51
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Gonçalves FB, Morais VA. PINK1: A Bridge between Mitochondria and Parkinson's Disease. Life (Basel) 2021; 11:life11050371. [PMID: 33919398 PMCID: PMC8143285 DOI: 10.3390/life11050371] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 12/31/2022] Open
Abstract
Mitochondria are known as highly dynamic organelles essential for energy production. Intriguingly, in the recent years, mitochondria have revealed the ability to maintain cell homeostasis and ultimately regulate cell fate. This regulation is achieved by evoking mitochondrial quality control pathways that are capable of sensing the overall status of the cellular environment. In a first instance, actions to maintain a robust pool of mitochondria take place; however, if unsuccessful, measures that lead to overall cell death occur. One of the central key players of these mitochondrial quality control pathways is PINK1 (PTEN-induce putative kinase), a mitochondrial targeted kinase. PINK1 is known to interact with several substrates to regulate mitochondrial functions, and not only is responsible for triggering mitochondrial clearance via mitophagy, but also participates in maintenance of mitochondrial functions and homeostasis, under healthy conditions. Moreover, PINK1 has been associated with the familial form of Parkinson’s disease (PD). Growing evidence has strongly linked mitochondrial homeostasis to the central nervous system (CNS), a system that is replenished with high energy demanding long-lasting neuronal cells. Moreover, sporadic cases of PD have also revealed mitochondrial impairments. Thus, one could speculate that mitochondrial homeostasis is the common denominator in these two forms of the disease, and PINK1 may play a central role in maintaining mitochondrial homeostasis. In this review, we will discuss the role of PINK1 in the mitochondrial physiology and scrutinize its role in the cascade of PD pathology.
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Abstract
Mitochondria are organelles central to myriad cellular processes. To maintain mitochondrial health, various processes co-operate at both the molecular and organelle level. At the molecular level, mitochondria can sense imbalances in their homeostasis and adapt to these by signaling to the nucleus. This mito-nuclear communication leads to the expression of nuclear stress response genes. Upon external stimuli, mitochondria can also alter their morphology accordingly, by inducing fission or fusion. In an extreme situation, mitochondria are degraded by mitophagy. Adequate function and regulation of these mitochondrial quality control pathways are crucial for cellular homeostasis. As we discuss, alterations in these processes have been linked to several pathologies including neurodegenerative diseases and cancer.
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53
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Morimoto D, Walinda E, Takashima S, Nishizawa M, Iwai K, Shirakawa M, Sugase K. Structural Dynamic Heterogeneity of Polyubiquitin Subunits Affects Phosphorylation Susceptibility. Biochemistry 2021; 60:573-583. [PMID: 33616406 DOI: 10.1021/acs.biochem.0c00619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polyubiquitin is a multifunctional protein tag formed by the covalent conjugation of ubiquitin molecules. Due to the high rigidity of the ubiquitin fold, the ubiquitin moieties in a polyubiquitin chain appear to be structurally equivalent to each other. It is therefore unclear how a specific ubiquitin moiety in a chain may be preferentially recognized by some proteins, such as the kinase PINK1. Here we show that there is structural dynamic heterogeneity in the two ubiquitin moieties of K48-linked diubiquitin by NMR spectroscopic analyses. Our analyses capture subunit-asymmetric structural fluctuations that are not directly related to the closed-to-open transition of the two ubiquitin moieties in diubiquitin. Strikingly, these newly identified heterogeneous structural fluctuations may be linked to an increase in susceptibility to phosphorylation by PINK1. Coupled with the fact that there are almost no differences in static tertiary structure among ubiquitin moieties in a chain, the observed subunit-specific structural fluctuations may be an important factor that distinguishes individual ubiquitin moieties in a chain, thereby aiding both efficiency and specificity in post-translational modifications.
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Affiliation(s)
- Daichi Morimoto
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Shingo Takashima
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Mayu Nishizawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Kazuhiro Iwai
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Masahiro Shirakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Kenji Sugase
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
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54
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Huang C, Bian J, Cao Q, Chen XM, Pollock CA. The Mitochondrial Kinase PINK1 in Diabetic Kidney Disease. Int J Mol Sci 2021; 22:ijms22041525. [PMID: 33546409 PMCID: PMC7913536 DOI: 10.3390/ijms22041525] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 02/07/2023] Open
Abstract
Mitochondria are critical organelles that play a key role in cellular metabolism, survival, and homeostasis. Mitochondrial dysfunction has been implicated in the pathogenesis of diabetic kidney disease. The function of mitochondria is critically regulated by several mitochondrial protein kinases, including the phosphatase and tensin homolog (PTEN)-induced kinase 1 (PINK1). The focus of PINK1 research has been centered on neuronal diseases. Recent studies have revealed a close link between PINK1 and many other diseases including kidney diseases. This review will provide a concise summary of PINK1 and its regulation of mitochondrial function in health and disease. The physiological role of PINK1 in the major cells involved in diabetic kidney disease including proximal tubular cells and podocytes will also be summarized. Collectively, these studies suggested that targeting PINK1 may offer a promising alternative for the treatment of diabetic kidney disease.
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Affiliation(s)
- Chunling Huang
- Correspondence: (C.H.); (C.A.P.); Tel.: +61-2-9926-4784 (C.H.); +61-2-9926-4652 (C.A.P.)
| | | | | | | | - Carol A. Pollock
- Correspondence: (C.H.); (C.A.P.); Tel.: +61-2-9926-4784 (C.H.); +61-2-9926-4652 (C.A.P.)
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55
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Onishi M, Yamano K, Sato M, Matsuda N, Okamoto K. Molecular mechanisms and physiological functions of mitophagy. EMBO J 2021; 40:e104705. [PMID: 33438778 PMCID: PMC7849173 DOI: 10.15252/embj.2020104705] [Citation(s) in RCA: 570] [Impact Index Per Article: 190.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 08/03/2020] [Accepted: 10/02/2020] [Indexed: 12/12/2022] Open
Abstract
Degradation of mitochondria via a selective form of autophagy, named mitophagy, is a fundamental mechanism conserved from yeast to humans that regulates mitochondrial quality and quantity control. Mitophagy is promoted via specific mitochondrial outer membrane receptors, or ubiquitin molecules conjugated to proteins on the mitochondrial surface leading to the formation of autophagosomes surrounding mitochondria. Mitophagy-mediated elimination of mitochondria plays an important role in many processes including early embryonic development, cell differentiation, inflammation, and apoptosis. Recent advances in analyzing mitophagy in vivo also reveal high rates of steady-state mitochondrial turnover in diverse cell types, highlighting the intracellular housekeeping role of mitophagy. Defects in mitophagy are associated with various pathological conditions such as neurodegeneration, heart failure, cancer, and aging, further underscoring the biological relevance. Here, we review our current molecular understanding of mitophagy, and its physiological implications, and discuss how multiple mitophagy pathways coordinately modulate mitochondrial fitness and populations.
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Affiliation(s)
- Mashun Onishi
- Laboratory of Mitochondrial DynamicsGraduate School of Frontier BiosciencesOsaka UniversitySuitaJapan
| | - Koji Yamano
- The Ubiquitin ProjectTokyo Metropolitan Institute of Medical ScienceTokyoJapan
| | - Miyuki Sato
- Laboratory of Molecular Membrane BiologyInstitute for Molecular and Cellular RegulationGunma UniversityMaebashiJapan
| | - Noriyuki Matsuda
- The Ubiquitin ProjectTokyo Metropolitan Institute of Medical ScienceTokyoJapan
| | - Koji Okamoto
- Laboratory of Mitochondrial DynamicsGraduate School of Frontier BiosciencesOsaka UniversitySuitaJapan
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56
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Clark EH, Vázquez de la Torre A, Hoshikawa T, Briston T. Targeting mitophagy in Parkinson's disease. J Biol Chem 2021; 296:100209. [PMID: 33372898 PMCID: PMC7948953 DOI: 10.1074/jbc.rev120.014294] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 12/22/2022] Open
Abstract
The genetics and pathophysiology of Parkinson's disease (PD) strongly implicate mitochondria in disease aetiology. Elegant studies over the last two decades have elucidated complex molecular signaling governing the identification and removal of dysfunctional mitochondria from the cell, a process of mitochondrial quality control known as mitophagy. Mitochondrial deficits and specifically reduced mitophagy are evident in both sporadic and familial PD. Mendelian genetics attributes loss-of-function mutations in key mitophagy regulators PINK1 and Parkin to early-onset PD. Pharmacologically enhancing mitophagy and accelerating the removal of damaged mitochondria are of interest for developing a disease-modifying PD therapeutic. However, despite significant understanding of both PINK1-Parkin-dependent and -independent mitochondrial quality control pathways, the therapeutic potential of targeting mitophagy remains to be fully explored. Here, we provide a summary of the genetic evidence supporting the role for mitophagy failure as a pathogenic mechanism in PD. We assess the tractability of mitophagy pathways and prospects for drug discovery and consider intervention points for mitophagy enhancement. We explore the numerous hit molecules beginning to emerge from high-content/high-throughput screening as well as the biochemical and phenotypic assays that enabled these screens. The chemical and biological properties of these reference compounds suggest many could be used to interrogate and perturb mitochondrial biology to validate promising drug targets. Finally, we address key considerations and challenges in achieving preclinical proof-of-concept, including in vivo mitophagy reporter methodologies and disease models, as well as patient stratification and biomarker development for mitochondrial forms of the disease.
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Affiliation(s)
- Emily H Clark
- Hatfield Research Laboratories, Neurology Innovation Centre, Eisai Ltd, Hatfield, United Kingdom
| | | | - Tamaki Hoshikawa
- Hatfield Research Laboratories, Neurology Innovation Centre, Eisai Ltd, Hatfield, United Kingdom
| | - Thomas Briston
- Hatfield Research Laboratories, Neurology Innovation Centre, Eisai Ltd, Hatfield, United Kingdom.
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57
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Mitochondrial Dysfunction and Mitophagy in Parkinson's Disease: From Mechanism to Therapy. Trends Biochem Sci 2020; 46:329-343. [PMID: 33323315 DOI: 10.1016/j.tibs.2020.11.007] [Citation(s) in RCA: 228] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 12/12/2022]
Abstract
Mitochondrial dysfunction has been associated with neurodegeneration in Parkinson's disease (PD) for over 30 years. Despite this, the role of mitochondrial dysfunction as an initiator, propagator, or bystander remains undetermined. The discovery of the role of the PD familial genes PTEN-induced putative kinase 1 (PINK1) and parkin (PRKN) in mediating mitochondrial degradation (mitophagy) reaffirmed the importance of this process in PD aetiology. Recently, progress has been made in understanding the upstream and downstream regulators of canonical PINK1/parkin-mediated mitophagy, alongside noncanonical PINK1/parkin mitophagy, in response to mitochondrial damage. Progress has also been made in understanding the role of PD-associated genes, such as SNCA, LRRK2, and CHCHD2, in mitochondrial dysfunction and their overlap with sporadic PD (sPD), opening opportunities for therapeutically targeting mitochondria in PD.
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58
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Srivastava SP, Kanasaki K, Goodwin JE. Loss of Mitochondrial Control Impacts Renal Health. Front Pharmacol 2020; 11:543973. [PMID: 33362536 PMCID: PMC7756079 DOI: 10.3389/fphar.2020.543973] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 11/19/2020] [Indexed: 12/13/2022] Open
Abstract
Disruption of mitochondrial biosynthesis or dynamics, or loss of control over mitochondrial regulation leads to a significant alteration in fuel preference and metabolic shifts that potentially affect the health of kidney cells. Mitochondria regulate metabolic networks which affect multiple cellular processes. Indeed, mitochondria have established themselves as therapeutic targets in several diseases. The importance of mitochondria in regulating the pathogenesis of several diseases has been recognized, however, there is limited understanding of mitochondrial biology in the kidney. This review provides an overview of mitochondrial dysfunction in kidney diseases. We describe the importance of mitochondria and mitochondrial sirtuins in the regulation of renal metabolic shifts in diverse cells types, and review this loss of control leads to increased cell-to-cell transdifferentiation processes and myofibroblast-metabolic shifts, which affect the pathophysiology of several kidney diseases. In addition, we examine mitochondrial-targeted therapeutic agents that offer potential leads in combating kidney diseases.
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Affiliation(s)
- Swayam Prakash Srivastava
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, United States
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, United States
| | - Keizo Kanasaki
- Internal Medicine 1, Shimane University Faculty of Medicine, Izumo, Japan
| | - Julie E. Goodwin
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, United States
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, United States
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59
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Lin J, Chen K, Chen W, Yao Y, Ni S, Ye M, Zhuang G, Hu M, Gao J, Gao C, Liu Y, Yang M, Zhang Z, Zhang X, Huang J, Chen F, Sun L, Zhang X, Yu S, Chen Y, Jiang Y, Wang S, Yang X, Liu K, Zhou HM, Ji Z, Deng H, Haque ME, Li J, Mi LZ, Li Y, Yang Y. Paradoxical Mitophagy Regulation by PINK1 and TUFm. Mol Cell 2020; 80:607-620.e12. [PMID: 33113344 DOI: 10.1016/j.molcel.2020.10.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/25/2020] [Accepted: 10/06/2020] [Indexed: 01/19/2023]
Abstract
Aberrant mitophagy has been implicated in a broad spectrum of disorders. PINK1, Parkin, and ubiquitin have pivotal roles in priming mitophagy. However, the entire regulatory landscape and the precise control mechanisms of mitophagy remain to be elucidated. Here, we uncover fundamental mitophagy regulation involving PINK1 and a non-canonical role of the mitochondrial Tu translation elongation factor (TUFm). The mitochondrion-cytosol dual-localized TUFm interacts with PINK1 biochemically and genetically, which is an evolutionarily conserved Parkin-independent route toward mitophagy. A PINK1-dependent TUFm phosphoswitch at Ser222 determines conversion from activating to suppressing mitophagy. PINK1 modulates differential translocation of TUFm because p-S222-TUFm is restricted predominantly to the cytosol, where it inhibits mitophagy by impeding Atg5-Atg12 formation. The self-antagonizing feature of PINK1/TUFm is critical for the robustness of mitophagy regulation, achieved by the unique kinetic parameters of p-S222-TUFm, p-S65-ubiquitin, and their common kinase PINK1. Our findings provide new mechanistic insights into mitophagy and mitophagy-associated disorders.
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Affiliation(s)
- Jingjing Lin
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Kai Chen
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Wenfeng Chen
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Yizhou Yao
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Shiwei Ni
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Meina Ye
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Guifeng Zhuang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Minhuang Hu
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Jun Gao
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Caixi Gao
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Yan Liu
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Mingjuan Yang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Zhenkun Zhang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Xiaohui Zhang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Jiexiang Huang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Fei Chen
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Ling Sun
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Xi Zhang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Suhong Yu
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Yuling Chen
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yating Jiang
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Shujuan Wang
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Xiaozhen Yang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Ke Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Hai-Meng Zhou
- Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, Zhejiang Jiaxing 314006, China
| | - Zhiliang Ji
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - M Emdadul Haque
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, PO Box 17666, United Arab Emirates
| | - Junxiang Li
- AgeCode R&D Center, Yangtze Delta Region Institute of Tsinghua University, Zhejiang Jiaxing 314006, China
| | - Li-Zhi Mi
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Yuexi Li
- Huadong Research Institute for Medicine and Biotechniques, 293 East Zhongshan Road, Nanjing 210002, China.
| | - Yufeng Yang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China.
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60
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Sekine S. PINK1 import regulation at a crossroad of mitochondrial fate: the molecular mechanisms of PINK1 import. J Biochem 2020; 167:217-224. [PMID: 31504668 DOI: 10.1093/jb/mvz069] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 08/17/2019] [Indexed: 12/17/2022] Open
Abstract
PTEN-induced kinase 1 (PINK1) is a mitochondrial kinase whose activity is tightly regulated by the mitochondrial health status. In response to mitochondrial damage, activated PINK1 can promote mitophagy, an autophagic elimination of damaged mitochondria, by cooperating with Parkin ubiquitin ligase. Loss-of-function of PINK1/Parkin-mediated mitophagy results in the accumulation of dysfunctional mitochondria, which could be one aetiology of Parkinson's disease (PD). Within step-by-step signalling cascades of PINK1/Parkin-mediated mitophagy, mitochondrial damage-dependent PINK1 kinase activation is a critical step to trigger the mitophagy signal. Recent investigation of this process reveals that this stress-dependent PINK1 kinase activation is achieved by its regulated import into different mitochondrial compartments. Thus, PINK1 import regulation stands at an important crossroad to determine the mitochondrial fate-'keep' or 'remove'? In this review, we will summarize how the PINK1 import is regulated in a mitochondrial health status-dependent manner and how this process could be pharmacologically modulated to activate the PINK1/Parkin pathway.
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Affiliation(s)
- Shiori Sekine
- Aging Institute, Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
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61
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Bento-Pereira C, Dinkova-Kostova AT. Activation of transcription factor Nrf2 to counteract mitochondrial dysfunction in Parkinson's disease. Med Res Rev 2020; 41:785-802. [PMID: 32681666 DOI: 10.1002/med.21714] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/29/2020] [Accepted: 07/06/2020] [Indexed: 12/20/2022]
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disorder, for which no disease-modifying therapies are available to date. Although understanding of the precise aetiology of PD is incomplete, it is clear that age, genetic predisposition and environmental stressors increase the risk. At the cellular level, oxidative stress, chronic neuroinflammation, mitochondrial dysfunction and aberrant protein aggregation have been implicated as contributing factors. These detrimental processes are counteracted by elaborate networks of cellular defence mechanisms, one of which is orchestrated by transcription factor nuclear factor-erythroid 2 p45-related factor 2 (Nrf2; gene name NFE2L2). A wealth of preclinical evidence suggests that Nrf2 activation is beneficial in cellular and animal models of PD. In this review, we summarise the current understanding of mitochondrial dysfunction in PD, the role of Nrf2 in mitochondrial function and explore the potential of Nrf2 as a therapeutic target for mitochondrial dysfunction in PD.
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Affiliation(s)
- Claudia Bento-Pereira
- Division of Cellular Medicine, School of Medicine, Jacqui Wood Cancer Centre, University of Dundee, Dundee, Scotland, UK
| | - Albena T Dinkova-Kostova
- Division of Cellular Medicine, School of Medicine, Jacqui Wood Cancer Centre, University of Dundee, Dundee, Scotland, UK.,Departments of Medicine and Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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62
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Wang Y, Liu HH, Cao YT, Zhang LL, Huang F, Yi C. The Role of Mitochondrial Dynamics and Mitophagy in Carcinogenesis, Metastasis and Therapy. Front Cell Dev Biol 2020; 8:413. [PMID: 32587855 PMCID: PMC7297908 DOI: 10.3389/fcell.2020.00413] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 05/04/2020] [Indexed: 12/24/2022] Open
Abstract
Mitochondria are key cellular organelles and play vital roles in energy metabolism, apoptosis regulation and cellular homeostasis. Mitochondrial dynamics refers to the varying balance between mitochondrial fission and mitochondrial fusion that plays an important part in maintaining mitochondrial homeostasis and quality. Mitochondrial malfunction is involved in aging, metabolic disease, neurodegenerative disorders, and cancers. Mitophagy, a selective autophagy of mitochondria, can efficiently degrade, remove and recycle the malfunctioning or damaged mitochondria, and is crucial for quality control. In past decades, numerous studies have identified a series of factors that regulate mitophagy and are also involved in carcinogenesis, cancer cell migration and death. Therefore, it has become critically important to analyze signal pathways that regulate mitophagy to identify potential therapeutic targets. Here, we review recent progresses in mitochondrial dynamics, the mechanisms of mitophagy regulation, and the implications for understanding carcinogenesis, metastasis, treatment, and drug resistance.
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Affiliation(s)
- Yigang Wang
- Xinyuan Institute of Medicine and Biotechnology, School of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Hui-Hui Liu
- Xinyuan Institute of Medicine and Biotechnology, School of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yu-Ting Cao
- Xinyuan Institute of Medicine and Biotechnology, School of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Lei-Lei Zhang
- Xinyuan Institute of Medicine and Biotechnology, School of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Fang Huang
- Department of Pathology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Cong Yi
- Department of Biochemistry, Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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63
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Abstract
In 2004, PINK1 was established as a gene linked to early onset of autosomal recessive juvenile Parkinsonism. Since then, tremendous efforts allowed involving the gene product in diverse events but with a strong focus on its partnership with the protein Parkin for the degradation of damaged mitochondria through mitophagy. Yet, it is now clear that the importance of PINK1 encompasses a wider spectrum of intracellular processes. In this minireview, we highlight some of the PINK1 interplays and recent advances, including its growing involvement in immunity and also its emerging place in this era of mitochondria-organelles contact sites.
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Affiliation(s)
- Edgar Djaha Yoboue
- IRCCS Mondino Foundation, Pavia, Italy; Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Enza Maria Valente
- IRCCS Mondino Foundation, Pavia, Italy; Department of Molecular Medicine, University of Pavia, Pavia, Italy.
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64
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Deol KK, Eyles SJ, Strieter ER. Quantitative Middle-Down MS Analysis of Parkin-Mediated Ubiquitin Chain Assembly. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1132-1139. [PMID: 32297515 PMCID: PMC7333183 DOI: 10.1021/jasms.0c00058] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Misregulation of the E3 ubiquitin ligase Parkin and the kinase PINK1 underlie both inherited and idiopathic Parkinson's disease-associated neurodegeneration. Parkin and PINK1 work together to catalyze the assembly of ubiquitin chains on substrates located on the outer mitochondrial membrane to facilitate autophagic removal of damaged mitochondria through a process termed mitophagy. Quantitative measurements of Parkin-mediated chain assembly, both in vitro and on mitochondria, have revealed that chains are composed of Lys6, Lys11, Lys48, and Lys63 linkages. The combinatorial nature of these chains is further expanded by the ability of PINK1 to phosphorylate individual subunits. The precise architecture of chains produced by the coordinated action of PINK1 and Parkin, however, are unknown. Here, we demonstrate that quantitative middle-down mass spectrometry using uniformly 15N-labeled ubiquitin variants as internal standards informs on the extent of chain branching. We find that Parkin is a prolific branching enzyme in vitro. Quantitative middle-down mass spectrometry also reveals that phospho-Ser65-ubiquitin (pSer65-Ub)-a key activator of Parkin-is not incorporated into chains to a significant extent. Our results suggest that Parkin-mediated chain branching is "on-pathway", and branch points are the principal targets of the deubiquitinase USP30.
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Affiliation(s)
- Kirandeep K Deol
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - Stephen J Eyles
- Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - Eric R Strieter
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
- Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
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65
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Matsuda N, Yamano K. Two sides of a coin: Physiological significance and molecular mechanisms for damage-induced mitochondrial localization of PINK1 and Parkin. Neurosci Res 2020; 159:16-24. [PMID: 32201358 DOI: 10.1016/j.neures.2020.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/06/2020] [Accepted: 03/10/2020] [Indexed: 12/26/2022]
Abstract
In 1998, PARKIN was reported as a causal gene for hereditary recessive Parkinsonism by Kitada, Mizuno, Hattori, and Shimizu et al. Later in 2004, PINK1 was also reported as a causal gene for hereditary recessive Parkinsonism by Valente, Auburger, and Wood et al. Although many unsolved mysteries still remain, our knowledge of PINK1 and Parkin function has increased dramatically since then. Despite a number of milestone studies that advanced the PINK1 and Parkin research field, a critical turning point was undoubtedly the determination that their genuine subcellular localization was on depolarized mitochondria. In this review, we outline the key studies that have contributed to our current model for mitochondrial localization of PINK1 and Parkin. Interestingly, like two sides of a coin, our attempts to elucidate the mechanisms underlying the localization of PINK1 and Parkin were inextricably tied to the identification of the PINK1 substrate and molecular dissection of the Parkin activation mechanism.
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Affiliation(s)
- Noriyuki Matsuda
- The Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Room N-202, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan.
| | - Koji Yamano
- The Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Room N-202, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
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66
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N-degron-mediated degradation and regulation of mitochondrial PINK1 kinase. Curr Genet 2020; 66:693-701. [PMID: 32157382 DOI: 10.1007/s00294-020-01062-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 12/12/2022]
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative condition characterized by a gradual loss of a specific group of dopaminergic neurons in the substantia nigra. Importantly, current treatments only address the symptoms of PD, yet not the underlying molecular causes. Concomitantly, the function of genes that cause inherited forms of PD point to mitochondrial dysfunction as a major contributor in the etiology of PD. An inherent challenge that mitochondria face is the continuous exposure to diverse stresses including high levels of reactive oxygen species and protein misfolding, which increase their likelihood of dysregulation. In response, eukaryotic cells have evolved sophisticated quality control mechanisms to identify, repair and/or eliminate abnormal dysfunctional mitochondria. One such mechanism is mitophagy, a process which involves PTEN-induced putative kinase 1 (PINK1), a mitochondrial Ser/Thr kinase and Parkin, an E3 ubiquitin ligase, each encoded by genes responsible for early-onset autosomal recessive familial PD. Over 100 loss-of-function mutations in the PTEN-induced putative kinase 1 (PINK1) gene have been reported to cause autosomal recessive early-onset PD. PINK1 acts upstream of Parkin and is essential for the mitochondrial localization and activation of Parkin. Upon mitochondrial damage, PINK1 builds up on the outer mitochondrial membrane (OMM) and mediates the activation of Parkin. Activated Parkin then ubiquitinates numerous OMM proteins, eliciting mitochondrial autophagy (mitophagy). As a result, damaged mitochondrial components can be selectively eliminated. Thus, PINK1 acts a sensor of damage via fine-tuning of its levels on mitochondria, where it activates Parkin to orchestrate the clearance of unhealthy mitochondria. Previous work has unveiled that the Arg-N-end rule degradation pathway (Arg-N-degron pathway) mediates the degradation of PINK1, and thus fine-tune PINK1-dependent mitochondrial quality control pathway. Herein, we briefly discuss the interconnection between N-end rule degradation pathways and mitophagy in the context of N-degron mediated degradation of mitochondrial kinase PINK1 and highlight some of the future prospects.
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67
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Uchański T, Pardon E, Steyaert J. Nanobodies to study protein conformational states. Curr Opin Struct Biol 2020; 60:117-123. [DOI: 10.1016/j.sbi.2020.01.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 01/07/2023]
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68
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Abstract
Parkin is a protein involved in familial Parkinson's disease (PD), a neurodegenerative disorder with motor symptoms linked to the loss of dopaminergic neurons. More than 20 years have passed since the discovery of Parkin; since that time, another familial PD protein has been identified: PINK1, which acts upstream of Parkin. PINK1 is a protein kinase that monitors mitochondrial integrity by sensing disability status, whereas Parkin is a ubiquitin-protein ligase that attaches ubiquitin chains to malfunctioning mitochondria as a degradation signal. Both enzymes cooperatively facilitate autophagic clearance of damaged mitochondria (also known as mitophagy). Collectively, the PINK1-Parkin axis functions as the core machinery for mitophagy in neurons, and deficiency in this pathway causes early-onset PD. In this review, I will discuss how the PINK1-Parkin study has progressed, with the personal episodes I have experienced.
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69
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Tsai YCI, Johansson H, Dixon D, Martin S, Chung CW, Clarkson J, House D, Rittinger K. Single-Domain Antibodies as Crystallization Chaperones to Enable Structure-Based Inhibitor Development for RBR E3 Ubiquitin Ligases. Cell Chem Biol 2020; 27:83-93.e9. [PMID: 31813847 PMCID: PMC6963773 DOI: 10.1016/j.chembiol.2019.11.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/15/2019] [Accepted: 11/14/2019] [Indexed: 01/14/2023]
Abstract
Protein ubiquitination plays a key role in the regulation of cellular processes, and misregulation of the ubiquitin system is linked to many diseases. So far, development of tool compounds that target enzymes of the ubiquitin system has been slow and only a few specific inhibitors are available. Here, we report the selection of single-domain antibodies (single-dAbs) based on a human scaffold that recognize the catalytic domain of HOIP, a subunit of the multi-component E3 LUBAC and member of the RBR family of E3 ligases. Some of these dAbs affect ligase activity and provide mechanistic insight into the ubiquitin transfer mechanism of different E2-conjugating enzymes. Furthermore, we show that the co-crystal structure of a HOIP RBR/dAb complex serves as a robust platform for soaking of ligands that target the active site cysteine of HOIP, thereby providing easy access to structure-based ligand design for this important class of E3 ligases.
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Affiliation(s)
- Yi-Chun Isabella Tsai
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Henrik Johansson
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Crick-GSK Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - David Dixon
- R&D Medicinal Science & Technology, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Stephen Martin
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Chun-Wa Chung
- Crick-GSK Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK; R&D Medicinal Science & Technology, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Jane Clarkson
- R&D Medicinal Science & Technology, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - David House
- Crick-GSK Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Katrin Rittinger
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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70
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Wang L, Qi H, Tang Y, Shen HM. Post-translational Modifications of Key Machinery in the Control of Mitophagy. Trends Biochem Sci 2020; 45:58-75. [DOI: 10.1016/j.tibs.2019.08.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/05/2019] [Accepted: 08/16/2019] [Indexed: 12/12/2022]
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71
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Bayne AN, Trempe JF. Mechanisms of PINK1, ubiquitin and Parkin interactions in mitochondrial quality control and beyond. Cell Mol Life Sci 2019; 76:4589-4611. [PMID: 31254044 PMCID: PMC11105328 DOI: 10.1007/s00018-019-03203-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/13/2019] [Accepted: 06/19/2019] [Indexed: 12/20/2022]
Abstract
Parkinson's disease (PD) is a degenerative movement disorder resulting from the loss of specific neuron types in the midbrain. Early environmental and pathophysiological studies implicated mitochondrial damage and protein aggregation as the main causes of PD. These findings are now vindicated by the characterization of more than 20 genes implicated in rare familial forms of the disease. In particular, two proteins encoded by the Parkin and PINK1 genes, whose mutations cause early-onset autosomal recessive PD, function together in a mitochondrial quality control pathway. In this review, we will describe recent development in our understanding of their mechanisms of action, structure, and function. We explain how PINK1 acts as a mitochondrial damage sensor via the regulated proteolysis of its N-terminus and the phosphorylation of ubiquitin tethered to outer mitochondrial membrane proteins. In turn, phospho-ubiquitin recruits and activates Parkin via conformational changes that increase its ubiquitin ligase activity. We then describe how the formation of polyubiquitin chains on mitochondria triggers the recruitment of the autophagy machinery or the formation of mitochondria-derived vesicles. Finally, we discuss the evidence for the involvement of these mechanisms in physiological processes such as immunity and inflammation, as well as the links to other PD genes.
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Affiliation(s)
- Andrew N Bayne
- Department of Pharmacology and Therapeutics and Centre for Structural Biology, McGill University, 3655 Prom Sir William Osler, Montreal, QC, H3G 1Y6, Canada
| | - Jean-François Trempe
- Department of Pharmacology and Therapeutics and Centre for Structural Biology, McGill University, 3655 Prom Sir William Osler, Montreal, QC, H3G 1Y6, Canada.
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72
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Patel O, Roy MJ, Murphy JM, Lucet IS. The PEAK family of pseudokinases, their role in cell signalling and cancer. FEBS J 2019; 287:4183-4197. [PMID: 31599110 DOI: 10.1111/febs.15087] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/11/2019] [Accepted: 10/06/2019] [Indexed: 12/20/2022]
Abstract
The study of pseudokinases has uncovered that catalysis-independent functions play a critical role in cell signalling regulation. However, how pseudokinases dynamically assemble and regulate oncogenic signalling pathways remains, in most cases, unclear due to a limited knowledge of the structural determinants that are critical for their functions. Here, we review the recent progress made to unravel the role of the PEAK family of pseudokinases, which comprises SgK269, SgK223 and the recently identified PEAK3, in assembling specific oncogenic signalling pathways that contribute to the progression of several aggressive cancers. We focus on recent structural advances revealing that SgK269 and SgK223 can homo- and heteroassociate via a unique dimerisation domain, comprising conserved regulatory helices directly surrounding the pseudokinase domain, which is also conserved in PEAK3. We also highlight a potential oligomerisation mechanism driven by the pseudokinase domain. While it is likely that homo- or heterodimerisation and oligomerisation mechanisms contribute to the assembly of complex signalling hubs and provide a means to spatially and temporally modulate and diversify signalling outputs, the exact role that these oncogenic scaffolds play in regulating cell migration, invasion and morphology remains unclear. Here, we attempt to link their structural characteristics to their cellular functions by providing a thorough analysis of the signalling transduction pathways they are known to modulate.
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Affiliation(s)
- Onisha Patel
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Michael J Roy
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Isabelle S Lucet
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Australia
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73
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Heo JM, Harper NJ, Paulo JA, Li M, Xu Q, Coughlin M, Elledge SJ, Harper JW. Integrated proteogenetic analysis reveals the landscape of a mitochondrial-autophagosome synapse during PARK2-dependent mitophagy. SCIENCE ADVANCES 2019; 5:eaay4624. [PMID: 31723608 PMCID: PMC6834391 DOI: 10.1126/sciadv.aay4624] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/16/2019] [Indexed: 05/08/2023]
Abstract
The PINK1 protein kinase activates the PARK2 ubiquitin ligase to promote mitochondrial ubiquitylation and recruitment of ubiquitin-binding mitophagy receptors typified by OPTN and TAX1BP1. Here, we combine proximity biotinylation of OPTN and TAX1BP1 with CRISPR-Cas9-based screens for mitophagic flux to develop a spatial proteogenetic map of PARK2-dependent mitophagy. Proximity labeling of OPTN allowed visualization of a "mitochondrial-autophagosome synapse" upon mitochondrial depolarization. Proximity proteomics of OPTN and TAX1BP1 revealed numerous proteins at the synapse, including both PARK2 substrates and autophagy components. Parallel mitophagic flux screens identified proteins with roles in autophagy, vesicle formation and fusion, as well as PARK2 targets, many of which were also identified via proximity proteomics. One protein identified in both approaches, HK2, promotes assembly of a high-molecular weight complex of PINK1 and phosphorylation of ubiquitin in response to mitochondrial damage. This work provides a resource for understanding the spatial and molecular landscape of PARK2-dependent mitophagy.
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Affiliation(s)
- Jin-Mi Heo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Nathan J. Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Mamie Li
- Department of Genetics, Harvard Medical School, Howard Hughes Medical Institute; Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Qikai Xu
- Department of Genetics, Harvard Medical School, Howard Hughes Medical Institute; Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Margaret Coughlin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Stephen J. Elledge
- Department of Genetics, Harvard Medical School, Howard Hughes Medical Institute; Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - J. Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Corresponding author.
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74
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Tang C, Zhang WP. How Phosphorylation by PINK1 Remodels the Ubiquitin System: A Perspective from Structure and Dynamics. Biochemistry 2019; 59:26-33. [PMID: 31503455 DOI: 10.1021/acs.biochem.9b00715] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Ubiquitin is an important signaling protein in cells. It functions by covalent attachment to substrate proteins and by noncovalent interactions with target proteins. Ubiquitins are also concatenated, and the resulting polyubiquitins recognize target proteins multivalently with enhanced specificity. The function of ubiquitin is enabled by the conformational dynamics of ubiquitin and polyubiquitins, which spans over 12 orders of magnitude in a time scale. Recently, it was found that ubiquitin can be phosphorylated by PINK1 at residues S65 and T66. Only sparsely populated for the unmodified ubiquitin, a C-terminally retracted conformation is stabilized for phosphorylated ubiquitin and is further enriched at an increasing pH. The modulation of tertiary structure further impacts the quaternary arrangements of ubiquitin subunits in polyubiquitins. Additionally, ubiquitin phosphorylation inhibits the activities of many enzymes responsible for attaching and removing polyubiquitins, thus remodeling the composition and length of polyubiquitins. The phosphorylation-remolded polyubiquitins can then recognize different target proteins. As PINK1 and ubiquitin phosphorylation levels are up-regulated under certain pathophysiological conditions, the remodeled ubiquitin system may be involved in the divergence of cell fate.
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Affiliation(s)
- Chun Tang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan , Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences , Wuhan , Hubei 430071 , China
| | - Wei-Ping Zhang
- Department of Pharmacology, Key Laboratory of Medical Neurobiology of Ministry of Health of China , Zhejiang University School of Medicine , Hangzhou , Zhejiang 310058 , China
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75
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Insights into ubiquitin chain architecture using Ub-clipping. Nature 2019; 572:533-537. [PMID: 31413367 DOI: 10.1038/s41586-019-1482-y] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 07/17/2019] [Indexed: 01/17/2023]
Abstract
Protein ubiquitination is a multi-functional post-translational modification that affects all cellular processes. Its versatility arises from architecturally complex polyubiquitin chains, in which individual ubiquitin moieties may be ubiquitinated on one or multiple residues, and/or modified by phosphorylation and acetylation1-3. Advances in mass spectrometry have enabled the mapping of individual ubiquitin modifications that generate the ubiquitin code; however, the architecture of polyubiquitin signals has remained largely inaccessible. Here we introduce Ub-clipping as a methodology by which to understand polyubiquitin signals and architectures. Ub-clipping uses an engineered viral protease, Lbpro∗, to incompletely remove ubiquitin from substrates and leave the signature C-terminal GlyGly dipeptide attached to the modified residue; this simplifies the direct assessment of protein ubiquitination on substrates and within polyubiquitin. Monoubiquitin generated by Lbpro∗ retains GlyGly-modified residues, enabling the quantification of multiply GlyGly-modified branch-point ubiquitin. Notably, we find that a large amount (10-20%) of ubiquitin in polymers seems to exist as branched chains. Moreover, Ub-clipping enables the assessment of co-existing ubiquitin modifications. The analysis of depolarized mitochondria reveals that PINK1/parkin-mediated mitophagy predominantly exploits mono- and short-chain polyubiquitin, in which phosphorylated ubiquitin moieties are not further modified. Ub-clipping can therefore provide insight into the combinatorial complexity and architecture of the ubiquitin code.
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76
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Corti O. Neuronal Mitophagy: Lessons from a Pathway Linked to Parkinson's Disease. Neurotox Res 2019; 36:292-305. [PMID: 31102068 DOI: 10.1007/s12640-019-00060-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 04/17/2019] [Accepted: 05/06/2019] [Indexed: 02/06/2023]
Abstract
Neurons are specialized cells with complex and extended architecture and high energy requirements. Energy in the form of adenosine triphosphate, produced essentially by mitochondrial respiration, is necessary to preserve neuronal morphology, maintain resting potential, fire action potentials, and ensure neurotransmission. Pools of functional mitochondria are required in all neuronal compartments, including cell body and dendrites, nodes of Ranvier, growth cones, axons, and synapses. The mechanisms by which old or damaged mitochondria are removed and replaced in neurons remain to be fully understood. Mitophagy has gained considerable interest since the discovery of familial forms of Parkinson's disease caused by dysfunction of PINK1 and Parkin, two multifunctional proteins cooperating in the regulation of this process. Over the past 10 years, the molecular mechanisms by which PINK1 and Parkin jointly promote the degradation of defective mitochondria by autophagy have been dissected. However, our understanding of the relevance of mitophagy to mitochondrial homeostasis in neurons remains poor. Insight has been recently gained thanks to the development of fluorescent reporter systems for tracking mitochondria in the acidic compartment of the lysosome. Using these tools, mitophagy events have been visualized in primary neurons in culture and in vivo, under basal conditions and in response to toxic insults. Despite these advances, whether PINK1 and Parkin play a major role in promoting neuronal mitophagy under physiological conditions in adult animals and during aging remains a matter of debate. Future studies will have to clarify in how far dysfunction of neuronal mitophagy is central to the pathophysiology of Parkinson's disease.
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Affiliation(s)
- Olga Corti
- Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France.
- Inserm, U1127, F-75013, Paris, France.
- CNRS, UMR 7225, F-75013, Paris, France.
- Sorbonne Universités, F-75013, Paris, France.
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77
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Lucero M, Suarez AE, Chambers JW. Phosphoregulation on mitochondria: Integration of cell and organelle responses. CNS Neurosci Ther 2019; 25:837-858. [PMID: 31025544 PMCID: PMC6566066 DOI: 10.1111/cns.13141] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 03/29/2019] [Accepted: 04/04/2019] [Indexed: 12/20/2022] Open
Abstract
Mitochondria are highly integrated organelles that are crucial to cell adaptation and mitigating adverse physiology. Recent studies demonstrate that fundamental signal transduction pathways incorporate mitochondrial substrates into their biological programs. Reversible phosphorylation is emerging as a useful mechanism to modulate mitochondrial function in accordance with cellular changes. Critical serine/threonine protein kinases, such as the c-Jun N-terminal kinase (JNK), protein kinase A (PKA), PTEN-induced kinase-1 (PINK1), and AMP-dependent protein kinase (AMPK), readily translocate to the outer mitochondrial membrane (OMM), the interface of mitochondria-cell communication. OMM protein kinases phosphorylate diverse mitochondrial substrates that have discrete effects on organelle dynamics, protein import, respiratory complex activity, antioxidant capacity, and apoptosis. OMM phosphorylation events can be tempered through the actions of local protein phosphatases, such as mitogen-activated protein kinase phosphatase-1 (MKP-1) and protein phosphatase 2A (PP2A), to regulate the extent and duration of signaling. The central mediators of OMM signal transduction are the scaffold proteins because the relative abundance of these accessory proteins determines the magnitude and duration of a signaling event on the mitochondrial surface, which dictates the biological outcome of a local signal transduction pathway. The concentrations of scaffold proteins, such as A-kinase anchoring proteins (AKAPs) and Sab (or SH3 binding protein 5-SH3BP5), have been shown to influence neuronal survival and vulnerability, respectively, in models of Parkinson's disease (PD), highlighting the importance of OMM signaling to health and disease. Despite recent progress, much remains to be discovered concerning the mechanisms of OMM signaling. Nonetheless, enhancing beneficial OMM signaling events and inhibiting detrimental protein-protein interactions on the mitochondrial surface may represent highly selective approaches to restore mitochondrial health and homeostasis and mitigate organelle dysfunction in conditions such as PD.
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Affiliation(s)
- Maribel Lucero
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, the Biomolecular Sciences Institute, Florida International University, Miami, Florida
| | - Ana E Suarez
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, the Biomolecular Sciences Institute, Florida International University, Miami, Florida
| | - Jeremy W Chambers
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, the Biomolecular Sciences Institute, Florida International University, Miami, Florida
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78
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Wong AW, Urisman A, Burlingame AL, Shokat KM. Chemically reprogramming the phospho-transfer reaction to crosslink protein kinases to their substrates. Protein Sci 2019; 28:654-662. [PMID: 30636329 PMCID: PMC6371225 DOI: 10.1002/pro.3570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/03/2019] [Accepted: 01/07/2019] [Indexed: 12/24/2022]
Abstract
The proteomic mapping of enzyme-substrate interactions is challenged by their transient nature. A method to capture interacting protein kinases in complexes with a single substrate of interest would provide a new tool for mapping kinase signaling networks. Here, we describe a nucleotide-based substrate analog capable of reprogramming the wild-type phosphoryl-transfer reaction to produce a kinase-acrylamide-based thioether crosslink to mutant substrates with a cysteine nucleophile substituted at the native phosphorylation site. A previously reported ATP-based methacrylate crosslinker (ATP-MA) was capable of mediating kinase crosslinking to short peptides but not protein substrates. Exploration of structural variants of ATP-MA to enable crosslinking of protein substrates to kinases led to the discovery that an ADP-based methacrylate (ADP-MA) crosslinker was superior to the ATP scaffold at crosslinking in vitro. The improved efficiency of ADP-MA over ATP-MA is due to reduced inhibition of the second step of the kinase-substrate crosslinking reaction by the product of the first step of the reaction. The new probe, ADP-MA, demonstrated enhanced in vitro crosslinking between the Src tyrosine kinase and its substrate Cortactin in a phosphorylation site-specific manner. The kinase-substrate crosslinking reaction can be carried out in a complex mammalian cell lysate setting, although the low abundance of endogenous kinases remains a significant challenge for efficient capture.
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Affiliation(s)
- Allison W. Wong
- Department of Cellular and Molecular PharmacologyUniversity of California San FranciscoSan FranciscoCalifornia
| | - Anatoly Urisman
- Department of PathologyUniversity of California San FranciscoSan FranciscoCalifornia
- Department of Pharmaceutical ChemistryUniversity of California San FranciscoSan FranciscoCalifornia
| | - Alma L. Burlingame
- Department of Pharmaceutical ChemistryUniversity of California San FranciscoSan FranciscoCalifornia
| | - Kevan M. Shokat
- Department of Cellular and Molecular PharmacologyUniversity of California San FranciscoSan FranciscoCalifornia
- Howard Hughes Medical InstituteUniversity of California San FranciscoSan FranciscoCalifornia
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79
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Roche S, Lecointre C, Simon V, Labesse G. SHEDding light on the role of Pragmin pseudo-kinases in cancer. Am J Cancer Res 2019; 9:449-454. [PMID: 30906642 PMCID: PMC6405979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 11/27/2018] [Indexed: 06/09/2023] Open
Abstract
The human kinome comprises more than 50 pseudo-kinases with unclear biological function due to the absence of apparent catalytic activity, and therefore, with presumably little interest for cancer drug discovery. However, it is now acknowledged that several of them, such as Pragmin family members, play roles as important as those of active kinases in human cancer. How these pseudo-kinases promote tumor formation is largely unknown. Recently, independent structural analyses of three Pragmin pseudo-kinases (Pragmin, SGK223, and SGK269/PEAK1) revealed a split helical dimerization (SHED)-based mechanism of action. Additional sequence-structure analysis identified C19orf35 as a new member of the Pragmin family. Based on the results of these molecular studies, we present a unified model on how Pragmin pseudo-kinases may regulate oncogenic signaling, and suggest potential therapeutic strategies to block their tumor activity.
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Affiliation(s)
- Serge Roche
- CRBM, CNRS, University Montpellier, Equipe labellisée Ligue Contre le CancerF-34000 Montpellier, France
| | - Céline Lecointre
- CRBM, CNRS, University Montpellier, Equipe labellisée Ligue Contre le CancerF-34000 Montpellier, France
| | - Valérie Simon
- CRBM, CNRS, University Montpellier, Equipe labellisée Ligue Contre le CancerF-34000 Montpellier, France
| | - Gilles Labesse
- CBS, CNRS, INSERM, University MontpellierF34090 Montpellier, France
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80
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Phosphoproteomic identification and functional characterization of protein kinase substrates by 2D-DIGE and Phos-tag PAGE. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:57-61. [DOI: 10.1016/j.bbapap.2018.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 05/30/2018] [Accepted: 06/01/2018] [Indexed: 12/22/2022]
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81
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Quadri MM, Fatima SS, Che RC, Zhang AH. Mitochondria and Renal Fibrosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1165:501-524. [PMID: 31399982 DOI: 10.1007/978-981-13-8871-2_25] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mitochondria are important organelles in eukaryotic cells and perform a variety of biosynthetic and metabolic functions. Many human diseases are closely related to mitochondrial dysfunction. Kidney is an organ with high-energy requirements, which is distributed with a large number of mitochondria. Mitochondrial dysfunction plays a crucial role in the pathogenesis of kidney disease, and studies have shown that mitochondrial dysfunction is involved in the physiological process of renal fibrosis. This review introduced the biogenesis and pathophysiology of mitochondria, illustrated the involvement of mitochondrial dysfunction in renal fibrosis based on various kinds of cells, and finally summarized the latest mitochondria-targeted therapies.
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Affiliation(s)
| | - Syeda-Safoorah Fatima
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Ruo-Chen Che
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Ai-Hua Zhang
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China.
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82
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Abstract
A new conformation has recently been reported for ubiquitin (Ub). This invisible conformation (Ub-CR), where the C-terminal tail is retracted, has a key functional role in phosphorylation of the Ser65 residue, a trigger for PINK1 and Parkin dependent mitophagy. Here we calculate the transition mechanism and associated rates for the Ub to Ub-CR pathway in the wild-type protein and a selection of mutants. We predict a cooperative one-step process with a transition state that resembles the Ub configuration, characterized by a loss of all interactions of the C-terminal tail with surrounding residues, and an open ubiquitin scaffold. The calculated observables agree well with reported values, and we make a range of predictions to guide future experiments. In particular, the effect of mutations on the pathway and the corresponding structural ensembles should have observable consequences. This feedback between theory and experiment promises new insight into key cellular processes.
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Affiliation(s)
- Konstantin Röder
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , United Kingdom
| | - David J Wales
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , United Kingdom
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83
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Rasool S, Trempe JF. New insights into the structure of PINK1 and the mechanism of ubiquitin phosphorylation. Crit Rev Biochem Mol Biol 2018; 53:515-534. [PMID: 30238821 DOI: 10.1080/10409238.2018.1491525] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Mutations in PINK1 cause early-onset recessive Parkinson's disease. This gene encodes a protein kinase implicated in mitochondrial quality control via ubiquitin phosphorylation and activation of the E3 ubiquitin ligase Parkin. Here, we review and analyze functional features emerging from recent crystallographic, nuclear magnetic resonance (NMR) and mass spectrometry studies of PINK1. We compare the apo and ubiquitin-bound PINK1 structures and reveal an allosteric switch, regulated by autophosphorylation, which modulates substrate recognition. We critically assess the conformational changes taking place in ubiquitin and the Parkin ubiquitin-like domain in relation to its binding to PINK1. Finally, we discuss the implications of these biophysical findings in our understanding of the role of PINK1 in mitochondrial function, and analyze the potential for structure-based drug design.
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Affiliation(s)
- Shafqat Rasool
- a Department of Biochemistry , McGill University , Montréal , Canada.,b Groupe de Recherche Axé sur la Structure des Protéines (GRASP) , Montréal , Canada
| | - Jean-François Trempe
- b Groupe de Recherche Axé sur la Structure des Protéines (GRASP) , Montréal , Canada.,c Department of Pharmacology & Therapeutics , McGill University , Montréal , Canada
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84
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Mechanisms of mitophagy in cellular homeostasis, physiology and pathology. Nat Cell Biol 2018; 20:1013-1022. [PMID: 30154567 DOI: 10.1038/s41556-018-0176-2] [Citation(s) in RCA: 834] [Impact Index Per Article: 139.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/25/2018] [Indexed: 02/06/2023]
Abstract
Mitophagy is an evolutionarily conserved cellular process to remove dysfunctional or superfluous mitochondria, thus fine-tuning mitochondrial number and preserving energy metabolism. In this Review, we survey recent advances towards elucidating the molecular mechanisms that mediate mitochondrial elimination and the signalling pathways that govern mitophagy. We consider the contributions of mitophagy in physiological and pathological contexts and discuss emerging findings, highlighting the potential value of mitophagy modulation in therapeutic intervention.
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85
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Abstract
Ubiquitylation is an essential posttranslational modification that controls cell division, differentiation, and survival in all eukaryotes. By combining multiple E3 ligases (writers), ubiquitin-binding effectors (readers), and de-ubiquitylases (erasers) with functionally distinct ubiquitylation tags, the ubiquitin system constitutes a powerful signaling network that is employed in similar ways from yeast to humans. Here, we discuss conserved principles of ubiquitin-dependent signaling that illustrate how this posttranslational modification shapes intracellular signaling networks to establish robust development and homeostasis throughout the eukaryotic kingdom.
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Affiliation(s)
- Eugene Oh
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA; .,Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - David Akopian
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Michael Rape
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA; .,Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
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86
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Okatsu K, Sato Y, Yamano K, Matsuda N, Negishi L, Takahashi A, Yamagata A, Goto-Ito S, Mishima M, Ito Y, Oka T, Tanaka K, Fukai S. Structural insights into ubiquitin phosphorylation by PINK1. Sci Rep 2018; 8:10382. [PMID: 29991771 PMCID: PMC6039469 DOI: 10.1038/s41598-018-28656-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 05/31/2018] [Indexed: 11/09/2022] Open
Abstract
Mutations of PTEN-induced putative kinase 1 (PINK1) and the E3 ubiquitin (Ub) ligase parkin can cause familial parkinsonism. These two proteins are essential for ubiquitylation of damaged mitochondria and subsequent degradation. PINK1 phosphorylates Ser65 of Ub and the Ub-like (UBL) domain of parkin to allosterically relieve the autoinhibition of parkin. To understand the structural mechanism of the Ub/UBL-specific phosphorylation by PINK1, we determined the crystal structure of Tribolium castaneum PINK1 kinase domain (TcPINK1) in complex with a nonhydrolyzable ATP analogue at 2.5 Å resolution. TcPINK1 consists of the N- and C-terminal lobes with the PINK1-specific extension. The ATP analogue is bound in the cleft between the N- and C-terminal lobes. The adenine ring of the ATP analogue is bound to a hydrophobic pocket, whereas the triphosphate group of the ATP analogue and two coordinated Mg ions interact with the catalytic hydrophilic residues. Comparison with protein kinases A and C (PKA and PKC, respectively) unveils a putative Ub/UBL-binding groove, which is wider than the peptide-binding groove of PKA or PKC to accommodate the globular head of Ub or UBL. Further crosslinking analyses suggested a PINK1-interacting surface of Ub. Structure-guided mutational analyses support the findings from the present structural analysis of PINK1.
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Affiliation(s)
- Kei Okatsu
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Yusuke Sato
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan
| | - Koji Yamano
- Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
| | - Noriyuki Matsuda
- Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan.,PRESTO, Japan Science and Technology Agency, Saitama, 332-0012, Japan
| | - Lumi Negishi
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Akiko Takahashi
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Atsushi Yamagata
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan
| | - Sakurako Goto-Ito
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Masaki Mishima
- Graduate School of Science & Engineering, Tokyo Metropolitan University, Tokyo, 192-0397, Japan
| | - Yutaka Ito
- Graduate School of Science & Engineering, Tokyo Metropolitan University, Tokyo, 192-0397, Japan
| | - Toshihiko Oka
- Department of Life Science, Rikkyo University, Tokyo, 171-8501, Japan
| | - Keiji Tanaka
- Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
| | - Shuya Fukai
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan. .,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan. .,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan.
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87
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Abstract
Protein folding is often viewed in terms of a funneled potential or free energy landscape. A variety of experiments now indicate the existence of multifunnel landscapes, associated with multifunctional biomolecules. Here, we present evidence that these systems have evolved to exhibit the minimal number of funnels required to fulfill their cellular functions, suggesting an extension to the principle of minimum frustration. We find that minimal disruptive mutations result in additional funnels, and the associated structural ensembles become more diverse. The same trends are observed in an atomic cluster. These observations suggest guidelines for rational design of engineered multifunctional biomolecules.
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Affiliation(s)
- Konstantin Röder
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , U.K
| | - David J Wales
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , U.K
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88
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Abstract
Mutations in the E3 ubiquitin ligase parkin (PARK2, also known as PRKN) and the protein kinase PINK1 (also known as PARK6) are linked to autosomal-recessive juvenile parkinsonism (AR-JP)1,2; at the cellular level, these mutations cause defects in mitophagy, the process that organizes the destruction of damaged mitochondria3,4. Parkin is autoinhibited, and requires activation by PINK1, which phosphorylates Ser65 in ubiquitin and in the parkin ubiquitin-like (Ubl) domain. Parkin binds phospho-ubiquitin, which enables efficient parkin phosphorylation; however, the enzyme remains autoinhibited with an inaccessible active site5,6. It is unclear how phosphorylation of parkin activates the molecule. Here we follow the activation of full-length human parkin by hydrogen-deuterium exchange mass spectrometry, and reveal large-scale domain rearrangement in the activation process, during which the phospho-Ubl rebinds to the parkin core and releases the catalytic RING2 domain. A 1.8 Å crystal structure of phosphorylated human parkin reveals the binding site of the phospho-Ubl on the unique parkin domain (UPD), involving a phosphate-binding pocket lined by AR-JP mutations. Notably, a conserved linker region between Ubl and the UPD acts as an activating element (ACT) that contributes to RING2 release by mimicking RING2 interactions on the UPD, explaining further AR-JP mutations. Our data show how autoinhibition in parkin is resolved, and suggest a mechanism for how parkin ubiquitinates its substrates via an untethered RING2 domain. These findings open new avenues for the design of parkin activators for clinical use.
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89
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Bingol B. Autophagy and lysosomal pathways in nervous system disorders. Mol Cell Neurosci 2018; 91:167-208. [PMID: 29729319 DOI: 10.1016/j.mcn.2018.04.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 04/26/2018] [Accepted: 04/28/2018] [Indexed: 12/12/2022] Open
Abstract
Autophagy is an evolutionarily conserved pathway for delivering cytoplasmic cargo to lysosomes for degradation. In its classically studied form, autophagy is a stress response induced by starvation to recycle building blocks for essential cellular processes. In addition, autophagy maintains basal cellular homeostasis by degrading endogenous substrates such as cytoplasmic proteins, protein aggregates, damaged organelles, as well as exogenous substrates such as bacteria and viruses. Given their important role in homeostasis, autophagy and lysosomal machinery are genetically linked to multiple human disorders such as chronic inflammatory diseases, cardiomyopathies, cancer, and neurodegenerative diseases. Multiple targets within the autophagy and lysosomal pathways offer therapeutic opportunities to benefit patients with these disorders. Here, I will summarize the mechanisms of autophagy pathways, the evidence supporting a pathogenic role for disturbed autophagy and lysosomal degradation in nervous system disorders, and the therapeutic potential of autophagy modulators in the clinic.
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Affiliation(s)
- Baris Bingol
- Genentech, Inc., Department of Neuroscience, 1 DNA Way, South San Francisco 94080, United States.
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90
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Huyet J, Ozeir M, Burgevin MC, Pinson B, Chesney F, Remy JM, Siddiqi AR, Lupoli R, Pinon G, Saint-Marc C, Gibert JF, Morales R, Ceballos-Picot I, Barouki R, Daignan-Fornier B, Olivier-Bandini A, Augé F, Nioche P. Structural Insights into the Forward and Reverse Enzymatic Reactions in Human Adenine Phosphoribosyltransferase. Cell Chem Biol 2018; 25:666-676.e4. [PMID: 29576532 DOI: 10.1016/j.chembiol.2018.02.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 01/05/2018] [Accepted: 02/22/2018] [Indexed: 10/17/2022]
Abstract
Phosphoribosyltransferases catalyze the displacement of a PRPP α-1'-pyrophosphate to a nitrogen-containing nucleobase. How they control the balance of substrates/products binding and activities is poorly understood. Here, we investigated the human adenine phosphoribosyltransferase (hAPRT) that produces AMP in the purine salvage pathway. We show that a single oxygen atom from the Tyr105 side chain is responsible for selecting the active conformation of the 12 amino acid long catalytic loop. Using in vitro, cellular, and in crystallo approaches, we demonstrated that Tyr105 is key for the fine-tuning of the kinetic activity efficiencies of the forward and reverse reactions. Together, our results reveal an evolutionary pressure on the strictly conserved Tyr105 and on the dynamic motion of the flexible loop in phosphoribosyltransferases that is essential for purine biosynthesis in cells. These data also provide the framework for designing novel adenine derivatives that could modulate, through hAPRT, diseases-involved cellular pathways.
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Affiliation(s)
- Jessica Huyet
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR-S 1124, Centre Interdisciplinaire Chimie Biologie-Paris, 45, rue des Saints Pères, Paris 75006, France; INSERM, UMR-S 1124, Paris 75006, France
| | - Mohammad Ozeir
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR-S 1124, Centre Interdisciplinaire Chimie Biologie-Paris, 45, rue des Saints Pères, Paris 75006, France; INSERM, UMR-S 1124, Paris 75006, France
| | | | - Benoît Pinson
- Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, Bordeaux Cedex 33077, France
| | - Françoise Chesney
- Sanofi R&D, Translational Science Unit, Chilly-Mazarin 91385, France
| | - Jean-Marc Remy
- Sanofi R&D, Translational Science Unit, Chilly-Mazarin 91385, France
| | - Abdul Rauf Siddiqi
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Roland Lupoli
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR-S 1124, Centre Interdisciplinaire Chimie Biologie-Paris, 45, rue des Saints Pères, Paris 75006, France; INSERM, UMR-S 1124, Paris 75006, France; Université Paris Descartes, Structural and Molecular Analysis Platform, Paris 75006, France
| | - Gregory Pinon
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR-S 1124, Centre Interdisciplinaire Chimie Biologie-Paris, 45, rue des Saints Pères, Paris 75006, France; INSERM, UMR-S 1124, Paris 75006, France; Université Paris Descartes, Structural and Molecular Analysis Platform, Paris 75006, France
| | - Christelle Saint-Marc
- Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, Bordeaux Cedex 33077, France
| | | | - Renaud Morales
- Sanofi R&D, Translational Science Unit, Chilly-Mazarin 91385, France
| | - Irène Ceballos-Picot
- Laboratoire de Biochimie Métabolomique et Protéomique, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Faculté de Médecine Paris Descartes, Paris 75015, France
| | - Robert Barouki
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR-S 1124, Centre Interdisciplinaire Chimie Biologie-Paris, 45, rue des Saints Pères, Paris 75006, France; INSERM, UMR-S 1124, Paris 75006, France; Laboratoire de Biochimie Métabolomique et Protéomique, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Faculté de Médecine Paris Descartes, Paris 75015, France
| | - Bertrand Daignan-Fornier
- Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, Bordeaux Cedex 33077, France
| | | | - Franck Augé
- Sanofi R&D, Translational Science Unit, Chilly-Mazarin 91385, France.
| | - Pierre Nioche
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR-S 1124, Centre Interdisciplinaire Chimie Biologie-Paris, 45, rue des Saints Pères, Paris 75006, France; INSERM, UMR-S 1124, Paris 75006, France; Université Paris Descartes, Structural and Molecular Analysis Platform, Paris 75006, France.
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91
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Aguirre JD, Dunkerley KM, Lam R, Rusal M, Shaw GS. Impact of altered phosphorylation on loss of function of juvenile Parkinsonism-associated genetic variants of the E3 ligase parkin. J Biol Chem 2018. [PMID: 29530980 PMCID: PMC5925814 DOI: 10.1074/jbc.ra117.000605] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Autosomal recessive juvenile Parkinsonism (ARJP) is an inherited neurodegenerative disease in which 50% of affected individuals harbor mutations in the gene encoding the E3 ligase parkin. Parkin regulates the mitochondrial recycling pathway, which is induced by oxidative stress. In its native state, parkin is auto-inhibited by its N-terminal ubiquitin-like (Ubl) domain, which blocks the binding site for an incoming E2∼ubiquitin conjugate, needed for parkin's ubiquitination activity. Parkin is activated via phosphorylation of Ser-65 in its Ubl domain by PTEN-induced putative kinase 1 (PINK1) and a ubiquitin molecule phosphorylated at a position equivalent to Ser-65 in parkin. Here we have examined the underlying molecular mechanism of phosphorylation of parkin's Ubl domain carrying ARJP-associated substitutions and how altered phosphorylation modulates parkin activation and ubiquitination. We found that three substitutions in the Ubl domain (G12R, R33Q, and R42P) significantly decrease PINK1's ability to phosphorylate the Ubl domain. We noted that two basic loss-of-function substitutions (R33Q and R42P) are close to acidic patches in the proposed PINK1–parkin interface, indicating that ionic interactions at this site may be important for efficient parkin phosphorylation. Increased auto-ubiquitination with unique ubiquitin chain patterns was observed for two other Ubl domain substitutions (G12R and T55I), suggesting that these substitutions, along with phosphorylation, increase parkin degradation. Moreover, Ubl domain phosphorylation decreased its affinity for the potential effector protein ataxin-3, which edits ubiquitin chain building by parkin. Overall, our work provides a framework for the mechanisms of parkin's loss-of-function, indicating an interplay between ARJP-associated substitutions and phosphorylation of its Ubl domain.
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Affiliation(s)
- Jacob D Aguirre
- From the Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Karen M Dunkerley
- From the Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Rica Lam
- From the Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Michele Rusal
- From the Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Gary S Shaw
- From the Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
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92
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Rasool S, Soya N, Truong L, Croteau N, Lukacs GL, Trempe JF. PINK1 autophosphorylation is required for ubiquitin recognition. EMBO Rep 2018; 19:embr.201744981. [PMID: 29475881 DOI: 10.15252/embr.201744981] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 01/26/2018] [Accepted: 02/01/2018] [Indexed: 11/09/2022] Open
Abstract
Mutations in PINK1 cause autosomal recessive Parkinson's disease (PD), a neurodegenerative movement disorder. PINK1 is a kinase that acts as a sensor of mitochondrial damage and initiates Parkin-mediated clearance of the damaged organelle. PINK1 phosphorylates Ser65 in both ubiquitin and the ubiquitin-like (Ubl) domain of Parkin, which stimulates its E3 ligase activity. Autophosphorylation of PINK1 is required for Parkin activation, but how this modulates the ubiquitin kinase activity is unclear. Here, we show that autophosphorylation of Tribolium castaneum PINK1 is required for substrate recognition. Using enzyme kinetics and NMR spectroscopy, we reveal that PINK1 binds the Parkin Ubl with a 10-fold higher affinity than ubiquitin via a conserved interface that is also implicated in RING1 and SH3 binding. The interaction requires phosphorylation at Ser205, an invariant PINK1 residue (Ser228 in human). Using mass spectrometry, we demonstrate that PINK1 rapidly autophosphorylates in trans at Ser205. Small-angle X-ray scattering and hydrogen-deuterium exchange experiments provide insights into the structure of the PINK1 catalytic domain. Our findings suggest that multiple PINK1 molecules autophosphorylate first prior to binding and phosphorylating ubiquitin and Parkin.
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Affiliation(s)
- Shafqat Rasool
- Department of Pharmacology & Therapeutics and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, QC, Canada.,Department of Biochemistry, McGill University, Montréal, QC, Canada
| | - Naoto Soya
- Department of Physiology and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, QC, Canada
| | - Luc Truong
- Department of Pharmacology & Therapeutics and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, QC, Canada
| | - Nathalie Croteau
- Department of Pharmacology & Therapeutics and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, QC, Canada
| | - Gergely L Lukacs
- Department of Biochemistry, McGill University, Montréal, QC, Canada.,Department of Physiology and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, QC, Canada
| | - Jean-François Trempe
- Department of Pharmacology & Therapeutics and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, QC, Canada
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93
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Kazansky Y, Lai MY, Singh RK, Fushman D. Impact of different ionization states of phosphorylated Serine-65 on ubiquitin structure and interactions. Sci Rep 2018; 8:2651. [PMID: 29422536 PMCID: PMC5805711 DOI: 10.1038/s41598-018-20860-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 01/23/2018] [Indexed: 01/13/2023] Open
Abstract
The covalent attachment of ubiquitin (Ub) or Ub chains to cellular proteins is a versatile post-translational modification involved in a variety of eukaryotic cellular events. Recently, the post-translational modification of Ub itself by phosphorylation has emerged as an important component of the Ub-signaling system. Specifically, Ub phosphorylation at serine-65 was shown to activate parkin-mediated mitochondrial quality control. However, the impact of phosphorylation on Ub structure and interactions is poorly understood. Here we investigate the recently reported structural changes in Ub upon serine-65 phosphorylation, namely, the equilibrium between a native-like and a novel, alternate conformer of phosphorylated Ub (pUb). We show that this equilibrium is pH-dependent, and the two pUb conformers are linked to the different charge states of the phosphate group. We examined pUb binding to a known Ub-receptor and found that the alternate conformer is binding incompetent. Furthermore, serine-65 phosphorylation affects the conformational equilibrium of K48-linked Ub dimers. Lastly, our crystal structure of S65D Ub and NMR data indicate that phosphomimetic mutations do not adequately reproduce the salient features of pUb. Our results suggest that the pH-dependence of the conformations and binding properties of phosphorylated Ub and polyUb could provide an additional level of modulation in Ub-mediated signaling.
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Affiliation(s)
- Yaniv Kazansky
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - Ming-Yih Lai
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - Rajesh K Singh
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA.
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94
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Harper JW, Ordureau A, Heo JM. Building and decoding ubiquitin chains for mitophagy. Nat Rev Mol Cell Biol 2018; 19:93-108. [DOI: 10.1038/nrm.2017.129] [Citation(s) in RCA: 323] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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95
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VanHook AM. Papers of note in
Nature
552
(7683). Sci Signal 2017. [DOI: 10.1126/scisignal.aar6885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
This week’s articles highlight a potential therapeutic target for fibrosis; parasite receptors that contribute to malaria; a potential drawback of PD-1 inhibition for cancer immunotherapy; a noncoding RNA that regulates ribosome biogenesis; and a structural analysis of substrate binding by the kinase PINK1.
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96
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97
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Ha BH, Boggon TJ. The crystal structure of pseudokinase PEAK1 (Sugen kinase 269) reveals an unusual catalytic cleft and a novel mode of kinase fold dimerization. J Biol Chem 2017; 293:1642-1650. [PMID: 29212708 DOI: 10.1074/jbc.ra117.000751] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 11/30/2017] [Indexed: 01/18/2023] Open
Abstract
The pseudokinase group encompasses some 10% of protein kinases, but pseudokinases diverge from canonical kinases in key motifs. The two members of the small new kinase family 3 (NKF3) group are considered pseudokinases. These proteins, pseudopodium-enriched atypical kinase 1 (PEAK1, Sugen kinase 269, or SgK269) and pragmin (Sugen kinase 223 or SgK223), act as scaffolds in growth factor signaling pathways, and both contain a kinase fold with degraded kinase motifs at their C termini. These kinases may harbor regions that mediate oligomerization or control other aspects of signal transduction, but a lack of structural information has precluded detailed investigations into their functional roles. In this study, we determined the X-ray crystal structure of the PEAK1 pseudokinase domain to 2.3 Å resolution. The structure revealed that the PEAK1 kinase-like domain contains a closed nucleotide-binding cleft that in this conformation may deleteriously affect nucleotide binding. Moreover, we found that N- and C-terminal extensions create a highly unusual all α-helical split-dimerization region, termed here the split helical dimerization (SHED) region. Sequence conservation analysis suggested that this region facilitates a dimerization mode that is conserved between PEAK1 and pragmin. Finally, we observed structural similarities between the PEAK1 SHED region and the C-terminal extension of the Parkinson's disease-associated kinase PINK1. In summary, PEAK1's kinase cleft is occluded, and its newly identified SHED region may promote an unexpected dimerization mode. Similarities of PEAK1 with the active kinase PINK1 may reclassify the latter as a member of the new kinase family 3 group.
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Affiliation(s)
| | - Titus J Boggon
- From the Departments of Pharmacology and .,Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
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