1
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Li M, Zhang C, Xu Y, Li S, Huang C, Wu J, Lei M. Structural insights into human EMC and its interaction with VDAC. Aging (Albany NY) 2024; 16:5501-5525. [PMID: 38517390 PMCID: PMC11006472 DOI: 10.18632/aging.205660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 02/08/2024] [Indexed: 03/23/2024]
Abstract
The endoplasmic reticulum (ER) membrane protein complex (EMC) is a conserved, multi-subunit complex acting as an insertase at the ER membrane. Growing evidence shows that the EMC is also involved in stabilizing and trafficking membrane proteins. However, the structural basis and regulation of its multifunctionality remain elusive. Here, we report cryo-electron microscopy structures of human EMC in apo- and voltage-dependent anion channel (VDAC)-bound states at resolutions of 3.47 Å and 3.32 Å, respectively. We discovered a specific interaction between VDAC proteins and the EMC at mitochondria-ER contact sites, which is conserved from yeast to humans. Moreover, we identified a gating plug located inside the EMC hydrophilic vestibule, the substrate-binding pocket for client insertion. Conformation changes of this gating plug during the apo-to-VDAC-bound transition reveal that the EMC unlikely acts as an insertase in the VDAC1-bound state. Based on the data analysis, the gating plug may regulate EMC functions by modifying the hydrophilic vestibule in different states. Our discovery offers valuable insights into the structural basis of EMC's multifunctionality.
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Affiliation(s)
- Mingyue Li
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Chunli Zhang
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Yuntao Xu
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Shaobai Li
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Chenhui Huang
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Jian Wu
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Ming Lei
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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2
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Miliara X, Tatsuta T, Eiyama A, Langer T, Rouse SL, Matthews S. An intermolecular hydrogen bonded network in the PRELID-TRIAP protein family plays a role in lipid sensing. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140867. [PMID: 36309326 DOI: 10.1016/j.bbapap.2022.140867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022]
Abstract
The PRELID-TRIAP1 family of proteins is responsible for lipid transfer in mitochondria. Multiple structures have been resolved of apo and lipid substrate bound forms, allowing us to begin to piece together the molecular level details of the full lipid transfer cycle. Here, we used molecular dynamics simulations to demonstrate that the lipid binding is mediated by an extended, water-mediated hydrogen bonding network. A key mutation, R53E, was found to disrupt this network, causing lipid to be released from the complex. The X-ray crystal structure of R53E was captured in a fully closed and apo state. Lipid transfer assays and molecular simulations allow us to interpret the observed conformation in the context of the biological role. Together, our work provides further understanding of the mechanistic control of lipid transport by PRELID-TRIAP1 in mitochondria.
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Affiliation(s)
- Xeni Miliara
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, UK
| | - Takashi Tatsuta
- Max Planck Institute for Biology of Ageing, D-50931 Cologne, Germany
| | - Akinori Eiyama
- Max Planck Institute for Biology of Ageing, D-50931 Cologne, Germany
| | - Thomas Langer
- Max Planck Institute for Biology of Ageing, D-50931 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), D-50931 Cologne, Germany
| | - Sarah L Rouse
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, UK
| | - Steve Matthews
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, UK.
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3
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Kakimoto-Takeda Y, Kojima R, Shiino H, Shinmyo M, Kurokawa K, Nakano A, Endo T, Tamura Y. Dissociation of ERMES clusters plays a key role in attenuating the endoplasmic reticulum stress. iScience 2022; 25:105362. [PMID: 36339260 PMCID: PMC9626684 DOI: 10.1016/j.isci.2022.105362] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/24/2022] [Accepted: 10/12/2022] [Indexed: 11/27/2022] Open
Abstract
In yeast, ERMES, which mediates phospholipid transport between the ER and mitochondria, forms a limited number of oligomeric clusters at ER-mitochondria contact sites in a cell. Although the number of the ERMES clusters appears to be regulated to maintain proper inter-organelle phospholipid trafficking, its underlying mechanism and physiological relevance remain poorly understood. Here, we show that mitochondrial dynamics control the number of ERMES clusters. Moreover, we find that ER stress causes dissociation of the ERMES clusters independently of Ire1 and Hac1, canonical ER-stress response pathway components, leading to a delay in the phospholipid transport from the ER to mitochondria. Our biochemical and genetic analyses strongly suggest that the impaired phospholipid transport contributes to phospholipid accumulation in the ER, expanding the ER for ER stress attenuation. We thus propose that the ERMES dissociation constitutes an overlooked pathway of the ER stress response that operates in addition to the canonical Ire1/Hac1-dependent pathway. Mitochondrial fusion and division regulate the clustering of the ERMES complex ER stress leads to dissociation of the ERMES clusters independently of Ire1 and Hac1 The dissociated ERMES complexes have less activity in transporting phospholipids The defective phospholipid transport may cause the ER expansion to relieve ER stress
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Affiliation(s)
- Yuriko Kakimoto-Takeda
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, 2-2-2 Iidanishi, Yamagata 990-9585, Japan
| | - Rieko Kojima
- Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata 990-8560, Japan
| | - Hiroya Shiino
- Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata 990-8560, Japan
| | - Manatsu Shinmyo
- Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata 990-8560, Japan
| | - Kazuo Kurokawa
- Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Akihiko Nakano
- Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Toshiya Endo
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto 603-8555, Japan
- Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto 603-8555, Japan
| | - Yasushi Tamura
- Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata 990-8560, Japan
- Corresponding author
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4
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Song C, Pan S, Zhang J, Li N, Geng Q. Mitophagy: A novel perspective for insighting into cancer and cancer treatment. Cell Prolif 2022; 55:e13327. [PMID: 36200262 DOI: 10.1111/cpr.13327] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/13/2022] [Accepted: 08/02/2022] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Mitophagy refers to the selective self-elimination of mitochondria under damaged or certain developmental conditions. As an important regulatory mechanism to remove damaged mitochondria and maintain the internal and external cellular balance, mitophagy plays pivotal roles in carcinogenesis and progression as well as treatment. MATERIALS AND METHODS Here, we combined data from recent years to comprehensively describe the regulatory mechanisms of mitophagy and its multifaceted significance in cancer, and discusse the potential of targeted mitophagy as a cancer treatment strategy. RESULTS The molecular mechanisms regulating mitophagy are complex, diverse, and cross-talk. Inducing or blocking mitophagy has the same or completely different effects in different cancer contexts. Mitophagy plays an indispensable role in regulating cancer metabolic reprogramming, cell stemness, and chemotherapy resistance for better adaptation to tumor microenvironment. In cancer cell biology, mitophagy is considered to be a double-edged sword. And to fully understand the role of mitophagy in cancer development can provide new targets for cancer treatment in clinical practice. CONCLUSIONS This review synthesizes a large body of data to comprehensively describe the molecular mechanisms of mitophagy and its multidimensional significance in cancer and cancer treatment, which will undoubtedly deepen the understanding of mitophagy.
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Affiliation(s)
- Congkuan Song
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Shize Pan
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jinjin Zhang
- Department of Emergency, Taihe Hospital, Shiyan, China
| | - Ning Li
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Qing Geng
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
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5
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He H, Xiong L, Jian L, Li L, Wu Y, Qiao S. Role of mitochondria on UV-induced skin damage and molecular mechanisms of active chemical compounds targeting mitochondria. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 232:112464. [PMID: 35597147 DOI: 10.1016/j.jphotobiol.2022.112464] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/07/2022] [Accepted: 05/07/2022] [Indexed: 06/15/2023]
Abstract
Mitochondria are the principal place of energy metabolism and ROS production, leading to mtDNA being especially sensitive to the impacts of oxidative stress. Our review aims to elucidate and update the mechanisms of mitochondria in UV-induced skin damage. The mitochondrial deteriorative response to UV manifests morphological and functional alterations, including mitochondrial fusion and fission, mitochondrial biogenesis, mitochondrial energy metabolism and mitophagy. Additionally, we conclude the effect and molecular mechanisms of active chemical components to protect skin from UV-induced damage via mitochondrial protection which have been described in the last five years, showing prospective prospects in cosmetics as new therapeutic targets.
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Affiliation(s)
- Hailun He
- Department of Dermatology, The First Hospital of China Medical University, Shenyang, China; National joint Engineering Research Center for Theranostics of Immunological Skin Diseases, The First Hospital of China Medical University and Key Laboratory of Immunodermatology, Ministry of Health and Ministry of Education, Shenyang, China
| | - Lidan Xiong
- Cosmetics Safety and Efficacy Evaluation Center, West China Hospital, Sichuan University, Chengdu, China; Sichuan Engineering Technology Research Center of Cosmetic, Chengdu, China
| | - Linge Jian
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Liangman Li
- Orthopedics Department, the First Hospital of China Medical University, Shenyang, China
| | - Yan Wu
- Department of Dermatology, The First Hospital of China Medical University, Shenyang, China; National joint Engineering Research Center for Theranostics of Immunological Skin Diseases, The First Hospital of China Medical University and Key Laboratory of Immunodermatology, Ministry of Health and Ministry of Education, Shenyang, China.
| | - Shuai Qiao
- Department of Dermatology, The First Hospital of China Medical University, Shenyang, China; National joint Engineering Research Center for Theranostics of Immunological Skin Diseases, The First Hospital of China Medical University and Key Laboratory of Immunodermatology, Ministry of Health and Ministry of Education, Shenyang, China.
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6
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Egea PF. Mechanisms of Non-Vesicular Exchange of Lipids at Membrane Contact Sites: Of Shuttles, Tunnels and, Funnels. Front Cell Dev Biol 2021; 9:784367. [PMID: 34912813 PMCID: PMC8667587 DOI: 10.3389/fcell.2021.784367] [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: 09/27/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
Eukaryotic cells are characterized by their exquisite compartmentalization resulting from a cornucopia of membrane-bound organelles. Each of these compartments hosts a flurry of biochemical reactions and supports biological functions such as genome storage, membrane protein and lipid biosynthesis/degradation and ATP synthesis, all essential to cellular life. Acting as hubs for the transfer of matter and signals between organelles and throughout the cell, membrane contacts sites (MCSs), sites of close apposition between membranes from different organelles, are essential to cellular homeostasis. One of the now well-acknowledged function of MCSs involves the non-vesicular trafficking of lipids; its characterization answered one long-standing question of eukaryotic cell biology revealing how some organelles receive and distribute their membrane lipids in absence of vesicular trafficking. The endoplasmic reticulum (ER) in synergy with the mitochondria, stands as the nexus for the biosynthesis and distribution of phospholipids (PLs) throughout the cell by contacting nearly all other organelle types. MCSs create and maintain lipid fluxes and gradients essential to the functional asymmetry and polarity of biological membranes throughout the cell. Membrane apposition is mediated by proteinaceous tethers some of which function as lipid transfer proteins (LTPs). We summarize here the current state of mechanistic knowledge of some of the major classes of LTPs and tethers based on the available atomic to near-atomic resolution structures of several "model" MCSs from yeast but also in Metazoans; we describe different models of lipid transfer at MCSs and analyze the determinants of their specificity and directionality. Each of these systems illustrate fundamental principles and mechanisms for the non-vesicular exchange of lipids between eukaryotic membrane-bound organelles essential to a wide range of cellular processes such as at PL biosynthesis and distribution, lipid storage, autophagy and organelle biogenesis.
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Affiliation(s)
- Pascal F Egea
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
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7
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Bennett JP, Onyango IG. Energy, Entropy and Quantum Tunneling of Protons and Electrons in Brain Mitochondria: Relation to Mitochondrial Impairment in Aging-Related Human Brain Diseases and Therapeutic Measures. Biomedicines 2021; 9:225. [PMID: 33671585 PMCID: PMC7927033 DOI: 10.3390/biomedicines9020225] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/18/2021] [Accepted: 02/18/2021] [Indexed: 11/16/2022] Open
Abstract
Adult human brains consume a disproportionate amount of energy substrates (2-3% of body weight; 20-25% of total glucose and oxygen). Adenosine triphosphate (ATP) is a universal energy currency in brains and is produced by oxidative phosphorylation (OXPHOS) using ATP synthase, a nano-rotor powered by the proton gradient generated from proton-coupled electron transfer (PCET) in the multi-complex electron transport chain (ETC). ETC catalysis rates are reduced in brains from humans with neurodegenerative diseases (NDDs). Declines of ETC function in NDDs may result from combinations of nitrative stress (NS)-oxidative stress (OS) damage; mitochondrial and/or nuclear genomic mutations of ETC/OXPHOS genes; epigenetic modifications of ETC/OXPHOS genes; or defects in importation or assembly of ETC/OXPHOS proteins or complexes, respectively; or alterations in mitochondrial dynamics (fusion, fission, mitophagy). Substantial free energy is gained by direct O2-mediated oxidation of NADH. Traditional ETC mechanisms require separation between O2 and electrons flowing from NADH/FADH2 through the ETC. Quantum tunneling of electrons and much larger protons may facilitate this separation. Neuronal death may be viewed as a local increase in entropy requiring constant energy input to avoid. The ATP requirement of the brain may partially be used for avoidance of local entropy increase. Mitochondrial therapeutics seeks to correct deficiencies in ETC and OXPHOS.
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Affiliation(s)
| | - Isaac G. Onyango
- International Clinical Research Center, St. Anne’s University Hospital, CZ-65691 Brno, Czech Republic;
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8
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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: 587] [Impact Index Per Article: 195.7] [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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9
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Fernández-Del-Río L, Kelly ME, Contreras J, Bradley MC, James AM, Murphy MP, Payne GS, Clarke CF. Genes and lipids that impact uptake and assimilation of exogenous coenzyme Q in Saccharomyces cerevisiae. Free Radic Biol Med 2020; 154:105-118. [PMID: 32387128 PMCID: PMC7611304 DOI: 10.1016/j.freeradbiomed.2020.04.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/18/2020] [Accepted: 04/28/2020] [Indexed: 12/13/2022]
Abstract
Coenzyme Q (CoQ) is an essential player in the respiratory electron transport chain and is the only lipid-soluble antioxidant synthesized endogenously in mammalian and yeast cells. In humans, genetic mutations, pathologies, certain medical treatments, and aging, result in CoQ deficiencies, which are linked to mitochondrial, cardiovascular, and neurodegenerative diseases. The only strategy available for these patients is CoQ supplementation. CoQ supplements benefit a small subset of patients, but the poor solubility of CoQ greatly limits treatment efficacy. Consequently, the efficient delivery of CoQ to the mitochondria and restoration of respiratory function remains a major challenge. A better understanding of CoQ uptake and mitochondrial delivery is crucial to make this molecule a more efficient and effective therapeutic tool. In this study, we investigated the mechanism of CoQ uptake and distribution using the yeast Saccharomyces cerevisiae as a model organism. The addition of exogenous CoQ was tested for the ability to restore growth on non-fermentable medium in several strains that lack CoQ synthesis (coq mutants). Surprisingly, we discovered that the presence of CoQ biosynthetic intermediates impairs assimilation of CoQ into a functional respiratory chain in yeast cells. Moreover, a screen of 40 gene deletions considered to be candidates to prevent exogenous CoQ from rescuing growth of the CoQ-less coq2Δ mutant, identified six novel genes (CDC10, RTS1, RVS161, RVS167, VPS1, and NAT3) as necessary for efficient trafficking of CoQ to mitochondria. The proteins encoded by these genes represent essential steps in the pathways responsible for transport of exogenously supplied CoQ to its functional sites in the cell, and definitively associate CoQ distribution with endocytosis and intracellular vesicular trafficking pathways conserved from yeast to human cells.
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Affiliation(s)
- Lucía Fernández-Del-Río
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, USA
| | - Miranda E Kelly
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, USA
| | - Jaime Contreras
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, USA
| | - Michelle C Bradley
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, USA
| | - Andrew M James
- MRC Mitochondrial Biology Unit, University of Cambridge, UK
| | - Michael P Murphy
- MRC Mitochondrial Biology Unit, University of Cambridge, UK; Department of Medicine, University of Cambridge, UK
| | - Gregory S Payne
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Catherine F Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, USA.
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10
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Eberhardt EL, Ludlam AV, Tan Z, Cianfrocco MA. Miro: A molecular switch at the center of mitochondrial regulation. Protein Sci 2020; 29:1269-1284. [PMID: 32056317 PMCID: PMC7255519 DOI: 10.1002/pro.3839] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/03/2020] [Accepted: 02/06/2020] [Indexed: 12/24/2022]
Abstract
The orchestration of mitochondria within the cell represents a critical aspect of cell biology. At the center of this process is the outer mitochondrial membrane protein, Miro. Miro coordinates diverse cellular processes by regulating connections between organelles and the cytoskeleton that range from mediating contacts between the endoplasmic reticulum and mitochondria to the regulation of both actin and microtubule motor proteins. Recently, a number of cell biological, biochemical, and protein structure studies have helped to characterize the myriad roles played by Miro. In addition to answering questions regarding Miro's function, these studies have opened the door to new avenues in the study of Miro in the cell. This review will focus on summarizing recent findings for Miro's structure, function, and activity while highlighting key questions that remain unanswered.
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Affiliation(s)
- Emily L. Eberhardt
- Life Sciences Institute, Department of Biological ChemistryUniversity of MichiganAnn ArborMichigan
- Cellular and Molecular Biology ProgramUniversity of MichiganAnn ArborMichigan
| | - Anthony V. Ludlam
- Life Sciences Institute, Department of Biological ChemistryUniversity of MichiganAnn ArborMichigan
| | - Zhenyu Tan
- Life Sciences Institute, Department of Biological ChemistryUniversity of MichiganAnn ArborMichigan
- Biophysics ProgramUniversity of MichiganAnn ArborMichigan
| | - Michael A. Cianfrocco
- Life Sciences Institute, Department of Biological ChemistryUniversity of MichiganAnn ArborMichigan
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11
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Watanabe Y, Tamura Y, Kakuta C, Watanabe S, Endo T. Structural basis for interorganelle phospholipid transport mediated by VAT-1. J Biol Chem 2020; 295:3257-3268. [PMID: 32005660 DOI: 10.1074/jbc.ra119.011019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/31/2020] [Indexed: 11/06/2022] Open
Abstract
Eukaryotic cells are compartmentalized to form organelles, whose functions rely on proper phospholipid and protein transport. Here we determined the crystal structure of human VAT-1, a cytosolic soluble protein that was suggested to transfer phosphatidylserine, at 2.2 Å resolution. We found that VAT-1 transferred not only phosphatidylserine but also other acidic phospholipids between membranes in vitro Structure-based mutational analyses showed the presence of a possible lipid-binding cavity at the interface between the two subdomains, and two tyrosine residues in the flexible loops facilitated phospholipid transfer, likely by functioning as a gate to this lipid-binding cavity. We also found that a basic and hydrophobic loop with two tryptophan residues protruded from the molecule and facilitated binding to the acidic-lipid membranes, thereby achieving efficient phospholipid transfer.
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Affiliation(s)
- Yasunori Watanabe
- Department of Bioscience, Graduate School of Agriculture, Ehime University, Matsuyama, Ehime 790-8566, Japan; Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto 603-8555, Japan
| | - Yasushi Tamura
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata 990-8560, Japan
| | - Chika Kakuta
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto 603-8555, Japan
| | - Seiya Watanabe
- Department of Bioscience, Graduate School of Agriculture, Ehime University, Matsuyama, Ehime 790-8566, Japan; Center for Marine Environmental Studies, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Toshiya Endo
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto 603-8555, Japan; Research Center for Protein Dynamics, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto 603-8555, Japan.
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12
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Udagawa O, Ishihara N. Mitochondrial dynamics and interorganellar communication in the development and dysmorphism of mammalian oocytes. J Biochem 2019; 167:257-266. [DOI: 10.1093/jb/mvz093] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 10/30/2019] [Indexed: 12/25/2022] Open
Abstract
AbstractMitochondria play many critical roles in cells, not only by supplying energy, but also by supplying metabolites, buffering Ca2+ levels and regulating apoptosis. During oocyte maturation and subsequent embryo development, mitochondria change their morphology by membrane fusion and fission, and coordinately undergo multiple cellular events with the endoplasmic reticulum (ER) closely apposed. Mitochondrial fusion and fission, known as mitochondrial dynamics, are regulated by family members of dynamin GTPases. Oocytes in animal models with these regulators artificially altered exhibit morphological abnormalities in nearby mitochondria and at the ER interface that are reminiscent of major cytoplasmic dysmorphisms in human assisted reproductive technology, in which a portion of mature oocytes retrieved from patients contain cytoplasmic dysmorphisms associated with mitochondria and ER abnormal morphologies. Understanding organelle morpho-homeostasis in oocytes obtained from animal models will contribute to the development of novel methods for determining oocyte health and for how to deal with dysmorphic oocytes.
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Affiliation(s)
- Osamu Udagawa
- Center for Health and Environmental Risk Research, Integrated Health Risk Research Section, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Naotada Ishihara
- Department of Biological Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- Department of Protein Biochemistry, Institute of Life Science, Kurume University, 67 Asahi, Kurume, Fukuoka 830-0011, Japan
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13
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Miliara X, Tatsuta T, Berry JL, Rouse SL, Solak K, Chorev DS, Wu D, Robinson CV, Matthews S, Langer T. Structural determinants of lipid specificity within Ups/PRELI lipid transfer proteins. Nat Commun 2019; 10:1130. [PMID: 30850607 PMCID: PMC6408443 DOI: 10.1038/s41467-019-09089-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/18/2019] [Indexed: 02/07/2023] Open
Abstract
Conserved lipid transfer proteins of the Ups/PRELI family regulate lipid accumulation in mitochondria by shuttling phospholipids in a lipid-specific manner across the intermembrane space. Here, we combine structural analysis, unbiased genetic approaches in yeast and molecular dynamics simulations to unravel determinants of lipid specificity within the conserved Ups/PRELI family. We present structures of human PRELID1-TRIAP1 and PRELID3b-TRIAP1 complexes, which exert lipid transfer activity for phosphatidic acid and phosphatidylserine, respectively. Reverse yeast genetic screens identify critical amino acid exchanges that broaden and swap their lipid specificities. We find that amino acids involved in head group recognition and the hydrophobicity of flexible loops regulate lipid entry into the binding cavity. Molecular dynamics simulations reveal different membrane orientations of PRELID1 and PRELID3b during the stepwise release of lipids. Our experiments thus define the structural determinants of lipid specificity and the dynamics of lipid interactions by Ups/PRELI proteins.
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Affiliation(s)
- Xeni Miliara
- Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, South Kensington, London, SW7 2AZ, UK
| | - Takashi Tatsuta
- Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Jamie-Lee Berry
- Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, South Kensington, London, SW7 2AZ, UK
| | - Sarah L Rouse
- Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, South Kensington, London, SW7 2AZ, UK
| | - Kübra Solak
- Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Dror S Chorev
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3TA, UK
| | - Di Wu
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3TA, UK
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3TA, UK
| | - Stephen Matthews
- Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, South Kensington, London, SW7 2AZ, UK.
| | - Thomas Langer
- Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931, Cologne, Germany.
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany.
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14
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An Isoprene Lipid-Binding Protein Promotes Eukaryotic Coenzyme Q Biosynthesis. Mol Cell 2019; 73:763-774.e10. [PMID: 30661980 DOI: 10.1016/j.molcel.2018.11.033] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/16/2018] [Accepted: 11/27/2018] [Indexed: 02/06/2023]
Abstract
The biosynthesis of coenzyme Q presents a paradigm for how cells surmount hydrophobic barriers in lipid biology. In eukaryotes, CoQ precursors-among nature's most hydrophobic molecules-must somehow be presented to a series of enzymes peripherally associated with the mitochondrial inner membrane. Here, we reveal that this process relies on custom lipid-binding properties of COQ9. We show that COQ9 repurposes the bacterial TetR fold to bind aromatic isoprenes with high specificity, including CoQ intermediates that likely reside entirely within the bilayer. We reveal a process by which COQ9 associates with cardiolipin-rich membranes and warps the membrane surface to access this cargo. Finally, we identify a molecular interface between COQ9 and the hydroxylase COQ7, motivating a model whereby COQ9 presents intermediates directly to CoQ enzymes. Overall, our results provide a mechanism for how a lipid-binding protein might access, select, and deliver specific cargo from a membrane to promote biosynthesis.
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15
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AhYoung AP, Egea PF. Determining the Lipid-Binding Specificity of SMP Domains: An ERMES Subunit as a Case Study. Methods Mol Biol 2019; 1949:213-235. [PMID: 30790259 DOI: 10.1007/978-1-4939-9136-5_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Membrane contact sites between the endoplasmic reticulum (ER) and mitochondria function as a central hub for the exchange of phospholipids and calcium. The yeast Endoplasmic Reticulum-Mitochondrion Encounter Structure (ERMES) complex is composed of five subunits that tether the ER and mitochondria. Three ERMES subunits (i.e., Mdm12, Mmm1, and Mdm34) contain the synaptotagmin-like mitochondrial lipid-binding protein (SMP) domain. The SMP domain belongs to the tubular lipid-binding protein (TULIP) superfamily, which consists of ubiquitous lipid scavenging and transfer proteins. Herein, we describe the methods for expression and purification of recombinant Mdm12, a bona fide SMP-containing protein, together with the subsequent identification of its bound phospholipids by high-performance thin-layer chromatography (HPTLC) and the characterization of its lipid exchange and transfer functions using lipid displacement and liposome flotation in vitro assays with liposomes as model biological membranes. These methods can be applied to the study and characterization of novel lipid-binding and lipid-transfer proteins.
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Affiliation(s)
- Andrew P AhYoung
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Early Discovery Biochemistry, Genentech Inc., South San Francisco, CA, USA
| | - Pascal F Egea
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- The Molecular Biology Institute, University of California, Los Angeles, CA, USA.
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16
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Lipid exchange at ER-mitochondria contact sites: a puzzle falling into place with quite a few pieces missing. Curr Opin Cell Biol 2018; 57:71-76. [PMID: 30554079 DOI: 10.1016/j.ceb.2018.11.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/20/2018] [Accepted: 11/21/2018] [Indexed: 12/31/2022]
Abstract
Over the last years, the importance of inter-organelle communication has become more and more evident, attested by the fast growing number of newly-identified membrane contact sites (MCS). At MCSs two organelles are connected via protein tethers that bring them in close proximity to facilitate metabolite exchange. In this review, we will focus on the MCSs connecting the ER and mitochondria, which have been implicated in phospholipid transport. While we already know the molecular identity of some tethers, we are still far from understanding the mechanisms underlying the phospholipid transport processes. In vitro studies suggest that some proteins in MCSs are capable of transporting lipids, however only at rates that do not meet the mitochondrial lipid demand. In vivo studies are even more puzzling as it appears that many redundant lipid transport routes, involving various lipid transport proteins and various MCSs, compensate for each other when necessary. Here, we will discuss the challenges in interpreting the data on lipid transport between ER and mitochondria from in vitro and in vivo experiments by highlighting some critical aspects that might be worth addressing in the future.
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17
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Sinzel M, Zeitler A, Dimmer KS. Interaction network of the mitochondrial outer membrane protein Mcp3. FEBS Lett 2018; 592:3210-3220. [PMID: 30192984 DOI: 10.1002/1873-3468.13243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/30/2018] [Accepted: 09/03/2018] [Indexed: 02/04/2023]
Abstract
Mitochondria are organelles containing two membranes that are distinct in composition and function. A role of the mitochondrial outer membrane (MOM) is to mediate contact of the organelle with the rest of the cell. In yeast, the MOM contains about 40 different integral proteins. Recently, we described the MOM protein Mcp3, which can serve as a multicopy suppressor of loss of ERMES complex that mediates mitochondria-endoplasmic reticulum contacts. To shed further light on the role of Mcp3 in the MOM, we analyzed its physical interaction with other proteins. We show that Mcp3 interacts with the MOM protein Om45 and the inner membrane protein Aim19. Our observations hint toward a potential involvement of Mcp3 in a structural and/or functional link between both mitochondrial membranes.
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Affiliation(s)
- Monika Sinzel
- Interfaculty Institute of Biochemistry, University of Tübingen, Germany
| | - Andreas Zeitler
- Interfaculty Institute of Biochemistry, University of Tübingen, Germany
| | - Kai S Dimmer
- Interfaculty Institute of Biochemistry, University of Tübingen, Germany
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18
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Rampelt H, Wollweber F, Gerke C, de Boer R, van der Klei IJ, Bohnert M, Pfanner N, van der Laan M. Assembly of the Mitochondrial Cristae Organizer Mic10 Is Regulated by Mic26–Mic27 Antagonism and Cardiolipin. J Mol Biol 2018; 430:1883-1890. [DOI: 10.1016/j.jmb.2018.04.037] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/20/2018] [Accepted: 04/27/2018] [Indexed: 01/05/2023]
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19
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Molecular hypotheses to explain the shared pathways and underlying pathobiological causes in catatonia and in catatonic presentations in neuropsychiatric disorders. Med Hypotheses 2018. [DOI: 10.1016/j.mehy.2018.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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20
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Non-vesicular lipid trafficking at the endoplasmic reticulum–mitochondria interface. Biochem Soc Trans 2018; 46:437-452. [DOI: 10.1042/bst20160185] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 02/20/2018] [Accepted: 02/22/2018] [Indexed: 12/14/2022]
Abstract
Mitochondria are highly dynamic organelles involved in various cellular processes such as energy production, regulation of calcium homeostasis, lipid trafficking, and apoptosis. To fulfill all these functions and preserve their morphology and dynamic behavior, mitochondria need to maintain a defined protein and lipid composition in both their membranes. The maintenance of mitochondrial membrane identity requires a selective and regulated transport of specific lipids from/to the endoplasmic reticulum (ER) and across the mitochondria outer and inner membranes. Since they are not integrated in the classical vesicular trafficking routes, mitochondria exchange lipids with the ER at sites of close apposition called membrane contact sites. Deregulation of such transport activities results in several pathologies including cancer and neurodegenerative disorders. However, we are just starting to understand the function of ER–mitochondria contact sites in lipid transport, what are the proteins involved and how they are regulated. In this review, we summarize recent insights into lipid transport pathways at the ER–mitochondria interface and discuss the implication of recently identified lipid transfer proteins in these processes.
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21
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Endo T, Tamura Y. Shuttle mission in the mitochondrial intermembrane space. EMBO J 2018; 37:embj.201898993. [PMID: 29382654 DOI: 10.15252/embj.201898993] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Toshiya Endo
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Yasushi Tamura
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata, Japan
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