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Domingues N, Pires J, Milosevic I, Raimundo N. Role of lipids in interorganelle communication. Trends Cell Biol 2024:S0962-8924(24)00095-3. [PMID: 38866684 DOI: 10.1016/j.tcb.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 06/14/2024]
Abstract
Cell homeostasis and function rely on well-orchestrated communication between different organelles. This communication is ensured by signaling pathways and membrane contact sites between organelles. Many players involved in organelle crosstalk have been identified, predominantly proteins and ions. The role of lipids in interorganelle communication remains poorly understood. With the development and broader availability of methods to quantify lipids, as well as improved spatiotemporal resolution in detecting different lipid species, the contribution of lipids to organelle interactions starts to be evident. However, the specific roles of various lipid molecules in intracellular communication remain to be studied systematically. We summarize new insights in the interorganelle communication field from the perspective of organelles and discuss the roles played by lipids in these complex processes.
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Affiliation(s)
- Neuza Domingues
- Multidisciplinary Institute of Ageing, University of Coimbra, Coimbra, Portugal
| | - Joana Pires
- Multidisciplinary Institute of Ageing, University of Coimbra, Coimbra, Portugal
| | - Ira Milosevic
- Multidisciplinary Institute of Ageing, University of Coimbra, Coimbra, Portugal; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nuno Raimundo
- Multidisciplinary Institute of Ageing, University of Coimbra, Coimbra, Portugal; Department of Cellular and Molecular Physiology, Penn State College of Medicine, Hershey, PA, USA; Penn State Cancer Institute, Hershey, PA, USA.
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2
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Campanella M, Kannan B. Mitochondrial sites of contact with the nucleus. J Cell Biol 2024; 223:e202305010. [PMID: 38669038 PMCID: PMC11046832 DOI: 10.1083/jcb.202305010] [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] [Indexed: 04/29/2024] Open
Abstract
Membrane contact sites (MCS) between mitochondria and the nucleus have been recently described. Termed nucleus associated mitochondria (NAM), they prime the expression of genes required for cellular resistance to stressors, thus offering a tethering mechanism for homeostatic communication. Here, we discuss the composition of NAM and their physiological and pathological significance.
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Affiliation(s)
- Michelangelo Campanella
- William Harvey Research Institute, Queen Mary University of London, London, UK
- Institute Gustave Roussy, Villejuif, France
- Department of Biomedical Science, University of Padua, Padua, Italy
| | - Brindha Kannan
- William Harvey Research Institute, Queen Mary University of London, London, UK
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3
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Keller J, Fernández-Busnadiego R. In situ studies of membrane biology by cryo-electron tomography. Curr Opin Cell Biol 2024; 88:102363. [PMID: 38677049 DOI: 10.1016/j.ceb.2024.102363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/26/2024] [Accepted: 04/08/2024] [Indexed: 04/29/2024]
Abstract
Cryo-electron tomography (cryo-ET) allows high resolution 3D imaging of biological samples in near-native environments. Thus, cryo-ET has become the method of choice to analyze the unperturbed organization of cellular membranes. Here, we briefly discuss current cryo-ET workflows and their application to study membrane biology in situ, under basal and pathological conditions.
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Affiliation(s)
- Jenny Keller
- University Medical Center Göttingen, Institute for Neuropathology, Göttingen, 37077, Germany; Collaborative Research Center 1190 "Compartmental Gates and Contact Sites in Cells", University of Göttingen, Göttingen, Germany.
| | - Rubén Fernández-Busnadiego
- University Medical Center Göttingen, Institute for Neuropathology, Göttingen, 37077, Germany; Collaborative Research Center 1190 "Compartmental Gates and Contact Sites in Cells", University of Göttingen, Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, 37077, Germany; Faculty of Physics, University of Göttingen, Göttingen, 37077, Germany.
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4
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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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5
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Ovciarikova J, Shikha S, Lacombe A, Courjol F, McCrone R, Hussain W, Maclean A, Lemgruber L, Martins-Duarte ES, Gissot M, Sheiner L. Two ancient membrane pores mediate mitochondrial-nucleus membrane contact sites. J Cell Biol 2024; 223:e202304075. [PMID: 38456969 PMCID: PMC10923651 DOI: 10.1083/jcb.202304075] [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: 04/22/2023] [Revised: 11/28/2023] [Accepted: 01/29/2024] [Indexed: 03/09/2024] Open
Abstract
Coordination between nucleus and mitochondria is essential for cell survival, and thus numerous communication routes have been established between these two organelles over eukaryotic cell evolution. One route for organelle communication is via membrane contact sites, functional appositions formed by molecular tethers. We describe a novel nuclear-mitochondrial membrane contact site in the protozoan Toxoplasma gondii. We have identified specific contacts occurring at the nuclear pore and demonstrated an interaction between components of the nuclear pore and the mitochondrial protein translocon, highlighting them as molecular tethers. Genetic disruption of the nuclear pore or the TOM translocon components, TgNup503 or TgTom40, respectively, result in contact site reduction, supporting their potential involvement in this tether. TgNup503 depletion further leads to specific mitochondrial morphology and functional defects, supporting a role for nuclear-mitochondrial contacts in mediating their communication. The discovery of a contact formed through interaction between two ancient mitochondrial and nuclear complexes sets the ground for better understanding of mitochondrial-nuclear crosstalk in eukaryotes.
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Affiliation(s)
- Jana Ovciarikova
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Shikha Shikha
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Alice Lacombe
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Flavie Courjol
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019—UMR 9017—CIIL—Center for Infection and Immunity of Lille, University of Lille, Lille, France
| | - Rosalind McCrone
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Wasim Hussain
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Andrew Maclean
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Leandro Lemgruber
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Erica S. Martins-Duarte
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Mathieu Gissot
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019—UMR 9017—CIIL—Center for Infection and Immunity of Lille, University of Lille, Lille, France
| | - Lilach Sheiner
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
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6
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Sun S, Zhao G, Jia M, Jiang Q, Li S, Wang H, Li W, Wang Y, Bian X, Zhao YG, Huang X, Yang G, Cai H, Pastor-Pareja JC, Ge L, Zhang C, Hu J. Stay in touch with the endoplasmic reticulum. SCIENCE CHINA. LIFE SCIENCES 2024; 67:230-257. [PMID: 38212460 DOI: 10.1007/s11427-023-2443-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 08/28/2023] [Indexed: 01/13/2024]
Abstract
The endoplasmic reticulum (ER), which is composed of a continuous network of tubules and sheets, forms the most widely distributed membrane system in eukaryotic cells. As a result, it engages a variety of organelles by establishing membrane contact sites (MCSs). These contacts regulate organelle positioning and remodeling, including fusion and fission, facilitate precise lipid exchange, and couple vital signaling events. Here, we systematically review recent advances and converging themes on ER-involved organellar contact. The molecular basis, cellular influence, and potential physiological functions for ER/nuclear envelope contacts with mitochondria, Golgi, endosomes, lysosomes, lipid droplets, autophagosomes, and plasma membrane are summarized.
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Affiliation(s)
- Sha Sun
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Gan Zhao
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Mingkang Jia
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Qing Jiang
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Shulin Li
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Haibin Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenjing Li
- Laboratory of Computational Biology & Machine Intelligence, School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunyun Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xin Bian
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Yan G Zhao
- Brain Research Center, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Xun Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Ge Yang
- Laboratory of Computational Biology & Machine Intelligence, School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Huaqing Cai
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jose C Pastor-Pareja
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Institute of Neurosciences, Consejo Superior de Investigaciones Cientfflcas-Universidad Miguel Hernandez, San Juan de Alicante, 03550, Spain.
| | - Liang Ge
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Chuanmao Zhang
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China.
| | - Junjie Hu
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China.
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7
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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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8
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Tracey-White D, Hayes MJ. Nucleus-Mitochondria Contact Sites Are Associated With Asynthetic Fission in Zebrafish Skin. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2024; 7:25152564241239445. [PMID: 38524404 PMCID: PMC10958491 DOI: 10.1177/25152564241239445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 02/13/2024] [Accepted: 02/19/2024] [Indexed: 03/26/2024]
Abstract
Rapid increase in body surface area of growing zebrafish larvae (Danio rario) is partially accomplished by asynthetic fission of superficial epithelial cells (SECs) of the skin. There are two cycles of this atypical form of cell division which is unaccompanied by DNA replication; resulting in cells with a variable DNA content. Here, electron microscopy of basal epithelium cells that give rise to these SECs in zebrafish larvae shows aggregation of mitochondria around the nucleus and the formation of nucleus-mitochondria membrane contact sites. Membrane aggregates appear in the lumen of the nuclear envelope at these sites of membrane contact in some cells, suggesting lipid turnover in this vicinity. As the epithelial cells mature and stratify, the mitochondria are engulfed by extensions arising from the nuclear envelope. The mitochondrial outer membrane fragments and mitochondria fuse with the nuclear envelope and parts of the endoplasmic reticulum. Other organelles, including the Golgi apparatus, progressively localize to a central region of the cell and lose their integrity. Thus, asynthetic fission is accompanied by an atypical pattern of organelle destruction and a prelude to this is the formation of nucleus-mitochondria membrane contact sites.
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9
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den Brave F, Schulte U, Fakler B, Pfanner N, Becker T. Mitochondrial complexome and import network. Trends Cell Biol 2023:S0962-8924(23)00208-8. [PMID: 37914576 DOI: 10.1016/j.tcb.2023.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 11/03/2023]
Abstract
Mitochondria perform crucial functions in cellular metabolism, protein and lipid biogenesis, quality control, and signaling. The systematic analysis of protein complexes and interaction networks provided exciting insights into the structural and functional organization of mitochondria. Most mitochondrial proteins do not act as independent units, but are interconnected by stable or dynamic protein-protein interactions. Protein translocases are responsible for importing precursor proteins into mitochondria and form central elements of several protein interaction networks. These networks include molecular chaperones and quality control factors, metabolite channels and respiratory chain complexes, and membrane and organellar contact sites. Protein translocases link the distinct networks into an overarching network, the mitochondrial import network (MitimNet), to coordinate biogenesis, membrane organization and function of mitochondria.
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Affiliation(s)
- Fabian den Brave
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, 53115 Bonn, Germany
| | - Uwe Schulte
- Institute of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Bernd Fakler
- Institute of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Nikolaus Pfanner
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, 53115 Bonn, Germany.
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10
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Lenhard S, Gerlich S, Khan A, Rödl S, Bökenkamp JE, Peker E, Zarges C, Faust J, Storchova Z, Räschle M, Riemer J, Herrmann JM. The Orf9b protein of SARS-CoV-2 modulates mitochondrial protein biogenesis. J Cell Biol 2023; 222:e202303002. [PMID: 37682539 PMCID: PMC10491932 DOI: 10.1083/jcb.202303002] [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: 03/01/2023] [Revised: 07/06/2023] [Accepted: 08/07/2023] [Indexed: 09/09/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) expresses high amounts of the protein Orf9b to target the mitochondrial outer membrane protein Tom70. Tom70 serves as an import receptor for mitochondrial precursors and, independently of this function, is critical for the cellular antiviral response. Previous studies suggested that Orf9b interferes with Tom70-mediated antiviral signaling, but its implication for mitochondrial biogenesis is unknown. In this study, we expressed Orf9b in human HEK293 cells and observed an Orf9b-mediated depletion of mitochondrial proteins, particularly in respiring cells. To exclude that the observed depletion was caused by the antiviral response, we generated a yeast system in which the function of human Tom70 could be recapitulated. Upon expression of Orf9b in these cells, we again observed a specific decline of a subset of mitochondrial proteins and a general reduction of mitochondrial volume. Thus, the SARS-CoV-2 virus is able to modulate the mitochondrial proteome by a direct effect of Orf9b on mitochondrial Tom70-dependent protein import.
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Affiliation(s)
- Svenja Lenhard
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Sarah Gerlich
- Biochemistry, University of Cologne, Cologne, Germany
- CECAD, University of Cologne, Cologne, Germany
| | - Azkia Khan
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Saskia Rödl
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Jan-Eric Bökenkamp
- Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Esra Peker
- Biochemistry, University of Cologne, Cologne, Germany
- CECAD, University of Cologne, Cologne, Germany
| | - Christine Zarges
- Biochemistry, University of Cologne, Cologne, Germany
- CECAD, University of Cologne, Cologne, Germany
| | - Janina Faust
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Zuzana Storchova
- Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Markus Räschle
- Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Jan Riemer
- Biochemistry, University of Cologne, Cologne, Germany
- CECAD, University of Cologne, Cologne, Germany
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11
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Benitez-Fuente F, Botella MA. Biological roles of plant synaptotagmins. Eur J Cell Biol 2023; 102:151335. [PMID: 37390668 DOI: 10.1016/j.ejcb.2023.151335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 06/19/2023] [Accepted: 06/19/2023] [Indexed: 07/02/2023] Open
Abstract
Plant synaptotagmins (SYTs) are resident proteins of the endoplasmic reticulum (ER). They are characterized by an N-terminal transmembrane region and C2 domains at the C-terminus, which tether the ER to the plasma membrane (PM). In addition to their tethering role, SYTs contain a lipid-harboring SMP domain, essential for shuttling lipids between the ER and the PM. There is now abundant literature on Arabidopsis SYT1, the best-characterized family member, which link it to biotic and abiotic responses as well as to ER morphology. Here, we review the current knowledge of SYT members, focusing on their role in stress, and discuss how these roles can be related to their tethering and lipid transport functions. Finally, we contextualize this information about SYTs with their homologs, the yeast tricalbins and the mammalian extended synaptotagmins.
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Affiliation(s)
- Francisco Benitez-Fuente
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga 12907, Spain
| | - Miguel A Botella
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga 12907, Spain.
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12
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Krishna CK, Schmidt N, Tippler BG, Schliebs W, Jung M, Winklhofer KF, Erdmann R, Kalel VC. Molecular basis of the glycosomal targeting of PEX11 and its mislocalization to mitochondrion in trypanosomes. Front Cell Dev Biol 2023; 11:1213761. [PMID: 37664461 PMCID: PMC10469627 DOI: 10.3389/fcell.2023.1213761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/03/2023] [Indexed: 09/05/2023] Open
Abstract
PEX19 binding sites are essential parts of the targeting signals of peroxisomal membrane proteins (mPTS). In this study, we characterized PEX19 binding sites of PEX11, the most abundant peroxisomal and glycosomal membrane protein from Trypanosoma brucei and Saccharomyces cerevisiae. TbPEX11 contains two PEX19 binding sites, one close to the N-terminus (BS1) and a second in proximity to the first transmembrane domain (BS2). The N-terminal BS1 is highly conserved across different organisms and is required for maintenance of the steady-state concentration and efficient targeting to peroxisomes and glycosomes in both baker's yeast and Trypanosoma brucei. The second PEX19 binding site in TbPEX11 is essential for its glycosomal localization. Deletion or mutations of the PEX19 binding sites in TbPEX11 or ScPEX11 results in mislocalization of the proteins to mitochondria. Bioinformatic analysis indicates that the N-terminal region of TbPEX11 contains an amphiphilic helix and several putative TOM20 recognition motifs. We show that the extreme N-terminal region of TbPEX11 contains a cryptic N-terminal signal that directs PEX11 to the mitochondrion if its glycosomal transport is blocked.
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Affiliation(s)
- Chethan K. Krishna
- Department of Systems Biochemistry, Institute for Biochemistry and Pathobiochemistry, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
| | - Nadine Schmidt
- Department of Systems Biochemistry, Institute for Biochemistry and Pathobiochemistry, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
| | - Bettina G. Tippler
- Department of Systems Biochemistry, Institute for Biochemistry and Pathobiochemistry, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
| | - Wolfgang Schliebs
- Department of Systems Biochemistry, Institute for Biochemistry and Pathobiochemistry, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
| | - Martin Jung
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Konstanze F. Winklhofer
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
| | - Ralf Erdmann
- Department of Systems Biochemistry, Institute for Biochemistry and Pathobiochemistry, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
| | - Vishal C. Kalel
- Department of Systems Biochemistry, Institute for Biochemistry and Pathobiochemistry, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
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13
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Jarrous N, Liu F. Human RNase P: overview of a ribonuclease of interrelated molecular networks and gene-targeting systems. RNA (NEW YORK, N.Y.) 2023; 29:300-307. [PMID: 36549864 PMCID: PMC9945436 DOI: 10.1261/rna.079475.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 12/09/2022] [Indexed: 05/14/2023]
Abstract
The seminal discovery of ribonuclease P (RNase P) and its catalytic RNA by Sidney Altman has not only revolutionized our understanding of life, but also opened new fields for scientific exploration and investigation. This review focuses on human RNase P and its use as a gene-targeting tool, two topics initiated in Altman's laboratory. We outline early works on human RNase P as a tRNA processing enzyme and comment on its expanding nonconventional functions in molecular networks of transcription, chromatin remodeling, homology-directed repair, and innate immunity. The important implications and insights from these discoveries on the potential use of RNase P as a gene-targeting tool are presented. This multifunctionality calls to a modified structure-function partitioning of domains in human RNase P, as well as its relative ribonucleoprotein, RNase MRP. The role of these two catalysts in innate immunity is of particular interest in molecular evolution, as this dynamic molecular network could have originated and evolved from primordial enzymes and sensors of RNA, including predecessors of these two ribonucleoproteins.
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Affiliation(s)
- Nayef Jarrous
- Department of Microbiology and Molecular Genetics, The Hebrew University-Hadassah Medical School, Jerusalem 9112010, Israel
| | - Fenyong Liu
- Division of Infectious Diseases, School of Public Health, University of California, Berkeley, California 94720, USA
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14
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Fenech EJ, Cohen N, Kupervaser M, Gazi Z, Schuldiner M. A toolbox for systematic discovery of stable and transient protein interactors in baker's yeast. Mol Syst Biol 2023; 19:e11084. [PMID: 36651308 PMCID: PMC9912024 DOI: 10.15252/msb.202211084] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 01/19/2023] Open
Abstract
Identification of both stable and transient interactions is essential for understanding protein function and regulation. While assessing stable interactions is more straightforward, capturing transient ones is challenging. In recent years, sophisticated tools have emerged to improve transient interactor discovery, with many harnessing the power of evolved biotin ligases for proximity labelling. However, biotinylation-based methods have lagged behind in the model eukaryote, Saccharomyces cerevisiae, possibly due to the presence of several abundant, endogenously biotinylated proteins. In this study, we optimised robust biotin-ligation methodologies in yeast and increased their sensitivity by creating a bespoke technique for downregulating endogenous biotinylation, which we term ABOLISH (Auxin-induced BiOtin LIgase diminiSHing). We used the endoplasmic reticulum insertase complex (EMC) to demonstrate our approaches and uncover new substrates. To make these tools available for systematic probing of both stable and transient interactions, we generated five full-genome collections of strains in which every yeast protein is tagged with each of the tested biotinylation machineries, some on the background of the ABOLISH system. This comprehensive toolkit enables functional interactomics of the entire yeast proteome.
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Affiliation(s)
- Emma J Fenech
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Nir Cohen
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Meital Kupervaser
- The de Botton Protein Profiling Institute of the Nancy and Stephen Grand Israel National Centre for Personalized MedicineWeizmann Institute of ScienceRehovotIsrael
| | - Zohar Gazi
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Maya Schuldiner
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
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15
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Wu Z, Berlemann LA, Bader V, Sehr DA, Dawin E, Covallero A, Meschede J, Angersbach L, Showkat C, Michaelis JB, Münch C, Rieger B, Namgaladze D, Herrera MG, Fiesel FC, Springer W, Mendes M, Stepien J, Barkovits K, Marcus K, Sickmann A, Dittmar G, Busch KB, Riedel D, Brini M, Tatzelt J, Cali T, Winklhofer KF. LUBAC assembles a ubiquitin signaling platform at mitochondria for signal amplification and transport of NF-κB to the nucleus. EMBO J 2022; 41:e112006. [PMID: 36398858 PMCID: PMC9753471 DOI: 10.15252/embj.2022112006] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/20/2022] [Accepted: 10/25/2022] [Indexed: 11/19/2022] Open
Abstract
Mitochondria are increasingly recognized as cellular hubs to orchestrate signaling pathways that regulate metabolism, redox homeostasis, and cell fate decisions. Recent research revealed a role of mitochondria also in innate immune signaling; however, the mechanisms of how mitochondria affect signal transduction are poorly understood. Here, we show that the NF-κB pathway activated by TNF employs mitochondria as a platform for signal amplification and shuttling of activated NF-κB to the nucleus. TNF treatment induces the recruitment of HOIP, the catalytic component of the linear ubiquitin chain assembly complex (LUBAC), and its substrate NEMO to the outer mitochondrial membrane, where M1- and K63-linked ubiquitin chains are generated. NF-κB is locally activated and transported to the nucleus by mitochondria, leading to an increase in mitochondria-nucleus contact sites in a HOIP-dependent manner. Notably, TNF-induced stabilization of the mitochondrial kinase PINK1 furthermore contributes to signal amplification by antagonizing the M1-ubiquitin-specific deubiquitinase OTULIN. Overall, our study reveals a role for mitochondria in amplifying TNF-mediated NF-κB activation, both serving as a signaling platform, as well as a transport mode for activated NF-κB to the nuclear.
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Affiliation(s)
- Zhixiao Wu
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Lena A Berlemann
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Verian Bader
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Dominik A Sehr
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Eva Dawin
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
- Leibniz‐Institut für Analytische Wissenschaften—ISAS—e.VDortmundGermany
| | | | - Jens Meschede
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Lena Angersbach
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Cathrin Showkat
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Jonas B Michaelis
- Faculty of Medicine, Institute of Biochemistry IIGoethe University FrankfurtFrankfurt am MainGermany
| | - Christian Münch
- Faculty of Medicine, Institute of Biochemistry IIGoethe University FrankfurtFrankfurt am MainGermany
| | - Bettina Rieger
- Institute for Integrative Cell Biology and Physiology, Faculty of BiologyUniversity of MünsterMünsterGermany
| | - Dmitry Namgaladze
- Institute of Biochemistry I, Faculty of MedicineGoethe‐University FrankfurtFrankfurtGermany
| | - Maria Georgina Herrera
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Fabienne C Fiesel
- Department of NeuroscienceMayo ClinicJacksonvilleFLUSA
- Neuroscience PhD ProgramMayo Clinic Graduate School of Biomedical SciencesJacksonvilleFLUSA
| | - Wolfdieter Springer
- Department of NeuroscienceMayo ClinicJacksonvilleFLUSA
- Neuroscience PhD ProgramMayo Clinic Graduate School of Biomedical SciencesJacksonvilleFLUSA
| | - Marta Mendes
- Proteomics of Cellular Signaling, Department of Infection and ImmunityLuxembourg Institute of HealthStrassenLuxembourg
| | - Jennifer Stepien
- Medizinisches Proteom‐CenterRuhr‐Universität BochumBochumGermany
- Medical Proteome Analysis, Center for Protein Diagnostics (PRODI)Ruhr‐University BochumBochumGermany
| | - Katalin Barkovits
- Medizinisches Proteom‐CenterRuhr‐Universität BochumBochumGermany
- Medical Proteome Analysis, Center for Protein Diagnostics (PRODI)Ruhr‐University BochumBochumGermany
| | - Katrin Marcus
- Medizinisches Proteom‐CenterRuhr‐Universität BochumBochumGermany
- Medical Proteome Analysis, Center for Protein Diagnostics (PRODI)Ruhr‐University BochumBochumGermany
| | - Albert Sickmann
- Leibniz‐Institut für Analytische Wissenschaften—ISAS—e.VDortmundGermany
| | - Gunnar Dittmar
- Proteomics of Cellular Signaling, Department of Infection and ImmunityLuxembourg Institute of HealthStrassenLuxembourg
- Department of Life Sciences and MedicineUniversity of LuxembourgBelvauxLuxembourg
| | - Karin B Busch
- Institute for Integrative Cell Biology and Physiology, Faculty of BiologyUniversity of MünsterMünsterGermany
| | - Dietmar Riedel
- Laboratory for Electron MicroscopyMax Planck Institute for Multidisciplinary SciencesGöttingenGermany
| | - Marisa Brini
- Department of BiologyUniversity of PaduaPaduaItaly
- Centro Studi per la Neurodegenerazione (CESNE)University of PadovaPaduaItaly
| | - Jörg Tatzelt
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
- RESOLV Cluster of ExcellenceRuhr University BochumBochumGermany
| | - Tito Cali
- Department of Biomedical SciencesUniversity of PaduaPaduaItaly
- Centro Studi per la Neurodegenerazione (CESNE)University of PadovaPaduaItaly
- Padua Neuroscience Center (PNC)University of PaduaPaduaItaly
| | - Konstanze F Winklhofer
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
- RESOLV Cluster of ExcellenceRuhr University BochumBochumGermany
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16
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Sing TL, Brar GA, Ünal E. Gametogenesis: Exploring an Endogenous Rejuvenation Program to Understand Cellular Aging and Quality Control. Annu Rev Genet 2022; 56:89-112. [PMID: 35878627 PMCID: PMC9712276 DOI: 10.1146/annurev-genet-080320-025104] [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] [Indexed: 01/07/2023]
Abstract
Gametogenesis is a conserved developmental program whereby a diploid progenitor cell differentiates into haploid gametes, the precursors for sexually reproducing organisms. In addition to ploidy reduction and extensive organelle remodeling, gametogenesis naturally rejuvenates the ensuing gametes, leading to resetting of life span. Excitingly, ectopic expression of the gametogenesis-specific transcription factor Ndt80 is sufficient to extend life span in mitotically dividing budding yeast, suggesting that meiotic rejuvenation pathways can be repurposed outside of their natural context. In this review, we highlight recent studies of gametogenesis that provide emerging insight into natural quality control, organelle remodeling, and rejuvenation strategies that exist within a cell. These include selective inheritance, programmed degradation, and de novo synthesis, all of which are governed by the meiotic gene expression program entailing many forms of noncanonical gene regulation. Finally, we highlight critical questions that remain in the field and provide perspective on the implications of gametogenesis research on human health span.
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Affiliation(s)
- Tina L Sing
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA;
| | - Gloria A Brar
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA;
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA;
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17
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Castro IG, Shortill SP, Dziurdzik SK, Cadou A, Ganesan S, Valenti R, David Y, Davey M, Mattes C, Thomas FB, Avraham RE, Meyer H, Fadel A, Fenech EJ, Ernst R, Zaremberg V, Levine TP, Stefan C, Conibear E, Schuldiner M. Systematic analysis of membrane contact sites in Saccharomyces cerevisiae uncovers modulators of cellular lipid distribution. eLife 2022; 11:74602. [DOI: 10.7554/elife.74602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
Actively maintained close appositions between organelle membranes, also known as contact sites, enable the efficient transfer of biomolecules between cellular compartments. Several such sites have been described as well as their tethering machineries. Despite these advances we are still far from a comprehensive understanding of the function and regulation of most contact sites. To systematically characterize contact site proteomes, we established a high-throughput screening approach in Saccharomyces cerevisiae based on co-localization imaging. We imaged split fluorescence reporters for six different contact sites, several of which are poorly characterized, on the background of 1165 strains expressing a mCherry-tagged yeast protein that has a cellular punctate distribution (a hallmark of contact sites), under regulation of the strong TEF2 promoter. By scoring both co-localization events and effects on reporter size and abundance, we discovered over 100 new potential contact site residents and effectors in yeast. Focusing on several of the newly identified residents, we identified three homologs of Vps13 and Atg2 that are residents of multiple contact sites. These proteins share their lipid transport domain, thus expanding this family of lipid transporters. Analysis of another candidate, Ypr097w, which we now call Lec1 (Lipid-droplet Ergosterol Cortex 1), revealed that this previously uncharacterized protein dynamically shifts between lipid droplets and the cell cortex, and plays a role in regulation of ergosterol distribution in the cell. Overall, our analysis expands the universe of contact site residents and effectors and creates a rich database to mine for new functions, tethers, and regulators.
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Affiliation(s)
| | - Shawn P Shortill
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia
- Department of Medical Genetics, University of British Columbia
| | - Samantha Katarzyna Dziurdzik
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia
- Department of Medical Genetics, University of British Columbia
| | - Angela Cadou
- Laboratory for Molecular Cell Biology, University College London
| | | | - Rosario Valenti
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Yotam David
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Michael Davey
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia
| | - Carsten Mattes
- Medical Biochemistry and Molecular Biology, PZMS, Medical Faculty, Saarland University
| | - Ffion B Thomas
- Laboratory for Molecular Cell Biology, University College London
| | | | - Hadar Meyer
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Amir Fadel
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Emma J Fenech
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Robert Ernst
- Medical Biochemistry and Molecular Biology, PZMS, Medical Faculty, Saarland University
| | | | - Tim P Levine
- UCL Institute of Ophthalmology, University College London
| | | | - Elizabeth Conibear
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia
- Department of Medical Genetics, University of British Columbia
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science
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18
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Kors S, Kurian SM, Costello JL, Schrader M. Controlling contacts-Molecular mechanisms to regulate organelle membrane tethering. Bioessays 2022; 44:e2200151. [PMID: 36180400 DOI: 10.1002/bies.202200151] [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: 08/03/2022] [Revised: 09/07/2022] [Accepted: 09/12/2022] [Indexed: 11/06/2022]
Abstract
In recent years, membrane contact sites (MCS), which mediate interactions between virtually all subcellular organelles, have been extensively characterized and shown to be essential for intracellular communication. In this review essay, we focus on an emerging topic: the regulation of MCS. Focusing on the tether proteins themselves, we discuss some of the known mechanisms which can control organelle tethering events and identify apparent common regulatory hubs, such as the VAP interface at the endoplasmic reticulum (ER). We also highlight several currently hypothetical concepts, including the idea of tether oligomerization and redox regulation playing a role in MCS formation. We identify gaps in our current understanding, such as the identity of the majority of kinases/phosphatases involved in tether modification and conclude that a holistic approach-incorporating the formation of multiple MCS, regulated by interconnected regulatory modulators-may be required to fully appreciate the true complexity of these fascinating intracellular communication systems.
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Affiliation(s)
- Suzan Kors
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, UK
| | - Smija M Kurian
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, UK
| | - Joseph L Costello
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, UK
| | - Michael Schrader
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, UK
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19
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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] [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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20
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Ovciarikova J, Oliveira Souza RO, Arrizabalaga G, Sheiner L. Protein control of membrane and organelle dynamics: Insights from the divergent eukaryote Toxoplasma gondii. Curr Opin Cell Biol 2022; 76:102085. [PMID: 35569259 PMCID: PMC9586877 DOI: 10.1016/j.ceb.2022.102085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/28/2022] [Accepted: 04/01/2022] [Indexed: 11/26/2022]
Abstract
Integral membrane protein complexes control key cellular functions in eukaryotes by defining membrane-bound spaces within organelles and mediating inter-organelles contacts. Despite the critical role of membrane complexes in cell biology, most of our knowledge is from a handful of model systems, primarily yeast and mammals, while a full functional and evolutionary understanding remains incomplete without the perspective from a broad range of divergent organisms. Apicomplexan parasites are single-cell eukaryotes whose survival depends on organelle compartmentalisation and communication. Studies of a model apicomplexan, Toxoplasma gondii, reveal unexpected divergence in the composition and function of complexes previously considered broadly conserved, such as the mitochondrial ATP synthase and the tethers mediating ER–mitochondria membrane contact sites. Thus, Toxoplasma joins the repertoire of divergent model eukaryotes whose research completes our understanding of fundamental cell biology.
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21
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Zaman M, Shutt TE. The Role of Impaired Mitochondrial Dynamics in MFN2-Mediated Pathology. Front Cell Dev Biol 2022; 10:858286. [PMID: 35399520 PMCID: PMC8989266 DOI: 10.3389/fcell.2022.858286] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/07/2022] [Indexed: 12/17/2022] Open
Abstract
The Mitofusin 2 protein (MFN2), encoded by the MFN2 gene, was first described for its role in mediating mitochondrial fusion. However, MFN2 is now recognized to play additional roles in mitochondrial autophagy (mitophagy), mitochondrial motility, lipid transfer, and as a tether to other organelles including the endoplasmic reticulum (ER) and lipid droplets. The tethering role of MFN2 is an important mediator of mitochondrial-ER contact sites (MERCs), which themselves have many important functions that regulate mitochondria, including calcium homeostasis and lipid metabolism. Exemplifying the importance of MFN2, pathogenic variants in MFN2 are established to cause the peripheral neuropathy Charcot-Marie-Tooth Disease Subtype 2A (CMT2A). However, the mechanistic basis for disease is not clear. Moreover, additional pathogenic phenotypes such as lipomatosis, distal myopathy, optic atrophy, and hearing loss, can also sometimes be present in patients with CMT2A. Given these variable patient phenotypes, and the many cellular roles played by MFN2, the mechanistic underpinnings of the cellular impairments by which MFN2 dysfunction leads to disease are likely to be complex. Here, we will review what is known about the various functions of MFN2 that are impaired by pathogenic variants causing CMT2A, with a specific emphasis on the ties between MFN2 variants and MERCs.
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Affiliation(s)
- Mashiat Zaman
- Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
- Alberta Children’s Hospital Research Institute (ACHRI), Calgary, AB, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Timothy E. Shutt
- Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
- Alberta Children’s Hospital Research Institute (ACHRI), Calgary, AB, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
- Department of Medical Genetics, University of Calgary, Calgary, AB, Canada
- *Correspondence: Timothy E. Shutt,
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22
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Dussouchaud A, Jacob J, Secq C, Verbavatz JM, Moras M, Larghero J, Fader CM, Ostuni MA, Lefevre SD. Transmission Electron Microscopy to Follow Ultrastructural Modifications of Erythroblasts Upon ex vivo Human Erythropoiesis. Front Physiol 2022; 12:791691. [PMID: 35222062 PMCID: PMC8864112 DOI: 10.3389/fphys.2021.791691] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/23/2021] [Indexed: 01/02/2023] Open
Abstract
Throughout mammal erythroid differentiation, erythroblasts undergo enucleation and organelle clearance becoming mature red blood cell. Organelles are cleared by autophagic pathways non-specifically targeting organelles and cytosolic content or by specific mitophagy targeting mitochondria. Mitochondrial functions are essential to coordinate metabolism reprogramming, cell death, and differentiation balance, and also synthesis of heme, the prosthetic group needed in hemoglobin assembly. In mammals, mitochondria subcellular localization and mitochondria interaction with other structures as endoplasmic reticulum and nucleus might be of importance for the removal of the nucleus, that is, the enucleation. Here, we aim to characterize by electron microscopy the changes in ultrastructure of cells over successive stages of human erythroblast differentiation. We focus on mitochondria to gain insights into intracellular localization, ultrastructure, and contact with other organelles. We found that mitochondria are progressively cleared with a significant switch between PolyE and OrthoE stages, acquiring a rounded shape and losing contact sites with both ER (MAM) and nucleus (NAM). We studied intracellular vesicle trafficking and found that endosomes and MVBs, known to be involved in iron traffic and heme synthesis, are increased during BasoE to PolyE transition; autophagic structures such as autophagosomes increase from ProE to OrthoE stages. Finally, consistent with metabolic switch, glycogen accumulation was observed in OrthoE stage.
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Affiliation(s)
- Alice Dussouchaud
- Université de Paris and Université des Antilles, INSERM, BIGR, Paris, France
| | - Julieta Jacob
- Laboratorio de Biología Celular y Molecular, Instituto de Histología y Embriología, CONICET, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Charles Secq
- Université de Paris and Université des Antilles, INSERM, BIGR, Paris, France
| | | | - Martina Moras
- Université de Paris and Université des Antilles, INSERM, BIGR, Paris, France
| | - Jérôme Larghero
- CNRS, UMR 7592, Institut Jacques Monod, Université de Paris, Paris, France
| | - Claudio M. Fader
- Laboratorio de Biología Celular y Molecular, Instituto de Histología y Embriología, CONICET, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Mariano A. Ostuni
- Université de Paris and Université des Antilles, INSERM, BIGR, Paris, France
| | - Sophie D. Lefevre
- Université de Paris and Université des Antilles, INSERM, BIGR, Paris, France
- *Correspondence: Sophie D. Lefevre,
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Ovciarikova J, Shikha S, Sheiner L. Nuclear Interactions: A Spotlight on Nuclear Mitochondrial Membrane Contact Sites. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2022; 5:25152564221096217. [PMID: 36338149 PMCID: PMC9623421 DOI: 10.1177/25152564221096217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Membrane contact sites (MCS) are critical for cellular functions of eukaryotes, as they enable communication and exchange between organelles. Research over the last decade unravelled the function and composition of MCS between a variety of organelles including mitochondria, ER, plasma membrane, lysosomes, lipid droplets, peroxisome and endosome, to name a few. In fact, MCS are found between any pair of organelles studied to date, with common functions including lipid exchange, calcium signalling and organelle positioning in the cell. Work in the past year has started addressing the composition and function of nuclear-mitochondrial MCS. Tether components mediating these contacts in yeast have been identified via comprehensive phenotypic screens, which also revealed a possible link between this contact and phosphatidylcholine metabolism. In human cells, and in the protozoan parasites causing malaria, proximity between these organelles is proposed to promote cell survival via a mitochondrial retrograde response. These pioneering studies should inspire the field to explore what cellular processes depend on the exchange between the nucleus and the mitochondrion, given that they play such central roles in cell biology.
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Affiliation(s)
- Jana Ovciarikova
- Wellcome Centre for Integrative Parasitology, University of Glasgow, UK
| | - Shikha Shikha
- Wellcome Centre for Integrative Parasitology, University of Glasgow, UK
| | - Lilach Sheiner
- Wellcome Centre for Integrative Parasitology, University of Glasgow, UK
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Pizzo P, Pozzan T. Mitochondrialand: What Will Come Next? FUNCTION (OXFORD, ENGLAND) 2021; 3:zqab073. [PMID: 35330923 PMCID: PMC8788370 DOI: 10.1093/function/zqab073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 01/07/2023]
Affiliation(s)
- Paola Pizzo
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
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25
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Casler JC, Lackner LL. Cnm1: A bridge between mitochondria and nuclear ER. J Cell Biol 2021; 220:212718. [PMID: 34694321 PMCID: PMC8548917 DOI: 10.1083/jcb.202109021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Few membrane contact sites have been defined at the molecular level. By using a high-throughput, microscopy-based screen, Eisenberg-Bord, Zung et al. (2021. J. Cell Biol.https://doi.org/10.1083/jcb.202104100) identify Cnm1 as a novel tethering protein that mediates contact between mitochondria and the nuclear ER in response to phospholipid levels.
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Affiliation(s)
- Jason C Casler
- Department of Molecular Biosciences, Northwestern University, Evanston, IL
| | - Laura L Lackner
- Department of Molecular Biosciences, Northwestern University, Evanston, IL
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