A pair of transporters controls mitochondrial Zn²⁺ levels to maintain mitochondrial homeostasis

Abstract

Zn²⁺ is required for the activity of many mitochondrial proteins, which regulate mitochondrial dynamics, apoptosis and mitophagy. However, it is not understood how the proper mitochondrial Zn²⁺ level is achieved to maintain mitochondrial homeostasis. Using Caenorhabditis elegans, we reveal here that a pair of mitochondrion-localized transporters controls the mitochondrial level of Zn²⁺. We demonstrate that SLC-30A9/ZnT9 is a mitochondrial Zn²⁺ exporter. Loss of SLC-30A9 leads to mitochondrial Zn²⁺ accumulation, which damages mitochondria, impairs animal development and shortens the life span. We further identify SLC-25A25/ SCaMC-2 as an important regulator of mitochondrial Zn²⁺ import. Loss of SLC-25A25 suppresses the abnormal mitochondrial Zn²⁺ accumulation and defective mitochondrial structure and functions caused by loss of SLC-30A9. Moreover, we reveal that the endoplasmic reticulum contains the Zn²⁺ pool from which mitochondrial Zn²⁺ is imported. These findings establish the molecular basis for controlling the correct mitochondrial Zn²⁺ levels for normal mitochondrial structure and functions.

Key words： mitochondria; Zn²⁺ transporter; C. elegans; ER-mitochondrial contact; development

References

1 Abuarab N, Munsey TS, Jiang LH, Li J, Sivaprasadarao A (2017) High glucose-induced ROS activates TRPM2 to trigger lysosomal membrane permeabilization and Zn²⁺-mediated mitochondrial fission. Sci Signal 10

2 Andreini C, Banci L, Bertini I, Rosato A (2006) Counting the zincproteins encoded in the human genome. J Proteome Res 5: 196- 201

3 Bian X, Teng T, Zhao H, Qin J, Qiao Z, Sun Y, Liun Z, Xu Z (2018) Zinc prevents mitochondrial superoxide generation by inducing mitophagy in the setting of hypoxia/reoxygenation in cardiac cells. Free Radic Res 52: 80- 91

4 Bossy-Wetzel E, Talantova MV, Lee WD, Scholzke MN, Harrop A, Mathews E, Gotz T, Han J, Ellisman MH, Perkins GA et al (2004) Crosstalk between nitric oxide and zinc pathways to neuronal cell death involving mitochondrial dysfunction and p38-activated K+ channels. Neuron 41: 351- 365

5 Bruinsma JJ, Jirakulaporn T, Muslin AJ, Kornfeld K (2002) Zinc ions and cation diffusion facilitator proteins regulate Ras-mediated signaling. Dev Cell 2: 567- 578

6 Chabosseau P, Tuncay E, Meur G, Bellomo EA, Hessels A, Hughes S, Johnson PR, Bugliani M, Marchetti P, Turan B et al (2014) Mitochondrial and ER-targeted eCALWY probes reveal high levels of free Zn2+. ACS Chem Biol 9: 2111- 2120

7 Cho HM, Ryu JR, Jo Y, Seo TW, Choi YN, Kim JH, Chung JM, Cho B, Kang HC, Yu SW et al (2019) Drp1-Zip1 interaction regulates mitochondrial quality surveillance system. Mol Cell 73: 364- 376

8 Colvin RA, Holmes WR, Fontaine CP, Maret W (2010) Cytosolic zinc buffering and muffling: their role in intracellular zinc homeostasis. Metallomics 2: 306- 317

9 del Arco A, Satrustegui J (2004) Identification of a novel human subfamily of mitochondrial carriers with calcium-binding domains. J Biol Chem 279: 24701- 24713

10 Dineley KE, Richards LL, Votyakova TV, Reynolds IJ (2005) Zinc causes loss of membrane potential and elevates reactive oxygen species in rat brain mitochondria. Mitochondrion 5: 55- 65

11 Dineley KE, Votyakova TV, Reynolds IJ (2003) Zinc inhibition of cellular energy production: implications for mitochondria and neurodegeneration. J Neurochem 85: 563- 570

12 Fiermonte G, De Leonardis F, Todisco S, Palmieri L, Lasorsa FM, Palmieri F (2004) Identification of the mitochondrial ATP-Mg/Pi transporter. Bacterial expression, reconstitution, functional characterization, and tissue distribution. J Biol Chem 279: 30722- 30730

13 Frederickson CJ, Koh JY, Bush AI (2005) The neurobiology of zinc in health and disease. Nat Rev Neurosci 6: 449- 462

14 Fukada T, Yamasaki S, Nishida K, Murakami M, Hirano T (2011) Zinc homeostasis and signaling in health and diseases: zinc signaling. J Biol Inorg Chem 16: 1123- 1134

15 Gartmann L, Wex T, Grungreiff K, Reinhold D, Kalinski T, Malfertheiner P, Schutte K (2018) Expression of zinc transporters ZIP4, ZIP14 and ZnT9 in hepatic carcinogenesis: an immunohistochemical study. J Trace Elem Med Biol 49: 35- 42

16 Gordon GW, Berry G, Liang XH, Levine B, Herman B (1998) Quantitative fluorescence resonance energy transfer measurements using fluorescence microscopy. Biophys J 74: 2702- 2713

17 Head B, Griparic L, Amiri M, Gandre-Babbe S, van der Bliek AM (2009) Inducible proteolytic inactivation of OPA1 mediated by the OMA1 protease in mammalian cells. J Cell Biol 187: 959- 966

18 Hofherr A, Seger C, Fitzpatrick F, Busch T, Michel E, Luan J, Osterried L, Linden F, Kramer-Zucker A, Wakimoto B et al (2018) The mitochondrial transporter SLC25A25 links ciliary TRPP2 signaling and cellular metabolism. PLoS Biol 16: e2005651

19 Huang YZ, Pan E, Xiong ZQ, McNamara JO (2008) Zinc-mediated transactivation of TrkB potentiates the hippocampal mossy fiberCA3 pyramid synapse. Neuron 57: 546- 558

20 Jiang D, Sullivan PG, Sensi SL, Steward O, Weiss JH (2001) Zn(2+) induces permeability transition pore opening and release of proapoptotic peptides from neuronal mitochondria. J Biol Chem 276: 47524- 47529

21 Joyal JL, Aprille JR (1992) The ATP-Mg/Pi carrier of rat liver mitochondria catalyzes a divalent electroneutral exchange. J Biol Chem 267: 19198- 19203

22 Kambe T, Tsuji T, Hashimoto A, Itsumura N (2015) The physiological, biochemical, and molecular roles of zinc transporters in zinc homeostasis and metabolism. Physiol Rev 95: 749- 784

23 Kanazawa T, Zappaterra M, Hasegawa A, Wright AP, NewmanSmith ED, Buttle KF, Mcdonald K, Mannella CA, Van der Bliek AM, Lu B et al (2008) The C. elegans Opa1 homologue EAT-3 Is essential for resistance to free radicals. PLoS Genet 4: 78- 84

24 Karabulut R, Turkyilmaz Z, Sonmez K, Kumas G, Ergun S, Ergun M, Basaklar A (2013) Twenty-four genes are upregulated in patients with hypospadias. Balkan J Med Genet 16: 39- 44

25 Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ (2015) The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc 10: 845- 858

26 Kido T, Lau YC (2019) The Y-linked proto-oncogene TSPY contributes to poor prognosis of the male hepatocellular carcinoma patients by promoting the pro-oncogenic and suppressing the anti-oncogenic gene expression. Cell Biosci 9: 22

27 Labrousse AM, Zappaterra M, Rube DA, Bliek A (1999) C. elegans dynamin-related protein DRP-1 controls severing of the mitochondrial outer membrane. Mol Cell 4: 815

28 Li J, Cai T, Wu P, Cui Z, Chen X, Hou J, Xie Z, Xue P, Shi L, Liu P et al (2009) Proteomic analysis of mitochondria from Caenorhabditis elegans. Proteomics 9: 4539- 4553

29 Lin W, Gao L, Chen X (2015) Protein-specific imaging of O-GlcNAcylation in single cells. ChemBioChem 16: 2571- 2575

30 Lin YF, Schulz AM, Pellegrino MW, Lu Y, Shaham S, Haynes CM (2016) Maintenance and propagation of a deleterious mitochondrial genome by the mitochondrial unfolded protein response. Nature 533: 416- 419

31 Lu M, Fu D (2007) Structure of the zinc transporter YiiP. Science 317: 1746- 1748

32 Malaiyandi LM, Honick AS, Rintoul GL, Wang QJ, Reynolds IJ (2005a) Zn2+ inhibits mitochondrial movement in neurons by phosphatidylinositol 3-kinase activation. J Neurosci 25: 9507- 9514

33 Malaiyandi LM, Vergun O, Dineley KE, Reynolds IJ (2005b) Direct visualization of mitochondrial zinc accumulation reveals uniporter-dependent and -independent transport mechanisms. J Neurochem 93: 1242- 1250

34 Mammadova-Bach E, Braun A (2019) Zinc homeostasis in plateletrelated diseases. Int J Mol Sci 20: 5258

35 Medvedeva YV, Weiss JH (2014) Intramitochondrial Zn2+ accumulation via the Ca2+ uniporter contributes to acute ischemic neurodegeneration. Neurobiol Dis 68: 137- 144

36 Mishra P, Chan DC (2016) Metabolic regulation of mitochondrial dynamics. J Cell Biol 212: 379- 387

37 Monne M, Daddabbo L, Giannossa LC, Nicolardi MC, Palmieri L, Miniero DV, Mangone A, Palmieri F (2017) Mitochondrial ATPMg/phosphate carriers transport divalent inorganic cations in complex with ATP. J Bioenerg Biomembr 49: 369- 380

38 Nargund AM, Fiorese CJ, Pellegrino MW, Deng P, Haynes CM (2015) Mitochondrial and nuclear accumulation of the transcription factor ATFS-1 promotes OXPHOS recovery during the UPR (mt). Mol Cell 58: 123- 133

39 Paix A, Wang Y, Smith HE, Lee CY, Calidas D, Lu T, Smith J, Schmidt H, Krause MW, Seydoux G et al (2014) Scalable and versatile genome editing using linear DNAs with microhomology to Cas9 Sites in Caenorhabditis elegans. Genetics 198: 1347- 1356

40 Paoletti P, Ascher P, Neyton J (1997) High-affinity zinc inhibition of NMDA NR1-NR2A receptors. J Neurosci 17: 5711- 5725

41 Park JA, Koh JY (1999) Induction of an immediate early gene egr-1 by zinc through extracellular signal-regulated kinase activation in cortical culture: its role in zinc-induced neuronal death. J Neurochem 73: 450- 456

42 Perez Y, Shorer Z, Liani-Leibson K, Chabosseau P, Kadir R, Volodarsky M, Halperin D, Barber-Zucker S, Shalev H, Schreiber R et al (2017) SLC30A9 mutation affecting intracellular zinc homeostasis causes a novel cerebro-renal syndrome. Brain 140: 928- 939

43 Pickles S, Vigie P, Youle RJ (2018) Mitophagy and quality control mechanisms in mitochondrial maintenance. Curr Biol 28: R170- R185

44 Satrustegui J, Pardo B, Del Arco A (2007) Mitochondrial transporters as novel targets for intracellular calcium signaling. Physiol Rev 87: 29- 67

45 Sensi SL, Paoletti P, Bush AI, Sekler I (2009) Zinc in the physiology and pathology of the CNS. Nat Rev Neurosci 10: 780- 791

46 Singh CK, Malas KM, Tydrick C, Siddiqui IA, Iczkowski KA, Ahmad N (2016) Analysis of zinc-exporters expression in prostate cancer. Sci Rep 6: 36772

47 Spinelli JB, Haigis MC (2018) The multifaceted contributions of mitochondria to cellular metabolism. Nat Cell Biol 20: 745- 754

48 Sun Y, Day RN, Periasamy A (2011) Investigating protein-protein interactions in living cells using fluorescence lifetime imaging microscopy. Nat Protoc 6: 1324- 1340

49 Tang R, Wang X, Zhou J, Zhang F, Zhao S, Gan Q, Zhao L, Wang F, Zhang Q, Zhang J et al (2020) Defective arginine metabolism impairs mitochondrial homeostasis in Caenorhabditis elegans. J Genet Genomics 47: 145- 156

50 Tewari SG, Dash RK, Beard DA, Bazil JN (2012) A biophysical model of the mitochondrial ATP-Mg/P(i) carrier. Biophys J 103: 1616- 1625

51 Xu S, Chisholm AD (2014) C. elegans epidermal wounding induces a mitochondrial ROS burst that promotes wound repair. Dev Cell 31: 48- 60

52 Yamasaki S, Sakata-Sogawa K, Hasegawa A, Suzuki T, Kabu K, Sato E, Kurosaki T, Yamashita S, Tokunaga M, Nishida K et al (2007) Zinc is a novel intracellular second messenger. J Cell Biol 177: 637- 645

53 Yang Q, Bruschweiler S, Chou JJ (2014) A self-sequestered calmodulin-like Ca2+ sensor of mitochondrial SCaMC carrier and its implication to Ca2+-dependent ATP-Mg/P(i) transport. Structure 22: 209- 217

54 Ye X, Zeng T, Kong W, Chen LL (2020) Integrative analyses of genes associated with fulminant type 1 diabetes. J Immunol Res 2020: 1025857

55 Yoder JH, Chong H, Guan KL, Han M (2004) Modulation of KSR activity in Caenorhabditis elegans by Zn ions, PAR-1 kinase and PP2A phosphatase. EMBO J 23: 111- 119

56 Youle RJ, van der Bliek AM (2012) Mitochondrial fission, fusion, and stress. Science 337: 1062- 1065

57 Zhou J, Wang X, Wang M, Chang Y, Zhang F, Ban Z, Tang R, Gan Q, Wu S, Guo Y et al (2019) The lysine catabolite saccharopine impairs development by disrupting mitochondrial homeostasis. J Cell Biol 218: 580- 597