Select E2 enzymes differentially regulate parkin activation and mitophagy
Open accessAbstract
Loss-of-function mutations in the genes encoding PINK1 and Parkin are the most common causes of recessive Parkinson's disease (PD). Both together mediate the selective degradation of mitochondrial proteins and whole organelles via the proteasome and the autophagy/lysosome pathway (mitophagy). The mitochondrial kinase PINK1 activates and recruits the E3 ubiquitin (Ub) ligase Parkin to de-energized mitochondria. However, Parkin's cognate E2 co-enzymes in this Ub-dependent pathway have not been investigated. Here, we discovered in total four E2s that either positively or negatively regulate Parkin's activation, translocation and enzymatic functions during mitochondrial quality control. UBE2D family members and UBE2L3 redundantly charge the RING/HECT hybrid ligase Parkin with Ub, resulting in its initial activation and translocation to mitochondria. UBE2N however primarily operates through a different mechanism to mediate the proper clustering of mitochondria a prerequisite for degradation. Strikingly, in contrast to UBE2D, UBE2L3 and UBE2N, depletion of UBE2R1 results in enhanced Parkin translocation and clustering upon mitochondrial uncoupling. Our study uncovered redundant, cooperative or antagonistic functions of distinct E2 enzymes in the regulation of Parkin and mitophagy may suggest a putative role in PD pathogenesis.
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The study used an established stable HeLa cell model with homogenous expression of GFP-PRKN.
“we used an established stable HeLa cell model with homogenous expression of GFP-PRKN [19].”
From miRNA family miR-29 inhibits PINK1-PRKN signaling via ATG9A (2026) · cites this paper as [19]
The machine-learning classifier had excellent agreement with the established GFP-PRKN ratio algorithm and a combined Z' score of 0.79.
“There was excellent agreement between the new classifier and the established ‘GFP-PRKN ratio’ algorithm [19, 20, 25, 30] (Fig. 1C, Table S4) but the new classifier was more robust in this screening setting and had a combined Z’ score of 0.79.”
From miRNA family miR-29 inhibits PINK1-PRKN signaling via ATG9A (2026) · cites this paper as [19]
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References 65 · Cited by 72
Research works printed but not linked: 49
- Anton, F., Dittmar, G., Langer, T. and Escobar-Henriques, M. (2013). Two deubiquitylases act on mitofusin and regulate mitochondrial fusion along independent pathways. Mol. Cell 49 , 487-498. http://dx.doi.org/10.1016/j.molcel.2012.12.003 · DOI
- Birsa, N., Norkett, R., Wauer, T., Mevissen, T. E., Wu, H. C., Foltynie, T., Bhatia, K., Hirst, W. D., Komander, D., Plun-Favreau, H. et al. (2014). K27 ubiquitination of the mitochondrial transport protein Miro is dependent on serine 65 of the Parkin ubiquitin ligase. J. Biol. Chem . http://dx.doi.org/10.1074/jbc.M114.563031 · DOI
- Burchell, V. S., Nelson, D. E., Sanchez-Martinez, A., Delgado-Camprubi, M., Ivatt, R. M., Pogson, J. H., Randle, S. J., Wray, S., Lewis, P. A., Houlden, H. et al. (2013). The Parkinson's disease-linked proteins Fbxo7 and Parkin interact to mediate mitophagy. Nat. Neurosci. 16 , 1257-1265. http://dx.doi.org/10.1038/nn.3489 · DOI
- Ceccarelli, D. F., Tang, X., Pelletier, B., Orlicky, S., Xie, W., Plantevin, V., Neculai, D., Chou, Y. C., Ogunjimi, A., Al-Hakim, A. et al. (2011). An allosteric inhibitor of the human Cdc34 ubiquitin-conjugating enzyme. Cell 145 , 10751087. http://dx.doi.org/10.1016/j.cell.2011.05.039 · DOI
- Chan, N. C., Salazar, A. M., Pham, A. H., Sweredoski, M. J., Kolawa, N. J., Graham, R. L., Hess, S. and Chan, D. C. (2011). Broad activation of the ubiquitin-proteasome system by Parkin is critical for mitophagy. Hum. Mol. Genet. 20 , 1726-1737. http://dx.doi.org/10.1093/hmg/ddr048 · DOI · Paper page
- Corti, O., Lesage, S. and Brice, A. (2011). What genetics tells us about the causes and mechanisms of Parkinson's disease. Physiol. Rev. 91 , 1161-1218. http://dx.doi.org/10.1152/physrev.00022.2010 · DOI
- de Leeuw, N., Bulk, S., Green, A., Jaeckle-Santos, L., Baker, L. A., Zinn, A. R., Kleefstra, T., van der Smagt, J. J., Vianne Morgante, A. M., de Vries, B. B. et al. (2010). UBE2A deficiency syndrome: Mild to severe intellectual disability accompanied by seizures, absent speech, urogenital, and skin anomalies in male patients. Am. J. Med. Genet. A. 152A , 3084-3090. http://dx.doi.org/10.1002/ajmg.a.33743 · DOI
- Di Fonzo, A., Dekker, M. C., Montagna, P., Baruzzi, A., Yonova, E. H., Correia Guedes, L., Szczerbinska, A., Zhao, T., Dubbel-Hulsman, L. O., Wouters, C. H. et al. (2009). FBXO7 mutations cause autosomal recessive, early-onset parkinsonian-pyramidal syndrome. Neurology 72 , 240-245. http://dx.doi.org/10.1212/01.wnl.0000338144.10967.2b · DOI
- Doris, K. S., Rumsby, E. L. and Morgan, B. A. (2012). Oxidative stress responses involve oxidation of a conserved ubiquitin pathway enzyme. Mol. Cell. Biol. 32 , 4472-4481. http://dx.doi.org/10.1128/MCB.00559-12 · DOI
- Duda, D. M., Olszewski, J. L., Schuermann, J. P., Kurinov, I., Miller, D. J., Nourse, A., Alpi, A. F. and Schulman, B. A. (2013). Structure of HHARI, a RING-IBR-RING ubiquitin ligase: autoinhibition of an Ariadne-family E3 and insights into ligation mechanism. Structure 21 , 1030-1041. http://dx.doi.org/10.1016/j.str.2013.04.019 · DOI
- Gegg, M. E., Cooper, J. M., Chau, K. Y., Rojo, M., Schapira, A. H. and Taanman, J. W. (2010). Mitofusin 1 and mitofusin 2 are ubiquitinated in a PINK1/parkin-dependent manner upon induction of mitophagy. Hum. Mol. Genet. 19 , 4861-4870. http://dx.doi.org/10.1093/hmg/ddq419 · DOI · Paper page
- Glauser, L., Sonnay, S., Stafa, K. and Moore, D. J. (2011). Parkin promotes the ubiquitination and degradation of the mitochondrial fusion factor mitofusin 1. J. Neurochem. 118 , 636-645. http://dx.doi.org/10.1111/j.1471-4159.2011.07318.x · DOI · Paper page
- Jahngen-Hodge, J., Obin, M. S., Gong, X., Shang, F., Nowell, T. R., Jr, Gong, J., Abasi, H., Blumberg, J. and Taylor, A. (1997). Regulation of ubiquitinconjugating enzymes by glutathione following oxidative stress. J. Biol. Chem. 272 , 28218-28226. http://dx.doi.org/10.1074/jbc.272.45.28218 · DOI
- Jin, J., Li, X., Gygi, S. P. and Harper, J. W. (2007). Dual E1 activation systems for ubiquitin differentially regulate E2 enzyme charging. Nature 447 , 1135-1138. http://dx.doi.org/10.1038/nature05902 · DOI
- Jin, S. M., Lazarou, M., Wang, C., Kane, L. A., Narendra, D. P. and Youle, R. J. (2010). Mitochondrial membrane potential regulates PINK1 import and proteolytic destabilization by PARL. J. Cell Biol. 191 , 933-942. http://dx.doi.org/10.1083/jcb.201008084 · DOI · Paper page
- Kim, N. C., Tresse, E., Kolaitis, R. M., Molliex, A., Thomas, R. E., Alami, N. H., Wang, B., Joshi, A., Smith, R. B., Ritson, G. P. et al. (2013). VCP is essential for mitochondrial quality control by PINK1/Parkin and this function is impaired by VCP mutations. Neuron 78 , 65-80. http://dx.doi.org/10.1016/j.neuron.2013.02.029 · DOI
- Kitada, T., Asakawa, S., Hattori, N., Matsumine, H., Yamamura, Y., Minoshima, S., Yokochi, M., Mizuno, Y. and Shimizu, N. (1998). Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism. Nature 392 , 605-608. http://dx.doi.org/10.1038/33416 · DOI · Paper page
- Komander, D. and Rape, M. (2012). The ubiquitin code. Annu. Rev. Biochem. 81 , 203-229. http://dx.doi.org/10.1146/annurev-biochem-060310-170328 · DOI · Paper page
- Koopman, W. J., Visch, H. J., Verkaart, S., van den Heuvel, L. W., Smeitink, J. A. and Willems, P. H. (2005). Mitochondrial network complexity and pathological decrease in complex I activity are tightly correlated in isolated human complex I deficiency. Am. J. Physiol. 289 , C881-C890. http://dx.doi.org/10.1152/ajpcell.00104.2005 · DOI
- Lazarou, M., Narendra, D. P., Jin, S. M., Tekle, E., Banerjee, S. and Youle, R. J. (2013). PINK1 drives Parkin self-association and HECT-like E3 activity upstream of mitochondrial binding. J. Cell Biol. 200 , 163-172. http://dx.doi.org/10.1083/jcb.201210111 · DOI
- Leboucher, G. P., Tsai, Y. C., Yang, M., Shaw, K. C., Zhou, M., Veenstra, T. D., Glickman, M. H. and Weissman, A. M. (2012). Stress-induced phosphorylation and proteasomal degradation of mitofusin 2 facilitates mitochondrial fragmentation and apoptosis. Mol. Cell 47 , 547-557. http://dx.doi.org/10.1016/j.molcel.2012.05.041 · DOI · Paper page
- Lee, J. Y., Nagano, Y., Taylor, J. P., Lim, K. L. and Yao, T. P. (2010). Diseasecausing mutations in parkin impair mitochondrial ubiquitination, aggregation, and HDAC6-dependent mitophagy. J. Cell Biol. 189 , 671-679. http://dx.doi.org/10.1083/jcb.201001039 · DOI
- Lefebvre, V., Du, Q., Baird, S., Ng, A. C., Nascimento, M., Campanella, M., McBride, H. M. and Screaton, R. A. (2013). Genome-wide RNAi screen identifies ATPase inhibitory factor 1 (ATPIF1) as essential for PARK2 recruitment and mitophagy. Autophagy 9 , 1770-1779. http://dx.doi.org/10.4161/auto.25413 · DOI
- Lydeard, J. R., Schulman, B. A. and Harper, J. W. (2013). Building and remodelling Cullin-RING E3 ubiquitin ligases. EMBO Rep. 14 , 1050-1061. http://dx.doi.org/10.1038/embor.2013.173 · DOI · Paper page
- Machida, Y. J., Machida, Y., Chen, Y., Gurtan, A. M., Kupfer, G. M., D'Andrea, A. D. and Dutta, A. (2006). UBE2T is the E2 in the Fanconi anemia pathway and undergoes negative autoregulation. Mol. Cell 23 , 589-596. http://dx.doi.org/10.1016/j.molcel.2006.06.024 · DOI
- Meissner, C., Lorenz, H., Weihofen, A., Selkoe, D. J. and Lemberg, M. K. (2011). The mitochondrial intramembrane protease PARL cleaves human Pink1 to regulate Pink1 trafficking. J. Neurochem. 117 , 856-867. http://dx.doi.org/10.1111/j.1471-4159.2011.07253.x · DOI
- Narendra, D., Tanaka, A., Suen, D. F. and Youle, R. J. (2008). Parkin is recruited selectively to impaired mitochondria and promotes their autophagy. J. Cell Biol. 183 , 795-803. http://dx.doi.org/10.1083/jcb.200809125 · DOI · Paper page
- Narendra, D., Kane, L. A., Hauser, D. N., Fearnley, I. M. and Youle, R. J. (2010a). p62/SQSTM1 is required for Parkin-induced mitochondrial clustering but not mitophagy; VDAC1 is dispensable for both. Autophagy 6 , 1090-1106. http://dx.doi.org/10.4161/auto.6.8.13426 · DOI
- Riley, B. E., Lougheed, J. C., Callaway, K., Velasquez, M., Brecht, E., Nguyen, L., Shaler, T., Walker, D., Yang, Y., Regnstrom, K. et al. (2013). Structure and function of Parkin E3 ubiquitin ligase reveals aspects of RING and HECT ligases. Nat. Commun. 4 , 1982. http://dx.doi.org/10.1038/ncomms2982 · DOI
- Sandebring, A. and Cedazo-Mı ´nguez, A. (2012). Parkin- an E3 ubiquitin ligase with multiple substrates. J. Alzheimers Dis. Parkinsonism S10 , 002. http://dx.doi.org/10.4172/2161-0460.S10-002 · DOI
- Sarraf, S. A., Raman, M., Guarani-Pereira, V., Sowa, M. E., Huttlin, E. L., Gygi, S. P. and Harper, J. W. (2013). Landscape of the http://dx.doi.org/10.1038/nature12043 · DOI
- Sha, D., Chin, L. S. and Li, L. (2010). Phosphorylation of parkin by Parkinson disease-linked kinase PINK1 activates parkin E3 ligase function and NF-kappaB signaling. Hum. Mol. Genet. 19 , 352-363. http://dx.doi.org/10.1093/hmg/ddp501 · DOI
- Sheng, Y., Hong, J. H., Doherty, R., Srikumar, T., Shloush, J., Avvakumov, G. V., Walker, J. R., Xue, S., Neculai, D., Wan, J. W. et al. (2012). A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen. Mol. Cell. Proteomics 11 , 329-341. http://dx.doi.org/10.1074/mcp.O111.013706 · DOI
- Spratt, D. E., Martinez-Torres, R. J., Noh, Y. J., Mercier, P., Manczyk, N., Barber, K. R., Aguirre, J. D., Burchell, L., Purkiss, A., Walden, H. et al. (2013). A molecular explanation for the recessive nature of parkin-linked Parkinson's disease. Nat. Commun. 4 , 1983. http://dx.doi.org/10.1038/ncomms2983 · DOI
- Staropoli, J. F., McDermott, C., Martinat, C., Schulman, B., Demireva, E. and Abeliovich, A. (2003). Parkin is a component of an SCF-like ubiquitin ligase complex and protects postmitotic neurons from kainate excitotoxicity. Neuron 37 , 735-749. http://dx.doi.org/10.1016/S0896-6273(0300084-9) · DOI
- Takada, K., Hirakawa, T., Yokosawa, H., Okawa, Y., Taguchi, H. and Ohkawa, K. (2001). Isolation of ubiquitin-E2 (ubiquitin-conjugating enzyme) complexes from erythroleukaemia cells using immunoaffinity techniques. Biochem. J. 356 , 199-206. http://dx.doi.org/10.1042/0264-6021:3560199 · DOI
- Trempe, J. F., Sauve ´, V., Grenier, K., Seirafi, M., Tang, M. Y., Me ´nade, M., Al-Abdul-Wahid, S., Krett, J., Wong, K., Kozlov, G. et al. (2013). Structure of parkin reveals mechanisms for ubiquitin ligase activation. Science 340 , 14511455. http://dx.doi.org/10.1126/science.1237908 · DOI
- Valente, E. M., Abou-Sleiman, P. M., Caputo, V., Muqit, M. M., Harvey, K., Gispert, S., Ali, Z., Del Turco, D., Bentivoglio, A. R., Healy, D. G. et al. (2004). Hereditary early-onset Parkinson's disease caused by mutations in PINK1. Science 304 , 1158-1160. http://dx.doi.org/10.1126/science.1096284 · DOI · Paper page
- van Wijk, S. J. and Timmers, H. T. (2010). The family of ubiquitin-conjugating enzymes (E2s): deciding between life and death of proteins. FASEB J. 24 , 981993. http://dx.doi.org/10.1096/fj.09-136259 · DOI
- Vives-Bauza, C., Zhou, C., Huang, Y., Cui, M., de Vries, R. L., Kim, J., May, J., Tocilescu, M. A., Liu, W., Ko, H. S. et al. (2010). PINK1-dependent recruitment of Parkin to mitochondria in mitophagy. Proc. Natl. Acad. Sci. USA 107 , 378383. http://dx.doi.org/10.1073/pnas.0911187107 · DOI · Paper page
- Walden, H. and Martinez-Torres, R. J. (2012). Regulation of Parkin E3 ubiquitin ligase activity. Cell. Mol. Life Sci. 69 , 3053-3067. http://dx.doi.org/10.1007/s00018-012-0978-5 · DOI
- Wauer, T. and Komander, D. (2013). Structure of the human Parkin ligase domain in an autoinhibited state. EMBO J. 32 , 2099-2112. http://dx.doi.org/10.1038/emboj.2013.125 · DOI
- Wenzel, D. M., Lissounov, A., Brzovic, P. S. and Klevit, R. E. (2011). UBCH7 reactivity profile reveals parkin and HHARI to be RING/HECT hybrids. Nature 474 , 105-108. http://dx.doi.org/10.1038/nature09966 · DOI
- Wiener, R., DiBello, A. T., Lombardi, P. M., Guzzo, C. M., Zhang, X., Matunis, M. J. and Wolberger, C. (2013). E2 ubiquitin-conjugating enzymes regulate the deubiquitinating activity of OTUB1. Nat. Struct. Mol. Biol. 20 , 1033-1039. http://dx.doi.org/10.1038/nsmb.2655 · DOI
- Williamson, A., Wickliffe, K. E., Mellone, B. G., Song, L., Karpen, G. H. and Rape, M. (2009). Identification of a physiological E2 module for the human anaphase-promoting complex. Proc. Natl. Acad. Sci. USA 106 , 18213-18218. http://dx.doi.org/10.1073/pnas.0907887106 · DOI
- Yamano, K. and Youle, R. J. (2013). PINK1 is degraded through the N-end rule http://dx.doi.org/10.4161/auto.24633 pathway. Autophagy 9 , 1758-1769. http://dx.doi.org/10.4161/auto.24633 · DOI
- Ye, Y. and Rape, M. (2009). Building ubiquitin chains: E2 enzymes at work. Nat. Rev. Mol. Cell Biol. 10 , 755-764. http://dx.doi.org/10.1038/nrm2780 · DOI · Paper page
- Yoshii, S. R., Kishi, C., Ishihara, N. and Mizushima, N. (2011). Parkin mediates proteasome-dependent protein degradation and rupture of the outer mitochondrial membrane. J. Biol. Chem. 286 , 19630-19640. http://dx.doi.org/10.1074/jbc.M110.209338 · DOI · Paper page
- Zheng, X. and Hunter, T. (2013). Parkin mitochondrial translocation is achieved through a novel catalytic activity coupled mechanism. Cell Res. 23 , 886-897. http://dx.doi.org/10.1038/cr.2013.66 · DOI
- Authors
- Fiesel, F. C., Moussaud-Lamodière, E. L., Ando, M., & Springer, W.
- Affiliations
- Mayo Clinic (US)
- Corresponding author
- Springer, Wolfdieter
- Venue
- Journal of Cell Science
- Publisher
- The Company of Biologists
- Published
- 2014-01-01
- Volume
- 127
- Issue
- Pt 16
- Pages
- 3488-504
- ISSN
- 0021-9533 (ISSN-L)
- 1477-9137
- PMC
- PMC4132391
- OpenAlex
- W2129750781
- Cited by
- 72
- References
- 65
- Citations by year
- 2026: 1 · 2024: 3 · 2023: 4 · 2022: 9 · 2021: 5 · 2020: 7 · 2019: 2 · 2018: 4 · 2017: 9 · 2016: 11 · 2015: 13 · 2014: 4
- FWCI
- 8.04
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Journal of Cell Science (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- National Institute of Neurological Disorders and Stroke (R01NS085070)
- Topics
- Health Sciences › Medicine › Neurology › Parkinson's Disease Mechanisms and Treatments
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
- Health Sciences › Medicine › Epidemiology › Autophagy in Disease and Therapy
- Keywords
- Parkin, PINK1, mitophagy, E2 ubiquitin-conjugating enzyme, UBE2L3, UBE2N, Parkinson's disease, mitochondrial quality control, ubiquitination, mitochondrial clustering, mitochondrial uncoupling
- MeSH terms
- Multigene Family, HeLa Cells, Humans, Mitochondria, Parkinson Disease, Ubiquitin-Conjugating Enzymes, Ubiquitin-Protein Ligases, Mitophagy
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