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Ungermann C, Moeller A. Structuring of the endolysosomal system by HOPS and CORVET tethering complexes. Curr Opin Cell Biol 2025; 94:102504. [PMID: 40187049 DOI: 10.1016/j.ceb.2025.102504] [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: 01/14/2025] [Revised: 02/26/2025] [Accepted: 03/04/2025] [Indexed: 04/07/2025]
Abstract
Eukaryotic cells depend on their endolysosomal system for membrane protein and organelle turnover, plasma membrane quality control, or regulation of their nutrient uptake. All material eventually ends up in the lytic environment of the lysosome for cellular recycling. At endosomes and lysosomes, the multisubunit complexes CORVET and HOPS tether membranes by binding both their cognate Rab GTPase and specific membrane lipids. Additionally, they carry one Sec1/Munc18-like subunit at their center and thus promote SNARE assembly and, subsequently, bilayer mixing. Recent structural and functional analysis provided insights into their organization and suggested how these complexes combine tethering with fusion catalysis. This review discusses the function and structural organization of HOPS and CORVET in the context of recent studies in yeast and metazoan cells.
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Affiliation(s)
- Christian Ungermann
- Department of Biology/Chemistry, Biochemistry Section, Osnabrück University, Barbarastrasse 13, 49076, Osnabrück, Germany; Center of Cellular Nanoanalytics Osnabrück (CellNanOs), Osnabrück University, Barbarastrasse 11, 49076, Osnabrück, Germany.
| | - Arne Moeller
- Center of Cellular Nanoanalytics Osnabrück (CellNanOs), Osnabrück University, Barbarastrasse 11, 49076, Osnabrück, Germany; Department of Biology/Chemistry, Structural Biology Section, Osnabrück University, Barbarastrasse 13, 49076, Osnabrück, Germany.
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2
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Diokmetzidou A, Scorrano L. Mitochondria-membranous organelle contacts at a glance. J Cell Sci 2025; 138:jcs263895. [PMID: 40357586 DOI: 10.1242/jcs.263895] [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: 05/15/2025] Open
Abstract
Mitochondrial contact sites are specialized interfaces where mitochondria physically interact with other organelles. Stabilized by molecular tethers and defined by unique proteomic and lipidomic profiles, these sites enable direct interorganellar communication and functional coordination, playing crucial roles in cellular physiology and homeostasis. Recent advances have expanded our knowledge of contact site-resident proteins, illuminated the dynamic and adaptive nature of these interfaces, and clarified their contribution to pathophysiology. In this Cell Science at a Glance article and the accompanying poster, we summarize the mitochondrial contacts that have been characterized in mammals, the molecular mechanisms underlying their formation, and their principal functions.
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Affiliation(s)
- Antigoni Diokmetzidou
- Department of Biology, University of Padova, 35121 Padova, Italy
- Veneto Institute of Molecular Medicine (VIMM), 35129 Padova, Italy
| | - Luca Scorrano
- Department of Biology, University of Padova, 35121 Padova, Italy
- Veneto Institute of Molecular Medicine (VIMM), 35129 Padova, Italy
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3
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Casler JC, Harper CS, Lackner LL. Mitochondria-plasma membrane contact sites regulate the ER-mitochondria encounter structure. J Cell Sci 2025; 138:JCS263685. [PMID: 39878621 PMCID: PMC11883241 DOI: 10.1242/jcs.263685] [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: 11/04/2024] [Accepted: 01/08/2025] [Indexed: 01/31/2025] Open
Abstract
Cells form multiple, molecularly distinct membrane contact sites (MCSs) between organelles. Despite knowing the molecular identity of several of these complexes, little is known about how MCSs are coordinately regulated in space and time to promote organelle function. Here, we examined two well-characterized mitochondria-endoplasmic reticulum (ER) MCSs - the ER-mitochondria encounter structure (ERMES) and the mitochondria-ER-cortex anchor (MECA) in Saccharomyces cerevisiae. We report that loss of MECA results in a substantial reduction in the number of ERMES contacts. Rather than reducing ERMES protein levels, loss of MECA results in an increase in the size of ERMES contacts. Using live-cell microscopy, we demonstrate that ERMES contacts display several dynamic behaviors, such as de novo formation, fusion and fission, that are altered in the absence of MECA or by changes in growth conditions. Unexpectedly, we find that the mitochondria-plasma membrane (PM) tethering, and not the mitochondria-ER tethering, function of MECA regulates ERMES contacts. Remarkably, synthetic tethering of mitochondria to the PM in the absence of MECA is sufficient to rescue the distribution of ERMES foci. Overall, our work reveals how one MCS can influence the regulation and function of another.
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Affiliation(s)
- Jason C. Casler
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Clare S. Harper
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Laura L. Lackner
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
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4
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Sánchez-León E, Bhalla K, Hu G, Lee CWJ, Lagace M, Jung WH, Kronstad JW. The HOPS and vCLAMP protein Vam6 connects polyphosphate with mitochondrial function and oxidative stress resistance in Cryptococcus neoformans. mBio 2025; 16:e0032825. [PMID: 39998208 PMCID: PMC11980578 DOI: 10.1128/mbio.00328-25] [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: 01/25/2025] [Accepted: 02/05/2025] [Indexed: 02/26/2025] Open
Abstract
Cryptococcus neoformans is considered one of the most dangerous fungal threats to human health, and the World Health Organization recently ranked it in the critical priority group for perceived public health importance. Proliferation of C. neoformans within mammalian hosts is supported by its ability to overcome nutritional limitations and endure stress conditions induced by the host immune response. Previously, we reported that the Vam6/Vps39/TRAP1-domain protein Vam6 was crucial for vacuolar morphology, iron acquisition, and virulence. However, the molecular mechanisms underlying the pleiotropic phenotypes resulting from loss of Vam6 remain poorly understood. In this study, we determined that Vam6 has roles in the HOPS complex for endomembrane trafficking to the vacuole and in the vCLAMP membrane contact site between the vacuole and mitochondria. Importantly, both of these roles regulate polyphosphate (polyP) metabolism, as demonstrated by a defect in trafficking of the VTC complex subunit Vtc2 for polyphosphate synthesis and by an influence on mitochondrial functions. In the latter case, Vam6 was required for polyP accumulation in response to electron transport chain inhibition and for overcoming oxidative stress. Overall, this work establishes connections between endomembrane trafficking, mitochondrial functions, and polyP homeostasis in C. neoformans.IMPORTANCEA detailed understanding of stress resistance by fungal pathogens of humans may provide new opportunities to improve antifungal therapy and combat life-threatening diseases. Here, we used a vam6 deletion mutant to investigate the role of the homotypic fusion and vacuole protein sorting (HOPS) complex in mitochondrial functions and polyphosphate homeostasis in Cryptococcus neoformans, an important fungal pathogen of immunocompromised people including those suffering from HIV/AIDS. Specifically, we made use of mutants defective in late endocytic trafficking steps to establish connections to oxidative stress and membrane trafficking with mitochondria. In particular, we found that mutants lacking the Vam6 protein had altered mitochondrial function, and that the mutants were perturbed for additional mitochondria and vacuole-related phenotypes (e.g., membrane composition, polyphosphate accumulation, and drug sensitivity). Overall, our study establishes connections between endomembrane trafficking components, mitochondrial functions, and polyphosphate homeostasis in an important fungal pathogen of humans.
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Affiliation(s)
- Eddy Sánchez-León
- The Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Kabir Bhalla
- The Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Guanggan Hu
- The Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Christopher W. J. Lee
- The Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Melissa Lagace
- The Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Won Hee Jung
- Department of Systems Biotechnology, Chung-Ang University, Anseong, South Korea
| | - James W. Kronstad
- The Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
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5
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Bi J, Sun Y, Guo M, Sun X, Sun J, Jiang R, Wang N, Huang G. Lysosomes: guardians and healers within cells- multifaceted perspective and outlook from injury repair to disease treatment. Cancer Cell Int 2025; 25:136. [PMID: 40205430 PMCID: PMC11984033 DOI: 10.1186/s12935-025-03771-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Accepted: 03/28/2025] [Indexed: 04/11/2025] Open
Abstract
Lysosomes, as crucial organelles within cells, carry out diverse biological functions such as waste degradation, regulation of the cellular environment, and precise control of cell signaling. This paper reviews the core functions and structural characteristics of lysosomes, and delves into the current research status of lysosomes damage repair mechanisms. Subsequently, we explore in depth the close association between lysosomes and various diseases, including but not limited to age-related chronic diseases, neuro-degenerative diseases, tumors, inflammation, and immune imbalance. Additionally, we also provide a detailed discussion of the application of lysosome-targeted substances in the field of regenerative medicine, especially the enormous potential demonstrated in key areas such as stem cell regulation and therapy, and myocardial cell repair. Though the integration of multidisciplinary research efforts, we believe that lysosomes damage repair mechanisms will demonstrate even greater application value in disease treatment and regenerative medicine.
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Affiliation(s)
- Jianlei Bi
- Department of Medical Oncology, The Second Hospital of Dalian Medical University, No. 467 Zhongshan Road, Shahekou District, Dalian, 116023, Liaoning, China
| | - Yincong Sun
- Institute for Genome Engineered Animal Models of Human Diseases, National Center of Genetically Engineered Animal Models for International Research, Dalian Medical University, Dalian, 116044, Liaoning, China
- College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, Liaoning, China
| | - Meihua Guo
- Institute for Genome Engineered Animal Models of Human Diseases, National Center of Genetically Engineered Animal Models for International Research, Dalian Medical University, Dalian, 116044, Liaoning, China
| | - Xiaoxin Sun
- College of Integrative Medicine, Dalian Medical University, Dalian, 116044, Liaoning, P.R. China
| | - Jie Sun
- Institute for Genome Engineered Animal Models of Human Diseases, National Center of Genetically Engineered Animal Models for International Research, Dalian Medical University, Dalian, 116044, Liaoning, China
| | - Rujiao Jiang
- Institute for Genome Engineered Animal Models of Human Diseases, National Center of Genetically Engineered Animal Models for International Research, Dalian Medical University, Dalian, 116044, Liaoning, China
| | - Ning Wang
- Institute for Genome Engineered Animal Models of Human Diseases, National Center of Genetically Engineered Animal Models for International Research, Dalian Medical University, Dalian, 116044, Liaoning, China.
| | - Gena Huang
- Department of Medical Oncology, The Second Hospital of Dalian Medical University, No. 467 Zhongshan Road, Shahekou District, Dalian, 116023, Liaoning, China.
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6
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Schwabl SI, Siegmann KA, Teis D. Lipid juggling: Any1 scrambles membranes for endosome biogenesis. J Cell Biol 2025; 224:e202502158. [PMID: 40094457 PMCID: PMC11912935 DOI: 10.1083/jcb.202502158] [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: 03/19/2025] Open
Abstract
Multivesicular bodies (MVBs) are crucial for membrane protein degradation and lipid homeostasis. A recent study by Gao and colleagues (https://doi.org/10.1083/jcb.202410013) identifies Any1 as a phospholipid scramblase that plays an important role in MVB biogenesis by coordinating membrane remodeling with lipid transfer through Vps13 at organelle contact sites.
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Affiliation(s)
- Sinead Iduna Schwabl
- Institute of Molecular Biochemistry, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | | | - David Teis
- Institute of Molecular Biochemistry, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
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7
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Kiraly S, Stanley J, Eden ER. Lysosome-Mitochondrial Crosstalk in Cellular Stress and Disease. Antioxidants (Basel) 2025; 14:125. [PMID: 40002312 PMCID: PMC11852311 DOI: 10.3390/antiox14020125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2024] [Revised: 12/23/2024] [Accepted: 01/11/2025] [Indexed: 02/27/2025] Open
Abstract
The perception of lysosomes and mitochondria as entirely separate and independent entities that degrade material and produce ATP, respectively, has been challenged in recent years as not only more complex roles for both organelles, but also an unanticipated level of interdependence are being uncovered. Coupled lysosome and mitochondrial function and dysfunction involve complex crosstalk between the two organelles which goes beyond mitochondrial quality control and lysosome-mediated clearance of damaged mitochondria through mitophagy. Our understanding of crosstalk between these two essential metabolic organelles has been transformed by major advances in the field of membrane contact sites biology. We now know that membrane contact sites between lysosomes and mitochondria play central roles in inter-organelle communication. This importance of mitochondria-lysosome contacts (MLCs) in cellular homeostasis, evinced by the growing number of diseases that have been associated with their dysregulation, is starting to be appreciated. How MLCs are regulated and how their coordination with other pathways of lysosome-mitochondria crosstalk is achieved are the subjects of ongoing scrutiny, but this review explores the current understanding of the complex crosstalk governing the function of the two organelles and its impact on cellular stress and disease.
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Affiliation(s)
| | | | - Emily R. Eden
- UCL Institute of Ophthalmology, London EC1V 9EL, UK; (S.K.); (J.S.)
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Lahimer M, Capelle S, Lefranc E, Bosquet D, Kazdar N, Ledu A, Agina M, Cabry R, BenKhalifa M. Micronutrient-Antioxidant Therapy and Male Fertility Improvement During ART Cycles. Nutrients 2025; 17:324. [PMID: 39861453 PMCID: PMC11768505 DOI: 10.3390/nu17020324] [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: 12/19/2024] [Revised: 01/10/2025] [Accepted: 01/14/2025] [Indexed: 01/27/2025] Open
Abstract
Today, accumulating evidence highlights the impact of oxidative stress (OS) on semen quality. It is considered to be a key factor contributing to the decline in male fertility. OS is detected in 30-80% of men with infertility, highlighting its strong association with impaired reproductive function and with clinical outcomes following the use of assisted reproductive technologies. Spermatozoa are particularly vulnerable to oxidative damage due to their high content of polyunsaturated fatty acids (PUFAs) and limited antioxidant defense abilities. OS arises from an imbalance between the production of reactive oxygen species and the capacity to neutralize or repair their adverse effects. Evidence indicates that OS leads to lipid peroxidation, protein oxidation, mitochondrial dysfunction, and genomic instability. Micronutrient-antioxidant therapies can play a key role in infertility improvement by neutralizing free radicals and preventing cellular damage. Many different micronutrients, including L-carnitine, L-glutathione, coenzyme Q10, selenium, and zinc, as well as vitamins complexes, are proposed to improve sperm parameters and male fertility potential. This study aims to review the impact of antioxidant supplementation on semen parameters, including sperm volume, motility, concentration, morphology, genome integrity (maturity and fragmentation), and in vitro fertilization (IVF) outcomes. Antioxidant intake and a balanced lifestyle reduce oxidative stress and mitochondrial dysfunction, enhancing the spermatogenesis and spermiogenesis processes, improving sperm quality, and protecting DNA integrity.
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Affiliation(s)
- Marwa Lahimer
- ART and Reproductive Biology Laboratory, University Hospital and School of Medicine, Picardie University Jules Verne, CHU Sud, 80000 Amiens, France; (S.C.); (E.L.); (D.B.); (R.C.); (M.B.)
- PERITOX-(UMR-I 01), UPJV/INERIS, UPJV, CURS, Chemin du Thil, 80025 Amiens, France
| | - Severine Capelle
- ART and Reproductive Biology Laboratory, University Hospital and School of Medicine, Picardie University Jules Verne, CHU Sud, 80000 Amiens, France; (S.C.); (E.L.); (D.B.); (R.C.); (M.B.)
| | - Elodie Lefranc
- ART and Reproductive Biology Laboratory, University Hospital and School of Medicine, Picardie University Jules Verne, CHU Sud, 80000 Amiens, France; (S.C.); (E.L.); (D.B.); (R.C.); (M.B.)
| | - Dorian Bosquet
- ART and Reproductive Biology Laboratory, University Hospital and School of Medicine, Picardie University Jules Verne, CHU Sud, 80000 Amiens, France; (S.C.); (E.L.); (D.B.); (R.C.); (M.B.)
| | - Nadia Kazdar
- Eylau/Unilabs, IVF Units Cherest et la Muette, 75116 Paris, France; (N.K.); (A.L.)
| | - Anne Ledu
- Eylau/Unilabs, IVF Units Cherest et la Muette, 75116 Paris, France; (N.K.); (A.L.)
| | - Mounir Agina
- Service of Reproductive Biology, University Hospital Farhat Hached, University of Sousse, Sousse 4000, Tunisia;
| | - Rosalie Cabry
- ART and Reproductive Biology Laboratory, University Hospital and School of Medicine, Picardie University Jules Verne, CHU Sud, 80000 Amiens, France; (S.C.); (E.L.); (D.B.); (R.C.); (M.B.)
- PERITOX-(UMR-I 01), UPJV/INERIS, UPJV, CURS, Chemin du Thil, 80025 Amiens, France
| | - Moncef BenKhalifa
- ART and Reproductive Biology Laboratory, University Hospital and School of Medicine, Picardie University Jules Verne, CHU Sud, 80000 Amiens, France; (S.C.); (E.L.); (D.B.); (R.C.); (M.B.)
- PERITOX-(UMR-I 01), UPJV/INERIS, UPJV, CURS, Chemin du Thil, 80025 Amiens, France
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9
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Lai Y, Zhang T, Huang L, Klymchenko AS, Lin W. An exchangeable SIM probe for monitoring organellar dynamics of necrosis cells and intracellular water heterogeneity in kidney repair. Proc Natl Acad Sci U S A 2025; 122:e2402348121. [PMID: 39752520 PMCID: PMC11725781 DOI: 10.1073/pnas.2402348121] [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: 02/06/2024] [Accepted: 11/25/2024] [Indexed: 01/15/2025] Open
Abstract
Monitoring subcellular organelle dynamics in real time and precisely assessing membrane heterogeneity in living cells are very important for studying fundamental biological mechanisms and gaining a comprehensive understanding of cellular processes. However, there remains a shortage of effective tools for these purposes. Herein, we propose a strategy to develop the exchangeable water-sensing probeAPBD for time-lapse imaging of dynamics in cellular membrane-bound organelle morphology with structured illumination microscopy at the nanoscale. In this work, our results reveal mitochondria as the first organelle to undergo morphological changes through swelling, fission, and fusion in cell necrosis, leading to the rupture of the endoplasmic reticulum (ER) sheet adhered to the mitochondria. Meanwhile, the ER tubules are then reconstructed by stretching and fusion of autophagosomes. Moreover, APBD allows us to directly visualize spatially resolved distribution of biomembranes vs. water inside single mammalian cells. Our findings show that the renal ischemia-reperfusion injury (IRI) model results in the increased biomembrane to cytoplasmic water ratio in the tissue. This reveals intracellular water heterogeneity between the nucleus and the cytoplasm during the IRI process. Overall, this study presents a strategy for development of the molecular tools for cellular water heterogeneity and organelle dynamics.
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Affiliation(s)
- Youbo Lai
- Institute of Optical Materials and Chemical Biology, Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning530004, Guangxi, People's Republic of China
| | - Tengteng Zhang
- Institute of Optical Materials and Chemical Biology, Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning530004, Guangxi, People's Republic of China
| | - Ling Huang
- Institute of Optical Materials and Chemical Biology, Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning530004, Guangxi, People's Republic of China
| | - Andrey S. Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch 67401, France
| | - Weiying Lin
- Institute of Optical Materials and Chemical Biology, Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning530004, Guangxi, People's Republic of China
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10
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Domingues N, Pires J, Milosevic I, Raimundo N. Role of lipids in interorganelle communication. Trends Cell Biol 2025; 35:46-58. [PMID: 38866684 PMCID: PMC11632148 DOI: 10.1016/j.tcb.2024.04.008] [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: 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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11
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Li H, Gong W, Sun W, Yao Y, Han Y. Role of VPS39, a key tethering protein for endolysosomal trafficking and mitochondria-lysosome crosstalk, in health and disease. J Cell Biochem 2024; 125:e30396. [PMID: 36924104 DOI: 10.1002/jcb.30396] [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: 10/20/2022] [Revised: 01/12/2023] [Accepted: 02/28/2023] [Indexed: 03/18/2023]
Abstract
The coordinated interaction between mitochondria and lysosomes, mainly manifested by mitophagy, mitochondria-derived vesicles, and direct physical contact, is essential for maintaining cellular life activities. The VPS39 subunit of the homotypic fusion and protein sorting complex could play a key role in the regulation of organelle dynamics, such as endolysosomal trafficking and mitochondria-vacuole/lysosome crosstalk, thus contributing to a variety of physiological functions. The abnormalities of VPS39 and related subunits have been reported to be involved in the pathological process of some diseases. Here, we analyze the potential mechanisms and the existing problems of VPS39 in regulating organelle dynamics, which, in turn, regulate physiological functions and disease pathogenesis, so as to provide new clues for facilitating the discovery of therapeutic targets for mitochondrial and lysosomal diseases.
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Affiliation(s)
- Hanbing Li
- Institute of Pharmacology, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Wenwen Gong
- Institute of Pharmacology, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Weiyun Sun
- Institute of Pharmacology, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Yuanfa Yao
- Institute of Pharmacology, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Yubing Han
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
- Britton Chance Center for Biomedical Photonics-MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China
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12
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Karmakar S, Klauda JB. Proposed dual membrane contact with full-length Osh4. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184365. [PMID: 38960299 DOI: 10.1016/j.bbamem.2024.184365] [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: 03/17/2024] [Revised: 06/03/2024] [Accepted: 06/25/2024] [Indexed: 07/05/2024]
Abstract
Membrane contacts sites (MCSs) play important roles in lipid trafficking across cellular compartments and maintain the widespread structural diversity of organelles. We have utilized microsecond long all-atom (AA) molecular dynamics (MD) simulations and enhanced sampling techniques to unravel the MCS structure targeting by yeast oxysterol binding protein (Osh4) in an environment that mimics the interface of membranes with an increased proportion of anionic lipids using CHARMM36m forcefield with additional CUFIX parameters for lipid-protein electrostatic interactions. In a dual-membrane environment, unbiased MD simulations show that Osh4 briefly interacts with both membranes, before aligning itself with a single membrane, adopting a β-crease-bound conformation similar to observations in a single-membrane scenario. Targeted molecular dynamics simulations followed by microsecond-long AA MD simulations have revealed a distinctive dual-membrane bound state of Osh4 at MCS, wherein the protein interacts with the lower membrane via the β-crease surface, featuring its PHE-239 residue positioned below the phosphate plane of membrane, while concurrently establishing contact with the opposite membrane through the extended α6-α7 region. Osh4 maintains these dual membrane contacts simultaneously over the course of microsecond-long MD simulations. Moreover, binding energy calculations highlighted the essential roles played by the phenylalanine loop and the α6 helix in dynamically stabilizing dual-membrane bound state of Osh4 at MCS. Our computational findings were corroborated through frequency of contact analysis, showcasing excellent agreement with past experimental cross-linking data. Our computational study reveals a dual-membrane bound conformation of Osh4, providing insights into protein-membrane interactions at membrane contact sites and their relevance to lipid transfer processes.
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Affiliation(s)
- Sharmistha Karmakar
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA; Biophysics Graduate Program, University of Maryland, College Park, MD 20742, USA.
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13
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Casler JC, Harper CS, White AJ, Anderson HL, Lackner LL. Mitochondria-ER-PM contacts regulate mitochondrial division and PI(4)P distribution. J Cell Biol 2024; 223:e202308144. [PMID: 38781029 PMCID: PMC11116812 DOI: 10.1083/jcb.202308144] [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: 08/18/2023] [Revised: 12/13/2023] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
The mitochondria-ER-cortex anchor (MECA) forms a tripartite membrane contact site between mitochondria, the endoplasmic reticulum (ER), and the plasma membrane (PM). The core component of MECA, Num1, interacts with the PM and mitochondria via two distinct lipid-binding domains; however, the molecular mechanism by which Num1 interacts with the ER is unclear. Here, we demonstrate that Num1 contains a FFAT motif in its C-terminus that interacts with the integral ER membrane protein Scs2. While dispensable for Num1's functions in mitochondrial tethering and dynein anchoring, the FFAT motif is required for Num1's role in promoting mitochondrial division. Unexpectedly, we also reveal a novel function of MECA in regulating the distribution of phosphatidylinositol-4-phosphate (PI(4)P). Breaking Num1 association with any of the three membranes it tethers results in an accumulation of PI(4)P on the PM, likely via disrupting Sac1-mediated PI(4)P turnover. This work establishes MECA as an important regulatory hub that spatially organizes mitochondria, ER, and PM to coordinate crucial cellular functions.
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Affiliation(s)
- Jason C. Casler
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Clare S. Harper
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Antoineen J. White
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Heidi L. Anderson
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Laura L. Lackner
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
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14
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Schlarmann P, Sakuragi K, Ikeda A, Yang Y, Sasaki S, Hanaoka K, Araki M, Shibata T, Kanai M, Funato K. The tricalbin family of membrane contact site tethers is involved in the transcriptional responses of Saccharomyces cerevisiae to glucose. J Biol Chem 2024; 300:107665. [PMID: 39128724 PMCID: PMC11408865 DOI: 10.1016/j.jbc.2024.107665] [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: 03/05/2024] [Revised: 07/24/2024] [Accepted: 08/05/2024] [Indexed: 08/13/2024] Open
Abstract
Cellular organelles maintain areas of close apposition with other organelles at which the cytosolic gap in between them is reduced to a minimum. These membrane contact sites (MCS) are vital for organelle communication and are formed by molecular tethers that physically connect opposing membranes. Although many regulatory pathways are known to converge at MCS, a link between MCS and transcriptional regulation-the primary mechanism through which cells adapt their metabolism to environmental cues-remains largely elusive. In this study, we performed RNA-sequencing on Saccharomyces cerevisiae cells lacking tricalbin proteins (Tcb1, Tcb2, and Tcb3), a family of tethering proteins that connect the endoplasmic reticulum with the plasma membrane and Golgi, to investigate if gene expression is altered when MCS are disrupted. Our results indicate that in the tcb1Δ2Δ3Δ strain, pathways responsive to a high-glucose environment, including glycolysis, fermentation, amino acid synthesis, and low-affinity glucose uptake, are upregulated. Conversely, pathways crucial during glucose depletion, such as the tricarboxylic acid cycle, respiration, high-affinity glucose uptake, and amino acid uptake are downregulated. In addition, we demonstrate that the altered gene expression of tcb1Δ2Δ3Δ in glucose metabolism correlates with increased growth, glucose consumption, CO2 production, and ethanol generation. In conclusion, our findings reveal that tricalbin protein deletion induces a shift in gene expression patterns mimicking cellular responses to a high-glucose environment. This suggests that MCS play a role in sensing and signaling pathways that modulate gene transcription in response to glucose availability.
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Affiliation(s)
- Philipp Schlarmann
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Keiko Sakuragi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Atsuko Ikeda
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yujia Yang
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Saku Sasaki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Kazuki Hanaoka
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Misako Araki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Tomoko Shibata
- National Research Institute of Brewing, Higashi-Hiroshima, Japan
| | - Muneyoshi Kanai
- National Research Institute of Brewing, Higashi-Hiroshima, Japan
| | - Kouichi Funato
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.
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15
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Lehmer M, Zoncu R. mTORC1 Signaling Inhibition Modulates Mitochondrial Function in Frataxin Deficiency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.06.606942. [PMID: 39211218 PMCID: PMC11360942 DOI: 10.1101/2024.08.06.606942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Lysosomes regulate mitochondrial function through multiple mechanisms including the master regulator, mechanistic Target of Rapamycin Complex 1 (mTORC1) protein kinase, which is activated at the lysosomal membrane by nutrient, growth factor and energy signals. mTORC1 promotes mitochondrial protein composition changes, respiratory capacity, and dynamics, though the full range of mitochondrial-regulating functions of this protein kinase remain undetermined. We find that acute chemical modulation of mTORC1 signaling decreased mitochondrial oxygen consumption, increased mitochondrial membrane potential and reduced susceptibility to stress-induced mitophagy. In cellular models of Friedreich's Ataxia (FA), where loss of the Frataxin (FXN) protein suppresses Fe-S cluster synthesis and mitochondrial respiration, the changes induced by mTORC1 inhibitors lead to improved cell survival. Proteomic-based profiling uncover compositional changes that could underlie mTORC1-dependent modulation of FXN-deficient mitochondria. These studies highlight mTORC1 signaling as a regulator of mitochondrial composition and function, prompting further evaluation of this pathway in the context of mitochondrial disease.
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16
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Hu G, Qu X, Bhalla K, Xue P, Bakkeren E, Lee CWJ, Kronstad JW. Loss of the putative Rab GTPase, Ypt7, impairs the virulence of Cryptococcus neoformans. Front Microbiol 2024; 15:1437579. [PMID: 39119141 PMCID: PMC11306161 DOI: 10.3389/fmicb.2024.1437579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 07/16/2024] [Indexed: 08/10/2024] Open
Abstract
Small GTPases of the Rab family coordinate multiple membrane fusion and trafficking events in eukaryotes. In fungi, the Rab GTPase, Ypt7, plays a critical role in late endosomal trafficking, and is required for homotypic fusion events in vacuole biogenesis and inheritance. In this study, we identified a putative YPT7 homologue in Cryptococcus neoformans, a fungal pathogen causing life threatening meningoencephalitis in immunocompromised individuals. As part of an ongoing effort to understand mechanisms of iron acquisition in C. neoformans, we established a role for Ypt7 in growth on heme as the sole iron source. Deletion of YPT7 also caused abnormal vacuolar morphology, defective endocytic trafficking and autophagy, and mislocalization of Aph1, a secreted vacuolar acid phosphatase. Ypt7 localized to the vacuolar membrane and membrane contact sites between the vacuole and mitochondria (vCLAMPs), and loss of the protein impaired growth on inhibitors of the electron transport chain. Additionally, Ypt7 was required for robust growth at 39°C, a phenotype likely involving the calcineurin signaling pathway because ypt7 mutants displayed increased susceptibility to the calcineurin-specific inhibitors, FK506 and cyclosporin A; the mutants also had impaired growth in either limiting or high levels of calcium. Finally, Ypt7 was required for survival during interactions with macrophages, and ypt7 mutants were attenuated for virulence in a mouse inhalation model thus demonstrating the importance of membrane trafficking functions in cryptococcosis.
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Affiliation(s)
- Guanggan Hu
- The Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Xianya Qu
- The Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Kabir Bhalla
- The Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Peng Xue
- The Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Erik Bakkeren
- The Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Christopher W. J. Lee
- The Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - James W. Kronstad
- The Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
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17
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den Brave F, Schulte U, Fakler B, Pfanner N, Becker T. Mitochondrial complexome and import network. Trends Cell Biol 2024; 34:578-594. [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] [MESH Headings] [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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18
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Saukko-Paavola AJ, Klemm RW. Remodelling of mitochondrial function by import of specific lipids at multiple membrane-contact sites. FEBS Lett 2024; 598:1274-1291. [PMID: 38311340 DOI: 10.1002/1873-3468.14813] [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: 11/29/2023] [Revised: 12/14/2023] [Accepted: 12/28/2023] [Indexed: 02/08/2024]
Abstract
Organelles form physical and functional contact between each other to exchange information, metabolic intermediates, and signaling molecules. Tethering factors and contact site complexes bring partnering organelles into close spatial proximity to establish membrane contact sites (MCSs), which specialize in unique functions like lipid transport or Ca2+ signaling. Here, we discuss how MCSs form dynamic platforms that are important for lipid metabolism. We provide a perspective on how import of specific lipids from the ER and other organelles may contribute to remodeling of mitochondria during nutrient starvation. We speculate that mitochondrial adaptation is achieved by connecting several compartments into a highly dynamic organelle network. The lipid droplet appears to be a central hub in coordinating the function of these organelle neighborhoods.
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Affiliation(s)
| | - Robin W Klemm
- Department of Physiology, Anatomy and Genetics, University of Oxford, UK
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19
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Mavuduru VA, Vadupu L, Ghosh KK, Chakrabortty S, Gulyás B, Padmanabhan P, Ball WB. Mitochondrial phospholipid transport: Role of contact sites and lipid transport proteins. Prog Lipid Res 2024; 94:101268. [PMID: 38195013 DOI: 10.1016/j.plipres.2024.101268] [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: 08/11/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 01/11/2024]
Abstract
One of the major constituents of mitochondrial membranes is the phospholipids, which play a key role in maintaining the structure and the functions of the mitochondria. However, mitochondria do not synthesize most of the phospholipids in situ, necessitating the presence of phospholipid import pathways. Even for the phospholipids, which are synthesized within the inner mitochondrial membrane (IMM), the phospholipid precursors must be imported from outside the mitochondria. Therefore, the mitochondria heavily rely on the phospholipid transport pathways for its proper functioning. Since, mitochondria are not part of a vesicular trafficking network, the molecular mechanisms of how mitochondria receive its phospholipids remain a relevant question. One of the major ways that hydrophobic phospholipids can cross the aqueous barrier of inter or intraorganellar spaces is by apposing membranes, thereby decreasing the distance of transport, or by being sequestered by lipid transport proteins (LTPs). Therefore, with the discovery of LTPs and membrane contact sites (MCSs), we are beginning to understand the molecular mechanisms of phospholipid transport pathways in the mitochondria. In this review, we will present a brief overview of the recent findings on the molecular architecture and the importance of the MCSs, both the intraorganellar and interorganellar contact sites, in facilitating the mitochondrial phospholipid transport. In addition, we will also discuss the role of LTPs for trafficking phospholipids through the intermembrane space (IMS) of the mitochondria. Mechanistic insights into different phospholipid transport pathways of mitochondria could be exploited to vary the composition of membrane phospholipids and gain a better understanding of their precise role in membrane homeostasis and mitochondrial bioenergetics.
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Affiliation(s)
- Vijay Aditya Mavuduru
- Department of Biological Sciences, School of Engineering and Sciences, SRM University AP Andhra Pradesh, Guntur, Andhra Pradesh 522240, India
| | - Lavanya Vadupu
- Department of Biological Sciences, School of Engineering and Sciences, SRM University AP Andhra Pradesh, Guntur, Andhra Pradesh 522240, India
| | - Krishna Kanta Ghosh
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 59 Nanyang Drive, Singapore, 636921, Singapore
| | - Sabyasachi Chakrabortty
- Department of Chemistry, School of Engineering and Sciences, SRM University AP Andhra Pradesh, Guntur, Andhra Pradesh 522502, India
| | - Balázs Gulyás
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 59 Nanyang Drive, Singapore, 636921, Singapore; Cognitive Neuroimaging Centre, Nanyang Technological University, Singapore, 59 Nanyang Drive, 636921, Singapore; Department of Clinical Neuroscience, Karolinska Institute, Stockholm 17176, Sweden
| | - Parasuraman Padmanabhan
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 59 Nanyang Drive, Singapore, 636921, Singapore; Cognitive Neuroimaging Centre, Nanyang Technological University, Singapore, 59 Nanyang Drive, 636921, Singapore.
| | - Writoban Basu Ball
- Department of Biological Sciences, School of Engineering and Sciences, SRM University AP Andhra Pradesh, Guntur, Andhra Pradesh 522240, India.
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20
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Ersoy U, Kanakis I, Alameddine M, Pedraza-Vazquez G, Ozanne SE, Peffers MJ, Jackson MJ, Goljanek-Whysall K, Vasilaki A. Lifelong dietary protein restriction accelerates skeletal muscle loss and reduces muscle fibre size by impairing proteostasis and mitochondrial homeostasis. Redox Biol 2024; 69:102980. [PMID: 38064763 PMCID: PMC10755587 DOI: 10.1016/j.redox.2023.102980] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 01/01/2024] Open
Abstract
The early life environment significantly affects the development of age-related skeletal muscle disorders. However, the long-term effects of lactational protein restriction on skeletal muscle are still poorly defined. Our study revealed that male mice nursed by dams fed a low-protein diet during lactation exhibited skeletal muscle growth restriction. This was associated with a dysregulation in the expression levels of genes related to the ribosome, mitochondria and skeletal muscle development. We reported that lifelong protein restriction accelerated loss of type-IIa muscle fibres and reduced muscle fibre size by impairing mitochondrial homeostasis and proteostasis at 18 months of age. However, feeding a normal-protein diet following lactational protein restriction prevented accelerated fibre loss and fibre size reduction in later life. These findings provide novel insight into the mechanisms by which lactational protein restriction hinders skeletal muscle growth and includes evidence that lifelong dietary protein restriction accelerated skeletal muscle loss in later life.
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Affiliation(s)
- Ufuk Ersoy
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences (ILCaMS), The MRC - Versus Arthritis Centre for Integrated Research Into Musculoskeletal Ageing (CIMA), University of Liverpool, Liverpool, UK
| | - Ioannis Kanakis
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences (ILCaMS), The MRC - Versus Arthritis Centre for Integrated Research Into Musculoskeletal Ageing (CIMA), University of Liverpool, Liverpool, UK; Chester Medical School, Faculty of Medicine and Life Sciences, University of Chester, Chester, UK
| | - Moussira Alameddine
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences (ILCaMS), The MRC - Versus Arthritis Centre for Integrated Research Into Musculoskeletal Ageing (CIMA), University of Liverpool, Liverpool, UK
| | - Gibran Pedraza-Vazquez
- Department of Physiology, School of Medicine and REMEDI, CMNHS, University of Galway, Galway, Ireland
| | - Susan E Ozanne
- MRC Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, University of Cambridge Metabolic Research Laboratories, Cambridge, UK
| | - Mandy Jayne Peffers
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences (ILCaMS), The MRC - Versus Arthritis Centre for Integrated Research Into Musculoskeletal Ageing (CIMA), University of Liverpool, Liverpool, UK
| | - Malcolm J Jackson
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences (ILCaMS), The MRC - Versus Arthritis Centre for Integrated Research Into Musculoskeletal Ageing (CIMA), University of Liverpool, Liverpool, UK
| | - Katarzyna Goljanek-Whysall
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences (ILCaMS), The MRC - Versus Arthritis Centre for Integrated Research Into Musculoskeletal Ageing (CIMA), University of Liverpool, Liverpool, UK; Department of Physiology, School of Medicine and REMEDI, CMNHS, University of Galway, Galway, Ireland
| | - Aphrodite Vasilaki
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences (ILCaMS), The MRC - Versus Arthritis Centre for Integrated Research Into Musculoskeletal Ageing (CIMA), University of Liverpool, Liverpool, UK.
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21
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Voeltz GK, Sawyer EM, Hajnóczky G, Prinz WA. Making the connection: How membrane contact sites have changed our view of organelle biology. Cell 2024; 187:257-270. [PMID: 38242082 PMCID: PMC11830234 DOI: 10.1016/j.cell.2023.11.040] [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: 09/19/2023] [Revised: 11/13/2023] [Accepted: 11/29/2023] [Indexed: 01/21/2024]
Abstract
The view of organelles and how they operate together has changed dramatically over the last two decades. The textbook view of organelles was that they operated largely independently and were connected by vesicular trafficking and the diffusion of signals through the cytoplasm. We now know that all organelles make functional close contacts with one another, often called membrane contact sites. The study of these sites has moved to center stage in cell biology as it has become clear that they play critical roles in healthy and developing cells and during cell stress and disease states. Contact sites have important roles in intracellular signaling, lipid metabolism, motor-protein-mediated membrane dynamics, organelle division, and organelle biogenesis. Here, we summarize the major conceptual changes that have occurred in cell biology as we have come to appreciate how contact sites integrate the activities of organelles.
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Affiliation(s)
- G K Voeltz
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Boulder, CO 80309, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - E M Sawyer
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Boulder, CO 80309, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - G Hajnóczky
- MitoCare Center, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - W A Prinz
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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22
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Kubala JM, Laursen KB, Schreiner R, Williams RM, van der Mijn JC, Crowley MJ, Mongan NP, Nanus DM, Heller DA, Gudas LJ. NDUFA4L2 reduces mitochondrial respiration resulting in defective lysosomal trafficking in clear cell renal cell carcinoma. Cancer Biol Ther 2023; 24:2170669. [PMID: 36722045 PMCID: PMC9897797 DOI: 10.1080/15384047.2023.2170669] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/23/2022] [Indexed: 02/02/2023] Open
Abstract
In clear cell renal cell carcinoma (ccRCC), activation of hypoxic signaling induces NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4-like 2 (NDUFA4L2) expression. Over 90% of ccRCCs exhibit overexpression of NDUFA4L2, which we previously showed contributes to ccRCC proliferation and survival. The function of NDUFA4L2 in ccRCC has not been fully elucidated. NDUFA4L2 was reported to reduce mitochondrial respiration via mitochondrial complex I inhibition. We found that NDUFA4L2 expression in human ccRCC cells increases the extracellular acidification rate, indicative of elevated glycolysis. Conversely, NDUFA4L2 expression in non-cancerous kidney epithelial cells decreases oxygen consumption rate while increasing extracellular acidification rate, suggesting that a Warburg-like effect is induced by NDUFA4L2 alone. We performed mass-spectrometry (MS)-based proteomics of NDUFA4L2 associated complexes. Comparing RCC4-P (parental) ccRCC cells with RCC4 in which NDUFA4L2 is knocked out by CRISPR-Cas9 (RCC4-KO-643), we identified 3,215 proteins enriched in the NDUFA4L2 immunoprecipitates. Among the top-ranking pathways were "Metabolic Reprogramming in Cancer" and "Glycolysis Activation in Cancer (Warburg Effect)." We also show that NDUFA4L2 enhances mitochondrial fragmentation, interacts with lysosomes, and increases mitochondrial-lysosomal associations, as assessed by high-resolution fluorescence microscopy and live cell imaging. We identified 161 lysosomal proteins, including Niemann-Pick Disease Type C Intracellular Cholesterol Transporters 1 and 2 (NPC1, NPC2), that are associated with NDUFA4L2 in RCC4-P cells. RCC4-P cells have larger and decreased numbers of lysosomes relative to RCC4 NDUFA4L2 knockout cells. These findings suggest that NDUFA4L2 regulates mitochondrial-lysosomal associations and potentially lysosomal size and abundance. Consequently, NDUFA4L2 may regulate not only mitochondrial, but also lysosomal functions in ccRCC.
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Affiliation(s)
- Jaclyn M. Kubala
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | | | - Ryan Schreiner
- Division of Regenerative Medicine Research, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ryan M. Williams
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Biomedical Engineering, the City College of New York, New York, NY, USA
| | | | - Michael J. Crowley
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - Nigel P. Mongan
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
- Faculty of Medicine and Health Sciences, Center for Cancer Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - David M. Nanus
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Urology; New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY, USA
| | - Daniel A. Heller
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - Lorraine J. Gudas
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Urology; New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY, USA
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23
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Yagi M, Do Y, Hirai H, Miki K, Toshima T, Fukahori Y, Setoyama D, Abe C, Nabeshima YI, Kang D, Uchiumi T. Improving lysosomal ferroptosis with NMN administration protects against heart failure. Life Sci Alliance 2023; 6:e202302116. [PMID: 37793777 PMCID: PMC10551641 DOI: 10.26508/lsa.202302116] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023] Open
Abstract
Myocardial mitochondria are primary sites of myocardial energy metabolism. Mitochondrial disorders are associated with various cardiac diseases. We previously showed that mice with cardiomyocyte-specific knockout of the mitochondrial translation factor p32 developed heart failure from dilated cardiomyopathy. Mitochondrial translation defects cause not only mitochondrial dysfunction but also decreased nicotinamide adenine dinucleotide (NAD+) levels, leading to impaired lysosomal acidification and autophagy. In this study, we investigated whether nicotinamide mononucleotide (NMN) administration, which compensates for decreased NAD+ levels, improves heart failure because of mitochondrial dysfunction. NMN administration reduced damaged lysosomes and improved autophagy, thereby reducing heart failure and extending the lifespan in p32cKO mice. We found that lysosomal damage due to mitochondrial dysfunction induced ferroptosis, involving the accumulation of iron in lysosomes and lipid peroxide. The ameliorative effects of NMN supplementation were found to strongly affect lysosomal function rather than mitochondrial function, particularly lysosome-mediated ferroptosis. NMN supplementation can improve lysosomal, rather than mitochondrial, function and prevent chronic heart failure.
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Affiliation(s)
- Mikako Yagi
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Department of Health Sciences, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yura Do
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Haruka Hirai
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Department of Health Sciences, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kenji Miki
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takahiro Toshima
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yukina Fukahori
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Daiki Setoyama
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Chiaki Abe
- Department of Aging Science and Medicine, Graduate School of Medicine Kyoto University Medical Innovation Center, Kyoto, Japan
| | - Yo-Ichi Nabeshima
- Department of Aging Science and Medicine, Graduate School of Medicine Kyoto University Medical Innovation Center, Kyoto, Japan
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takeshi Uchiumi
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Department of Health Sciences, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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24
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Sarhadi TR, Panse JS, Nagotu S. Mind the gap: Methods to study membrane contact sites. Exp Cell Res 2023; 431:113756. [PMID: 37633408 DOI: 10.1016/j.yexcr.2023.113756] [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: 03/28/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/28/2023]
Abstract
Organelles are dynamic entities whose functions are essential for the optimum functioning of cells. It is now known that the juxtaposition of organellar membranes is essential for the exchange of metabolites and their communication. These functional apposition sites are termed membrane contact sites. Dynamic membrane contact sites between various sub-cellular structures such as mitochondria, endoplasmic reticulum, peroxisomes, Golgi apparatus, lysosomes, lipid droplets, plasma membrane, endosomes, etc. have been reported in various model systems. The burgeoning area of research on membrane contact sites has witnessed several manuscripts in recent years that identified the contact sites and components involved. Several methods have been developed to identify, measure and analyze the membrane contact sites. In this manuscript, we aim to discuss important methods developed to date that are used to study membrane contact sites.
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Affiliation(s)
- Tanveera Rounaque Sarhadi
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Janhavee Shirish Panse
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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25
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Abstract
Studies of rare human genetic disorders of mitochondrial phospholipid metabolism have highlighted the crucial role that membrane phospholipids play in mitochondrial bioenergetics and human health. The phospholipid composition of mitochondrial membranes is highly conserved from yeast to humans, with each class of phospholipid performing a specific function in the assembly and activity of various mitochondrial membrane proteins, including the oxidative phosphorylation complexes. Recent studies have uncovered novel roles of cardiolipin and phosphatidylethanolamine, two crucial mitochondrial phospholipids, in organismal physiology. Studies on inter-organellar and intramitochondrial phospholipid transport have significantly advanced our understanding of the mechanisms that maintain mitochondrial phospholipid homeostasis. Here, we discuss these recent advances in the function and transport of mitochondrial phospholipids while describing their biochemical and biophysical properties and biosynthetic pathways. Additionally, we highlight the roles of mitochondrial phospholipids in human health by describing the various genetic diseases caused by disruptions in their biosynthesis and discuss advances in therapeutic strategies for Barth syndrome, the best-studied disorder of mitochondrial phospholipid metabolism.
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Affiliation(s)
- Alaumy Joshi
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Travis H. Richard
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Vishal M. Gohil
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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26
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Del Vecchio M, Amado L, Cogan AP, Meert E, Rosseels J, Franssens V, Govers SK, Winderickx J, Montoro AG. Multiple tethers of organelle contact sites are involved in α-synuclein toxicity in yeast. Mol Biol Cell 2023; 34:ar84. [PMID: 37074954 PMCID: PMC10398879 DOI: 10.1091/mbc.e23-01-0029] [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: 01/31/2023] [Revised: 04/05/2023] [Accepted: 04/12/2023] [Indexed: 04/20/2023] Open
Abstract
The protein α-synuclein (α-syn) is one of the major factors linked to Parkinson's disease, yet how its misfolding and deposition contribute to the pathology remains largely elusive. Recently, contact sites among organelles were implicated in the development of this disease. Here, we used the budding yeast Saccharomyces cerevisiae, in which organelle contact sites have been characterized extensively, as a model to investigate their role in α-syn cytotoxicity. We observed that lack of specific tethers that anchor the endoplasmic reticulum to the plasma membrane resulted in cells with increased resistance to α-syn expression. Additionally, we found that strains lacking two dual-function proteins involved in contact sites, Mdm10 and Vps39, were resistant to the expression of α-syn. In the case of Mdm10, we found that this is related to its function in mitochondrial protein biogenesis and not to its role as a contact site tether. In contrast, both functions of Vps39, in vesicular transport and as a tether of the vacuole-mitochondria contact site, were required to support α-syn toxicity. Overall, our findings support that interorganelle communication through membrane contact sites is highly relevant for α-syn-mediated toxicity.
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Affiliation(s)
- Mara Del Vecchio
- Department of Biology, Functional Biology Laboratory, KU Leuven, 3001 Heverlee, Belgium
- Department of Biology, Microbial Systems Cell Biology Laboratory, KU Leuven, 3001 Heverlee, Belgium
| | - Lucia Amado
- Department of Biology/Chemistry, Cellular Communication Laboratory, Osnabrück University, 49076 Osnabrück, Germany
| | - Alexandra P. Cogan
- Department of Biology/Chemistry, Cellular Communication Laboratory, Osnabrück University, 49076 Osnabrück, Germany
| | - Els Meert
- Department of Biology, Functional Biology Laboratory, KU Leuven, 3001 Heverlee, Belgium
| | - Joelle Rosseels
- Department of Biology, Functional Biology Laboratory, KU Leuven, 3001 Heverlee, Belgium
| | - Vanessa Franssens
- Department of Biology, Functional Biology Laboratory, KU Leuven, 3001 Heverlee, Belgium
| | - Sander K. Govers
- Department of Biology, Microbial Systems Cell Biology Laboratory, KU Leuven, 3001 Heverlee, Belgium
| | - Joris Winderickx
- Department of Biology, Functional Biology Laboratory, KU Leuven, 3001 Heverlee, Belgium
| | - Ayelén González Montoro
- Department of Biology/Chemistry, Cellular Communication Laboratory, Osnabrück University, 49076 Osnabrück, Germany
- Center of Cellular Nanoanalytics Osnabrück, 49076 Osnabrück, Germany
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27
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Vormittag S, Ende RJ, Derré I, Hilbi H. Pathogen vacuole membrane contact sites - close encounters of the fifth kind. MICROLIFE 2023; 4:uqad018. [PMID: 37223745 PMCID: PMC10117887 DOI: 10.1093/femsml/uqad018] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/30/2023] [Accepted: 04/06/2023] [Indexed: 05/25/2023]
Abstract
Vesicular trafficking and membrane fusion are well-characterized, versatile, and sophisticated means of 'long range' intracellular protein and lipid delivery. Membrane contact sites (MCS) have been studied in far less detail, but are crucial for 'short range' (10-30 nm) communication between organelles, as well as between pathogen vacuoles and organelles. MCS are specialized in the non-vesicular trafficking of small molecules such as calcium and lipids. Pivotal MCS components important for lipid transfer are the VAP receptor/tether protein, oxysterol binding proteins (OSBPs), the ceramide transport protein CERT, the phosphoinositide phosphatase Sac1, and the lipid phosphatidylinositol 4-phosphate (PtdIns(4)P). In this review, we discuss how these MCS components are subverted by bacterial pathogens and their secreted effector proteins to promote intracellular survival and replication.
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Affiliation(s)
| | | | - Isabelle Derré
- Corresponding author. Department of Microbiology, Immunology and Cancer Biology, University of Virginia, 1340 Jefferson Park Ave, Charlottesville, VA 22908, United States. Tel: +1-434-924-2330; E-mail:
| | - Hubert Hilbi
- Corresponding author. Institute of Medical Microbiology, University of Zürich, Gloriastrasse 30, 8006 Zürich, Switzerland. Tel: +41-44-634-2650; E-mail:
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28
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XUE P, SÁNCHEZ-LEÓN E, DAMOO D, HU G, JUNG WH, KRONSTAD JW. Heme sensing and trafficking in fungi. FUNGAL BIOL REV 2023; 43:100286. [PMID: 37781717 PMCID: PMC10540271 DOI: 10.1016/j.fbr.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Fungal pathogens cause life-threatening diseases in humans, and the increasing prevalence of these diseases emphasizes the need for new targets for therapeutic intervention. Nutrient acquisition during infection is a promising target, and recent studies highlight the contributions of endomembrane trafficking, mitochondria, and vacuoles in the sensing and acquisition of heme by fungi. These studies have been facilitated by genetically encoded biosensors and other tools to quantitate heme in subcellular compartments and to investigate the dynamics of trafficking in living cells. In particular, the applications of biosensors in fungi have been extended beyond the detection of metabolites, cofactors, pH, and redox status to include the detection of heme. Here, we focus on studies that make use of biosensors to examine mechanisms of heme uptake and degradation, with guidance from the model fungus Saccharomyces cerevisiae and an emphasis on the pathogenic fungi Candida albicans and Cryptococcus neoformans that threaten human health. These studies emphasize a role for endocytosis in heme uptake, and highlight membrane contact sites involving mitochondria, the endoplasmic reticulum and vacuoles as mediators of intracellular iron and heme trafficking.
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Affiliation(s)
- Peng XUE
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eddy SÁNCHEZ-LEÓN
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Djihane DAMOO
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Guanggan HU
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Won Hee JUNG
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Korea
| | - James W. KRONSTAD
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
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29
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Fujimoto S, Tashiro S, Tamura Y. Complementation Assay Using Fusion of Split-GFP and TurboID (CsFiND) Enables Simultaneous Visualization and Proximity Labeling of Organelle Contact Sites in Yeast. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2023; 6:25152564231153621. [PMID: 37366411 PMCID: PMC10243572 DOI: 10.1177/25152564231153621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Numerous studies have revealed that organelle membrane contact sites (MCSs) play important roles in diverse cellular events, including the transport of lipids and ions between connected organelles. To understand MCS functions, it is essential to uncover proteins that accumulate at MCSs. Here, we develop a complementation assay system termed CsFiND (Complementation assay using Fusion of split-GFP and TurboID) for the simultaneous visualization of MCSs and identification of MCS-localized proteins. We express the CsFiND proteins on the endoplasmic reticulum and mitochondrial outer membrane in yeast to verify the reliability of CsFiND as a tool for identifying MCS-localized proteins.
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Affiliation(s)
| | - Shinya Tashiro
- Faculty of Science, Yamagata University, Yamagata, Japan
| | - Yasushi Tamura
- Faculty of Science, Yamagata University, Yamagata, Japan
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30
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Genovese I, Fornetti E, Ruocco G. Mitochondria inter-organelle relationships in cancer protein aggregation. Front Cell Dev Biol 2022; 10:1062993. [PMID: 36601538 PMCID: PMC9806238 DOI: 10.3389/fcell.2022.1062993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Mitochondria are physically associated with other organelles, such as ER and lysosomes, forming a complex network that is crucial for cell homeostasis regulation. Inter-organelle relationships are finely regulated by both tether systems, which maintain physical proximity, and by signaling cues that induce the exchange of molecular information to regulate metabolism, Ca2+ homeostasis, redox state, nutrient availability, and proteostasis. The coordinated action of the organelles is engaged in the cellular integrated stress response. In any case, pathological conditions alter functional communication and efficient rescue pathway activation, leading to cell distress exacerbation and eventually cell death. Among these detrimental signals, misfolded protein accumulation and aggregation cause major damage to the cells, since defects in protein clearance systems worsen cell toxicity. A cause for protein aggregation is often a defective mitochondrial redox balance, and the ER freshly translated misfolded proteins and/or a deficient lysosome-mediated clearance system. All these features aggravate mitochondrial damage and enhance proteotoxic stress. This review aims to gather the current knowledge about the complex liaison between mitochondria, ER, and lysosomes in facing proteotoxic stress and protein aggregation, highlighting both causes and consequences. Particularly, specific focus will be pointed to cancer, a pathology in which inter-organelle relations in protein aggregation have been poorly investigated.
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Affiliation(s)
- Ilaria Genovese
- Center for Life Nano and Neuro Science, Istituto Italiano di Tecnologia (IIT), Rome, Italy,*Correspondence: Ilaria Genovese,
| | - Ersilia Fornetti
- Center for Life Nano and Neuro Science, Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Giancarlo Ruocco
- Center for Life Nano and Neuro Science, Istituto Italiano di Tecnologia (IIT), Rome, Italy,Department of Physics, Sapienza University of Rome, Rome, Italy
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31
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Renne MF, Bao X, Hokken MWJ, Bierhuizen AS, Hermansson M, Sprenger RR, Ewing TA, Ma X, Cox RC, Brouwers JF, De Smet CH, Ejsing CS, de Kroon AIPM. Molecular species selectivity of lipid transport creates a mitochondrial sink for di-unsaturated phospholipids. EMBO J 2022; 41:e106837. [PMID: 34873731 PMCID: PMC8762554 DOI: 10.15252/embj.2020106837] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 11/09/2022] Open
Abstract
Mitochondria depend on the import of phospholipid precursors for the biosynthesis of phosphatidylethanolamine (PE) and cardiolipin, yet the mechanism of their transport remains elusive. A dynamic lipidomics approach revealed that mitochondria preferentially import di-unsaturated phosphatidylserine (PS) for subsequent conversion to PE by the mitochondrial PS decarboxylase Psd1p. Several protein complexes tethering mitochondria to the endomembrane system have been implicated in lipid transport in yeast, including the endoplasmic reticulum (ER)-mitochondrial encounter structure (ERMES), ER-membrane complex (EMC), and the vacuole and mitochondria patch (vCLAMP). By limiting the availability of unsaturated phospholipids, we created conditions to investigate the mechanism of lipid transfer and the contributions of the tethering complexes in vivo. Under these conditions, inactivation of ERMES components or of the vCLAMP component Vps39p exacerbated accumulation of saturated lipid acyl chains, indicating that ERMES and Vps39p contribute to the mitochondrial sink for unsaturated acyl chains by mediating transfer of di-unsaturated phospholipids. These results support the concept that intermembrane lipid flow is rate-limited by molecular species-dependent lipid efflux from the donor membrane and driven by the lipid species' concentration gradient between donor and acceptor membrane.
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Affiliation(s)
- Mike F Renne
- Membrane Biochemistry & BiophysicsDepartment of ChemistryUtrecht UniversityUtrechtThe Netherlands
- Present address:
Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
| | - Xue Bao
- Membrane Biochemistry & BiophysicsDepartment of ChemistryUtrecht UniversityUtrechtThe Netherlands
| | - Margriet WJ Hokken
- Membrane Biochemistry & BiophysicsDepartment of ChemistryUtrecht UniversityUtrechtThe Netherlands
- Present address:
Department of Medical MicrobiologyRadboud University Medical CenterRadboud Institute for Molecular Life SciencesNijmegenThe Netherlands
| | - Adolf S Bierhuizen
- Membrane Biochemistry & BiophysicsDepartment of ChemistryUtrecht UniversityUtrechtThe Netherlands
| | - Martin Hermansson
- Department of Biochemistry and Molecular BiologyVILLUM Center for Bioanalytical SciencesUniversity of Southern DenmarkOdenseDenmark
| | - Richard R Sprenger
- Department of Biochemistry and Molecular BiologyVILLUM Center for Bioanalytical SciencesUniversity of Southern DenmarkOdenseDenmark
| | - Tom A Ewing
- Membrane Biochemistry & BiophysicsDepartment of ChemistryUtrecht UniversityUtrechtThe Netherlands
- Present address:
Wageningen Food & Biobased ResearchWageningen University & ResearchWageningenThe Netherlands
| | - Xiao Ma
- Membrane Biochemistry & BiophysicsDepartment of ChemistryUtrecht UniversityUtrechtThe Netherlands
| | - Ruud C Cox
- Membrane Biochemistry & BiophysicsDepartment of ChemistryUtrecht UniversityUtrechtThe Netherlands
| | - Jos F Brouwers
- Biochemistry and Cell BiologyDepartment of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
- Present address:
Center for Molecular MedicineUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Cedric H De Smet
- Membrane Biochemistry & BiophysicsDepartment of ChemistryUtrecht UniversityUtrechtThe Netherlands
| | - Christer S Ejsing
- Department of Biochemistry and Molecular BiologyVILLUM Center for Bioanalytical SciencesUniversity of Southern DenmarkOdenseDenmark
- Cell Biology and Biophysics UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Anton IPM de Kroon
- Membrane Biochemistry & BiophysicsDepartment of ChemistryUtrecht UniversityUtrechtThe Netherlands
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32
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Kümmel D, Herrmann E, Langemeyer L, Ungermann C. Molecular insights into endolysosomal microcompartment formation and maintenance. Biol Chem 2022; 404:441-454. [PMID: 36503831 DOI: 10.1515/hsz-2022-0294] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022]
Abstract
Abstract
The endolysosomal system of eukaryotic cells has a key role in the homeostasis of the plasma membrane, in signaling and nutrient uptake, and is abused by viruses and pathogens for entry. Endocytosis of plasma membrane proteins results in vesicles, which fuse with the early endosome. If destined for lysosomal degradation, these proteins are packaged into intraluminal vesicles, converting an early endosome to a late endosome, which finally fuses with the lysosome. Each of these organelles has a unique membrane surface composition, which can form segmented membrane microcompartments by membrane contact sites or fission proteins. Furthermore, these organelles are in continuous exchange due to fission and fusion events. The underlying machinery, which maintains organelle identity along the pathway, is regulated by signaling processes. Here, we will focus on the Rab5 and Rab7 GTPases of early and late endosomes. As molecular switches, Rabs depend on activating guanine nucleotide exchange factors (GEFs). Over the last years, we characterized the Rab7 GEF, the Mon1-Ccz1 (MC1) complex, and key Rab7 effectors, the HOPS complex and retromer. Structural and functional analyses of these complexes lead to a molecular understanding of their function in the context of organelle biogenesis.
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Affiliation(s)
- Daniel Kümmel
- Institute of Biochemistry, University of Münster , Corrensstraße 36 , D-48149 Münster , Germany
| | - Eric Herrmann
- Institute of Biochemistry, University of Münster , Corrensstraße 36 , D-48149 Münster , Germany
| | - Lars Langemeyer
- Department of Biology/Chemistry, Biochemistry section , Osnabrück University , Barbarastraße 13 , D-49076 Osnabrück , Germany
- Center of Cellular Nanoanalytics (CellNanOs) , Osnabrück University , Barbarastraße 11 , D-49076 Osnabrück , Germany
| | - Christian Ungermann
- Department of Biology/Chemistry, Biochemistry section , Osnabrück University , Barbarastraße 13 , D-49076 Osnabrück , Germany
- Center of Cellular Nanoanalytics (CellNanOs) , Osnabrück University , Barbarastraße 11 , D-49076 Osnabrück , Germany
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33
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Kakimoto-Takeda Y, Kojima R, Shiino H, Shinmyo M, Kurokawa K, Nakano A, Endo T, Tamura Y. Dissociation of ERMES clusters plays a key role in attenuating the endoplasmic reticulum stress. iScience 2022; 25:105362. [PMID: 36339260 PMCID: PMC9626684 DOI: 10.1016/j.isci.2022.105362] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/24/2022] [Accepted: 10/12/2022] [Indexed: 11/27/2022] Open
Abstract
In yeast, ERMES, which mediates phospholipid transport between the ER and mitochondria, forms a limited number of oligomeric clusters at ER-mitochondria contact sites in a cell. Although the number of the ERMES clusters appears to be regulated to maintain proper inter-organelle phospholipid trafficking, its underlying mechanism and physiological relevance remain poorly understood. Here, we show that mitochondrial dynamics control the number of ERMES clusters. Moreover, we find that ER stress causes dissociation of the ERMES clusters independently of Ire1 and Hac1, canonical ER-stress response pathway components, leading to a delay in the phospholipid transport from the ER to mitochondria. Our biochemical and genetic analyses strongly suggest that the impaired phospholipid transport contributes to phospholipid accumulation in the ER, expanding the ER for ER stress attenuation. We thus propose that the ERMES dissociation constitutes an overlooked pathway of the ER stress response that operates in addition to the canonical Ire1/Hac1-dependent pathway. Mitochondrial fusion and division regulate the clustering of the ERMES complex ER stress leads to dissociation of the ERMES clusters independently of Ire1 and Hac1 The dissociated ERMES complexes have less activity in transporting phospholipids The defective phospholipid transport may cause the ER expansion to relieve ER stress
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Affiliation(s)
- Yuriko Kakimoto-Takeda
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, 2-2-2 Iidanishi, Yamagata 990-9585, Japan
| | - Rieko Kojima
- Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata 990-8560, Japan
| | - Hiroya Shiino
- Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata 990-8560, Japan
| | - Manatsu Shinmyo
- Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata 990-8560, Japan
| | - Kazuo Kurokawa
- Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Akihiko Nakano
- Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Toshiya Endo
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto 603-8555, Japan
- Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto 603-8555, Japan
| | - Yasushi Tamura
- Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata 990-8560, Japan
- Corresponding author
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34
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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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35
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White AJ, Harper CS, Rosario EM, Dietz JV, Addis HG, Fox JL, Khalimonchuk O, Lackner LL. Loss of Num1-mediated cortical dynein anchoring negatively impacts respiratory growth. J Cell Sci 2022; 135:jcs259980. [PMID: 36185004 PMCID: PMC9687553 DOI: 10.1242/jcs.259980] [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: 03/02/2022] [Accepted: 09/26/2022] [Indexed: 01/29/2023] Open
Abstract
Num1 is a multifunctional protein that both tethers mitochondria to the plasma membrane and anchors dynein to the cell cortex during nuclear inheritance. Previous work has examined the impact loss of Num1-based mitochondrial tethering has on dynein function in Saccharomyces cerevisiae; here, we elucidate its impact on mitochondrial function. We find that like mitochondria, Num1 is regulated by changes in metabolic state, with the protein levels and cortical distribution of Num1 differing between fermentative and respiratory growth conditions. In cells lacking Num1, we observe a reproducible respiratory growth defect, suggesting a role for Num1 in not only maintaining mitochondrial morphology, but also function. A structure-function approach revealed that, unexpectedly, Num1-mediated cortical dynein anchoring is important for normal growth under respiratory conditions. The severe respiratory growth defect in Δnum1 cells is not specifically due to the canonical functions of dynein in nuclear migration but is dependent on the presence of dynein, as deletion of DYN1 in Δnum1 cells partially rescues respiratory growth. We hypothesize that misregulated dynein present in cells that lack Num1 negatively impacts mitochondrial function resulting in defects in respiratory growth.
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Affiliation(s)
- Antoineen J. White
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Clare S. Harper
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Erica M. Rosario
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Jonathan V. Dietz
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Hannah G. Addis
- Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC 29424, USA
| | - Jennifer L. Fox
- Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC 29424, USA
| | - Oleh Khalimonchuk
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA
- Nebraska Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA
- Fred & Pamela Buffett Cancer Center, Omaha, NE 68198, USA
| | - Laura L. Lackner
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
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36
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Kim S, Coukos R, Gao F, Krainc D. Dysregulation of organelle membrane contact sites in neurological diseases. Neuron 2022; 110:2386-2408. [PMID: 35561676 PMCID: PMC9357093 DOI: 10.1016/j.neuron.2022.04.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/21/2022] [Accepted: 04/18/2022] [Indexed: 10/18/2022]
Abstract
The defining evolutionary feature of eukaryotic cells is the emergence of membrane-bound organelles. Compartmentalization allows each organelle to maintain a spatially, physically, and chemically distinct environment, which greatly bolsters individual organelle function. However, the activities of each organelle must be balanced and are interdependent for cellular homeostasis. Therefore, properly regulated interactions between organelles, either physically or functionally, remain critical for overall cellular health and behavior. In particular, neuronal homeostasis depends heavily on the proper regulation of organelle function and cross talk, and deficits in these functions are frequently associated with diseases. In this review, we examine the emerging role of organelle contacts in neurological diseases and discuss how the disruption of contacts contributes to disease pathogenesis. Understanding the molecular mechanisms underlying the formation and regulation of organelle contacts will broaden our knowledge of their role in health and disease, laying the groundwork for the development of new therapies targeting interorganelle cross talk and function.
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Affiliation(s)
- Soojin Kim
- Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E Chicago Avenue, Chicago, IL, 60611, USA
| | - Robert Coukos
- Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E Chicago Avenue, Chicago, IL, 60611, USA
| | - Fanding Gao
- Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E Chicago Avenue, Chicago, IL, 60611, USA
| | - Dimitri Krainc
- Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E Chicago Avenue, Chicago, IL 60611, USA.
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37
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Schuster EM, Epple MW, Glaser KM, Mihlan M, Lucht K, Zimmermann JA, Bremser A, Polyzou A, Obier N, Cabezas-Wallscheid N, Trompouki E, Ballabio A, Vogel J, Buescher JM, Westermann AJ, Rambold AS. TFEB induces mitochondrial itaconate synthesis to suppress bacterial growth in macrophages. Nat Metab 2022; 4:856-866. [PMID: 35864246 PMCID: PMC9314259 DOI: 10.1038/s42255-022-00605-w] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 06/13/2022] [Indexed: 01/04/2023]
Abstract
Successful elimination of bacteria in phagocytes occurs in the phago-lysosomal system, but also depends on mitochondrial pathways. Yet, how these two organelle systems communicate is largely unknown. Here we identify the lysosomal biogenesis factor transcription factor EB (TFEB) as regulator for phago-lysosome-mitochondria crosstalk in macrophages. By combining cellular imaging and metabolic profiling, we find that TFEB activation, in response to bacterial stimuli, promotes the transcription of aconitate decarboxylase (Acod1, Irg1) and synthesis of its product itaconate, a mitochondrial metabolite with antimicrobial activity. Activation of the TFEB-Irg1-itaconate signalling axis reduces the survival of the intravacuolar pathogen Salmonella enterica serovar Typhimurium. TFEB-driven itaconate is subsequently transferred via the Irg1-Rab32-BLOC3 system into the Salmonella-containing vacuole, thereby exposing the pathogen to elevated itaconate levels. By activating itaconate production, TFEB selectively restricts proliferating Salmonella, a bacterial subpopulation that normally escapes macrophage control, which contrasts TFEB's role in autophagy-mediated pathogen degradation. Together, our data define a TFEB-driven metabolic pathway between phago-lysosomes and mitochondria that restrains Salmonella Typhimurium burden in macrophages in vitro and in vivo.
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Affiliation(s)
- Ev-Marie Schuster
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- International Max Planck Research School for Immunobiology, Epigenetics and Metabolism (IMPRS-IEM), Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Maximilian W Epple
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- International Max Planck Research School for Immunobiology, Epigenetics and Metabolism (IMPRS-IEM), Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Katharina M Glaser
- International Max Planck Research School for Immunobiology, Epigenetics and Metabolism (IMPRS-IEM), Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Michael Mihlan
- Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Kerstin Lucht
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Julia A Zimmermann
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- International Max Planck Research School for Immunobiology, Epigenetics and Metabolism (IMPRS-IEM), Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Center of Chronic Immunodeficiency, Medical Center University of Freiburg, Freiburg, Germany
| | - Anna Bremser
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Aikaterini Polyzou
- International Max Planck Research School for Immunobiology, Epigenetics and Metabolism (IMPRS-IEM), Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Department of Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Nadine Obier
- Department of Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Nina Cabezas-Wallscheid
- Department of Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Eirini Trompouki
- Department of Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- IRCAN Institute for Research on Cancer and Aging, INSERM Unité 1081, CNRS UMR 7284, Université Côte d'Azur, Nice, France
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine, Medical Genetics Unit, Department of Medical and Translational Science and SSM School for Advanced Studies, Federico II University, Naples, Italy
- Department of Molecular and Human Genetics, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research (HZI), University of Würzburg, Würzburg, Germany
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Joerg M Buescher
- Metabolomics Core Facility, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Alexander J Westermann
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research (HZI), University of Würzburg, Würzburg, Germany
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Angelika S Rambold
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
- Center of Chronic Immunodeficiency, Medical Center University of Freiburg, Freiburg, Germany.
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Bisinski DD, Gomes Castro I, Mari M, Walter S, Fröhlich F, Schuldiner M, González Montoro A. Cvm1 is a component of multiple vacuolar contact sites required for sphingolipid homeostasis. J Biophys Biochem Cytol 2022; 221:213309. [PMID: 35766971 PMCID: PMC9247719 DOI: 10.1083/jcb.202103048] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/05/2022] [Accepted: 06/13/2022] [Indexed: 02/03/2023] Open
Abstract
Membrane contact sites are specialized platforms formed between most organelles that enable them to exchange metabolites and influence the dynamics of each other. The yeast vacuole is a degradative organelle equivalent to the lysosome in higher eukaryotes with important roles in ion homeostasis and metabolism. Using a high-content microscopy screen, we identified Ymr160w (Cvm1, for contact of the vacuole membrane 1) as a novel component of three different contact sites of the vacuole: with the nuclear endoplasmic reticulum, the mitochondria, and the peroxisomes. At the vacuole-mitochondria contact site, Cvm1 acts as a tether independently of previously known tethers. We show that changes in Cvm1 levels affect sphingolipid homeostasis, altering the levels of multiple sphingolipid classes and the response of sphingolipid-sensing signaling pathways. Furthermore, the contact sites formed by Cvm1 are induced upon a decrease in sphingolipid levels. Altogether, our work identifies a novel protein that forms multiple contact sites and supports a role of lysosomal contacts in sphingolipid homeostasis.
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Affiliation(s)
- Daniel D. Bisinski
- Department of Biology/Chemistry, Cellular Communication Laboratory, University of Osnabrück, Osnabrück, Germany
| | - Inês Gomes Castro
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Muriel Mari
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Stefan Walter
- Center of Cellular Nanoanalytics Osnabrück, Osnabrück, Germany
| | - Florian Fröhlich
- Center of Cellular Nanoanalytics Osnabrück, Osnabrück, Germany,Department of Biology/Chemistry, Molecular Membrane Biology Group, University of Osnabrück, Osnabrück, Germany
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ayelén González Montoro
- Department of Biology/Chemistry, Cellular Communication Laboratory, University of Osnabrück, Osnabrück, Germany,Center of Cellular Nanoanalytics Osnabrück, Osnabrück, Germany
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39
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Vrijsen S, Vrancx C, Del Vecchio M, Swinnen JV, Agostinis P, Winderickx J, Vangheluwe P, Annaert W. Inter-organellar Communication in Parkinson's and Alzheimer's Disease: Looking Beyond Endoplasmic Reticulum-Mitochondria Contact Sites. Front Neurosci 2022; 16:900338. [PMID: 35801175 PMCID: PMC9253489 DOI: 10.3389/fnins.2022.900338] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 05/05/2022] [Indexed: 01/13/2023] Open
Abstract
Neurodegenerative diseases (NDs) are generally considered proteinopathies but whereas this may initiate disease in familial cases, onset in sporadic diseases may originate from a gradually disrupted organellar homeostasis. Herein, endolysosomal abnormalities, mitochondrial dysfunction, endoplasmic reticulum (ER) stress, and altered lipid metabolism are commonly observed in early preclinical stages of major NDs, including Parkinson's disease (PD) and Alzheimer's disease (AD). Among the multitude of underlying defective molecular mechanisms that have been suggested in the past decades, dysregulation of inter-organellar communication through the so-called membrane contact sites (MCSs) is becoming increasingly apparent. Although MCSs exist between almost every other type of subcellular organelle, to date, most focus has been put on defective communication between the ER and mitochondria in NDs, given these compartments are critical in neuronal survival. Contributions of other MCSs, notably those with endolysosomes and lipid droplets are emerging, supported as well by genetic studies, identifying genes functionally involved in lysosomal homeostasis. In this review, we summarize the molecular identity of the organelle interactome in yeast and mammalian cells, and critically evaluate the evidence supporting the contribution of disturbed MCSs to the general disrupted inter-organellar homeostasis in NDs, taking PD and AD as major examples.
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Affiliation(s)
- Stephanie Vrijsen
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, KU Leuven, Leuven, Belgium
| | - Céline Vrancx
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, KU Leuven, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Mara Del Vecchio
- Laboratory of Functional Biology, Department of Biology, KU Leuven, Heverlee, Belgium
| | - Johannes V. Swinnen
- Laboratory of Lipid Metabolism and Cancer, Department of Oncology, Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
| | - Patrizia Agostinis
- Laboratory of Cell Death Research and Therapy, VIB-Center for Cancer Research, KU Leuven, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Joris Winderickx
- Laboratory of Functional Biology, Department of Biology, KU Leuven, Heverlee, Belgium
| | - Peter Vangheluwe
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, KU Leuven, Leuven, Belgium
| | - Wim Annaert
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, KU Leuven, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Leuven, Belgium
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40
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Jain A, Zoncu R. Organelle transporters and inter-organelle communication as drivers of metabolic regulation and cellular homeostasis. Mol Metab 2022; 60:101481. [PMID: 35342037 PMCID: PMC9043965 DOI: 10.1016/j.molmet.2022.101481] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/14/2022] [Accepted: 03/21/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Spatial compartmentalization of metabolic pathways within membrane-separated organelles is key to the ability of eukaryotic cells to precisely regulate their biochemical functions. Membrane-bound organelles such as mitochondria, endoplasmic reticulum (ER) and lysosomes enable the concentration of metabolic precursors within optimized chemical environments, greatly accelerating the efficiency of both anabolic and catabolic reactions, enabling division of labor and optimal utilization of resources. However, metabolic compartmentalization also poses a challenge to cells because it creates spatial discontinuities that must be bridged for reaction cascades to be connected and completed. To do so, cells employ different methods to coordinate metabolic fluxes occurring in different organelles, such as membrane-localized transporters to facilitate regulated metabolite exchange between mitochondria and lysosomes, non-vesicular transport pathways via physical contact sites connecting the ER with both mitochondria and lysosomes, as well as localized regulatory signaling processes that coordinately regulate the activity of all these organelles. SCOPE OF REVIEW This review covers how cells use membrane transporters, membrane contact sites, and localized signaling pathways to mediate inter-organelle communication and coordinate metabolism. We also describe how disruption of inter-organelle communication is an emerging driver in a multitude of diseases, from cancer to neurodegeneration. MAJOR CONCLUSIONS Effective communication among organelles is essential to cellular health and function. Identifying the major molecular players involved in mediating metabolic coordination between organelles will further our understanding of cellular metabolism in health and lead us to design better therapeutics against dysregulated metabolism in disease.
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Affiliation(s)
- Aakriti Jain
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Roberto Zoncu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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41
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Hoffmann JJ, Becker T. Crosstalk between Mitochondrial Protein Import and Lipids. Int J Mol Sci 2022; 23:ijms23095274. [PMID: 35563660 PMCID: PMC9101885 DOI: 10.3390/ijms23095274] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/29/2022] [Accepted: 05/05/2022] [Indexed: 12/10/2022] Open
Abstract
Mitochondria import about 1000 precursor proteins from the cytosol. The translocase of the outer membrane (TOM complex) forms the major entry site for precursor proteins. Subsequently, membrane-bound protein translocases sort the precursor proteins into the outer and inner membrane, the intermembrane space, and the matrix. The phospholipid composition of mitochondrial membranes is critical for protein import. Structural and biochemical data revealed that phospholipids affect the stability and activity of mitochondrial protein translocases. Integration of proteins into the target membrane involves rearrangement of phospholipids and distortion of the lipid bilayer. Phospholipids are present in the interface between subunits of protein translocases and affect the dynamic coupling of partner proteins. Phospholipids are required for full activity of the respiratory chain to generate membrane potential, which in turn drives protein import across and into the inner membrane. Finally, outer membrane protein translocases are closely linked to organellar contact sites that mediate lipid trafficking. Altogether, intensive crosstalk between mitochondrial protein import and lipid biogenesis controls mitochondrial biogenesis.
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42
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Loginov SV, Fermie J, Fokkema J, Agronskaia AV, De Heus C, Blab GA, Klumperman J, Gerritsen HC, Liv N. Correlative Organelle Microscopy: Fluorescence Guided Volume Electron Microscopy of Intracellular Processes. Front Cell Dev Biol 2022; 10:829545. [PMID: 35478966 PMCID: PMC9035751 DOI: 10.3389/fcell.2022.829545] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/04/2022] [Indexed: 01/19/2023] Open
Abstract
Intracellular processes depend on a strict spatial and temporal organization of proteins and organelles. Therefore, directly linking molecular to nanoscale ultrastructural information is crucial in understanding cellular physiology. Volume or three-dimensional (3D) correlative light and electron microscopy (volume-CLEM) holds unique potential to explore cellular physiology at high-resolution ultrastructural detail across cell volumes. However, the application of volume-CLEM is hampered by limitations in throughput and 3D correlation efficiency. In order to address these limitations, we describe a novel pipeline for volume-CLEM that provides high-precision (<100 nm) registration between 3D fluorescence microscopy (FM) and 3D electron microscopy (EM) datasets with significantly increased throughput. Using multi-modal fiducial nanoparticles that remain fluorescent in epoxy resins and a 3D confocal fluorescence microscope integrated into a Focused Ion Beam Scanning Electron Microscope (FIB.SEM), our approach uses FM to target extremely small volumes of even single organelles for imaging in volume EM and obviates the need for post-correlation of big 3D datasets. We extend our targeted volume-CLEM approach to include live-cell imaging, adding information on the motility of intracellular membranes selected for volume-CLEM. We demonstrate the power of our approach by targeted imaging of rare and transient contact sites between the endoplasmic reticulum (ER) and lysosomes within hours rather than days. Our data suggest that extensive ER-lysosome and mitochondria-lysosome interactions restrict lysosome motility, highlighting the unique capabilities of our integrated CLEM pipeline for linking molecular dynamic data to high-resolution ultrastructural detail in 3D.
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Affiliation(s)
- Sergey V. Loginov
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Job Fermie
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Jantina Fokkema
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Alexandra V. Agronskaia
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Cilia De Heus
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Gerhard A. Blab
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Judith Klumperman
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Hans C. Gerritsen
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Nalan Liv
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- *Correspondence: Nalan Liv,
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Duarte PV, Hardenberg R, Mari M, Walter S, Reggiori F, Fröhlich F, Montoro AG, Ungermann C. The yeast LYST homolog Bph1 is a Rab5 effector and prevents Atg8 lipidation at endosomes. J Cell Sci 2022; 135:274866. [PMID: 35343566 DOI: 10.1242/jcs.259421] [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: 09/30/2021] [Accepted: 03/18/2022] [Indexed: 01/18/2023] Open
Abstract
Lysosomes mediate degradation of macromolecules to their precursors for their cellular recycling. Additionally, lysosome-related organelles mediate cell type-specific functions. The Chédiak-Higashi syndrome is an autosomal, recessive disease, in which loss of the protein LYST causes defects in lysosomes and lysosome-related organelles. The molecular function of LYST, however, is largely unknown. Here, we dissected the function of the yeast LYST homolog, Bph1. We show that Bph1 is an endosomal protein, and an effector of the minor Rab5 isoform Ypt52. Strikingly, the bph1▵ mutant has lipidated Atg8 on their endosomes, which is sorted via late endosomes into the vacuole lumen under non-autophagy inducing conditions. In agreement, proteomics of bph1▵ vacuoles reveal an accumulation of Atg8, reduced flux via selective autophagy, and defective endocytosis. Additionally, bph1▵ cells have reduced autophagic flux under starvation conditions. Our observations suggest that Bph1 is a novel Rab5 effector that maintains endosomal functioning. When lost, Atg8 is lipidated at endosomes even during normal growth and ends up in the vacuole lumen. Thus, our results contribute to the understanding of the role of LYST-related proteins and associated diseases.
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Affiliation(s)
- Prado Vargas Duarte
- Osnabrück University, Department of Biology/Chemistry, Biochemistry section, Barbarastrasse 13, 49076 Osnabrück, Germany
| | - Ralph Hardenberg
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Muriel Mari
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Stefan Walter
- Osnabrück University, Center of Cellular Nanoanalytic Osnabrück (CellNanOs), Barbarastrasse 11, 49076 Osnabrück, Germany
| | - Fulvio Reggiori
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Florian Fröhlich
- Osnabrück University, Center of Cellular Nanoanalytic Osnabrück (CellNanOs), Barbarastrasse 11, 49076 Osnabrück, Germany.,Osnabrück University, Department of Biology/Chemistry, Molecular Membrane Biology section, Barbarastrasse 13, 49076 Osnabrück, Germany
| | - Ayelén González Montoro
- Osnabrück University, Center of Cellular Nanoanalytic Osnabrück (CellNanOs), Barbarastrasse 11, 49076 Osnabrück, Germany.,Osnabrück University, Department of Biology/Chemistry, Cellular Communication Laboratory, Barbarastrasse 13, 49076 Osnabrück, Germany
| | - Christian Ungermann
- Osnabrück University, Department of Biology/Chemistry, Biochemistry section, Barbarastrasse 13, 49076 Osnabrück, Germany.,Osnabrück University, Center of Cellular Nanoanalytic Osnabrück (CellNanOs), Barbarastrasse 11, 49076 Osnabrück, Germany
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44
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Mitochondria-lysosome contact site dynamics and misregulation in neurodegenerative diseases. Trends Neurosci 2022; 45:312-322. [PMID: 35249745 PMCID: PMC8930467 DOI: 10.1016/j.tins.2022.01.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/11/2022] [Accepted: 01/26/2022] [Indexed: 02/06/2023]
Abstract
Neurons rely heavily on properly regulated mitochondrial and lysosomal homeostasis, with multiple neurodegenerative diseases linked to dysfunction in these two organelles. Interestingly, mitochondria-lysosome membrane contact sites have been identified as a key pathway mediating their crosstalk in neurons. Recent studies have further elucidated the regulation of mitochondria-lysosome contact dynamics via distinct tethering/untethering protein machinery. Moreover, this pathway has been shown to have additional functions in regulating organelle network dynamics and metabolite transfer between lysosomes and mitochondria. In this review, we highlight recent advances in the field of mitochondria-lysosome contact sites and their misregulation across multiple neurodegenerative disorders, which further underscore a potential role for this pathway in neuronal homeostasis and disease.
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45
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John Peter AT, Schie SNS, Cheung NJ, Michel AH, Peter M, Kornmann B. Rewiring phospholipid biosynthesis reveals resilience to membrane perturbations and uncovers regulators of lipid homeostasis. EMBO J 2022; 41:e109998. [PMID: 35188676 PMCID: PMC8982615 DOI: 10.15252/embj.2021109998] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/20/2021] [Accepted: 01/07/2022] [Indexed: 02/01/2023] Open
Abstract
The organelles of eukaryotic cells differ in their membrane lipid composition. This heterogeneity is achieved by the localization of lipid synthesizing and modifying enzymes to specific compartments, as well as by intracellular lipid transport that utilizes vesicular and non‐vesicular routes to ferry lipids from their place of synthesis to their destination. For instance, the major and essential phospholipids, phosphatidylethanolamine (PE) and phosphatidylcholine (PC), can be produced by multiple pathways and, in the case of PE, also at multiple locations. However, the molecular components that underlie lipid homeostasis as well as the routes allowing their distribution remain unclear. Here, we present an approach in which we simplify and rewire yeast phospholipid synthesis by redirecting PE and PC synthesis reactions to distinct subcellular locations using chimeric enzymes fused to specific organelle targeting motifs. In rewired conditions, viability is expected to depend on homeostatic adaptation to the ensuing lipostatic perturbations and on efficient interorganelle lipid transport. We therefore performed genetic screens to identify factors involved in both of these processes. Among the candidates identified, we find genes linked to transcriptional regulation of lipid homeostasis, lipid metabolism, and transport. In particular, we identify a requirement for Csf1—an uncharacterized protein harboring a Chorein‐N lipid transport motif—for survival under certain rewired conditions as well as lipidomic adaptation to cold, implicating Csf1 in interorganelle lipid transport and homeostatic adaptation.
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Affiliation(s)
| | | | - Ngaam J Cheung
- Department of Biochemistry University of Oxford Oxford UK
| | - Agnès H Michel
- Department of Biochemistry University of Oxford Oxford UK
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46
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Zhao M, Lian A, Zhong L, Guo R. The regulatory mechanism between lysosomes and mitochondria in the aetiology of cardiovascular diseases. Acta Physiol (Oxf) 2022; 234:e13757. [PMID: 34978753 DOI: 10.1111/apha.13757] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/16/2021] [Accepted: 01/01/2022] [Indexed: 11/28/2022]
Abstract
Coordinated action among various organelles maintains cellular functions. For instance, mitochondria and lysosomes are the main organelles contributing to cellular metabolism and provide energy for cardiomyocyte contraction. They also provide essential signalling platforms in the cell that regulate many key processes such as autophagy, apoptosis, oxidative stress, inflammation and cell death. Often, abnormalities in mitochondrial or lysosomal structures and functions bring about cardiovascular diseases (CVDs). Although the communication between mitochondria and lysosomes throughout the cardiovascular system is intensely studied, the regulatory mechanisms have not been completely understood. Thus, we summarize the most recent studies related to mitochondria and lysosomes' role in CVDs and their potential connections and communications under cardiac pathophysiological conditions. Further, we discuss limitations and future perspectives regarding diagnosis, therapeutic strategies and drug discovery in CVDs.
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Affiliation(s)
- Mengxue Zhao
- College of Life Sciences Institute of Life Science and Green Development Hebei University Baoding China
| | - Andrew Lian
- College of Osteopathic Medicine of the Pacific Western University of Health Sciences Pomona California USA
| | - Li Zhong
- College of Life Sciences Institute of Life Science and Green Development Hebei University Baoding China
- College of Osteopathic Medicine of the Pacific Western University of Health Sciences Pomona California USA
| | - Rui Guo
- College of Life Sciences Institute of Life Science and Green Development Hebei University Baoding China
- The Key Laboratory of Zoological Systematics and Application College of Life Sciences Hebei University Baoding China
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Poggio E, Brini M, Calì T. Get Closer to the World of Contact Sites: A Beginner's Guide to Proximity-Driven Fluorescent Probes. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2022; 5:25152564221135748. [PMID: 37366505 PMCID: PMC10243574 DOI: 10.1177/25152564221135748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
To maintain cellular homeostasis and to coordinate the proper response to a specific stimulus, information must be integrated throughout the cell in a well-organized network, in which organelles are the crucial nodes and membrane contact sites are the main edges. Membrane contact sites are the cellular subdomains where two or more organelles come into close apposition and interact with each other. Even though many inter-organelle contacts have been identified, most of them are still not fully characterized, therefore their study is an appealing and expanding field of research. Thanks to significant technological progress, many tools are now available or are in rapid development, making it difficult to choose which one is the most suitable for answering a specific biological question. Here we distinguish two different experimental approaches for studying inter-organelle contact sites. The first one aims to morphologically characterize the sites of membrane contact and to identify the molecular players involved, relying mainly on the application of biochemical and electron microscopy (EM)-related methods. The second approach aims to understand the functional importance of a specific contact, focusing on spatio-temporal details. For this purpose, proximity-driven fluorescent probes are the experimental tools of choice, since they allow the monitoring and quantification of membrane contact sites and their dynamics in living cells under different cellular conditions or upon different stimuli. In this review, we focus on these tools with the purpose of highlighting their great versatility and how they can be applied in the study of membrane contacts. We will extensively describe all the different types of proximity-driven fluorescent tools, discussing their benefits and drawbacks, ultimately providing some suggestions to choose and apply the appropriate methods on a case-to-case basis and to obtain the best experimental outcomes.
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Affiliation(s)
- Elena Poggio
- Department of Biology (DiBio), University of
Padova, Padova, Italy
| | - Marisa Brini
- Department of Biology (DiBio), University of
Padova, Padova, Italy
- Study Center for Neurodegeneration (CESNE),
University of Padova, Padova, Italy
| | - Tito Calì
- Study Center for Neurodegeneration (CESNE),
University of Padova, Padova, Italy
- Department of Biomedical Sciences (DSB),
University of Padova, Padova, Italy
- Padova Neuroscience Center (PNC), University
of Padova, Padova, Italy
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48
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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; 5:25152564221133267. [PMID: 36329759 PMCID: PMC9629538 DOI: 10.1177/25152564221133267] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 09/29/2022] [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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González Montoro A, Vargas Duarte P, Auffarth K, Walter S, Fröhlich F, Ungermann C. Subunit exchange among endolysosomal tethering complexes is linked to contact site formation at the vacuole. Mol Biol Cell 2021; 32:br14. [PMID: 34668759 PMCID: PMC8694092 DOI: 10.1091/mbc.e21-05-0227] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The hexameric HOPS (homotypic fusion and protein sorting) complex is a conserved tethering complex at the lysosome-like vacuole, where it mediates tethering and promotes all fusion events involving this organelle. The Vps39 subunit of this complex also engages in a membrane contact site between the vacuole and the mitochondria, called vCLAMP. Additionally, four subunits of HOPS are also part of the endosomal CORVET tethering complex. Here, we analyzed the partition of HOPS and CORVET subunits between the different complexes by tracing their localization and function. We find that Vps39 has a specific role in vCLAMP formation beyond tethering, and that vCLAMPs and HOPS compete for the same pool of Vps39. In agreement, we find that the CORVET subunit Vps3 can take the position of Vps39 in HOPS. This endogenous pool of a Vps3-hybrid complex is affected by Vps3 or Vps39 levels, suggesting that HOPS and CORVET assembly is dynamic. Our data shed light on how individual subunits of tethering complexes such as Vps39 can participate in other functions, while maintaining the remaining subcomplex available for its function in tethering and fusion.
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Affiliation(s)
- Ayelén González Montoro
- Cellular Communication Laboratory, Osnabrück University, 49076 Osnabrück, Germany.,Center of Cellular Nanoanalytic Osnabrück (CellNanOs), Osnabrück University, 49076 Osnabrück, Germany
| | | | - Kathrin Auffarth
- Biochemistry section, Osnabrück University, 49076 Osnabrück, Germany
| | - Stefan Walter
- Center of Cellular Nanoanalytic Osnabrück (CellNanOs), Osnabrück University, 49076 Osnabrück, Germany
| | - Florian Fröhlich
- Molecular Membrane Biology section, Department of Biology/Chemistry, Osnabrück University, 49076 Osnabrück, Germany.,Center of Cellular Nanoanalytic Osnabrück (CellNanOs), Osnabrück University, 49076 Osnabrück, Germany
| | - Christian Ungermann
- Biochemistry section, Osnabrück University, 49076 Osnabrück, Germany.,Center of Cellular Nanoanalytic Osnabrück (CellNanOs), Osnabrück University, 49076 Osnabrück, Germany
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50
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Egea PF. Mechanisms of Non-Vesicular Exchange of Lipids at Membrane Contact Sites: Of Shuttles, Tunnels and, Funnels. Front Cell Dev Biol 2021; 9:784367. [PMID: 34912813 PMCID: PMC8667587 DOI: 10.3389/fcell.2021.784367] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
Eukaryotic cells are characterized by their exquisite compartmentalization resulting from a cornucopia of membrane-bound organelles. Each of these compartments hosts a flurry of biochemical reactions and supports biological functions such as genome storage, membrane protein and lipid biosynthesis/degradation and ATP synthesis, all essential to cellular life. Acting as hubs for the transfer of matter and signals between organelles and throughout the cell, membrane contacts sites (MCSs), sites of close apposition between membranes from different organelles, are essential to cellular homeostasis. One of the now well-acknowledged function of MCSs involves the non-vesicular trafficking of lipids; its characterization answered one long-standing question of eukaryotic cell biology revealing how some organelles receive and distribute their membrane lipids in absence of vesicular trafficking. The endoplasmic reticulum (ER) in synergy with the mitochondria, stands as the nexus for the biosynthesis and distribution of phospholipids (PLs) throughout the cell by contacting nearly all other organelle types. MCSs create and maintain lipid fluxes and gradients essential to the functional asymmetry and polarity of biological membranes throughout the cell. Membrane apposition is mediated by proteinaceous tethers some of which function as lipid transfer proteins (LTPs). We summarize here the current state of mechanistic knowledge of some of the major classes of LTPs and tethers based on the available atomic to near-atomic resolution structures of several "model" MCSs from yeast but also in Metazoans; we describe different models of lipid transfer at MCSs and analyze the determinants of their specificity and directionality. Each of these systems illustrate fundamental principles and mechanisms for the non-vesicular exchange of lipids between eukaryotic membrane-bound organelles essential to a wide range of cellular processes such as at PL biosynthesis and distribution, lipid storage, autophagy and organelle biogenesis.
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Affiliation(s)
- Pascal F. Egea
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
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