/j.molcel.2007.04.005. PubMed DOI

Prezant TR, et al. Mitochondrial ribosomal RNA mutation associated with both antibiotic-induced and non-syndromic deafness. Nat. Genet. 1993;4:289–294. doi: 10.1038/ng0793-289. PubMed DOI

Ramachandran A, et al. Inhibition of mitochondrial protein synthesis results in increased endothelial cell susceptibility to nitric oxide-induced apoptosis. Proc. Natl Acad. Sci. USA. 2002;99:6643–6648. doi: 10.1073/pnas.102019899. PubMed DOI PMC

Maio N, et al. Disease-causing SDHAF1 mutations impair transfer of Fe-S clusters to SDHB. Cell Metab. 2016;23:292–302. doi: 10.1016/j.cmet.2015.12.005. PubMed DOI PMC

van Nederveen FH, et al. An immunohistochemical procedure to detect patients with paraganglioma and phaeochromocytoma with germline SDHB, SDHC, or SDHD gene mutations: a retrospective and prospective analysis. Lancet Oncol. 2009;10:764–771. doi: 10.1016/S1470-2045(09)70164-0. PubMed DOI PMC

Bezawork-Geleta A, Saiyed T, Dougan DA, Truscott KN. Mitochondrial matrix proteostasis is linked to hereditary paraganglioma: LON-mediated turnover of the human flavinylation factor SDH5 is regulated by its interaction with SDHA. FASEB J. 2014;28:1794–1804. doi: 10.1096/fj.13-242420. PubMed DOI

Sun F, et al. Crystal structure of mitochondrial respiratory membrane protein complex II. Cell. 2005;121:1043–1057. doi: 10.1016/j.cell.2005.05.025. PubMed DOI

Robinson BH, Petrova-Benedict R, Buncic JR, Wallace DC. Nonviability of cells with oxidative defects in galactose medium: a screening test for affected patient fibroblasts. Biochem. Med. Metab. Biol. 1992;48:122–126. doi: 10.1016/0885-4505(92)90056-5. PubMed DOI

Benard G, Rossignol R. Ultrastructure of the mitochondrion and its bearing on function and bioenergetics. Antioxid. Redox Signal. 2008;10:1313–1342. doi: 10.1089/ars.2007.2000. PubMed DOI

Stroud DA, Formosa LE, Wijeyeratne XW, Nguyen TN, Ryan MT. Gene knockout using transcription activator-like effector nucleases (TALENs) reveals that human NDUFA9 protein is essential for stabilizing the junction between membrane and matrix arms of complex I. J. Biol. Chem. 2013;288:1685–1690. doi: 10.1074/jbc.C112.436766. PubMed DOI PMC

Oostveen FG, Au HC, Meijer PJ, Scheffler IE. A Chinese hamster mutant cell line with a defect in the integral membrane protein CII-3 of complex II of the mitochondrial electron transport chain. J. Biol. Chem. 1995;270:26104–26108. doi: 10.1074/jbc.270.44.26104. PubMed DOI

Housley SL, et al. Renal carcinoma with giant mitochondria associated with germ-line mutation and somatic loss of the succinate dehydrogenase B gene. Histopathology. 2010;56:405–408. doi: 10.1111/j.1365-2559.2010.03482.x. PubMed DOI

Rost HL, et al. OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nat. Biotechnol. 2014;32:219–223. doi: 10.1038/nbt.2841. PubMed DOI

Ghazalpour A, et al. Comparative analysis of proteome and transcriptome variation in mouse. PLoS Genet. 2011;7:e1001393. doi: 10.1371/journal.pgen.1001393. PubMed DOI PMC

Huang S, et al. Complementary iTRAQ proteomics and RNA-seq transcriptomics reveal multiple levels of regulation in response to nitrogen starvation in Synechocystis sp. PCC 6803. Mol. Biosyst. 2013;9:2565–2574. doi: 10.1039/c3mb70188c. PubMed DOI

Cenik C, et al. Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans. Genome Res. 2015;25:1610–1621. doi: 10.1101/gr.193342.115. PubMed DOI PMC

Liu Y, Beyer A, Aebersold R. On the dependency of cellular protein levels on mRNA abundance. Cell. 2016;165:535–550. doi: 10.1016/j.cell.2016.03.014. PubMed DOI

Bauernfeind AL, Babbitt CC. The predictive nature of transcript expression levels on protein expression in adult human brain. BMC Genomics. 2017;18:322. doi: 10.1186/s12864-017-3674-x. PubMed DOI PMC

Mitchell AD, Hoogenraad NJ. De novo pyrimidine nucleotide biosynthesis in synchronized rat hepatoma (HTC) cells and mouse embryo fibroblast (3T3) cells. Exp. Cell Res. 1975;93:105–110. doi: 10.1016/0014-4827(75)90428-0. PubMed DOI

Sigoillot FD, Berkowski JA, Sigoillot SM, Kotsis DH, Guy HI. Cell cycle-dependent regulation of pyrimidine biosynthesis. J. Biol. Chem. 2003;278:3403–3409. doi: 10.1074/jbc.M211078200. PubMed DOI

Lane AN, Fan TW. Regulation of mammalian nucleotide metabolism and biosynthesis. Nucleic Acids Res. 2015;43:2466–2485. doi: 10.1093/nar/gkv047. PubMed DOI PMC

Vander Heiden MG, Cantley LC, Thompson CB. Understanding the Warburg effect: the metabolic requirements of cell proliferation. Science. 2009;324:1029–1033. doi: 10.1126/science.1160809. PubMed DOI PMC

Ackerman D, Simon MC. Hypoxia, lipids, and cancer: surviving the harsh tumor microenvironment. Trends Cell Biol. 2014;24:472–478. doi: 10.1016/j.tcb.2014.06.001. PubMed DOI PMC

Wen H, An YJ, Xu WJ, Kang KW, Park S. Real-time monitoring of cancer cell metabolism and effects of an anticancer agent using 2D in-cell NMR spectroscopy. Angew. Chem. Int. Ed. Engl. 2015;54:5374–5377. doi: 10.1002/anie.201410380. PubMed DOI

Killian JK, et al. Succinate dehydrogenase mutation underlies global epigenomic divergence in gastrointestinal stromal tumor. Cancer Discov. 2013;3:648–657. doi: 10.1158/2159-8290.CD-13-0092. PubMed DOI PMC

Kitazawa S, et al. Succinate dehydrogenase B-deficient cancer cells are highly sensitive to bromodomain and extra-terminal inhibitors. Oncotarget. 2017;8:28922–28938. doi: 10.18632/oncotarget.15959. PubMed DOI PMC

Letouze E, et al. SDH mutations establish a hypermethylator phenotype in paraganglioma. Cancer Cell. 2013;23:739–752. doi: 10.1016/j.ccr.2013.04.018. PubMed DOI

Lussey-Lepoutre C, et al. Loss of succinate dehydrogenase activity results in dependency on pyruvate carboxylation for cellular anabolism. Nat. Commun. 2015;6:8784. doi: 10.1038/ncomms9784. PubMed DOI PMC

Cardaci S, et al. Pyruvate carboxylation enables growth of SDH-deficient cells by supporting aspartate biosynthesis. Nat. Cell Biol. 2015;17:1317–1326. doi: 10.1038/ncb3233. PubMed DOI PMC

DeBerardinis RJ, Chandel NS. Fundamentals of cancer metabolism. Sci. Adv. 2016;2:e1600200. doi: 10.1126/sciadv.1600200. PubMed DOI PMC

Boroughs LK, DeBerardinis RJ. Metabolic pathways promoting cancer cell survival and growth. Nat. Cell Biol. 2015;17:351–359. doi: 10.1038/ncb3124. PubMed DOI PMC

Yang C, et al. Glutamine oxidation maintains the TCA cycle and cell survival during impaired mitochondrial pyruvate transport. Mol. Cell. 2014;56:414–424. doi: 10.1016/j.molcel.2014.09.025. PubMed DOI PMC

Mullen AR, et al. Reductive carboxylation supports growth in tumour cells with defective mitochondria. Nature. 2011;481:385–388. doi: 10.1038/nature10642. PubMed DOI PMC

Lendvai N, et al. Succinate-to-fumarate ratio as a new metabolic marker to detect the presence of SDHB/D-related paraganglioma: initial experimental and ex vivo findings. Endocrinology. 2014;155:27–32. doi: 10.1210/en.2013-1549. PubMed DOI PMC

Kluckova K, et al. Ubiquinone-binding site mutagenesis reveals the role of mitochondrial complex II in cell death initiation. Cell Death Dis. 2015;6:e1749. doi: 10.1038/cddis.2015.110. PubMed DOI PMC

Cecchini G. Function and structure of complex II of the respiratory chain. Annu. Rev. Biochem. 2003;72:77–109. doi: 10.1146/annurev.biochem.72.121801.161700. PubMed DOI

Hao HX, et al. SDH5, a gene required for flavination of succinate dehydrogenase, is mutated in paraganglioma. Science. 2009;325:1139–1142. doi: 10.1126/science.1175689. PubMed DOI PMC

Qi W, et al. Pyruvate kinase M2 activation may protect against the progression of diabetic glomerular pathology and mitochondrial dysfunction. Nat. Med. 2017;23:753–762. doi: 10.1038/nm.4328. PubMed DOI PMC

Ye J, et al. Pyruvate kinase M2 promotes de novo serine synthesis to sustain mTORC1 activity and cell proliferation. Proc. Natl Acad. Sci. USA. 2012;109:6904–6909. doi: 10.1073/pnas.1204176109. PubMed DOI PMC

Schulze A, Harris AL. How cancer metabolism is tuned for proliferation and vulnerable to disruption. Nature. 2012;491:364–373. doi: 10.1038/nature11706. PubMed DOI

Christofk HR, Vander Heiden MG, Wu N, Asara JM, Cantley LC. Pyruvate kinase M2 is a phosphotyrosine-binding protein. Nature. 2008;452:181–186. doi: 10.1038/nature06667. PubMed DOI

Bezawork-Geleta A, Dong L, Rohlena J, Neuzil J. The assembly factor SDHAF2 is dispensable for flavination of the catalytic subunit of mitochondrial complex II in breast cancer cells. J. Biol. Chem. 2016;291:21414–21420. doi: 10.1074/jbc.C116.755017. PubMed DOI PMC

Brown KK, Spinelli JB, Asara JM, Toker A. Adaptive reprogramming of De Novo pyrimidine synthesis is a metabolic vulnerability in triple-negative breast cancer. Cancer Discov. 2017;7:391–399. doi: 10.1158/2159-8290.CD-16-0611. PubMed DOI PMC

Mathur D, et al. PTEN regulates glutamine flux to pyrimidine synthesis and sensitivity to dihydroorotate dehydrogenase inhibition. Cancer Discov. 2017;7:380–390. doi: 10.1158/2159-8290.CD-16-0612. PubMed DOI PMC

Rabinovich S, et al. Diversion of aspartate in ASS1-deficient tumours fosters de novo pyrimidine synthesis. Nature. 2015;527:379–383. doi: 10.1038/nature15529. PubMed DOI PMC

Zong H, et al. AMP kinase is required for mitochondrial biogenesis in skeletal muscle in response to chronic energy deprivation. Proc. Natl Acad. Sci. USA. 2002;99:15983–15987. doi: 10.1073/pnas.252625599. PubMed DOI PMC

Hardie DG, Ross FA, Hawley SA. AMPK: a nutrient and energy sensor that maintains energy homeostasis. Nat. Rev. Mol. Cell Biol. 2012;13:251–262. doi: 10.1038/nrm3311. PubMed DOI PMC

Canto C, et al. AMPK regulates energy expenditure by modulating NAD+metabolism and SIRT1 activity. Nature. 2009;458:1056–1060. doi: 10.1038/nature07813. PubMed DOI PMC

Guaras A, et al. The CoQH2/CoQ ratio serves as a sensor of respiratory chain efficiency. Cell Rep. 2016;15:197–209. doi: 10.1016/j.celrep.2016.03.009. PubMed DOI

Benn DE, et al. Clinical presentation and penetrance of pheochromocytoma/paraganglioma syndromes. J. Clin. Endocrinol. Metab. 2006;91:827–836. doi: 10.1210/jc.2005-1862. PubMed DOI

Fishbein L, et al. Comprehensive molecular characterization of pheochromocytoma and paraganglioma. Cancer Cell. 2017;31:181–193. doi: 10.1016/j.ccell.2017.01.001. PubMed DOI PMC

Jochmanova I, Pacak K. Pheochromocytoma: the first metabolic endocrine cancer. Clin. Cancer Res. 2016;22:5001–5011. doi: 10.1158/1078-0432.CCR-16-0606. PubMed DOI PMC

Sancak Y, et al. EMRE is an essential component of the mitochondrial calcium uniporter complex. Science. 2013;342:1379–1382. doi: 10.1126/science.1242993. PubMed DOI PMC

Blecha J, et al. Antioxidant defense in quiescent cells determines selectivity of electron transport chain inhibition-induced cell death. Free Radic. Biol. Med. 2017;112:253–266. doi: 10.1016/j.freeradbiomed.2017.07.033. PubMed DOI

Rohlenova K, et al. Selective disruption of respiratory supercomplexes as a new strategy to suppress Her2high breast cancer. Antioxid. Redox Signal. 2017;26:84–103. doi: 10.1089/ars.2016.6677. PubMed DOI PMC

Vondrusova M, Bezawork-Geleta A, Sachaphibulkij K, Truksa J, Neuzil J. The effect of mitochondrially targeted anticancer agents on mitochondrial (super)complexes. Methods Mol. Biol. 2015;1265:195–208. doi: 10.1007/978-1-4939-2288-8_15. PubMed DOI

Pasdar EA, et al. Characterisation of mesothelioma-initiating cells and their susceptibility to anti-cancer agents. PLoS ONE. 2015;10:e0119549. doi: 10.1371/journal.pone.0119549. PubMed DOI PMC

Yan B, et al. Mitochondrially targeted vitamin E succinate efficiently kills breast tumour-initiating cells in a complex II-dependent manner. BMC Cancer. 2015;15:401. doi: 10.1186/s12885-015-1394-7. PubMed DOI PMC

Dong LF, et al. Horizontal transfer of whole mitochondria restores tumorigenic potential in mitochondrial DNA-deficient cancer cells. Elife. 2017;6:1–22. PubMed PMC

Wu JX, et al. SWATH mass spectrometry performance using extended peptide MS/MS assay libraries. Mol. Cell. Proteom. 2016;15:2501–2514. doi: 10.1074/mcp.M115.055558. PubMed DOI PMC

Huang da W, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009;37:1–13. doi: 10.1093/nar/gkn923. PubMed DOI PMC

Wen H, et al. Enhanced phase II detoxification contributes to beneficial effects of dietary restriction as revealed by multi-platform metabolomics studies. Mol. Cell. Proteomics. 2013;12:575–586. doi: 10.1074/mcp.M112.021352. PubMed DOI PMC

Wen H, et al. A new NMR-based metabolomics approach for the diagnosis of biliary tract cancer. J. Hepatol. 2010;52:228–233. doi: 10.1016/j.jhep.2009.11.002. PubMed DOI

Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–2120. doi: 10.1093/bioinformatics/btu170. PubMed DOI PMC

Kopylova E, Noe L, Touzet H. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics. 2012;28:3211–3217. doi: 10.1093/bioinformatics/bts611. PubMed DOI

Dobin A, et al. Bioinformatics. 2013. STAR: ultrafast universal RNA-seq aligner; pp. 15–21. PubMed PMC

Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550. doi: 10.1186/s13059-014-0550-8. PubMed DOI PMC

Sekula M, Datta S, Datta S. optCluster: an R Package for Determining the Optimal Clustering Algorithm. Bioinformation. 2017;13:101–103. doi: 10.6026/97320630013101. PubMed DOI PMC

Reimand J, et al. g:Profiler-a web server for functional interpretation of gene lists (2016 update) Nucleic Acids Res. 2016;44:W83–W89. doi: 10.1093/nar/gkw199. PubMed DOI PMC

Supek F, Bosnjak M, Skunca N, Smuc T. REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS ONE. 2011;6:e21800. doi: 10.1371/journal.pone.0021800. PubMed DOI PMC

Papathomas TG, et al. SDHB/SDHA immunohistochemistry in pheochromocytomas and paragangliomas: a multicenter interobserver variation analysis using virtual microscopy: a Multinational Study of the European Network for the Study of Adrenal Tumors (ENS@T) Mod. Pathol. 2015;28:807–821. doi: 10.1038/modpathol.2015.41. PubMed DOI

Disordered-to-ordered transitions in assembly factors allow the complex II catalytic subunit to switch binding partners

Germline SUCLG2 Variants in Patients With Pheochromocytoma and Paraganglioma

Mitochondrial complex II and reactive oxygen species in disease and therapy

Reactivation of Dihydroorotate Dehydrogenase-Driven Pyrimidine Biosynthesis Restores Tumor Growth of Respiration-Deficient Cancer Cells