1
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Messina M, Vaz FM, Rahman S. Mitochondrial membrane synthesis, remodelling and cellular trafficking. J Inherit Metab Dis 2024. [PMID: 38872485 DOI: 10.1002/jimd.12766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/14/2024] [Accepted: 05/21/2024] [Indexed: 06/15/2024]
Abstract
Mitochondria are dynamic cellular organelles with complex roles in metabolism and signalling. Primary mitochondrial disorders are a group of approximately 400 monogenic disorders arising from pathogenic genetic variants impacting mitochondrial structure, ultrastructure and/or function. Amongst these disorders, defects of complex lipid biosynthesis, especially of the unique mitochondrial membrane lipid cardiolipin, and membrane biology are an emerging group characterised by clinical heterogeneity, but with recurrent features including cardiomyopathy, encephalopathy, neurodegeneration, neuropathy and 3-methylglutaconic aciduria. This review discusses lipid synthesis in the mitochondrial membrane, the mitochondrial contact site and cristae organising system (MICOS), mitochondrial dynamics and trafficking, and the disorders associated with defects of each of these processes. We highlight overlapping functions of proteins involved in lipid biosynthesis and protein import into the mitochondria, pointing to an overarching coordination and synchronisation of mitochondrial functions. This review also focuses on membrane interactions between mitochondria and other organelles, namely the endoplasmic reticulum, peroxisomes, lysosomes and lipid droplets. We signpost disorders of these membrane interactions that may explain the observation of secondary mitochondrial dysfunction in heterogeneous pathological processes. Disruption of these organellar interactions ultimately impairs cellular homeostasis and organismal health, highlighting the central role of mitochondria in human health and disease.
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Affiliation(s)
- Martina Messina
- Mitochondrial Research Group, Genetics and Genomic Medicine Department, UCL Great Ormond Street Institute of Child Health, London, UK
- Metabolic Unit, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Frédéric M Vaz
- Department of Laboratory Medicine and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of Metabolism, Amsterdam, The Netherlands
| | - Shamima Rahman
- Mitochondrial Research Group, Genetics and Genomic Medicine Department, UCL Great Ormond Street Institute of Child Health, London, UK
- Metabolic Unit, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
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2
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Launay N, Lopez-Erauskin J, Bianchi P, Guha S, Parameswaran J, Coppa A, Torreni L, Schlüter A, Fourcade S, Paredes-Fuentes AJ, Artuch R, Casasnovas C, Ruiz M, Pujol A. Imbalanced mitochondrial dynamics contributes to the pathogenesis of X-linked adrenoleukodystrophy. Brain 2024; 147:2069-2084. [PMID: 38763511 DOI: 10.1093/brain/awae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/20/2023] [Accepted: 01/21/2024] [Indexed: 05/21/2024] Open
Abstract
The peroxisomal disease adrenoleukodystrophy (X-ALD) is caused by loss of the transporter of very-long-chain fatty acids (VLCFAs), ABCD1. An excess of VLCFAs disrupts essential homeostatic functions crucial for axonal maintenance, including redox metabolism, glycolysis and mitochondrial respiration. As mitochondrial function and morphology are intertwined, we set out to investigate the role of mitochondrial dynamics in X-ALD models. Using quantitative 3D transmission electron microscopy, we revealed mitochondrial fragmentation in corticospinal axons in Abcd1- mice. In patient fibroblasts, an excess of VLCFAs triggers mitochondrial fragmentation through the redox-dependent phosphorylation of DRP1 (DRP1S616). The blockade of DRP1-driven fission by the peptide P110 effectively preserved mitochondrial morphology. Furthermore, mRNA inhibition of DRP1 not only prevented mitochondrial fragmentation but also protected axonal health in a Caenorhabditis elegans model of X-ALD, underscoring DRP1 as a potential therapeutic target. Elevated levels of circulating cell-free mtDNA in patients' CSF align this leukodystrophy with primary mitochondrial disorders. Our findings underscore the intricate interplay between peroxisomal dysfunction, mitochondrial dynamics and axonal integrity in X-ALD, shedding light on potential avenues for therapeutic intervention.
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Affiliation(s)
- Nathalie Launay
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, 28029 Madrid, Spain
| | - Jone Lopez-Erauskin
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
- Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA 92093, USA
| | - Patrizia Bianchi
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
- Physiology and Immunology, Facultat de Medicina, Institut de Neurociències and Department of Cell Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Sanjib Guha
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
- Nautilus Biotechnology, San Carlos, CA 94070, USA
| | - Janani Parameswaran
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
- Department of Cell Biology, Emory University, Atlanta, GA 30322, USA
| | - Andrea Coppa
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Lorenzo Torreni
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
- Programa de Doctorat en Biomedicina, Universitat de Barcelona, 08193 Barcelona, Spain
| | - Agatha Schlüter
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, 28029 Madrid, Spain
| | - Stéphane Fourcade
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, 28029 Madrid, Spain
| | - Abraham J Paredes-Fuentes
- Division of Inborn Errors of Metabolism-IBC, Biochemistry and Molecular Genetics Department, Hospital Clínic de Barcelona, 08028 Barcelona, Spain
| | - Rafael Artuch
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, 28029 Madrid, Spain
- Clinical Biochemistry Department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, 08950 Barcelona, Spain
| | - Carlos Casasnovas
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, 28029 Madrid, Spain
- Neuromuscular Unit, Neurology Department, Bellvitge University Hospital, Universitat de Barcelona, 08907 Lhospitalet de Llobregat, Barcelona, Spain
| | - Montserrat Ruiz
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, 28029 Madrid, Spain
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, 28029 Madrid, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
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3
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Zung N, Aravindan N, Boshnakovska A, Valenti R, Preminger N, Jonas F, Yaakov G, Willoughby MM, Homberg B, Keller J, Kupervaser M, Dezorella N, Dadosh T, Wolf SG, Itkin M, Malitsky S, Brandis A, Barkai N, Fernández-Busnadiego R, Reddi AR, Rehling P, Rapaport D, Schuldiner M. The molecular mechanism of on-demand sterol biosynthesis at organelle contact sites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593285. [PMID: 38766039 PMCID: PMC11100823 DOI: 10.1101/2024.05.09.593285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Contact-sites are specialized zones of proximity between two organelles, essential for organelle communication and coordination. The formation of contacts between the Endoplasmic Reticulum (ER), and other organelles, relies on a unique membrane environment enriched in sterols. However, how these sterol-rich domains are formed and maintained had not been understood. We found that the yeast membrane protein Yet3, the homolog of human BAP31, is localized to multiple ER contact sites. We show that Yet3 interacts with all the enzymes of the post-squalene ergosterol biosynthesis pathway and recruits them to create sterol-rich domains. Increasing sterol levels at ER contacts causes its depletion from the plasma membrane leading to a compensatory reaction and altered cell metabolism. Our data shows that Yet3 provides on-demand sterols at contacts thus shaping organellar structure and function. A molecular understanding of this protein's functions gives new insights into the role of BAP31 in development and pathology.
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Affiliation(s)
- Naama Zung
- Department of Molecular Genetics, Weizmann Institute of Science, Israel
| | - Nitya Aravindan
- Interfaculty Institute of Biochemistry, University of Tuebingen, Germany
| | - Angela Boshnakovska
- Department of Cellular Biochemistry, University Medical Center Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Translational Neuroinflammation and Automated Microscopy, Germany
- Max Planck Institute for Multidisciplinary Sciences, D-37077, Germany
| | - Rosario Valenti
- Department of Molecular Genetics, Weizmann Institute of Science, Israel
| | - Noga Preminger
- Department of Molecular Genetics, Weizmann Institute of Science, Israel
| | - Felix Jonas
- Department of Molecular Genetics, Weizmann Institute of Science, Israel
| | - Gilad Yaakov
- Department of Molecular Genetics, Weizmann Institute of Science, Israel
| | - Mathilda M Willoughby
- School of Chemistry and Biochemistry, Georgia Institute of Technology, USA
- Biochemistry and Molecular Biology Department, University of Nebraska Medical Center, USA
| | - Bettina Homberg
- Department of Cellular Biochemistry, University Medical Center Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Translational Neuroinflammation and Automated Microscopy, Germany
- Max Planck Institute for Multidisciplinary Sciences, D-37077, Germany
| | - Jenny Keller
- University Medical Center Göttingen, Institute for Neuropathology, 37077, Germany
- Collaborative Research Center 1190 "Compartmental Gates and Contact Sites in Cells", University of Göttingen, Germany
| | - Meital Kupervaser
- The De Botton Protein Profiling institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Israel
| | - Nili Dezorella
- Electron Microscopy Unit, Chemical Research Support, Weizmann Institute of Science, Israel
| | - Tali Dadosh
- Electron Microscopy Unit, Chemical Research Support, Weizmann Institute of Science, Israel
| | - Sharon G Wolf
- Electron Microscopy Unit, Chemical Research Support, Weizmann Institute of Science, Israel
| | - Maxim Itkin
- Life Sciences Core Facilities, Weizmann Institute of Science, Israel
| | - Sergey Malitsky
- Life Sciences Core Facilities, Weizmann Institute of Science, Israel
| | - Alexander Brandis
- Life Sciences Core Facilities, Weizmann Institute of Science, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Israel
| | - Rubén Fernández-Busnadiego
- University Medical Center Göttingen, Institute for Neuropathology, 37077, Germany
- Collaborative Research Center 1190 "Compartmental Gates and Contact Sites in Cells", University of Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077, Germany
- Faculty of Physics, University of Göttingen, 37077, Germany
| | - Amit R Reddi
- School of Chemistry and Biochemistry, Georgia Institute of Technology, USA
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Translational Neuroinflammation and Automated Microscopy, Germany
- Max Planck Institute for Multidisciplinary Sciences, D-37077, Germany
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tuebingen, Germany
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Israel
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4
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Enkler L, Spang A. Functional interplay of lipid droplets and mitochondria. FEBS Lett 2024; 598:1235-1251. [PMID: 38268392 DOI: 10.1002/1873-3468.14809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/12/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024]
Abstract
Our body stores energy mostly in form of fatty acids (FAs) in lipid droplets (LDs). From there the FAs can be mobilized and transferred to peroxisomes and mitochondria. This transfer is dependent on close opposition of LDs and mitochondria and peroxisomes and happens at membrane contact sites. However, the composition and the dynamics of these contact sites is not well understood, which is in part due to the dependence on the metabolic state of the cell and on the cell- and tissue-type. Here, we summarize the current knowledge on the contacts between lipid droplets and mitochondria both in mammals and in the yeast Saccharomyces cerevisiae, in which various contact sites are well studied. We discuss possible functions of the contact site and their implication in disease.
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Affiliation(s)
| | - Anne Spang
- Biozentrum, University of Basel, Switzerland
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5
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Bittner E, Stehlik T, Lam J, Dimitrov L, Heimerl T, Schöck I, Harberding J, Dornes A, Heymons N, Bange G, Schuldiner M, Zalckvar E, Bölker M, Schekman R, Freitag J. Proteins that carry dual targeting signals can act as tethers between peroxisomes and partner organelles. PLoS Biol 2024; 22:e3002508. [PMID: 38377076 PMCID: PMC10906886 DOI: 10.1371/journal.pbio.3002508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 03/01/2024] [Accepted: 01/19/2024] [Indexed: 02/22/2024] Open
Abstract
Peroxisomes are organelles with crucial functions in oxidative metabolism. To correctly target to peroxisomes, proteins require specialized targeting signals. A mystery in the field is the sorting of proteins that carry a targeting signal for peroxisomes and as well as for other organelles, such as mitochondria or the endoplasmic reticulum (ER). Exploring several of these proteins in fungal model systems, we observed that they can act as tethers bridging organelles together to create contact sites. We show that in Saccharomyces cerevisiae this mode of tethering involves the peroxisome import machinery, the ER-mitochondria encounter structure (ERMES) at mitochondria and the guided entry of tail-anchored proteins (GET) pathway at the ER. Our findings introduce a previously unexplored concept of how dual affinity proteins can regulate organelle attachment and communication.
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Affiliation(s)
- Elena Bittner
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Thorsten Stehlik
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Jason Lam
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Lazar Dimitrov
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Thomas Heimerl
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Isabelle Schöck
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Jannik Harberding
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Anita Dornes
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Nikola Heymons
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Michael Bölker
- Department of Biology, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Randy Schekman
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Johannes Freitag
- Department of Biology, Philipps-University Marburg, Marburg, Germany
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
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6
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Enkler L, Szentgyörgyi V, Pennauer M, Prescianotto-Baschong C, Riezman I, Wiesyk A, Avraham RE, Spiess M, Zalckvar E, Kucharczyk R, Riezman H, Spang A. Arf1 coordinates fatty acid metabolism and mitochondrial homeostasis. Nat Cell Biol 2023; 25:1157-1172. [PMID: 37400497 PMCID: PMC10415182 DOI: 10.1038/s41556-023-01180-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/05/2023] [Indexed: 07/05/2023]
Abstract
Lipid mobilization through fatty acid β-oxidation is a central process essential for energy production during nutrient shortage. In yeast, this catabolic process starts in the peroxisome from where β-oxidation products enter mitochondria and fuel the tricarboxylic acid cycle. Little is known about the physical and metabolic cooperation between these organelles. Here we found that expression of fatty acid transporters and of the rate-limiting enzyme involved in β-oxidation is decreased in cells expressing a hyperactive mutant of the small GTPase Arf1, leading to an accumulation of fatty acids in lipid droplets. Consequently, mitochondria became fragmented and ATP synthesis decreased. Genetic and pharmacological depletion of fatty acids phenocopied the arf1 mutant mitochondrial phenotype. Although β-oxidation occurs in both mitochondria and peroxisomes in mammals, Arf1's role in fatty acid metabolism is conserved. Together, our results indicate that Arf1 integrates metabolism into energy production by regulating fatty acid storage and utilization, and presumably organelle contact sites.
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Affiliation(s)
| | | | | | | | - Isabelle Riezman
- Department of Biochemistry, NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Aneta Wiesyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Reut Ester Avraham
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | | | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Howard Riezman
- Department of Biochemistry, NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Anne Spang
- Biozentrum, University of Basel, Basel, Switzerland.
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7
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Wozny MR, Di Luca A, Morado DR, Picco A, Khaddaj R, Campomanes P, Ivanović L, Hoffmann PC, Miller EA, Vanni S, Kukulski W. In situ architecture of the ER-mitochondria encounter structure. Nature 2023:10.1038/s41586-023-06050-3. [PMID: 37165187 DOI: 10.1038/s41586-023-06050-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 04/04/2023] [Indexed: 05/12/2023]
Abstract
The endoplasmic reticulum and mitochondria are main hubs of eukaryotic membrane biogenesis that rely on lipid exchange via membrane contact sites1-3, but the underpinning mechanisms remain poorly understood. In yeast, tethering and lipid transfer between the two organelles is mediated by the endoplasmic reticulum-mitochondria encounter structure (ERMES), a four-subunit complex of unresolved stoichiometry and architecture4-6. Here we determined the molecular organization of ERMES within Saccharomyces cerevisiae cells using integrative structural biology by combining quantitative live imaging, cryo-correlative microscopy, subtomogram averaging and molecular modelling. We found that ERMES assembles into approximately 25 discrete bridge-like complexes distributed irregularly across a contact site. Each bridge consists of three synaptotagmin-like mitochondrial lipid binding protein domains oriented in a zig-zag arrangement. Our molecular model of ERMES reveals a pathway for lipids. These findings resolve the in situ supramolecular architecture of a major inter-organelle lipid transfer machinery and provide a basis for the mechanistic understanding of lipid fluxes in eukaryotic cells.
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Affiliation(s)
- Michael R Wozny
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Andrea Di Luca
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Dustin R Morado
- MRC Laboratory of Molecular Biology, Cambridge, UK
- SciLifeLab, Solna, Sweden
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Andrea Picco
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Rasha Khaddaj
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Pablo Campomanes
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Lazar Ivanović
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Patrick C Hoffmann
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | | | - Stefano Vanni
- Department of Biology, University of Fribourg, Fribourg, Switzerland.
| | - Wanda Kukulski
- MRC Laboratory of Molecular Biology, Cambridge, UK.
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland.
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8
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Jansen RL, van den Noort M, Krikken AM, Bibi C, Böhm A, Schuldiner M, Zalckvar E, van der Klei IJ. Novel targeting assay uncovers targeting information within peroxisomal ABC transporter Pxa1. BIOCHIMICA ET BIOPHYSICA ACTA (BBA) - MOLECULAR CELL RESEARCH 2023; 1870:119471. [PMID: 37028652 DOI: 10.1016/j.bbamcr.2023.119471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 03/08/2023] [Accepted: 03/23/2023] [Indexed: 04/08/2023]
Abstract
The mechanism behind peroxisomal membrane protein targeting is still poorly understood, with only two yeast proteins believed to be involved and no consensus targeting sequence. Pex19 is thought to bind peroxisomal membrane proteins in the cytosol, and is subsequently recruited by Pex3 at the peroxisomal surface, followed by protein insertion via a mechanism that is as-yet-unknown. However, some peroxisomal membrane proteins still correctly sort in the absence of Pex3 or Pex19, suggesting that multiple sorting pathways exist. Here, we studied sorting of yeast peroxisomal ABC transporter Pxa1. Co-localization analysis of Pxa1-GFP in a collection of 86 peroxisome-related deletion strains revealed that Pxa1 sorting requires Pex3 and Pex19, while none of the other 84 proteins tested were essential. To identify regions with peroxisomal targeting information in Pxa1, we developed a novel in vivo re-targeting assay, using a reporter consisting of the mitochondrial ABC transporter Mdl1 lacking its N-terminal mitochondrial targeting signal. Using this assay, we showed that the N-terminal 95 residues of Pxa1 are sufficient for retargeting this reporter to peroxisomes. Interestingly, truncated Pxa1 lacking residues 1-95 still localized to peroxisomes. This was confirmed via localization of various Pxa1 truncation and deletion constructs. However, localisation of Pxa1 lacking residues 1-95 depended on the presence of its interaction partner Pxa2, indicating that this truncated protein does not contain a true targeting signal.
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9
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New discoveries in ER-mitochondria communication. Biochem Soc Trans 2023; 51:571-577. [PMID: 36892405 DOI: 10.1042/bst20221305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/17/2023] [Accepted: 02/17/2023] [Indexed: 03/10/2023]
Abstract
The study of endoplasmic reticulum (ER)-mitochondria communication is a vast and expanding field with many novel developments in the past few years. In this mini-review, we focus on several recent publications that identify novel functions of tether complexes, in particular autophagy regulation and lipid droplet biogenesis. We review novel findings that shed light on the role of triple contacts between ER and mitochondria with peroxisomes or lipid droplets as the third player. We also summarize recent findings on the role of ER-mitochondria contacts in human neurodegenerative diseases, which implicate either enhanced or reduced ER-mitochondria contacts in neurodegeneration. Taken together, the discussed studies highlight the need for further research into the role of triple organelle contacts, as well as into the exact mechanisms of increased and decreased ER-mitochondria contacts in neurodegeneration.
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10
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Deori NM, Nagotu S. Peroxisome biogenesis and inter-organelle communication: an indispensable role for Pex11 and Pex30 family proteins in yeast. Curr Genet 2022; 68:537-550. [PMID: 36242632 DOI: 10.1007/s00294-022-01254-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 11/26/2022]
Abstract
Peroxisomes are highly dynamic organelles present in most eukaryotic cells. They also play an important role in human health and the optimum functioning of cells. An extensive repertoire of proteins is associated with the biogenesis and function of these organelles. Two protein families that are involved in regulating peroxisome number in a cell directly or indirectly are Pex11 and Pex30. Interestingly, these proteins are also reported to regulate the contact sites between peroxisomes and other cell organelles such as mitochondria, endoplasmic reticulum and lipid droplets. In this manuscript, we review our current knowledge of the role of these proteins in peroxisome biogenesis in various yeast species. Further, we also discuss in detail the role of these protein families in the regulation of inter-organelle contacts in yeast.
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Affiliation(s)
- Nayan Moni Deori
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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11
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Bittner E, Stehlik T, Freitag J. Sharing the wealth: The versatility of proteins targeted to peroxisomes and other organelles. Front Cell Dev Biol 2022; 10:934331. [PMID: 36225313 PMCID: PMC9549241 DOI: 10.3389/fcell.2022.934331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Peroxisomes are eukaryotic organelles with critical functions in cellular energy and lipid metabolism. Depending on the organism, cell type, and developmental stage, they are involved in numerous other metabolic and regulatory pathways. Many peroxisomal functions require factors also relevant to other cellular compartments. Here, we review proteins shared by peroxisomes and at least one different site within the cell. We discuss the mechanisms to achieve dual targeting, their regulation, and functional consequences. Characterization of dual targeting is fundamental to understand how peroxisomes are integrated into the metabolic and regulatory circuits of eukaryotic cells.
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Affiliation(s)
| | | | - Johannes Freitag
- Department of Biology, Philipps-University Marburg, Marburg, Germany
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12
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Asif N, Lin F, Li L, Zhu X, Nawaz S. Regulation of Autophagy Machinery in Magnaporthe oryzae. Int J Mol Sci 2022; 23:8366. [PMID: 35955497 PMCID: PMC9369213 DOI: 10.3390/ijms23158366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/15/2022] [Accepted: 07/26/2022] [Indexed: 01/18/2023] Open
Abstract
Plant diseases cause substantial loss to crops all over the world, reducing the quality and quantity of agricultural goods significantly. One of the world's most damaging plant diseases, rice blast poses a substantial threat to global food security. Magnaporthe oryzae causes rice blast disease, which challenges world food security by causing substantial damage in rice production annually. Autophagy is an evolutionarily conserved breakdown and recycling system in eukaryotes that regulate homeostasis, stress adaption, and programmed cell death. Recently, new studies found that the autophagy process plays a vital role in the pathogenicity of M. oryzae and the regulation mechanisms are gradually clarified. Here we present a brief summary of the recent advances, concentrating on the new findings of autophagy regulation mechanisms and summarize some autophagy-related techniques in rice blast fungus. This review will help readers to better understand the relationship between autophagy and the virulence of plant pathogenic fungi.
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Affiliation(s)
- Nida Asif
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China;
| | - Fucheng Lin
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China;
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (L.L.); (X.Z.)
| | - Lin Li
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (L.L.); (X.Z.)
| | - Xueming Zhu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (L.L.); (X.Z.)
| | - Sehar Nawaz
- Center of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture Faisalabad, Faisalabad 38040, Pakistan;
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13
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Goto-Yamada S, Oikawa K, Yamato KT, Kanai M, Hikino K, Nishimura M, Mano S. Image-Based Analysis Revealing the Molecular Mechanism of Peroxisome Dynamics in Plants. Front Cell Dev Biol 2022; 10:883491. [PMID: 35592252 PMCID: PMC9110829 DOI: 10.3389/fcell.2022.883491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/15/2022] [Indexed: 11/13/2022] Open
Abstract
Peroxisomes are present in eukaryotic cells and have essential roles in various biological processes. Plant peroxisomes proliferate by de novo biosynthesis or division of pre-existing peroxisomes, degrade, or replace metabolic enzymes, in response to developmental stages, environmental changes, or external stimuli. Defects of peroxisome functions and biogenesis alter a variety of biological processes and cause aberrant plant growth. Traditionally, peroxisomal function-based screening has been employed to isolate Arabidopsis thaliana mutants that are defective in peroxisomal metabolism, such as lipid degradation and photorespiration. These analyses have revealed that the number, subcellular localization, and activity of peroxisomes are closely related to their efficient function, and the molecular mechanisms underlying peroxisome dynamics including organelle biogenesis, protein transport, and organelle interactions must be understood. Various approaches have been adopted to identify factors involved in peroxisome dynamics. With the development of imaging techniques and fluorescent proteins, peroxisome research has been accelerated. Image-based analyses provide intriguing results concerning the movement, morphology, and number of peroxisomes that were hard to obtain by other approaches. This review addresses image-based analysis of peroxisome dynamics in plants, especially A. thaliana and Marchantia polymorpha.
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Affiliation(s)
- Shino Goto-Yamada
- Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Kazusato Oikawa
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Katsuyuki T. Yamato
- Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
| | - Masatake Kanai
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
| | - Kazumi Hikino
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
| | - Mikio Nishimura
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe, Japan
| | - Shoji Mano
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
- *Correspondence: Shoji Mano
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14
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Hijazi I, Wang E, Orozco M, Pelton S, Chang A. Peroxisomal support of mitochondrial respiratory efficiency promotes ER stress survival. J Cell Sci 2022; 135:273605. [PMID: 34854901 PMCID: PMC8767275 DOI: 10.1242/jcs.259254] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/18/2021] [Indexed: 01/12/2023] Open
Abstract
Endoplasmic reticulum stress (ERS) occurs when cellular demand for protein folding exceeds the capacity of the organelle. Adaptation and cell survival in response to ERS requires a critical contribution by mitochondria and peroxisomes. During ERS responses, mitochondrial respiration increases to ameliorate reactive oxygen species (ROS) accumulation. We now show in yeast that peroxisome abundance also increases to promote an adaptive response. In pox1Δ cells, which are defective in peroxisomal β-oxidation of fatty acids, the respiratory response to ERS is impaired and ROS accrues. However, the respiratory response to ERS is rescued and ROS production is mitigated in pox1Δ cells overexpressing Mpc1, the mitochondrial pyruvate carrier that provides another source of acetyl CoA to fuel the tricarboxylic acid cycle and oxidative phosphorylation. Using proteomics, select mitochondrial proteins were identified that undergo upregulation upon ERS to remodel the respiratory machinery. The abundance of several peroxisome-based proteins was also increased, corroborating the role of peroxisomes in ERS adaptation. Finally, ERS stimulates assembly of respiratory complexes into higher-order supercomplexes, underlying increased electron transfer efficiency. Our results highlight peroxisomal and mitochondrial support for ERS adaptation to favor cell survival.
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15
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Friedman JR. Mitochondria from the Outside in: The Relationship Between Inter-Organelle Crosstalk and Mitochondrial Internal Organization. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2022; 5:10.1177/25152564221133267. [PMID: 36329759 PMCID: PMC9629538 DOI: 10.1177/25152564221133267] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A fundamental role of membrane-bound organelles is the compartmentalization and organization of cellular processes. Mitochondria perform an immense number of metabolic chemical reactions and to efficiently regulate these, the organelle organizes its inner membrane into distinct morphological domains, including its characteristic cristae membranes. In recent years, a structural feature of increasing apparent importance is the inter-connection between the mitochondrial exterior and other organelles at membrane contact sites (MCSs). Mitochondria form MCSs with almost every other organelle in the cell, including the endoplasmic reticulum, lipid droplets, and lysosomes, to coordinate global cellular metabolism with mitochondrial metabolism. However, these MCSs not only facilitate the transport of metabolites between organelles, but also directly impinge on the physical shape and functional organization inside mitochondria. In this review, we highlight recent advances in our understanding of how physical connections between other organelles and mitochondria both directly and indirectly influence the internal architecture of mitochondria.
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Affiliation(s)
- Jonathan R Friedman
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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16
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Joshi AS. Peroxisomal Membrane Contact Sites in Yeasts. Front Cell Dev Biol 2021; 9:735031. [PMID: 34869317 PMCID: PMC8640217 DOI: 10.3389/fcell.2021.735031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/29/2021] [Indexed: 11/13/2022] Open
Abstract
Peroxisomes are ubiquitous, single membrane-bound organelles that play a crucial role in lipid metabolism and human health. While peroxisome number is maintained by the division of existing peroxisomes, nascent peroxisomes can be generated from the endoplasmic reticulum (ER) membrane in yeasts. During formation and proliferation, peroxisomes maintain membrane contacts with the ER. In addition to the ER, contacts between peroxisomes and other organelles such as lipid droplets, mitochondria, vacuole, and plasma membrane have been reported. These membrane contact sites (MCS) are dynamic and important for cellular function. This review focuses on the recent developments in peroxisome biogenesis and the functional importance of peroxisomal MCS in yeasts.
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Affiliation(s)
- Amit S Joshi
- Department of Biochemistry and Cell and Molecular Biology, University of Tennessee, Knoxville, TN, United States
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17
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Valli M, Grillitsch K, Grünwald-Gruber C, Tatto NE, Hrobath B, Klug L, Ivashov V, Hauzmayer S, Koller M, Tir N, Leisch F, Gasser B, Graf AB, Altmann F, Daum G, Mattanovich D. A subcellular proteome atlas of the yeast Komagataella phaffii. FEMS Yeast Res 2021; 20:5700286. [PMID: 31922548 PMCID: PMC6981350 DOI: 10.1093/femsyr/foaa001] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/09/2020] [Indexed: 12/11/2022] Open
Abstract
The compartmentalization of metabolic and regulatory pathways is a common pattern of living organisms. Eukaryotic cells are subdivided into several organelles enclosed by lipid membranes. Organelle proteomes define their functions. Yeasts, as simple eukaryotic single cell organisms, are valuable models for higher eukaryotes and frequently used for biotechnological applications. While the subcellular distribution of proteins is well studied in Saccharomyces cerevisiae, this is not the case for other yeasts like Komagataella phaffii (syn. Pichia pastoris). Different to most well-studied yeasts, K. phaffii can grow on methanol, which provides specific features for production of heterologous proteins and as a model for peroxisome biology. We isolated microsomes, very early Golgi, early Golgi, plasma membrane, vacuole, cytosol, peroxisomes and mitochondria of K. phaffii from glucose- and methanol-grown cultures, quantified their proteomes by liquid chromatography-electrospray ionization-mass spectrometry of either unlabeled or tandem mass tag-labeled samples. Classification of the proteins by their relative enrichment, allowed the separation of enriched proteins from potential contaminants in all cellular compartments except the peroxisomes. We discuss differences to S. cerevisiae, outline organelle specific findings and the major metabolic pathways and provide an interactive map of the subcellular localization of proteins in K. phaffii.
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Affiliation(s)
- Minoska Valli
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Karlheinz Grillitsch
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria
| | - Clemens Grünwald-Gruber
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Nadine E Tatto
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Bernhard Hrobath
- Institute of Statistics, University of Natural Resources and Life Sciences, Peter-Jordan-Straße 82, 1190 Vienna, Austria
| | - Lisa Klug
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010, Graz, Austria
| | - Vasyl Ivashov
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010, Graz, Austria
| | - Sandra Hauzmayer
- School of Bioengineering, University of Applied Sciences FH-Campus Vienna, Muthgasse 11, 1190 Vienna, Austria
| | - Martina Koller
- School of Bioengineering, University of Applied Sciences FH-Campus Vienna, Muthgasse 11, 1190 Vienna, Austria
| | - Nora Tir
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Friedrich Leisch
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Institute of Statistics, University of Natural Resources and Life Sciences, Peter-Jordan-Straße 82, 1190 Vienna, Austria
| | - Brigitte Gasser
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Alexandra B Graf
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,School of Bioengineering, University of Applied Sciences FH-Campus Vienna, Muthgasse 11, 1190 Vienna, Austria
| | - Friedrich Altmann
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Günther Daum
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010, Graz, Austria
| | - Diethard Mattanovich
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
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18
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Frankovsky J, Vozáriková V, Nosek J, Tomáška Ľ. Mitochondrial protein phosphorylation in yeast revisited. Mitochondrion 2021; 57:148-162. [PMID: 33412333 DOI: 10.1016/j.mito.2020.12.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/23/2020] [Accepted: 12/30/2020] [Indexed: 12/16/2022]
Abstract
Protein phosphorylation is one of the best-known post-translational modifications occurring in all domains of life. In eukaryotes, protein phosphorylation affects all cellular compartments including mitochondria. High-throughput techniques of mass spectrometry combined with cell fractionation and biochemical methods yielded thousands of phospho-sites on hundreds of mitochondrial proteins. We have compiled the information on mitochondrial protein kinases and phosphatases and their substrates in Saccharomyces cerevisiae and provide the current state-of-the-art overview of mitochondrial protein phosphorylation in this model eukaryote. Using several examples, we describe emerging features of the yeast mitochondrial phosphoproteome and present challenges lying ahead in this exciting field.
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Affiliation(s)
- Jan Frankovsky
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Veronika Vozáriková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Ľubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia.
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19
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Ray B, Bhat A, Mahalakshmi AM, Tuladhar S, Bishir M, Mohan SK, Veeraraghavan VP, Chandra R, Essa MM, Chidambaram SB, Sakharkar MK. Mitochondrial and Organellar Crosstalk in Parkinson's Disease. ASN Neuro 2021; 13:17590914211028364. [PMID: 34304614 PMCID: PMC8317254 DOI: 10.1177/17590914211028364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/04/2021] [Accepted: 06/07/2021] [Indexed: 12/17/2022] Open
Abstract
Mitochondrial dysfunction is a well-established pathological event in Parkinson's disease (PD). Proteins misfolding and its impaired cellular clearance due to altered autophagy/mitophagy/pexophagy contribute to PD progression. It has been shown that mitochondria have contact sites with endoplasmic reticulum (ER), peroxisomes and lysosomes that are involved in regulating various physiological processes. In pathological conditions, the crosstalk at the contact sites initiates alterations in intracellular vesicular transport, calcium homeostasis and causes activation of proteases, protein misfolding and impairment of autophagy. Apart from the well-reported molecular changes like mitochondrial dysfunction, impaired autophagy/mitophagy and oxidative stress in PD, here we have summarized the recent scientific reports to provide the mechanistic insights on the altered communications between ER, peroxisomes, and lysosomes at mitochondrial contact sites. Furthermore, the manuscript elaborates on the contributions of mitochondrial contact sites and organelles dysfunction to the pathogenesis of PD and suggests potential therapeutic targets.
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Affiliation(s)
- Bipul Ray
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru, India
- Centre for Experimental Pharmacology and Toxicology, Central Animal Facility, JSS Academy of Higher Education & Research, Mysuru, India
| | - Abid Bhat
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru, India
- Centre for Experimental Pharmacology and Toxicology, Central Animal Facility, JSS Academy of Higher Education & Research, Mysuru, India
| | | | - Sunanda Tuladhar
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru, India
- Centre for Experimental Pharmacology and Toxicology, Central Animal Facility, JSS Academy of Higher Education & Research, Mysuru, India
| | - Muhammed Bishir
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru, India
| | - Surapaneni Krishna Mohan
- Department of Biochemistry, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai – 600123, India
| | - Vishnu Priya Veeraraghavan
- Department of Biochemistry, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai - 600 077, India
| | - Ramesh Chandra
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi, 110007, India
- Dr. B. R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi, 110007, India
| | - Musthafa Mohamed Essa
- Department of Food Science and Nutrition, CAMS, Sultan Qaboos University, Muscat, Oman
- Aging and Dementia Research Group, Sultan Qaboos University, Muscat, Sultanate of Oman
- Visiting Professor, Biomedical Sciences department, University of Pacific, Sacramento, CA, USA
| | - Saravana Babu Chidambaram
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru, India
- Centre for Experimental Pharmacology and Toxicology, Central Animal Facility, JSS Academy of Higher Education & Research, Mysuru, India
| | - Meena Kishore Sakharkar
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, SK- S7N 5A2, Canada
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20
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Shin JJH, Crook OM, Borgeaud AC, Cattin-Ortolá J, Peak-Chew SY, Breckels LM, Gillingham AK, Chadwick J, Lilley KS, Munro S. Spatial proteomics defines the content of trafficking vesicles captured by golgin tethers. Nat Commun 2020; 11:5987. [PMID: 33239640 PMCID: PMC7689464 DOI: 10.1038/s41467-020-19840-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023] Open
Abstract
Intracellular traffic between compartments of the secretory and endocytic pathways is mediated by vesicle-based carriers. The proteomes of carriers destined for many organelles are ill-defined because the vesicular intermediates are transient, low-abundance and difficult to purify. Here, we combine vesicle relocalisation with organelle proteomics and Bayesian analysis to define the content of different endosome-derived vesicles destined for the trans-Golgi network (TGN). The golgin coiled-coil proteins golgin-97 and GCC88, shown previously to capture endosome-derived vesicles at the TGN, were individually relocalised to mitochondria and the content of the subsequently re-routed vesicles was determined by organelle proteomics. Our findings reveal 45 integral and 51 peripheral membrane proteins re-routed by golgin-97, evidence for a distinct class of vesicles shared by golgin-97 and GCC88, and various cargoes specific to individual golgins. These results illustrate a general strategy for analysing intracellular sub-proteomes by combining acute cellular re-wiring with high-resolution spatial proteomics.
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Affiliation(s)
- John J H Shin
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Oliver M Crook
- The Milner Therapeutics Institute, University of Cambridge, Cambridge, CB2 0AW, UK
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
- MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SR, UK
| | - Alicia C Borgeaud
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Jérôme Cattin-Ortolá
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Sew Y Peak-Chew
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Lisa M Breckels
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Alison K Gillingham
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Jessica Chadwick
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Kathryn S Lilley
- The Milner Therapeutics Institute, University of Cambridge, Cambridge, CB2 0AW, UK
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Sean Munro
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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21
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Navarro-Espíndola R, Suaste-Olmos F, Peraza-Reyes L. Dynamic Regulation of Peroxisomes and Mitochondria during Fungal Development. J Fungi (Basel) 2020; 6:E302. [PMID: 33233491 PMCID: PMC7711908 DOI: 10.3390/jof6040302] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 12/11/2022] Open
Abstract
Peroxisomes and mitochondria are organelles that perform major functions in the cell and whose activity is very closely associated. In fungi, the function of these organelles is critical for many developmental processes. Recent studies have disclosed that, additionally, fungal development comprises a dynamic regulation of the activity of these organelles, which involves a developmental regulation of organelle assembly, as well as a dynamic modulation of the abundance, distribution, and morphology of these organelles. Furthermore, for many of these processes, the dynamics of peroxisomes and mitochondria are governed by common factors. Notably, intense research has revealed that the process that drives the division of mitochondria and peroxisomes contributes to several developmental processes-including the formation of asexual spores, the differentiation of infective structures by pathogenic fungi, and sexual development-and that these processes rely on selective removal of these organelles via autophagy. Furthermore, evidence has been obtained suggesting a coordinated regulation of organelle assembly and dynamics during development and supporting the existence of regulatory systems controlling fungal development in response to mitochondrial activity. Gathered information underscores an important role for mitochondrial and peroxisome dynamics in fungal development and suggests that this process involves the concerted activity of these organelles.
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Affiliation(s)
| | | | - Leonardo Peraza-Reyes
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (R.N.-E.); (F.S.-O.)
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22
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Grossmann D, Berenguer-Escuder C, Chemla A, Arena G, Krüger R. The Emerging Role of RHOT1/Miro1 in the Pathogenesis of Parkinson's Disease. Front Neurol 2020; 11:587. [PMID: 33041957 PMCID: PMC7523470 DOI: 10.3389/fneur.2020.00587] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/22/2020] [Indexed: 12/16/2022] Open
Abstract
The expected increase in prevalence of Parkinson's disease (PD) as the most common neurodegenerative movement disorder over the next years underscores the need for a better understanding of the underlying molecular pathogenesis. Here, first insights provided by genetics over the last two decades, such as dysfunction of molecular and organellar quality control, are described. The mechanisms involved relate to impaired intracellular calcium homeostasis and mitochondrial dynamics, which are tightly linked to the cross talk between the endoplasmic reticulum (ER) and mitochondria. A number of proteins related to monogenic forms of PD have been mapped to these pathways, i.e., PINK1, Parkin, LRRK2, and α-synuclein. Recently, Miro1 was identified as an important player, as several studies linked Miro1 to mitochondrial quality control by PINK1/Parkin-mediated mitophagy and mitochondrial transport. Moreover, Miro1 is an important regulator of mitochondria-ER contact sites (MERCs), where it acts as a sensor for cytosolic calcium levels. The involvement of Miro1 in the pathogenesis of PD was recently confirmed by genetic evidence based on the first PD patients with heterozygous mutations in RHOT1/Miro1. Patient-based cellular models from RHOT1/Miro1 mutation carriers showed impaired calcium homeostasis, structural alterations of MERCs, and increased mitochondrial clearance. To account for the emerging role of Miro1, we present a comprehensive overview focusing on the role of this protein in PD-related neurodegeneration and highlighting new developments in our understanding of Miro1, which provide new avenues for neuroprotective therapies for PD patients.
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Affiliation(s)
- Dajana Grossmann
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg.,Section for Translational Neurodegeneration "Albrecht Kossel", Department of Neurology, Universitätsmedizin Rostock, Rostock, Germany
| | - Clara Berenguer-Escuder
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Axel Chemla
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Giuseppe Arena
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Rejko Krüger
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg.,Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg, Luxembourg.,Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
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23
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Peruzzo R, Costa R, Bachmann M, Leanza L, Szabò I. Mitochondrial Metabolism, Contact Sites and Cellular Calcium Signaling: Implications for Tumorigenesis. Cancers (Basel) 2020; 12:E2574. [PMID: 32927611 PMCID: PMC7564994 DOI: 10.3390/cancers12092574] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/01/2020] [Accepted: 09/07/2020] [Indexed: 12/11/2022] Open
Abstract
Mitochondria are organelles that are mainly involved in the generation of ATP by cellular respiration. In addition, they modulate several intracellular functions, ranging from cell proliferation and differentiation to cell death. Importantly, mitochondria are social and can interact with other organelles, such as the Endoplasmic Reticulum, lysosomes and peroxisomes. This symbiotic relationship gives advantages to both partners in regulating some of their functions related to several aspects of cell survival, metabolism, sensitivity to cell death and metastasis, which can all finally contribute to tumorigenesis. Moreover, growing evidence indicates that modulation of the length and/or numbers of these contacts, as well as of the distance between the two engaged organelles, impacts both on their function as well as on cellular signaling. In this review, we discuss recent advances in the field of contacts and communication between mitochondria and other intracellular organelles, focusing on how the tuning of mitochondrial function might impact on both the interaction with other organelles as well as on intracellular signaling in cancer development and progression, with a special focus on calcium signaling.
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Affiliation(s)
| | | | | | - Luigi Leanza
- Department of Biology, University of Padova, 35131 Padova, Italy; (R.P.); (R.C.); (M.B.); (I.S.)
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24
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Liao Y, Dong Y, Cheng J. The Molecular Determinants of Mitochondrial Membrane Contact With ER, Lysosomes and Peroxisomes in Neuronal Physiology and Pathology. Front Cell Neurosci 2020; 14:194. [PMID: 32848610 PMCID: PMC7427582 DOI: 10.3389/fncel.2020.00194] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 06/05/2020] [Indexed: 11/24/2022] Open
Abstract
Membrane tethering is an important communication method for membrane-packaged organelles. Mitochondria are organelles with a bilayer membrane, and the membrane contact between mitochondria and other organelles is indispensable for maintaining cellular homeostasis. Increased levels of molecular determinants that mediate the membrane contact between mitochondria and other organelles, and their functions, have been revealed in recent years. In this review article, we aim to summarize the findings on the tethering between mitochondria and other organelles in physiological or pathological conditions, and discuss their roles in cellular homeostasis, neural activity, and neurodegenerative diseases.
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Affiliation(s)
- Yajin Liao
- Center on Translational Neuroscience, College of Life & Environmental Science, Minzu University of China, Beijing, China
| | - Yuan Dong
- Department of Biochemistry, Medical College, Qingdao University, Qingdao, China
| | - Jinbo Cheng
- Center on Translational Neuroscience, College of Life & Environmental Science, Minzu University of China, Beijing, China
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25
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Silva BSC, DiGiovanni L, Kumar R, Carmichael RE, Kim PK, Schrader M. Maintaining social contacts: The physiological relevance of organelle interactions. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118800. [PMID: 32712071 PMCID: PMC7377706 DOI: 10.1016/j.bbamcr.2020.118800] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/12/2020] [Accepted: 07/19/2020] [Indexed: 02/07/2023]
Abstract
Membrane-bound organelles in eukaryotic cells form an interactive network to coordinate and facilitate cellular functions. The formation of close contacts, termed "membrane contact sites" (MCSs), represents an intriguing strategy for organelle interaction and coordinated interplay. Emerging research is rapidly revealing new details of MCSs. They represent ubiquitous and diverse structures, which are important for many aspects of cell physiology and homeostasis. Here, we provide a comprehensive overview of the physiological relevance of organelle contacts. We focus on mitochondria, peroxisomes, the Golgi complex and the plasma membrane, and discuss the most recent findings on their interactions with other subcellular organelles and their multiple functions, including membrane contacts with the ER, lipid droplets and the endosomal/lysosomal compartment.
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Affiliation(s)
- Beatriz S C Silva
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter EX4 4QD, Devon, UK
| | - Laura DiGiovanni
- Program in Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Rechal Kumar
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter EX4 4QD, Devon, UK
| | - Ruth E Carmichael
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter EX4 4QD, Devon, UK.
| | - Peter K Kim
- Program in Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| | - Michael Schrader
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter EX4 4QD, Devon, UK.
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26
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Bohnert M. Tether Me, Tether Me Not—Dynamic Organelle Contact Sites in Metabolic Rewiring. Dev Cell 2020; 54:212-225. [DOI: 10.1016/j.devcel.2020.06.026] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/17/2020] [Accepted: 06/20/2020] [Indexed: 02/04/2023]
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27
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Zung N, Schuldiner M. New horizons in mitochondrial contact site research. Biol Chem 2020; 401:793-809. [PMID: 32324151 DOI: 10.1515/hsz-2020-0133] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/14/2020] [Indexed: 12/18/2022]
Abstract
Contact sites, areas where two organelles are held in close proximity through the action of molecular tethers, enable non-vesicular communication between compartments. Mitochondria have been center stage in the contact site field since the discovery of the first contact between mitochondria and the endoplasmic reticulum (ER) over 60 years ago. However, only now, in the last decade, has there been a burst of discoveries regarding contact site biology in general and mitochondrial contacts specifically. The number and types of characterized contacts increased dramatically, new molecular mechanisms enabling contact formation were discovered, additional unexpected functions for contacts were shown, and their roles in cellular and organismal physiology were emphasized. Here, we focus on mitochondria as we highlight the most recent developments, future goals and unresolved questions in the field.
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Affiliation(s)
- Naama Zung
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
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28
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Germain K, Kim PK. Pexophagy: A Model for Selective Autophagy. Int J Mol Sci 2020; 21:ijms21020578. [PMID: 31963200 PMCID: PMC7013971 DOI: 10.3390/ijms21020578] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/09/2020] [Accepted: 01/13/2020] [Indexed: 01/03/2023] Open
Abstract
The removal of damaged or superfluous organelles from the cytosol by selective autophagy is required to maintain organelle function, quality control and overall cellular homeostasis. Precisely how substrate selectivity is achieved, and how individual substrates are degraded during selective autophagy in response to both extracellular and intracellular cues is not well understood. The aim of this review is to highlight pexophagy, the autophagic degradation of peroxisomes, as a model for selective autophagy. Peroxisomes are dynamic organelles whose abundance is rapidly modulated in response to metabolic demands. Peroxisomes are routinely turned over by pexophagy for organelle quality control yet can also be degraded by pexophagy in response to external stimuli such as amino acid starvation or hypoxia. This review discusses the molecular machinery and regulatory mechanisms governing substrate selectivity during both quality-control pexophagy and pexophagy in response to external stimuli, in yeast and mammalian systems. We draw lessons from pexophagy to infer how the cell may coordinate the degradation of individual substrates by selective autophagy across different cellular cues.
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Affiliation(s)
- Kyla Germain
- Cell Biology Program, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada;
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Peter K. Kim
- Cell Biology Program, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada;
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
- Correspondence: ; Tel.: +1-416-813-5983
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29
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Schrader M, Kamoshita M, Islinger M. Organelle interplay-peroxisome interactions in health and disease. J Inherit Metab Dis 2020; 43:71-89. [PMID: 30864148 PMCID: PMC7041636 DOI: 10.1002/jimd.12083] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/28/2019] [Accepted: 03/06/2019] [Indexed: 01/04/2023]
Abstract
Peroxisomes are multifunctional, dynamic, membrane-bound organelles with important functions in cellular lipid metabolism, rendering them essential for human health and development. Important roles for peroxisomes in signaling and the fine-tuning of cellular processes are emerging, which integrate them in a complex network of interacting cellular compartments. Like many other organelles, peroxisomes communicate through membrane contact sites. For example, peroxisomal growth, positioning, and lipid metabolism involves contacts with the endoplasmic reticulum (ER). Here, we discuss the most recent findings on peroxisome-organelle interactions including peroxisome-ER interplay at membrane contacts sites, and functional interplay with mitochondria, lysosomes, and lipid droplets in mammalian cells. We address tether proteins, metabolic cooperation, and the impact of peroxisome interactions on human health and disease.
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Affiliation(s)
- Michael Schrader
- College of Life and Environmental Sciences, BiosciencesUniversity of ExeterExeterUK
| | - Maki Kamoshita
- College of Life and Environmental Sciences, BiosciencesUniversity of ExeterExeterUK
| | - Markus Islinger
- Institute of Neuroanatomy, Center for Biomedicine and Medical Technology Mannheim, Medical Faculty ManheimUniversity of HeidelbergMannheimGermany
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30
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Staying in Healthy Contact: How Peroxisomes Interact with Other Cell Organelles. Trends Mol Med 2019; 26:201-214. [PMID: 31727543 DOI: 10.1016/j.molmed.2019.09.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/24/2019] [Accepted: 09/24/2019] [Indexed: 11/24/2022]
Abstract
Peroxisomes share extensive metabolic connections with other cell organelles. Membrane contact sites (MCSs) establish and maintain such interactions, and they are vital for organelle positioning and motility. In the past few years peroxisome interactions and MCSs with other cellular organelles have been explored extensively, resulting in the identification of new MCSs, the tethering molecules involved, and their functional characterization. Defective tethering and compartmental communication can lead to pathological conditions that can be termed 'organelle interaction diseases'. We review peroxisome-organelle interactions in mammals and summarize the most recent knowledge of mammalian peroxisomal organelle contacts in health and disease.
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31
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Komath SS, Singh SL, Pratyusha VA, Sah SK. Generating anchors only to lose them: The unusual story of glycosylphosphatidylinositol anchor biosynthesis and remodeling in yeast and fungi. IUBMB Life 2019; 70:355-383. [PMID: 29679465 DOI: 10.1002/iub.1734] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 02/16/2018] [Accepted: 02/22/2018] [Indexed: 02/06/2023]
Abstract
Glycosylphosphatidylinositol (GPI)-anchored proteins (GPI-APs) are present ubiquitously at the cell surface in all eukaryotes. They play a crucial role in the interaction of the cell with its external environment, allowing the cell to receive signals, respond to challenges, and mediate adhesion. In yeast and fungi, they also participate in the structural integrity of the cell wall and are often essential for survival. Roughly four decades after the discovery of the first GPI-APs, this review provides an overview of the insights gained from studies of the GPI biosynthetic pathway and the future challenges in the field. In particular, we focus on the biosynthetic pathway in Saccharomyces cerevisiae, which has for long been studied as a model organism. Where available, we also provide information about the GPI biosynthetic steps in other yeast/ fungi. Although the core structure of the GPI anchor is conserved across organisms, several variations are built into the biosynthetic pathway. The present Review specifically highlights these variations and their implications. There is growing evidence to suggest that several phenotypes are common to GPI deficiency and should be expected in GPI biosynthetic mutants. However, it appears that several phenotypes are unique to a specific step in the pathway and may even be species-specific. These could suggest the points at which the GPI biosynthetic pathway intersects with other important cellular pathways and could be points of regulation. They could be of particular significance in the study of pathogenic fungi and in identification of new and specific antifungal drugs/ drug targets. © 2018 IUBMB Life, 70(5):355-383, 2018.
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Affiliation(s)
| | - Sneh Lata Singh
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | - Sudisht Kumar Sah
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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32
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Tsui HS, Pham NVB, Amer BR, Bradley MC, Gosschalk JE, Gallagher-Jones M, Ibarra H, Clubb RT, Blaby-Haas CE, Clarke CF. Human COQ10A and COQ10B are distinct lipid-binding START domain proteins required for coenzyme Q function. J Lipid Res 2019; 60:1293-1310. [PMID: 31048406 DOI: 10.1194/jlr.m093534] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/12/2019] [Indexed: 12/18/2022] Open
Abstract
Coenzyme Q (CoQ or ubiquinone) serves as an essential redox-active lipid in respiratory electron and proton transport during cellular energy metabolism. CoQ also functions as a membrane-localized antioxidant protecting cells against lipid peroxidation. CoQ deficiency is associated with multiple human diseases; CoQ10 supplementation in particular has noted cardioprotective benefits. In Saccharomyces cerevisiae, Coq10, a putative START domain protein, is believed to chaperone CoQ to sites where it functions. Yeast coq10 deletion mutants (coq10Δ) synthesize CoQ inefficiently during log phase growth and are respiratory defective and sensitive to oxidative stress. Humans have two orthologs of yeast COQ10, COQ10A and COQ10B Here, we tested the human co-orthologs for their ability to rescue the yeast mutant. We showed that expression of either human ortholog, COQ10A or COQ10B, rescues yeast coq10Δ mutant phenotypes, restoring the function of respiratory-dependent growth on a nonfermentable carbon source and sensitivity to oxidative stress induced by treatment with PUFAs. These effects indicate a strong functional conservation of Coq10 across different organisms. However, neither COQ10A nor COQ10B restored CoQ biosynthesis when expressed in the yeast coq10Δ mutant. The involvement of yeast Coq10 in CoQ biosynthesis may rely on its interactions with another protein, possibly Coq11, which is not found in humans. Coexpression analyses of yeast COQ10 and human COQ10A and COQ10B provide additional insights to functions of these START domain proteins and their potential roles in other biologic pathways.
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Affiliation(s)
- Hui S Tsui
- Department of Chemistry and Biochemistry and Molecular Biology Institute,University of California, Los Angeles, Los Angeles, CA 90095
| | - Nguyen V B Pham
- Department of Chemistry and Biochemistry and Molecular Biology Institute,University of California, Los Angeles, Los Angeles, CA 90095
| | - Brendan R Amer
- Department of Chemistry and Biochemistry and Molecular Biology Institute,University of California, Los Angeles, Los Angeles, CA 90095
| | - Michelle C Bradley
- Department of Chemistry and Biochemistry and Molecular Biology Institute,University of California, Los Angeles, Los Angeles, CA 90095
| | - Jason E Gosschalk
- Department of Chemistry and Biochemistry and Molecular Biology Institute,University of California, Los Angeles, Los Angeles, CA 90095.,UCLA-Department of Energy Institute of Genomics and Proteomics University of California, Los Angeles, Los Angeles, CA 90095
| | - Marcus Gallagher-Jones
- Department of Chemistry and Biochemistry and Molecular Biology Institute,University of California, Los Angeles, Los Angeles, CA 90095
| | - Hope Ibarra
- Department of Chemistry and Biochemistry and Molecular Biology Institute,University of California, Los Angeles, Los Angeles, CA 90095
| | - Robert T Clubb
- Department of Chemistry and Biochemistry and Molecular Biology Institute,University of California, Los Angeles, Los Angeles, CA 90095
| | | | - Catherine F Clarke
- Department of Chemistry and Biochemistry and Molecular Biology Institute,University of California, Los Angeles, Los Angeles, CA 90095
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33
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Esposito M, Hermann-Le Denmat S, Delahodde A. Contribution of ERMES subunits to mature peroxisome abundance. PLoS One 2019; 14:e0214287. [PMID: 30908556 PMCID: PMC6433259 DOI: 10.1371/journal.pone.0214287] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 03/11/2019] [Indexed: 11/26/2022] Open
Abstract
Eukaryotic organelles share different components and establish physical contacts to communicate throughout the cell. One of the best-recognized examples of such interplay is the metabolic cooperation and crosstalk between mitochondria and peroxisomes, both organelles being functionally and physically connected and linked to the endoplasmic reticulum (ER). In Saccharomyces cerevisiae, mitochondria are linked to the ER by the ERMES complex that facilitates inter-organelle calcium and phospholipid exchanges. Recently, peroxisome-mitochondria contact sites (PerMit) have been reported and among Permit tethers, one component of the ERMES complex (Mdm34) was shown to interact with the peroxin Pex11, suggesting that the ERMES complex or part of it may be involved in two membrane contact sites (ER-mitochondria and peroxisome- mitochondria). This opens the possibility of exchanges between these three membrane compartments. Here, we investigated in details the role of each ERMES subunit on peroxisome abundance. First, we confirmed previous studies from other groups showing that absence of Mdm10 or Mdm12 leads to an increased number of mature peroxisomes. Secondly, we showed that this is not simply due to respiratory function defect, mitochondrial DNA (mtDNA) loss or mitochondrial network alteration. Finally, we present evidence that the contribution of ERMES subunits Mdm10 and Mdm12 to peroxisome number involves two different mechanisms.
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Affiliation(s)
- Michela Esposito
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette cedex, France
| | - Sylvie Hermann-Le Denmat
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette cedex, France
- Ecole Normale Supérieure, PSL Research University, Paris, France
| | - Agnès Delahodde
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette cedex, France
- * E-mail:
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34
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Xia M, Zhang Y, Jin K, Lu Z, Zeng Z, Xiong W. Communication between mitochondria and other organelles: a brand-new perspective on mitochondria in cancer. Cell Biosci 2019; 9:27. [PMID: 30931098 PMCID: PMC6425566 DOI: 10.1186/s13578-019-0289-8] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/09/2019] [Indexed: 12/24/2022] Open
Abstract
Mitochondria are energy factories of cells and are important pivots for intracellular interactions with other organelles. They interact with the endoplasmic reticulum, peroxisomes, and nucleus through signal transduction, vesicle transport, and membrane contact sites to regulate energy metabolism, biosynthesis, immune response, and cell turnover. However, when the communication between organelles fails and the mitochondria are dysfunctional, it may induce tumorigenesis. In this review, we elaborate on how mitochondria interact with the endoplasmic reticulum, peroxisomes, and cell nuclei, as well as the relation between organelle communication and tumor development .
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Affiliation(s)
- MengFang Xia
- 1NHC Key Laboratory of Carcinogenesis, Xiangya Hospital, Central South University, Changsha, Hunan China.,2The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan China.,3Hunan Key Laboratory of Non Resolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan China
| | - YaZhuo Zhang
- 1NHC Key Laboratory of Carcinogenesis, Xiangya Hospital, Central South University, Changsha, Hunan China.,2The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan China.,3Hunan Key Laboratory of Non Resolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan China
| | - Ke Jin
- 2The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan China
| | - ZiTong Lu
- 2The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan China
| | - Zhaoyang Zeng
- 1NHC Key Laboratory of Carcinogenesis, Xiangya Hospital, Central South University, Changsha, Hunan China.,2The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan China.,3Hunan Key Laboratory of Non Resolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan China
| | - Wei Xiong
- 1NHC Key Laboratory of Carcinogenesis, Xiangya Hospital, Central South University, Changsha, Hunan China.,2The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan China.,3Hunan Key Laboratory of Non Resolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan China
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35
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Eisenberg-Bord M, Tsui HS, Antunes D, Fernández-Del-Río L, Bradley MC, Dunn CD, Nguyen TPT, Rapaport D, Clarke CF, Schuldiner M. The Endoplasmic Reticulum-Mitochondria Encounter Structure Complex Coordinates Coenzyme Q Biosynthesis. ACTA ACUST UNITED AC 2019; 2:2515256418825409. [PMID: 30937424 PMCID: PMC6441334 DOI: 10.1177/2515256418825409] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Loss of the endoplasmic reticulum (ER)-mitochondria encounter structure (ERMES) complex that resides in contact sites between the yeast ER and mitochondria leads to impaired respiration; however, the reason for that is not clear. We find that in ERMES null mutants, there is an increase in the level of mRNAs encoding for biosynthetic enzymes of coenzyme Q6 (CoQ6), an essential electron carrier of the mitochondrial respiratory chain. We show that the mega complexes involved in CoQ6 biosynthesis (CoQ synthomes) are destabilized in ERMES mutants. This, in turn, affects the level and distribution of CoQ6 within the cell, resulting in reduced mitochondrial CoQ6. We suggest that these outcomes contribute to the reduced respiration observed in ERMES mutants. Fluorescence microscopy experiments demonstrate close proximity between the CoQ synthome and ERMES, suggesting a spatial coordination. The involvement of the ER-mitochondria contact site in regulation of CoQ6 biogenesis highlights an additional level of communication between these two organelles.
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Affiliation(s)
| | - Hui S Tsui
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, CA, USA
| | - Diana Antunes
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Lucía Fernández-Del-Río
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, CA, USA
| | - Michelle C Bradley
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, CA, USA
| | - Cory D Dunn
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | | | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Catherine F Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, CA, USA
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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36
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Liu X, Wen X, Klionsky DJ. ER-mitochondria contacts are required for pexophagy in Saccharomyces cerevisiae. ACTA ACUST UNITED AC 2019; 2. [PMID: 30859155 DOI: 10.1177/2515256418821584] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Peroxisomes play important roles in lipid metabolism. Surplus or damaged peroxisomes can be selectively targeted for autophagic degradation, a process termed pexophagy. Maintaining a proper level of pexophagy is critical for cellular homeostasis. Here we found that endoplasmic reticulum (ER)-mitochondria contact sites are necessary for efficient pexophagy. During pexophagy, the peroxisomes destined for degradation are adjacent to the ER-mitochondria encounter structure (ERMES) that mediates formation of ER- mitochondria contacts; disruption of the ERMES results in a severe defect in pexophagy. We show that a mutant form of Mdm34, a component of the ERMES, which impairs ERMES formation and diminishes its association with the peroxisomal membrane protein Pex11, also leads to defects in pexophagy. The dynamin-related GTPase Vps1, which is specific for peroxisomal fission, is recruited to the peroxisomes at ER-mitochondria contacts by the selective autophagy scaffold Atg11 and the pexophagy receptor Atg36, facilitating peroxisome degradation.
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Affiliation(s)
- Xu Liu
- Life Sciences Institute, and the Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xin Wen
- Life Sciences Institute, and the Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel J Klionsky
- Life Sciences Institute, and the Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
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37
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Tanaka H, Okazaki T, Aoyama S, Yokota M, Koike M, Okada Y, Fujiki Y, Gotoh Y. Peroxisomes control mitochondrial dynamics and the mitochondrion-dependent pathway of apoptosis. J Cell Sci 2019; 132:jcs.224766. [DOI: 10.1242/jcs.224766] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 05/01/2019] [Indexed: 01/03/2023] Open
Abstract
Peroxisomes cooperate with mitochondria in the performance of cellular metabolic functions such as fatty acid oxidation and maintenance of redox homeostasis. Whether peroxisomes also regulate mitochondrial fission-fusion dynamics or mitochondrion-dependent apoptosis has remained unclear, however. We now show that genetic ablation of the peroxins Pex3 or Pex5, which are essential for peroxisome biogenesis, resulted in mitochondrial fragmentation in MEFs in a manner dependent on Drp1. Conversely, treatment with 4-PBA, a peroxisome proliferator, resulted in mitochondrial elongation in wild-type MEFs, but not in Pex3-deficient MEFs. We further found that peroxisome deficiency increased the levels of cytosolic cytochrome c and caspase activity under basal conditions without inducing apoptosis. It also greatly enhanced etoposide-induced caspase activation and apoptosis, indicative of an enhanced cellular sensitivity to death signals. Together, our data unveil a previously unrecognized role of peroxisomes in the regulation of mitochondrial dynamics and mitochondrion-dependent apoptosis. Effects of peroxin genes mutations on mitochondrion-dependent apoptosis may contribute to pathogenesis of peroxisome biogenesis disorders.
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Affiliation(s)
- Hideaki Tanaka
- Graduate School of Pharmaceutical Sciences, IRCN, The University of Tokyo, Tokyo 113-0033, Japan
| | - Tomohiko Okazaki
- Graduate School of Pharmaceutical Sciences, IRCN, The University of Tokyo, Tokyo 113-0033, Japan
| | - Saeko Aoyama
- Graduate School of Pharmaceutical Sciences, IRCN, The University of Tokyo, Tokyo 113-0033, Japan
| | - Mutsumi Yokota
- Department of Cell Biology and Neuroscience, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - Masato Koike
- Department of Cell Biology and Neuroscience, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - Yasushi Okada
- Laboratory for Cell Dynamics Observation, Center for Biosystems Dynamics Research (BDR), RIKEN, Osaka 565-0874, Japan
- Department of Physics, Universal Biology Institute (UBI), and the International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo 113-0033, Japan
| | - Yukio Fujiki
- Division of Organelle Homeostasis, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Yukiko Gotoh
- Graduate School of Pharmaceutical Sciences, IRCN, The University of Tokyo, Tokyo 113-0033, Japan
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Wang Y, Metz J, Costello JL, Passmore J, Schrader M, Schultz C, Islinger M. Intracellular redistribution of neuronal peroxisomes in response to ACBD5 expression. PLoS One 2018; 13:e0209507. [PMID: 30589881 PMCID: PMC6307868 DOI: 10.1371/journal.pone.0209507] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/06/2018] [Indexed: 12/21/2022] Open
Abstract
Peroxisomes can be frequently found in proximity to other subcellular organelles such as the endoplasmic reticulum (ER), mitochondria or lysosomes. The tail-anchored protein ACBD5 was recently identified as part of a tethering complex at peroxisome-ER contact sites, interacting with the ER resident protein VAPB. Contact site disruption was found to significantly increase peroxisome motility, apparently interfering with intracellular positioning systems. Unlike other somatic cells, neurons have to distribute organelles across relatively long distances in order to maintain their extraordinary cellular polarity. Using confocal live imaging microscopy in cultured hippocampal neurons we observed that peroxisomes and mitochondria show a strikingly similar motility with approximately 10% performing microtubule-driven long range movements. In order to investigate if ER contacts influence overall peroxisome motility and cellular distribution patterns, hippocampal neurons were transfected with plasmids encoding ACBD5 to stimulate peroxisome-ER interactions. Overexpression of ACBD5 reduced peroxisomal long range movements in the neurites of the hippocampal cells by 70%, implying that ER attachment counteracts microtubule-driven peroxisome transport, while mitochondrial motility was unaffected. Moreover, the analyses of peroxisome distribution in fixed neurons unveiled a significant redistribution of peroxisomes towards the periphery of the perikaryon underneath the plasma membrane and into neurites, where peroxisomes are frequently found in close proximity to mitochondria. Surprisingly, further analysis of peroxisome and VAPB distribution upon ACBD5 expression did not reveal a substantial colocalization, implying this effect may be independent of VAPB. In line with these findings, expression of an ACBD5 variant unable to bind to VAPB still altered the localization of peroxisomes in the same way as the wild-type ACBD5. Thus, we conclude, that the VAPB-ACBD5 facilitated peroxisome-ER interaction is not responsible for the observed organelle redistribution in neurons. Rather, we suggest that additional ACBD5-binding proteins in neurons may tether peroxisomes to contact sites at or near the plasma membrane of neurons.
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Affiliation(s)
- Yunhong Wang
- Institute of Neuroanatomy, Center for Biomedicine & Medical Technology Mannheim, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Jeremy Metz
- Biosciences, University of Exeter, Exeter, United Kingdom
| | | | | | | | - Christian Schultz
- Institute of Neuroanatomy, Center for Biomedicine & Medical Technology Mannheim, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Markus Islinger
- Institute of Neuroanatomy, Center for Biomedicine & Medical Technology Mannheim, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
- * E-mail:
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39
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Lutfullahoğlu-Bal G, Seferoğlu AB, Keskin A, Akdoğan E, Dunn CD. A bacteria-derived tail anchor localizes to peroxisomes in yeast and mammalian cells. Sci Rep 2018; 8:16374. [PMID: 30401812 PMCID: PMC6219538 DOI: 10.1038/s41598-018-34646-7] [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: 06/22/2018] [Accepted: 10/18/2018] [Indexed: 11/18/2022] Open
Abstract
Prokaryotes can provide new genetic information to eukaryotes by horizontal gene transfer (HGT), and such transfers are likely to have been particularly consequential in the era of eukaryogenesis. Since eukaryotes are highly compartmentalized, it is worthwhile to consider the mechanisms by which newly transferred proteins might reach diverse organellar destinations. Toward this goal, we have focused our attention upon the behavior of bacteria-derived tail anchors (TAs) expressed in the eukaryote Saccharomyces cerevisiae. In this study, we report that a predicted membrane-associated domain of the Escherichia coli YgiM protein is specifically trafficked to peroxisomes in budding yeast, can be found at a pre-peroxisomal compartment (PPC) upon disruption of peroxisomal biogenesis, and can functionally replace an endogenous, peroxisome-directed TA. Furthermore, the YgiM(TA) can localize to peroxisomes in mammalian cells. Since the YgiM(TA) plays no endogenous role in peroxisomal function or assembly, this domain is likely to serve as an excellent tool allowing further illumination of the mechanisms by which TAs can travel to peroxisomes. Moreover, our findings emphasize the ease with which bacteria-derived sequences might target to organelles in eukaryotic cells following HGT, and we discuss the importance of flexible recognition of organelle targeting information during and after eukaryogenesis.
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Affiliation(s)
- Güleycan Lutfullahoğlu-Bal
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00014, Helsinki, Finland
- Department of Molecular Biology and Genetics, Koç University, 34450, Sarıyer, İstanbul, Turkey
| | - Ayşe Bengisu Seferoğlu
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00014, Helsinki, Finland
| | - Abdurrahman Keskin
- Department of Molecular Biology and Genetics, Koç University, 34450, Sarıyer, İstanbul, Turkey
- Department of Biological Sciences, Columbia University, New York, NY, 10027, United States of America
| | - Emel Akdoğan
- Department of Molecular Biology and Genetics, Koç University, 34450, Sarıyer, İstanbul, Turkey
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, 95616, United States of America
| | - Cory D Dunn
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00014, Helsinki, Finland.
- Department of Molecular Biology and Genetics, Koç University, 34450, Sarıyer, İstanbul, Turkey.
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40
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Abstract
Peroxisomes are key metabolic organelles, which contribute to cellular lipid metabolism, e.g. the β-oxidation of fatty acids and the synthesis of myelin sheath lipids, as well as cellular redox balance. Peroxisomal dysfunction has been linked to severe metabolic disorders in man, but peroxisomes are now also recognized as protective organelles with a wider significance in human health and potential impact on a large number of globally important human diseases such as neurodegeneration, obesity, cancer, and age-related disorders. Therefore, the interest in peroxisomes and their physiological functions has significantly increased in recent years. In this review, we intend to highlight recent discoveries, advancements and trends in peroxisome research, and present an update as well as a continuation of two former review articles addressing the unsolved mysteries of this astonishing organelle. We summarize novel findings on the biological functions of peroxisomes, their biogenesis, formation, membrane dynamics and division, as well as on peroxisome-organelle contacts and cooperation. Furthermore, novel peroxisomal proteins and machineries at the peroxisomal membrane are discussed. Finally, we address recent findings on the role of peroxisomes in the brain, in neurological disorders, and in the development of cancer.
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Affiliation(s)
- Markus Islinger
- Institute of Neuroanatomy, Center for Biomedicine and Medical Technology Mannheim, Medical Faculty Manheim, University of Heidelberg, 68167, Mannheim, Germany
| | - Alfred Voelkl
- Institute for Anatomy and Cell Biology, University of Heidelberg, 69120, Heidelberg, Germany
| | - H Dariush Fahimi
- Institute for Anatomy and Cell Biology, University of Heidelberg, 69120, Heidelberg, Germany
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41
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Yu SB, Pekkurnaz G. Mechanisms Orchestrating Mitochondrial Dynamics for Energy Homeostasis. J Mol Biol 2018; 430:3922-3941. [PMID: 30089235 PMCID: PMC6186503 DOI: 10.1016/j.jmb.2018.07.027] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 07/23/2018] [Accepted: 07/30/2018] [Indexed: 12/13/2022]
Abstract
To maintain homeostasis, every cell must constantly monitor its energy level and appropriately adjust energy, in the form of ATP, production rates based on metabolic demand. Continuous fulfillment of this energy demand depends on the ability of cells to sense, metabolize, and convert nutrients into chemical energy. Mitochondria are the main energy conversion sites for many cell types. Cellular metabolic states dictate the mitochondrial size, shape, function, and positioning. Mitochondrial shape varies from singular discrete organelles to interconnected reticular networks within cells. The morphological adaptations of mitochondria to metabolic cues are facilitated by the dynamic events categorized as transport, fusion, fission, and quality control. By changing their dynamics and strategic positioning within the cytoplasm, mitochondria carry out critical functions and also participate actively in inter-organelle cross-talk, assisting metabolite transfer, degradation, and biogenesis. Mitochondrial dynamics has become an active area of research because of its particular importance in cancer, metabolic diseases, and neurological disorders. In this review, we will highlight the molecular pathways involved in the regulation of mitochondrial dynamics and their roles in maintaining energy homeostasis.
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Affiliation(s)
- Seungyoon B Yu
- Neurobiology Section, Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, United States
| | - Gulcin Pekkurnaz
- Neurobiology Section, Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, United States.
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42
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Akşit A, van der Klei IJ. Yeast peroxisomes: How are they formed and how do they grow? Int J Biochem Cell Biol 2018; 105:24-34. [PMID: 30268746 DOI: 10.1016/j.biocel.2018.09.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 01/01/2023]
Abstract
Peroxisomes are single membrane enclosed cell organelles, which are present in almost all eukaryotic cells. In addition to the common peroxisomal pathways such as β-oxidation of fatty acids and decomposition of H2O2, these organelles fulfil a range of metabolic and non-metabolic functions. Peroxisomes are very important since various human disorders exist that are caused by a defect in peroxisome function. Here we describe our current knowledge on the molecular mechanisms of peroxisome biogenesis in yeast, including peroxisomal protein sorting, organelle dynamics and peroxisomal membrane contact sites.
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Affiliation(s)
- Arman Akşit
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, the Netherlands
| | - Ida J van der Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, the Netherlands.
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43
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Wu H, de Boer R, Krikken AM, Akşit A, Yuan W, van der Klei IJ. Peroxisome development in yeast is associated with the formation of Pex3-dependent peroxisome-vacuole contact sites. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1866:349-359. [PMID: 30595161 DOI: 10.1016/j.bbamcr.2018.08.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/28/2018] [Accepted: 08/30/2018] [Indexed: 12/29/2022]
Abstract
Using electron and fluorescence microscopy techniques, we identified various physical contacts between peroxisomes and other cell organelles in the yeast Hansenula polymorpha. In exponential glucose-grown cells, which typically contain a single small peroxisome, contacts were only observed with the endoplasmic reticulum and the plasma membrane. Here we focus on a novel peroxisome-vacuole contact site that is formed when glucose-grown cells are shifted to methanol containing media, conditions that induce strong peroxisome development. At these conditions, the small peroxisomes rapidly increase in size, a phenomenon that is paralleled by the formation of distinct intimate contacts with the vacuole. Localization studies showed that the peroxin Pex3 accumulated in patches at the peroxisome-vacuole contact sites. In wild-type cells growing exponentially on medium containing glucose, peroxisome-vacuole contact sites were never observed. However, upon overproduction of Pex3 peroxisomes also associated to vacuoles at these growth conditions. Our observations strongly suggest a role for Pex3 in the formation of a novel peroxisome-vacuole contact site. This contact likely plays a role in membrane growth as it is formed solely at conditions of strong peroxisome expansion.
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Affiliation(s)
- Huala Wu
- Molecular Cell Biology, University of Groningen, PO Box 11103, 9300, CC, Groningen, the Netherlands
| | - Rinse de Boer
- Molecular Cell Biology, University of Groningen, PO Box 11103, 9300, CC, Groningen, the Netherlands
| | - Arjen M Krikken
- Molecular Cell Biology, University of Groningen, PO Box 11103, 9300, CC, Groningen, the Netherlands
| | - Arman Akşit
- Molecular Cell Biology, University of Groningen, PO Box 11103, 9300, CC, Groningen, the Netherlands
| | - Wei Yuan
- Molecular Cell Biology, University of Groningen, PO Box 11103, 9300, CC, Groningen, the Netherlands
| | - Ida J van der Klei
- Molecular Cell Biology, University of Groningen, PO Box 11103, 9300, CC, Groningen, the Netherlands.
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44
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Deori NM, Kale A, Maurya PK, Nagotu S. Peroxisomes: role in cellular ageing and age related disorders. Biogerontology 2018; 19:303-324. [PMID: 29968207 DOI: 10.1007/s10522-018-9761-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/27/2018] [Indexed: 12/12/2022]
Abstract
Peroxisomes are dynamic organelles essential for optimum functioning of a eukaryotic cell. Biogenesis of these organelles and the diverse functions performed by them have been extensively studied in the past decade. Their ability to perform functions depending on the cell type and growth conditions is unique and remarkable. Oxidation of fatty acids and reactive oxygen species metabolism are the two most important functions of these ubiquitous organelles. They are often referred to as both source and sink of reactive oxygen species in a cell. Recent research connects peroxisome dysfunction to fatal oxidative damage associated with ageing-related diseases/disorders. It is now widely accepted that mitochondria and peroxisomes are required to maintain oxidative balance in a cell. However, our understanding on the inter-dependence of these organelles to maintain cellular homeostasis of reactive oxygen species is still in its infancy. Herein, we summarize findings that highlight the role of peroxisomes in cellular reactive oxygen species metabolism, ageing and age-related disorders.
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Affiliation(s)
- Nayan M Deori
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Avinash Kale
- UM-DAE, Centre for Excellence in Basic Sciences, Health Centre, University of Mumbai, Mumbai, 400098, India
| | - Pawan K Maurya
- Interdisciplinary Laboratory for Clinical Neuroscience (LiNC), Universidade Federal de Sao Paulo-UNIFESP, Sao Paulo, Brazil
| | - Shirisha Nagotu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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45
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Diogo CV, Yambire KF, Fernández Mosquera L, Branco F T, Raimundo N. Mitochondrial adventures at the organelle society. Biochem Biophys Res Commun 2018; 500:87-93. [PMID: 28456629 PMCID: PMC5930832 DOI: 10.1016/j.bbrc.2017.04.124] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 04/23/2017] [Indexed: 01/16/2023]
Abstract
Mitochondria are constantly communicating with the rest of the cell. Defects in mitochondria underlie severe pathologies, whose mechanisms remain poorly understood. It is becoming increasingly evident that mitochondrial malfunction resonates in other organelles, perturbing their function and their biogenesis. In this manuscript, we review the current knowledge on the cross-talk between mitochondria and other organelles, particularly lysosomes, peroxisomes and the endoplasmic reticulum. Several organelle interactions are mediated by transcriptional programs, and other signaling mechanisms are likely mediating organelle dysfunction downstream of mitochondrial impairments. Many of these organelle crosstalk pathways are likely to have a role in pathological processes.
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Affiliation(s)
- Cátia V Diogo
- Universitätsmedizin Göttingen, Institute fur Zellbiochemie, Humboldtallee 23, room 01.423, 37073 Göttingen, Germany
| | - King Faisal Yambire
- Universitätsmedizin Göttingen, Institute fur Zellbiochemie, Humboldtallee 23, room 01.423, 37073 Göttingen, Germany; International Max-Planck Research School in Neuroscience, Göttingen, Germany
| | - Lorena Fernández Mosquera
- Universitätsmedizin Göttingen, Institute fur Zellbiochemie, Humboldtallee 23, room 01.423, 37073 Göttingen, Germany
| | - Tiago Branco F
- Universitätsmedizin Göttingen, Institute fur Zellbiochemie, Humboldtallee 23, room 01.423, 37073 Göttingen, Germany
| | - Nuno Raimundo
- Universitätsmedizin Göttingen, Institute fur Zellbiochemie, Humboldtallee 23, room 01.423, 37073 Göttingen, Germany.
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46
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Chuartzman SG, Schuldiner M. Database for High Throughput Screening Hits (dHITS): a simple tool to retrieve gene specific phenotypes from systematic screens done in yeast. Yeast 2018; 35:477-483. [PMID: 29574976 PMCID: PMC6055851 DOI: 10.1002/yea.3312] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/04/2018] [Accepted: 03/07/2018] [Indexed: 12/21/2022] Open
Abstract
In the last decade several collections of Saccharomyces cerevisiae yeast strains have been created. In these collections every gene is modified in a similar manner such as by a deletion or the addition of a protein tag. Such libraries have enabled a diversity of systematic screens, giving rise to large amounts of information regarding gene functions. However, often papers describing such screens focus on a single gene or a small set of genes and all other loci affecting the phenotype of choice (‘hits’) are only mentioned in tables that are provided as supplementary material and are often hard to retrieve or search. To help unify and make such data accessible, we have created a Database of High Throughput Screening Hits (dHITS). The dHITS database enables information to be obtained about screens in which genes of interest were found as well as the other genes that came up in that screen – all in a readily accessible and downloadable format. The ability to query large lists of genes at the same time provides a platform to easily analyse hits obtained from transcriptional analyses or other screens. We hope that this platform will serve as a tool to facilitate investigation of protein functions to the yeast community.
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Affiliation(s)
- Silvia G Chuartzman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
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47
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Systematic mapping of contact sites reveals tethers and a function for the peroxisome-mitochondria contact. Nat Commun 2018; 9:1761. [PMID: 29720625 PMCID: PMC5932058 DOI: 10.1038/s41467-018-03957-8] [Citation(s) in RCA: 198] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/22/2018] [Indexed: 12/15/2022] Open
Abstract
The understanding that organelles are not floating in the cytosol, but rather held in an organized yet dynamic interplay through membrane contact sites, is altering the way we grasp cell biological phenomena. However, we still have not identified the entire repertoire of contact sites, their tethering molecules and functions. To systematically characterize contact sites and their tethering molecules here we employ a proximity detection method based on split fluorophores and discover four potential new yeast contact sites. We then focus on a little-studied yet highly disease-relevant contact, the Peroxisome-Mitochondria (PerMit) proximity, and uncover and characterize two tether proteins: Fzo1 and Pex34. We genetically expand the PerMit contact site and demonstrate a physiological function in β-oxidation of fatty acids. Our work showcases how systematic analysis of contact site machinery and functions can deepen our understanding of these structures in health and disease.
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48
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Extramitochondrial Assembly of Mitochondrial Targeting Signal Disrupted Mitochondrial Enzyme Aldehyde Dehydrogenase. Sci Rep 2018; 8:6186. [PMID: 29670139 PMCID: PMC5906672 DOI: 10.1038/s41598-018-24586-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/06/2018] [Indexed: 11/17/2022] Open
Abstract
Supramolecular assembly of metabolic enzymes has been studied both in vivo and in vitro for nearly a decade. Experimental evidence has suggested a close relationship between enzymatic activity and enzyme assembly/disassembly. However, most cases were studied with the cytosolic enzymes. Here, I report the evidence for a mitochondrial enzyme with its ability in forming visible intracellular structures. By removing the mitochondrial targeting sequence, yeast mitochondrial enzyme aldehyde dehydrogenase (Ald4p) exhibits reversible supramolecular assembly in the cytoplasm, thus creating a useful system for further characterization of the regulatory factors that modulate the assembly/disassembly of this mitochondrial enzyme.
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49
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Kakimoto Y, Tashiro S, Kojima R, Morozumi Y, Endo T, Tamura Y. Visualizing multiple inter-organelle contact sites using the organelle-targeted split-GFP system. Sci Rep 2018; 8:6175. [PMID: 29670150 PMCID: PMC5906596 DOI: 10.1038/s41598-018-24466-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 04/04/2018] [Indexed: 12/18/2022] Open
Abstract
Functional integrity of eukaryotic organelles relies on direct physical contacts between distinct organelles. However, the entity of organelle-tethering factors is not well understood due to lack of means to analyze inter-organelle interactions in living cells. Here we evaluate the split-GFP system for visualizing organelle contact sites in vivo and show its advantages and disadvantages. We observed punctate GFP signals from the split-GFP fragments targeted to any pairs of organelles among the ER, mitochondria, peroxisomes, vacuole and lipid droplets in yeast cells, which suggests that these organelles form contact sites with multiple organelles simultaneously although it is difficult to rule out the possibilities that these organelle contacts sites are artificially formed by the irreversible associations of the split-GFP probes. Importantly, split-GFP signals in the overlapped regions of the ER and mitochondria were mainly co-localized with ERMES, an authentic ER-mitochondria tethering structure, suggesting that split-GFP assembly depends on the preexisting inter-organelle contact sites. We also confirmed that the split-GFP system can be applied to detection of the ER-mitochondria contact sites in HeLa cells. We thus propose that the split-GFP system is a potential tool to observe and analyze inter-organelle contact sites in living yeast and mammalian cells.
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Affiliation(s)
- Yuriko Kakimoto
- Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata, Yamagata, 990-8560, Japan
| | - Shinya Tashiro
- Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata, Yamagata, 990-8560, Japan
| | - Rieko Kojima
- Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata, Yamagata, 990-8560, Japan
| | - Yuki Morozumi
- Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata, Yamagata, 990-8560, Japan
| | - Toshiya Endo
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
| | - Yasushi Tamura
- Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata, Yamagata, 990-8560, Japan.
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50
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Castro IG, Schuldiner M, Zalckvar E. Mind the Organelle Gap - Peroxisome Contact Sites in Disease. Trends Biochem Sci 2018; 43:199-210. [PMID: 29395653 PMCID: PMC6252078 DOI: 10.1016/j.tibs.2018.01.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 12/23/2017] [Accepted: 01/02/2018] [Indexed: 12/20/2022]
Abstract
The eukaryotic cell is organized as a complex grid system where membrane-bound cellular compartments, organelles, must be localized to the right place at the right time. One way to facilitate correct organelle localization and organelle cooperation is through membrane contact sites, areas of close proximity between two organelles that are bridged by protein/lipid complexes. It is now clear that all organelles physically contact each other. The main focus of this review is contact sites of peroxisomes, central metabolic hubs whose defects lead to a variety of diseases. New peroxisome contacts, their tethering complexes and functions have been recently discovered. However, if and how peroxisome contacts contribute to the development of peroxisome-related diseases is still a mystery.
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Affiliation(s)
- Inês Gomes Castro
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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