PPTC7 antagonizes mitophagy by promoting BNIP3 and NIX degradation via SCFFBXL4
Tóm tắt
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
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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