PPTC7 antagonizes mitophagy by promoting BNIP3 and NIX degradation via SCFFBXL4

EMBO Reports - Tập 25 Số 8 - Trang 3324-3347
Giang Nguyen1,2, Brendan Townsend2, Prajakta Gosavi2, Keri‐Lyn Kozul3,2, Soo Siang Ooi2, Denaye Eldershaw4, Saroja Weeratunga4, Meihan Liu4, Mathew V. Jones5,6, S. Sean Millard2, Dominic C.H. Ng2, Michele Pagano7,8,9, Alexis Bonfim‐Melo6, Tobias Schneider10,11, David Komander10,11, Michael Lazarou12,10,11, Brett M. Collins13, Julia K. Pagan14
1Department of Biotechnology, School of Biotechnology, Viet Nam National University-International University, Ho Chi Minh City, Vietnam.
2Faculty of Medicine, School of Biomedical Sciences, University of Queensland, Brisbane, QLD, Australia.
3Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, MO, 63110, St Louis, USA.
4The University of Queensland, Institute for Molecular Bioscience, Brisbane, QLD 4072, Australia
5School of Chemistry & Molecular Biosciences, University of Queensland, Brisbane, QLD, 4072, Australia.
6The University of Queensland Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
7Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
8Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY, 10065, USA.
9Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY, 10016, USA
10Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3068, Australia.
11Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
12Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3068, Australia.
13The University of Queensland, Institute for Molecular Bioscience, Brisbane, QLD, 4072, Australia. [email protected].
14Faculty of Medicine, School of Biomedical Sciences, University of Queensland, Brisbane, QLD, Australia. [email protected].

Tóm tắt

Abstract

Mitophagy must be carefully regulated to ensure that cells maintain appropriate numbers of functional mitochondria. The SCFFBXL4 ubiquitin ligase complex suppresses mitophagy by controlling the degradation of BNIP3 and NIX mitophagy receptors, and FBXL4 mutations result in mitochondrial disease as a consequence of elevated mitophagy. Here, we reveal that the mitochondrial phosphatase PPTC7 is an essential cofactor for SCFFBXL4-mediated destruction of BNIP3 and NIX, suppressing both steady-state and induced mitophagy. Disruption of the phosphatase activity of PPTC7 does not influence BNIP3 and NIX turnover. Rather, a pool of PPTC7 on the mitochondrial outer membrane acts as an adaptor linking BNIP3 and NIX to FBXL4, facilitating the turnover of these mitophagy receptors. PPTC7 accumulates on the outer mitochondrial membrane in response to mitophagy induction or the absence of FBXL4, suggesting a homoeostatic feedback mechanism that attenuates high levels of mitophagy. We mapped critical residues required for PPTC7–BNIP3/NIX and PPTC7-FBXL4 interactions and their disruption interferes with both BNIP3/NIX degradation and mitophagy suppression. Collectively, these findings delineate a complex regulatory mechanism that restricts BNIP3/NIX-induced mitophagy.

Từ khóa


Tài liệu tham khảo

Adriaenssens E, Asselbergh B, Rivera-Mejias P, Bervoets S, Vendredy L, De Winter V, Spaas K, de Rycke R, van Isterdael G, Impens F et al (2023) Small heat shock proteins operate as molecular chaperones in the mitochondrial intermembrane space. Nat Cell Biol 25:467–480

Allen GF, Toth R, James J, Ganley IG (2013) Loss of iron triggers PINK1/Parkin-independent mitophagy. EMBO Rep 14:1127–1135

Alsina D, Lytovchenko O, Schab A, Atanassov I, Schober FA, Jiang M, Koolmeister C, Wedell A, Taylor RW, Wredenberg A et al (2020) FBXL4 deficiency increases mitochondrial removal by autophagy. EMBO Mol Med 12:e11659

Baek K, Krist DT, Prabu JR, Hill S, Klügel M, Neumaier L-M, von Gronau S, Kleiger G, Schulman BA (2020) NEDD8 nucleates a multivalent cullin–RING–UBE2D ubiquitin ligation assembly. Nature 578:461–466

Bellot G, Garcia-Medina R, Gounon P, Chiche J, Roux D, Pouyssegur J, Mazure NM (2009) Hypoxia-induced autophagy is mediated through hypoxia-inducible factor induction of BNIP3 and BNIP3L via their BH3 domains. Mol Cell Biol 29:2570–2581

Bonnen PE, Yarham JW, Besse A, Wu P, Faqeih EA, Al-Asmari AM, Saleh MA, Eyaid W, Hadeel A, He L et al (2013) Mutations in FBXL4 cause mitochondrial encephalopathy and a disorder of mitochondrial DNA maintenance. Am J Hum Genet 93:471–481

Bryant P, Pozzati G, Elofsson A (2022) Improved prediction of protein-protein interactions using AlphaFold2. Nat Commun 13:1265

Cao Y, Zheng J, Wan H, Sun Y, Fu S, Liu S, He B, Cai G, Cao Y, Huang H et al (2023) A mitochondrial SCF-FBXL4 ubiquitin E3 ligase complex degrades BNIP3 and NIX to restrain mitophagy and prevent mitochondrial disease. EMBO J 42:e113033

Chen Y, Jiao D, Liu Y, Xu X, Wang Y, Luo X, Saiyin H, Li Y, Gao K, Chen Y et al (2023) FBXL4 mutations cause excessive mitophagy via BNIP3/BNIP3L accumulation leading to mitochondrial DNA depletion syndrome. Cell Death Differ 30:2351–2363

Elcocks H, Brazel AJ, McCarron KR, Kaulich M, Husnjak K, Mortiboys H, Clague MJ, Urbe S (2023) FBXL4 ubiquitin ligase deficiency promotes mitophagy by elevating NIX levels. EMBO J 42:e112799

Esteban-Martinez L, Sierra-Filardi E, McGreal RS, Salazar-Roa M, Marino G, Seco E, Durand S, Enot D, Grana O, Malumbres M et al (2017) Programmed mitophagy is essential for the glycolytic switch during cell differentiation. EMBO J 36:1688–1706

Evans R, O’Neill M, Pritzel A, Antropova N, Senior A, Green T, Žídek A, Bates R, Blackwell S, Yim J et al (2022) Protein complex prediction with AlphaFold-Multimer. Preprint at https://www.biorxiv.org/content/10.1101/2021.10.04.463034v1

Gai X, Ghezzi D, Johnson MA, Biagosch CA, Shamseldin HE, Haack TB, Reyes A, Tsukikawa M, Sheldon CA, Srinivasan S et al (2013) Mutations in FBXL4, encoding a mitochondrial protein, cause early-onset mitochondrial encephalomyopathy. Am J Hum Genet 93:482–495

Guo X, Niemi NM, Hutchins PD, Condon SGF, Jochem A, Ulbrich A, Higbee AJ, Russell JD, Senes A, Coon JJ et al (2017) Ptc7p dephosphorylates select mitochondrial proteins to enhance metabolic function. Cell Rep 18:307–313

Hanna RA, Quinsay MN, Orogo AM, Giang K, Rikka S, Gustafsson AB (2012) Microtubule-associated protein 1 light chain 3 (LC3) interacts with Bnip3 protein to selectively remove endoplasmic reticulum and mitochondria via autophagy. J Biol Chem 287:19094–19104

Hao B, Zheng N, Schulman BA, Wu G, Miller JJ, Pagano M, Pavletich NP (2005) Structural basis of the Cks1-dependent recognition of p27(Kip1) by the SCF(Skp2) ubiquitin ligase. Mol Cell 20:9–19

He YL, Li J, Gong SH, Cheng X, Zhao M, Cao Y, Zhao T, Zhao YQ, Fan M, Wu HT et al (2022) BNIP3 phosphorylation by JNK1/2 promotes mitophagy via enhancing its stability under hypoxia. Cell Death Dis 13:966

Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C (2006) Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins 65:712–725

Huttlin EL, Bruckner RJ, Navarrete-Perea J, Cannon JR, Baltier K, Gebreab F, Gygi MP, Thornock A, Zarraga G, Tam S et al (2021) Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell 184:3022–3040 e3028

Huttlin EL, Bruckner RJ, Paulo JA, Cannon JR, Ting L, Baltier K, Colby G, Gebreab F, Gygi MP, Parzen H et al (2017) Architecture of the human interactome defines protein communities and disease networks. Nature 545:505–509

Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, Tunyasuvunakool K, Bates R, Zidek A, Potapenko A et al (2021) Highly accurate protein structure prediction with AlphaFold. Nature 596:583–589

Kuchay S, Duan S, Schenkein E, Peschiaroli A, Saraf A, Florens L, Washburn MP, Pagano M (2013) FBXL2- and PTPL1-mediated degradation of p110-free p85beta regulatory subunit controls the PI(3)K signalling cascade. Nat Cell Biol 15:472–480

Lampert MA, Orogo AM, Najor RH, Hammerling BC, Leon LJ, Wang BJ, Kim T, Sussman MA, Gustafsson AB (2019) BNIP3L/NIX and FUNDC1-mediated mitophagy is required for mitochondrial network remodeling during cardiac progenitor cell differentiation. Autophagy 15:1182–1198

Liu X, Chai J, Ou X, Li M, Liu Z (2019) Structural insights into substrate selectivity, catalytic mechanism, and redox regulation of rice photosystem II core phosphatase. Mol Plant 12:86–98

Luck K, Kim DK, Lambourne L, Spirohn K, Begg BE, Bian W, Brignall R, Cafarelli T, Campos-Laborie FJ, Charloteaux B et al (2020) A reference map of the human binary protein interactome. Nature 580:402–408

Marinkovic M, Novak I (2021) A brief overview of BNIP3L/NIX receptor-mediated mitophagy. FEBS Open Bio 11:3230–3236

Marinkovic M, Sprung M, Novak I (2021) Dimerization of mitophagy receptor BNIP3L/NIX is essential for recruitment of autophagic machinery. Autophagy 17:1232–1243

Meyer JG, Niemi NM, Pagliarini DJ, Coon JJ (2020) Quantitative shotgun proteome analysis by direct infusion. Nat Methods 17:1222–1228

Mirdita M, Schutze K, Moriwaki Y, Heo L, Ovchinnikov S, Steinegger M (2022) ColabFold: making protein folding accessible to all. Nat Methods 19:679–682

Mirdita M, Steinegger M, Soding J (2019) MMseqs2 desktop and local web server app for fast, interactive sequence searches. Bioinformatics 35:2856–2858

Nguyen-Dien GT, Kozul KL, Cui Y, Townsend B, Kulkarni PG, Ooi SS, Marzio A, Carrodus N, Zuryn S, Pagano M et al (2023) FBXL4 suppresses mitophagy by restricting the accumulation of NIX and BNIP3 mitophagy receptors. EMBO J 42:e112767

Niemi NM, Serrano LR, Muehlbauer LK, Balnis CE, Wei L, Smith AJ, Kozul KL, Forny M, Connor OM, Rashan EH et al (2023) PPTC7 maintains mitochondrial protein content by suppressing receptor-mediated mitophagy. Nat Commun 14:6431

Niemi NM, Wilson GM, Overmyer KA, Vogtle FN, Myketin L, Lohman DC, Schueler KL, Attie AD, Meisinger C, Coon JJ et al (2019) Pptc7 is an essential phosphatase for promoting mammalian mitochondrial metabolism and biogenesis. Nat Commun 10:3197

Novak I, Kirkin V, McEwan DG, Zhang J, Wild P, Rozenknop A, Rogov V, Lohr F, Popovic D, Occhipinti A et al (2010) Nix is a selective autophagy receptor for mitochondrial clearance. EMBO Rep 11:45–51

Onishi M, Yamano K, Sato M, Matsuda N, Okamoto K (2021) Molecular mechanisms and physiological functions of mitophagy. EMBO J 40:e104705

Ordureau A, Kraus F, Zhang J, An H, Park S, Ahfeldt T, Paulo JA, Harper JW (2021) Temporal proteomics during neurogenesis reveals large-scale proteome and organelle remodeling via selective autophagy. Mol Cell 81:5082–5098 e5011

Pagan JK, Marzio A, Jones MJ, Saraf A, Jallepalli PV, Florens L, Washburn MP, Pagano M (2015) Degradation of Cep68 and PCNT cleavage mediate Cep215 removal from the PCM to allow centriole separation, disengagement and licensing. Nat Cell Biol 17:31–43

Pagliarini DJ, Calvo SE, Chang B, Sheth SA, Vafai SB, Ong SE, Walford GA, Sugiana C, Boneh A, Chen WK et al (2008) A mitochondrial protein compendium elucidates complex I disease biology. Cell 134:112–123

Poole LP, Bock-Hughes A, Berardi DE, Macleod KF (2021) ULK1 promotes mitophagy via phosphorylation and stabilization of BNIP3. Sci Rep 11:20526

Rhee HW, Zou P, Udeshi ND, Martell JD, Mootha VK, Carr SA, Ting AY (2013) Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging. Science 339:1328–1331

Rogov VV, Suzuki H, Marinkovic M, Lang V, Kato R, Kawasaki M, Buljubasic M, Sprung M, Rogova N, Wakatsuki S et al (2017) Phosphorylation of the mitochondrial autophagy receptor Nix enhances its interaction with LC3 proteins. Sci Rep 7:1131

Sandoval H, Thiagarajan P, Dasgupta SK, Schumacher A, Prchal JT, Chen M, Wang J (2008) Essential role for Nix in autophagic maturation of erythroid cells. Nature 454:232–235

Schweers RL, Zhang J, Randall MS, Loyd MR, Li W, Dorsey FC, Kundu M, Opferman JT, Cleveland JL, Miller JL et al (2007) NIX is required for programmed mitochondrial clearance during reticulocyte maturation. Proc Natl Acad Sci USA 104:19500–19505

Simpson CL, Tokito MK, Uppala R, Sarkar MK, Gudjonsson JE, Holzbaur ELF (2021) NIX initiates mitochondrial fragmentation via DRP1 to drive epidermal differentiation. Cell Rep 34:108689

Sowter HM, Ratcliffe PJ, Watson P, Greenberg AH, Harris AL (2001) HIF-1-dependent regulation of hypoxic induction of the cell death factors BNIP3 and NIX in human tumors. Cancer Res 61:6669–6673

Stojanovski D, Pfanner N, Wiedemann N (2007) Import of proteins into mitochondria. Methods Cell Biol 80:783–806

Sun N, Malide D, Liu J, Rovira II, Combs CA, Finkel T (2017) A fluorescence-based imaging method to measure in vitro and in vivo mitophagy using mt-Keima. Nat Protoc 12:1576–1587

Sun Y, Cao Y, Wan H, Memetimin A, Cao Y, Li L, Wu C, Wang M, Chen S, Li Q et al (2024) A mitophagy sensor PPTC7 controls BNIP3 and NIX degradation to regulate mitochondrial mass. Mol Cell 84:327–344 e329

Tracy K, Dibling BC, Spike BT, Knabb JR, Schumacker P, Macleod KF (2007) BNIP3 is an RB/E2F target gene required for hypoxia-induced autophagy. Mol Cell Biol 27:6229–6242

Uoselis L, Nguyen TN, Lazarou M (2023) Mitochondrial degradation: mitophagy and beyond. Mol Cell 83:3404–3420

Wei L, Oguz Gok M, Svoboda JD, Forny M, Friedman JR, Niemi NM (2024) PPTC7 limits mitophagy through proximal and dynamic interactions with BNIP3 and NIX. Preprint at bioRxiv https://doi.org/10.1101/2024.01.24.576953

Yuan Y, Zheng Y, Zhang X, Chen Y, Wu X, Wu J, Shen Z, Jiang L, Wang L, Yang W et al (2017) BNIP3L/NIX-mediated mitophagy protects against ischemic brain injury independent of PARK2. Autophagy 13:1754–1766

Zhao JF, Rodger CE, Allen GFG, Weidlich S, Ganley IG (2020) HIF1alpha-dependent mitophagy facilitates cardiomyoblast differentiation. Cell Stress 4:99–113