1
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Enkler L, Spang A. Functional interplay of lipid droplets and mitochondria. FEBS Lett 2024; 598:1235-1251. [PMID: 38268392 DOI: 10.1002/1873-3468.14809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/12/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024]
Abstract
Our body stores energy mostly in form of fatty acids (FAs) in lipid droplets (LDs). From there the FAs can be mobilized and transferred to peroxisomes and mitochondria. This transfer is dependent on close opposition of LDs and mitochondria and peroxisomes and happens at membrane contact sites. However, the composition and the dynamics of these contact sites is not well understood, which is in part due to the dependence on the metabolic state of the cell and on the cell- and tissue-type. Here, we summarize the current knowledge on the contacts between lipid droplets and mitochondria both in mammals and in the yeast Saccharomyces cerevisiae, in which various contact sites are well studied. We discuss possible functions of the contact site and their implication in disease.
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Affiliation(s)
| | - Anne Spang
- Biozentrum, University of Basel, Switzerland
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2
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Erazo-Oliveras A, Muñoz-Vega M, Salinas ML, Wang X, Chapkin RS. Dysregulation of cellular membrane homeostasis as a crucial modulator of cancer risk. FEBS J 2024; 291:1299-1352. [PMID: 36282100 PMCID: PMC10126207 DOI: 10.1111/febs.16665] [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: 06/18/2022] [Revised: 09/09/2022] [Accepted: 10/24/2022] [Indexed: 11/07/2022]
Abstract
Cellular membranes serve as an epicentre combining extracellular and cytosolic components with membranous effectors, which together support numerous fundamental cellular signalling pathways that mediate biological responses. To execute their functions, membrane proteins, lipids and carbohydrates arrange, in a highly coordinated manner, into well-defined assemblies displaying diverse biological and biophysical characteristics that modulate several signalling events. The loss of membrane homeostasis can trigger oncogenic signalling. More recently, it has been documented that select membrane active dietaries (MADs) can reshape biological membranes and subsequently decrease cancer risk. In this review, we emphasize the significance of membrane domain structure, organization and their signalling functionalities as well as how loss of membrane homeostasis can steer aberrant signalling. Moreover, we describe in detail the complexities associated with the examination of these membrane domains and their association with cancer. Finally, we summarize the current literature on MADs and their effects on cellular membranes, including various mechanisms of dietary chemoprevention/interception and the functional links between nutritional bioactives, membrane homeostasis and cancer biology.
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Affiliation(s)
- Alfredo Erazo-Oliveras
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Mónica Muñoz-Vega
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Michael L. Salinas
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Xiaoli Wang
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Robert S. Chapkin
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
- Center for Environmental Health Research; Texas A&M University; College Station, Texas, 77843; USA
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3
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Pan X, Ren L, Yang Y, Xu Y, Ning L, Zhang Y, Luo H, Zou Q, Zhang Y. MCSdb, a database of proteins residing in membrane contact sites. Sci Data 2024; 11:281. [PMID: 38459036 PMCID: PMC10923927 DOI: 10.1038/s41597-024-03104-7] [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: 05/08/2023] [Accepted: 02/29/2024] [Indexed: 03/10/2024] Open
Abstract
Organelles do not act as autonomous discrete units but rather as interconnected hubs that engage in extensive communication by forming close contacts called "membrane contact sites (MCSs)". And many proteins have been identified as residing in MCS and playing important roles in maintaining and fulfilling specific functions within these microdomains. However, a comprehensive compilation of these MCS proteins is still lacking. Therefore, we developed MCSdb, a manually curated resource of MCS proteins and complexes from publications. MCSdb documents 7010 MCS protein entries and 263 complexes, involving 24 organelles and 44 MCSs across 11 species. Additionally, MCSdb orchestrates all data into different categories with multitudinous information for presenting MCS proteins. In summary, MCSdb provides a valuable resource for accelerating MCS functional interpretation and interorganelle communication deciphering.
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Affiliation(s)
- Xianrun Pan
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Liping Ren
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, China
| | - Yu Yang
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, China
| | - Yi Xu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Lin Ning
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, China
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yibing Zhang
- Glasgow College, University of Electronic Science and Technology of China, Chengdu, China
| | - Huaichao Luo
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China.
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China.
| | - Yang Zhang
- Innovative Institute of Chinese Medicine and Pharmacy, Academy for Interdiscipline, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
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4
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Jerabkova-Roda K, Marwaha R, Das T, Goetz JG. Organelle morphology and positioning orchestrate physiological and disease-associated processes. Curr Opin Cell Biol 2024; 86:102293. [PMID: 38096602 DOI: 10.1016/j.ceb.2023.102293] [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: 08/28/2023] [Revised: 10/24/2023] [Accepted: 11/19/2023] [Indexed: 02/15/2024]
Abstract
In cells, organelles are distributed nonrandomly to regulate cells' physiological and disease-associated processes. Based on their morphology, position within the cell, and contacts with other organelles, they exert different biological functions. Endo-lysosomes are critical cell metabolism and nutrient-sensing regulators modulating cell growth and cellular adaptation in response to nutrient availability. Their spatial distribution is intimately linked to their function. In this review, we will discuss the role of endolysosomes under physiological conditions and in the context of cancer progression, with a special focus on their morphology, the molecular mechanisms determining their subcellular position, and the contacts they form with other organelles. We aim to highlight the relationship between cell architecture and cell function and its impact on maintaining organismal homeostasis.
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Affiliation(s)
- Katerina Jerabkova-Roda
- Tumor Biomechanics, INSERM UMR_S1109, Strasbourg, France; Université de Strasbourg, Strasbourg, France; Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France; Equipe Labellisée Ligue Contre le Cancer, France.
| | - Rituraj Marwaha
- Tata Institute of Fundamental Research Hyderabad (TIFR-H), Hyderabad, 500 046, India
| | - Tamal Das
- Tata Institute of Fundamental Research Hyderabad (TIFR-H), Hyderabad, 500 046, India
| | - Jacky G Goetz
- Tumor Biomechanics, INSERM UMR_S1109, Strasbourg, France; Université de Strasbourg, Strasbourg, France; Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France; Equipe Labellisée Ligue Contre le Cancer, France
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5
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Kumar R, Islinger M, Worthy H, Carmichael R, Schrader M. The peroxisome: an update on mysteries 3.0. Histochem Cell Biol 2024; 161:99-132. [PMID: 38244103 PMCID: PMC10822820 DOI: 10.1007/s00418-023-02259-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2023] [Indexed: 01/22/2024]
Abstract
Peroxisomes are highly dynamic, oxidative organelles with key metabolic functions in cellular lipid metabolism, such as the β-oxidation of fatty acids and the synthesis of myelin sheath lipids, as well as the regulation of cellular redox balance. Loss of peroxisomal functions causes severe metabolic disorders in humans. Furthermore, peroxisomes also fulfil protective roles in pathogen and viral defence and immunity, highlighting their wider significance in human health and disease. This has sparked increasing interest in peroxisome biology and their physiological functions. This review presents an update and a continuation of three previous review articles addressing the unsolved mysteries of this remarkable organelle. We continue to highlight recent discoveries, advancements, and trends in peroxisome research, and address novel findings on the metabolic functions of peroxisomes, their biogenesis, protein import, membrane dynamics and division, as well as on peroxisome-organelle membrane contact sites and organelle cooperation. Furthermore, recent insights into peroxisome organisation through super-resolution microscopy are discussed. Finally, we address new roles for peroxisomes in immune and defence mechanisms and in human disorders, and for peroxisomal functions in different cell/tissue types, in particular their contribution to organ-specific pathologies.
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Grants
- BB/W015420/1, BB/V018167/1, BB/T002255/1, BB/R016844/1 Biotechnology and Biological Sciences Research Council
- BB/W015420/1, BB/V018167/1, BB/T002255/1, BB/R016844/1 Biotechnology and Biological Sciences Research Council
- BB/W015420/1, BB/V018167/1, BB/T002255/1, BB/R016844/1 Biotechnology and Biological Sciences Research Council
- European Union’s Horizon 2020 research and innovation programme
- Deutsches Zentrum für Herz-Kreislaufforschung
- German Research Foundation
- Medical Faculty Mannheim, University of Heidelberg
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Affiliation(s)
- Rechal Kumar
- Faculty of Health and Life Sciences, Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
| | - Markus Islinger
- Institute of Neuroanatomy, Medical Faculty Mannheim, Mannheim Centre for Translational Neuroscience, University of Heidelberg, 68167, Mannheim, Germany
| | - Harley Worthy
- Faculty of Health and Life Sciences, Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
| | - Ruth Carmichael
- Faculty of Health and Life Sciences, Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
| | - Michael Schrader
- Faculty of Health and Life Sciences, Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
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6
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Andhare D, Ragusa MJ. A new GUV-based assay to reconstitute membrane tethering in vitro demonstrates the vesicle tethering ability of the selective autophagy scaffold Atg11. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.19.572332. [PMID: 38187578 PMCID: PMC10769207 DOI: 10.1101/2023.12.19.572332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Membrane tethering is essential for the generation of organelle contact sites and to anchor incoming vesicles to their target membranes before vesicle fusion. During autophagy in yeast, tethering of 30 nm vesicles to cargo is one of the first steps in the generation of the isolation membrane that engulfs the cargo to be degraded. While membrane tethering is critical for cellular function, many of the current biochemical techniques to assay for membrane tethering rely on indirect readouts and are limited in their ability to monitor protein localization at sites of tethering. As such, we developed a fluorescence-microscopy-based GUV liposome tethering assay (GLT) to directly visualize membrane tethering and monitor protein localization at tethering sites simultaneously. We initially used GLT with engineered membrane tethers to demonstrate the ease of use, versatility and sensitivity of the assay. We also demonstrated that the selective autophagy scaffolding protein Atg11 can bind, and tether negatively charged membranes but is unable to bind GUVs mimicking the charge of the outer mitochondrial membrane. Atg11 instead requires the selective autophagy receptor Atg32 to be recruited to mitochondrial membranes. Lastly, we demonstrate that Atg11 bound to Atg32 on GUVs can tether negatively charged vesicles to GUVs. Collectively, our results reconstitute one of the first steps during the initiation of mitochondrial autophagy and highlight the versatility of GLT to study a range of membrane tethering events biochemically.
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Affiliation(s)
- Devika Andhare
- Department of Chemistry, Dartmouth College, Hanover, NH 03755, USA
| | - Michael J Ragusa
- Department of Chemistry, Dartmouth College, Hanover, NH 03755, USA
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7
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Peggion C, Barazzuol L, Poggio E, Calì T, Brini M. Ca 2+ signalling: A common language for organelles crosstalk in Parkinson's disease. Cell Calcium 2023; 115:102783. [PMID: 37597300 DOI: 10.1016/j.ceca.2023.102783] [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: 06/13/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/21/2023]
Abstract
Parkinson's disease (PD) is a neurodegenerative disease caused by multifactorial pathogenic mechanisms. Familial PD is linked with genetic mutations in genes whose products are either associated with mitochondrial function or endo-lysosomal pathways. Of note, mitochondria are essential to sustain high energy demanding synaptic activity of neurons and alterations in mitochondrial Ca2+ signaling have been proposed as causal events for neurodegenerative process, although the mechanisms responsible for the selective loss of specific neuronal populations in the different neurodegenerative diseases is still not clear. Here, we specifically discuss the importance of a correct mitochondrial communication with the other organelles occurring at regions where their membranes become in close contact. We discuss the nature and the role of contact sites that mitochondria establish with ER, lysosomes, and peroxisomes, and how PD related proteins participate in the regulation/dysregulation of the tethering complexes. Unravelling molecular details of mitochondria tethering could contribute to identify specific therapeutic targets and develop new strategies to counteract the progression of the disease.
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Affiliation(s)
| | | | - Elena Poggio
- Department of Biology (DIBIO), University of Padova, Italy
| | - Tito Calì
- Department of Biomedical Sciences (DSB), University of Padova, Italy; Study Center for Neurodegeneration (CESNE), University of Padova, Italy; Padova Neuroscience Center (PNC), University of Padova, Padova, Italy.
| | - Marisa Brini
- Department of Biology (DIBIO), University of Padova, Italy; Study Center for Neurodegeneration (CESNE), University of Padova, Italy.
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8
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Liu L, Gray JL, Tate EW, Yang A. Bacterial enzymes: powerful tools for protein labeling, cell signaling, and therapeutic discovery. Trends Biotechnol 2023; 41:1385-1399. [PMID: 37328400 DOI: 10.1016/j.tibtech.2023.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/01/2023] [Accepted: 05/16/2023] [Indexed: 06/18/2023]
Abstract
Bacteria have evolved a diverse set of enzymes that enable them to subvert host defense mechanisms as well as to form part of the prokaryotic immune system. Due to their unique and varied biochemical activities, these bacterial enzymes have emerged as key tools for understanding and investigating biological systems. In this review, we summarize and discuss some of the most prominent bacterial enzymes used for the site-specific modification of proteins, in vivo protein labeling, proximity labeling, interactome mapping, signaling pathway manipulation, and therapeutic discovery. Finally, we provide a perspective on the complementary advantages and limitations of using bacterial enzymes compared with chemical probes for exploring biological systems.
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Affiliation(s)
- Lu Liu
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Janine L Gray
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK.
| | - Aimin Yang
- School of Life Sciences, Chongqing University, Chongqing 401331, China.
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9
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Vardar Acar N, Özgül RK. A big picture of the mitochondria-mediated signals: From mitochondria to organism. Biochem Biophys Res Commun 2023; 678:45-61. [PMID: 37619311 DOI: 10.1016/j.bbrc.2023.08.032] [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: 06/06/2023] [Revised: 08/02/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023]
Abstract
Mitochondria, well-known for years as the powerhouse and biosynthetic center of the cell, are dynamic signaling organelles beyond their energy production and biosynthesis functions. The metabolic functions of mitochondria, playing an important role in various biological events both in physiological and stress conditions, transform them into important cellular stress sensors. Mitochondria constantly communicate with the rest of the cell and even from other cells to the organism, transmitting stress signals including oxidative and reductive stress or adaptive signals such as mitohormesis. Mitochondrial signal transduction has a vital function in regulating integrity of human genome, organelles, cells, and ultimately organism.
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Affiliation(s)
- Neşe Vardar Acar
- Department of Pediatric Metabolism, Institute of Child Health, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - R Köksal Özgül
- Department of Pediatric Metabolism, Institute of Child Health, Faculty of Medicine, Hacettepe University, Ankara, Turkey.
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10
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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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11
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Zhou M, Kong B, Zhang X, Xiao K, Lu J, Li W, Li M, Li Z, Ji W, Hou J, Xu T. A proximity labeling strategy enables proteomic analysis of inter-organelle membrane contacts. iScience 2023; 26:107159. [PMID: 37485370 PMCID: PMC10362359 DOI: 10.1016/j.isci.2023.107159] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/03/2023] [Accepted: 06/13/2023] [Indexed: 07/25/2023] Open
Abstract
Inter-organelle membrane contacts are highly dynamic and act as central hubs for many biological processes, but the protein compositions remain largely unknown due to the lack of efficient tools. Here, we developed BiFCPL to analyze the contact proteome in living cells by a bimolecular fluorescence complementation (BiFC)-based proximity labeling (PL) strategy. BiFCPL was applied to study mitochondria-endoplasmic reticulum contacts (MERCs) and mitochondria-lipid droplet (LD) contacts. We identified 403 highly confident MERC proteins, including many transiently resident proteins and potential tethers. Moreover, we demonstrated that mitochondria-LD contacts are sensitive to nutrient status. A comparative proteomic analysis revealed that 60 proteins are up- or downregulated at contact sites under metabolic challenge. We verified that SQLE, an enzyme for cholesterol synthesis, accumulates at mitochondria-LD contact sites probably to utilize local ATP for cholesterol synthesis. This work provides an efficient method to identify key proteins at inter-organelle membrane contacts in living cells.
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Affiliation(s)
- Maoge Zhou
- Guangzhou Laboratory, Guangzhou, Guangdong 510005, China
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bingjie Kong
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiang Zhang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ke Xiao
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Lu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Weixing Li
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Min Li
- Guangzhou Laboratory, Guangzhou, Guangdong 510005, China
| | - Zonghong Li
- Guangzhou Laboratory, Guangzhou, Guangdong 510005, China
| | - Wei Ji
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junjie Hou
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Tao Xu
- Guangzhou Laboratory, Guangzhou, Guangdong 510005, China
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Biomedical Engineering, Guangzhou Medical University, Guangzhou, Guangdong 511436, China
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12
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Yun H, Jung M, Lee H, Jung S, Kim T, Kim N, Park SY, Kim WJ, Mun JY, Yoo JY. Homotypic SCOTIN assemblies form ER-endosome membrane contacts and regulate endosome dynamics. EMBO Rep 2023:e56538. [PMID: 37377038 PMCID: PMC10398665 DOI: 10.15252/embr.202256538] [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: 11/23/2022] [Revised: 05/25/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
The ER regulates the spatiotemporal organization of endolysosomal systems by membrane contact. In addition to tethering via heterotypic interactions on both organelles, we present a novel ER-endosome tethering mechanism mediated by homotypic interactions. The single-pass transmembrane protein SCOTIN is detected in the membrane of the ER and endosomes. In SCOTIN-knockout (KO) cells, the ER-late endosome contacts are reduced, and the perinuclear positioning of endosomes is disturbed. The cytosolic proline-rich domain (PRD) of SCOTIN forms homotypic assemblies in vitro and is necessary for ER-endosome membrane tethering in cells. A region of 28 amino acids spanning 150-177 within the SCOTIN PRD is essential to elicit membrane tethering and endosomal dynamics, as verified by reconstitution in SCOTIN-KO cells. The assembly of SCOTIN (PRD) is sufficient to mediate membrane tethering, as purified SCOTIN (PRD), but not SCOTIN (PRDΔ150-177), brings two different liposomes closer in vitro. Using organelle-specific targeting of a chimeric PRD domain shows that only the presence on both organellar membranes enables the ER-endosome membrane contact, indicating that the assembly of SCOTIN on heterologous membranes mediates organelle tethering.
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Affiliation(s)
- Hyeri Yun
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Minkyo Jung
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu, Republic of Korea
| | - Hojin Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Sungjin Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Taehyeon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Nari Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Seung-Yeol Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Won Jong Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Republic of Korea
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Ji Young Mun
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu, Republic of Korea
| | - Joo-Yeon Yoo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
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13
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Bian J, Su X, Yuan X, Zhang Y, Lin J, Li X. Endoplasmic reticulum membrane contact sites: cross-talk between membrane-bound organelles in plant cells. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2956-2967. [PMID: 36847172 DOI: 10.1093/jxb/erad068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/20/2023] [Indexed: 05/21/2023]
Abstract
Eukaryotic cells contain organelles surrounded by monolayer or bilayer membranes. Organelles take part in highly dynamic and organized interactions at membrane contact sites, which play vital roles during development and response to stress. The endoplasmic reticulum extends throughout the cell and acts as an architectural scaffold to maintain the spatial distribution of other membrane-bound organelles. In this review, we highlight the structural organization, dynamics, and physiological functions of membrane contact sites between the endoplasmic reticulum and various membrane-bound organelles, especially recent advances in plants. We briefly introduce how the combined use of dynamic and static imaging techniques can enable monitoring of the cross-talk between organelles via membrane contact sites. Finally, we discuss future directions for research fields related to membrane contact.
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Affiliation(s)
- Jiahui Bian
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Institute of Tree Development and Genome Editing, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xiao Su
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Institute of Tree Development and Genome Editing, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xiaoyan Yuan
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Institute of Tree Development and Genome Editing, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yuan Zhang
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Institute of Tree Development and Genome Editing, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Jinxing Lin
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Institute of Tree Development and Genome Editing, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Institute of Botany, Chinese Academy of Sciences, Beijing 100083, China
| | - Xiaojuan Li
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Institute of Tree Development and Genome Editing, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
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14
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Nieto-Garai JA, Olazar-Intxausti J, Anso I, Lorizate M, Terrones O, Contreras FX. Super-Resolution Microscopy to Study Interorganelle Contact Sites. Int J Mol Sci 2022; 23:ijms232315354. [PMID: 36499680 PMCID: PMC9739495 DOI: 10.3390/ijms232315354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/29/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
Interorganelle membrane contact sites (MCS) are areas of close vicinity between the membranes of two organelles that are maintained by protein tethers. Recently, a significant research effort has been made to study MCS, as they are implicated in a wide range of biological functions, such as organelle biogenesis and division, apoptosis, autophagy, and ion and phospholipid homeostasis. Their composition, characteristics, and dynamics can be studied by different techniques, but in recent years super-resolution fluorescence microscopy (SRFM) has emerged as a powerful tool for studying MCS. In this review, we first explore the main characteristics and biological functions of MCS and summarize the different approaches for studying them. Then, we center on SRFM techniques that have been used to study MCS. For each of the approaches, we summarize their working principle, discuss their advantages and limitations, and explore the main discoveries they have uncovered in the field of MCS.
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Affiliation(s)
- Jon Ander Nieto-Garai
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - June Olazar-Intxausti
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Itxaso Anso
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, 48903 Barakaldo, Spain
| | - Maier Lorizate
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Oihana Terrones
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
- Correspondence: (O.T.); (F.-X.C.); Tel.: +34-946-013-588 (O.T.); +34-946-012-106 (F.-X.C.)
| | - Francesc-Xabier Contreras
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
- Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, 48940 Leioa, Spain
- Ikerbasque, Basque Foundation of Science, 48011 Bilbao, Spain
- Correspondence: (O.T.); (F.-X.C.); Tel.: +34-946-013-588 (O.T.); +34-946-012-106 (F.-X.C.)
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15
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Bar-Peled L, Kory N. Principles and functions of metabolic compartmentalization. Nat Metab 2022; 4:1232-1244. [PMID: 36266543 PMCID: PMC10155461 DOI: 10.1038/s42255-022-00645-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/24/2022] [Indexed: 01/20/2023]
Abstract
Metabolism has historically been studied at the levels of whole cells, whole tissues and whole organisms. As a result, our understanding of how compartmentalization-the spatial and temporal separation of pathways and components-shapes organismal metabolism remains limited. At its essence, metabolic compartmentalization fulfils three important functions or 'pillars': establishing unique chemical environments, providing protection from reactive metabolites and enabling the regulation of metabolic pathways. However, how these pillars are established, regulated and maintained at both the cellular and systemic levels remains unclear. Here we discuss how the three pillars are established, maintained and regulated within the cell and discuss the consequences of dysregulation of metabolic compartmentalization in human disease. Organelles are increasingly emerging as 'command-and-control centres' and the increased understanding of metabolic compartmentalization is revealing new aspects of metabolic homeostasis, with this knowledge being translated into therapies for the treatment of cancer and certain neurodegenerative diseases.
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Affiliation(s)
- Liron Bar-Peled
- Center for Cancer Research, Massachusetts General Hospital and Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Nora Kory
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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16
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Proteomic mapping and optogenetic manipulation of membrane contact sites. Biochem J 2022; 479:1857-1875. [PMID: 36111979 PMCID: PMC9555801 DOI: 10.1042/bcj20220382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022]
Abstract
Membrane contact sites (MCSs) mediate crucial physiological processes in eukaryotic cells, including ion signaling, lipid metabolism, and autophagy. Dysregulation of MCSs is closely related to various diseases, such as type 2 diabetes mellitus (T2DM), neurodegenerative diseases, and cancers. Visualization, proteomic mapping and manipulation of MCSs may help the dissection of the physiology and pathology MCSs. Recent technical advances have enabled better understanding of the dynamics and functions of MCSs. Here we present a summary of currently known functions of MCSs, with a focus on optical approaches to visualize and manipulate MCSs, as well as proteomic mapping within MCSs.
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17
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Cook KC, Tsopurashvili E, Needham JM, Thompson SR, Cristea IM. Restructured membrane contacts rewire organelles for human cytomegalovirus infection. Nat Commun 2022; 13:4720. [PMID: 35953480 PMCID: PMC9366835 DOI: 10.1038/s41467-022-32488-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/30/2022] [Indexed: 12/24/2022] Open
Abstract
Membrane contact sites (MCSs) link organelles to coordinate cellular functions across space and time. Although viruses remodel organelles for their replication cycles, MCSs remain largely unexplored during infections. Here, we design a targeted proteomics platform for measuring MCS proteins at all organelles simultaneously and define functional virus-driven MCS alterations by the ancient beta-herpesvirus human cytomegalovirus (HCMV). Integration with super-resolution microscopy and comparisons to herpes simplex virus (HSV-1), Influenza A, and beta-coronavirus HCoV-OC43 infections reveals time-sensitive contact regulation that allows switching anti- to pro-viral organelle functions. We uncover a stabilized mitochondria-ER encapsulation structure (MENC). As HCMV infection progresses, MENCs become the predominant mitochondria-ER contact phenotype and sequentially recruit the tethering partners VAP-B and PTPIP51, supporting virus production. However, premature ER-mitochondria tethering activates STING and interferon response, priming cells against infection. At peroxisomes, ACBD5-mediated ER contacts balance peroxisome proliferation versus membrane expansion, with ACBD5 impacting the titers of each virus tested.
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Affiliation(s)
- Katelyn C Cook
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, US
| | - Elene Tsopurashvili
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, US
| | - Jason M Needham
- Department of Microbiology, University of Alabama Birmingham, Birmingham, AL, 35294, US
| | - Sunnie R Thompson
- Department of Microbiology, University of Alabama Birmingham, Birmingham, AL, 35294, US
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, US.
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18
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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: 14] [Impact Index Per Article: 7.0] [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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19
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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: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [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
- Johannes V. Swinnen
| | - 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
- Patrizia Agostinis
| | - Joris Winderickx
- Laboratory of Functional Biology, Department of Biology, KU Leuven, Heverlee, Belgium
- Joris Winderickx
| | - 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
- Peter Vangheluwe
| | - Wim Annaert
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, KU Leuven, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Leuven, Belgium
- *Correspondence: Wim Annaert
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20
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Girik V, Feng S, Hariri H, Henne WM, Riezman H. Vacuole-Specific Lipid Release for Tracking Intracellular Lipid Metabolism and Transport in Saccharomyces cerevisiae. ACS Chem Biol 2022; 17:1485-1494. [PMID: 35667650 PMCID: PMC9207805 DOI: 10.1021/acschembio.2c00120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lipid metabolism is spatiotemporally regulated within cells, yet intervention into lipid functions at subcellular resolution remains difficult. Here, we report a method that enables site-specific release of sphingolipids and cholesterol inside the vacuole in Saccharomyces cerevisiae. Using this approach, we monitored real-time sphingolipid metabolic flux out of the vacuole by mass spectrometry and found that the endoplasmic reticulum-vacuole-tethering protein Mdm1 facilitated the metabolism of sphingoid bases into ceramides. In addition, we showed that cholesterol, once delivered into yeast using our method, could restore cell proliferation induced by ergosterol deprivation, overcoming the previously described sterol-uptake barrier under aerobic conditions. Together, these data define a new way to study intracellular lipid metabolism and transport from the vacuole in yeast.
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Affiliation(s)
- Vladimir Girik
- Department of Biochemistry, University of Geneva, Geneva 1205, Switzerland
| | - Suihan Feng
- Department of Biochemistry, University of Geneva, Geneva 1205, Switzerland.,National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva 1205, Switzerland
| | - Hanaa Hariri
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, Texas 75390-9039 United States
| | - W Mike Henne
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, Texas 75390-9039 United States
| | - Howard Riezman
- Department of Biochemistry, University of Geneva, Geneva 1205, Switzerland
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21
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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: 3.5] [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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22
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Yang Z, Wang L, Yang C, Pu S, Guo Z, Wu Q, Zhou Z, Zhao H. Mitochondrial Membrane Remodeling. Front Bioeng Biotechnol 2022; 9:786806. [PMID: 35059386 PMCID: PMC8763711 DOI: 10.3389/fbioe.2021.786806] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/22/2021] [Indexed: 02/05/2023] Open
Abstract
Mitochondria are key regulators of many important cellular processes and their dysfunction has been implicated in a large number of human disorders. Importantly, mitochondrial function is tightly linked to their ultrastructure, which possesses an intricate membrane architecture defining specific submitochondrial compartments. In particular, the mitochondrial inner membrane is highly folded into membrane invaginations that are essential for oxidative phosphorylation. Furthermore, mitochondrial membranes are highly dynamic and undergo constant membrane remodeling during mitochondrial fusion and fission. It has remained enigmatic how these membrane curvatures are generated and maintained, and specific factors involved in these processes are largely unknown. This review focuses on the current understanding of the molecular mechanism of mitochondrial membrane architectural organization and factors critical for mitochondrial morphogenesis, as well as their functional link to human diseases.
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Affiliation(s)
- Ziyun Yang
- School of Life Sciences, Guangxi Normal University, Guilin, China.,Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China.,Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Liang Wang
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, West China Medical School, Sichuan University, High-Tech Development Zone, Chengdu, China
| | - Cheng Yang
- School of Life Sciences, Guangxi Normal University, Guilin, China.,Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China.,Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Shiming Pu
- School of Life Sciences, Guangxi Normal University, Guilin, China.,Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China.,Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Ziqi Guo
- School of Life Sciences, Guangxi Normal University, Guilin, China.,Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China.,Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Qiong Wu
- School of Life Sciences, Guangxi Normal University, Guilin, China.,Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China.,Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Zuping Zhou
- School of Life Sciences, Guangxi Normal University, Guilin, China.,Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China.,Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China
| | - Hongxia Zhao
- School of Life Sciences, Guangxi Normal University, Guilin, China.,Guangxi Universities, Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, China.,Research Center for Biomedical Sciences, Guangxi Normal University, Guilin, China.,Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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23
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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: 0] [Impact Index Per Article: 0] [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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24
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Benhammouda S, Vishwakarma A, Gatti P, Germain M. Mitochondria Endoplasmic Reticulum Contact Sites (MERCs): Proximity Ligation Assay as a Tool to Study Organelle Interaction. Front Cell Dev Biol 2021; 9:789959. [PMID: 34926468 PMCID: PMC8678465 DOI: 10.3389/fcell.2021.789959] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/18/2021] [Indexed: 01/17/2023] Open
Abstract
Organelles cooperate with each other to regulate vital cellular homoeostatic functions. This occurs through the formation of close connections through membrane contact sites. Mitochondria-Endoplasmic-Reticulum (ER) contact sites (MERCS) are one of such contact sites that regulate numerous biological processes by controlling calcium and metabolic homeostasis. However, the extent to which contact sites shape cellular biology and the underlying mechanisms remain to be fully elucidated. A number of biochemical and imaging approaches have been established to address these questions, resulting in the identification of a number of molecular tethers between mitochondria and the ER. Among these techniques, fluorescence-based imaging is widely used, including analysing signal overlap between two organelles and more selective techniques such as in-situ proximity ligation assay (PLA). While these two techniques allow the detection of endogenous proteins, preventing some problems associated with techniques relying on overexpression (FRET, split fluorescence probes), they come with their own issues. In addition, proper image analysis is required to minimise potential artefacts associated with these methods. In this review, we discuss the protocols and outline the limitations of fluorescence-based approaches used to assess MERCs using endogenous proteins.
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Affiliation(s)
- Sara Benhammouda
- Groupe de Recherche en Signalisation Cellulaire and Département de Biologie Médicale, Université Du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
- Centre D'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Université du Québec à Montréal, Montréal, QC, Canada
| | - Anjali Vishwakarma
- Groupe de Recherche en Signalisation Cellulaire and Département de Biologie Médicale, Université Du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
- Centre D'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Université du Québec à Montréal, Montréal, QC, Canada
| | - Priya Gatti
- Groupe de Recherche en Signalisation Cellulaire and Département de Biologie Médicale, Université Du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
- Centre D'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Université du Québec à Montréal, Montréal, QC, Canada
| | - Marc Germain
- Groupe de Recherche en Signalisation Cellulaire and Département de Biologie Médicale, Université Du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
- Centre D'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Université du Québec à Montréal, Montréal, QC, Canada
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25
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Hello from the other side: Membrane contact of lipid droplets with other organelles and subsequent functional implications. Prog Lipid Res 2021; 85:101141. [PMID: 34793861 DOI: 10.1016/j.plipres.2021.101141] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/10/2021] [Accepted: 11/10/2021] [Indexed: 02/06/2023]
Abstract
Lipid droplets (LDs) are ubiquitous organelles that play crucial roles in response to physiological and environmental cues. The identification of several neutral lipid synthesizing and regulatory protein complexes have propelled significant advance on the mechanisms of LD biogenesis in the endoplasmic reticulum (ER). Increasing evidence suggests that distinct proteins and regulatory factors, which localize to membrane contact sites (MCS), are involved not only in interorganellar lipid exchange and transport, but also function in other important cellular processes, including autophagy, mitochondrial dynamics and inheritance, ion signaling and inter-regulation of these MCS. More and more tethers and molecular determinants are associated to MCS and to a diversity of cellular and pathophysiological processes, demonstrating the dynamics and importance of these junctions in health and disease. The conjugation of lipids with proteins in supramolecular complexes is known to be paramount for many biological processes, namely membrane biosynthesis, cell homeostasis, regulation of organelle division and biogenesis, and cell growth. Ultimately, this physical organization allows the contact sites to function as crucial metabolic hubs that control the occurrence of chemical reactions. This leads to biochemical and metabolite compartmentalization for the purposes of energetic efficiency and cellular homeostasis. In this review, we will focus on the structural and functional aspects of LD-organelle interactions and how they ensure signaling exchange and metabolites transfer between organelles.
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Jiang C, Huang X, Yao J, Yu L, Wei F, Yang A. The role of membrane contact sites at the bacteria-host interface. Crit Rev Microbiol 2021; 48:270-282. [PMID: 34403642 DOI: 10.1080/1040841x.2021.1961678] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Membrane contact sites (MCSs) refer to the areas of close proximity between heterologous membranes. A growing body of evidence indicates that MCSs are involved in important cellular functions, such as cellular material transfer, organelle biogenesis, and cell growth. Importantly, the study of MCSs at the bacteria-host interface is an emerging popular research topic. Intracellular bacterial pathogens have evolved a variety of fascinating strategies to interfere with MCSs by injecting effectors into infected host cells. Bacteria-containing vacuoles establish direct physical contact with organelles within the host, ensuring vacuolar membrane integrity and energy supply from host organelles and protecting the vacuoles from the host endocytic pathway and lysosomal degradation. An increasing number of bacterial effectors from various bacterial pathogens hijack components of host MCSs to form the vacuole-organelle MCSs for material exchange. MCS-related events have been identified as new mechanisms of microbial pathogenesis to greatly improve bacterial survival and replication within host cells. In this review, we will discuss the recent advances in MCSs at the bacteria-host interface, focussing on the roles of MCSs mediated by bacterial effectors in microbial pathogenesis.
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Affiliation(s)
- Chen Jiang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Xue Huang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Jia Yao
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Lihua Yu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Fujing Wei
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Aimin Yang
- School of Life Sciences, Chongqing University, Chongqing, China
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Won J, Choi Y, Yun Y, Lee HH. Biochemical Characterization of the Num1-Mdm36 Complex at the Mitochondria-Plasma Membrane Contact Site. Mol Cells 2021; 44:207-213. [PMID: 33827993 PMCID: PMC8112169 DOI: 10.14348/molcells.2021.0016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/03/2021] [Accepted: 03/03/2021] [Indexed: 11/27/2022] Open
Abstract
Saccharomyces cerevisiae that tethers mitochondria to the plasma membrane and plays a key role in mitochondrial fission. The main components of MECA are Num1 and Mdm36, and it is known that Mdm36 binds to Num1 to enhance mitochondrial tethering. To better understand the biochemical characteristics of the Num1-Mdm36 complex at the molecular level, we purified the coiled-coil domain of Num1, full-length Mdm36, and Num1-Mdm36 complex and identified the oligomeric state and stoichiometric characteristics of the Num1-Mdm36 complex by chemical crosslinking, size-exclusion chromatography coupled with multi-angle light scattering, and isothermal titration calorimetry. Mdm36 exists as a dimer and interacts preferentially with Num1 with a stoichiometry of 2:2, forming a heterotetrameric complex. Furthermore, we narrowed down the specific binding region of Num1, which is essential for interacting with Mdm36, and showed that their binding affinity is strong enough to tether both mitochondrial and plasma membranes. Our biochemical characterizations suggest a stoichiometric model of the Num1-Mdm36 complex at the mitochondria-plasma membrane contact site in budding yeast.
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Affiliation(s)
- Jongdae Won
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Korea
| | - Yuri Choi
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Korea
| | - Yaejin Yun
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Korea
| | - Hyung Ho Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Korea
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28
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Abstract
Our cells are comprised of billions of proteins, lipids, and other small molecules packed into their respective subcellular organelles, with the daunting task of maintaining cellular homeostasis over a lifetime. However, it is becoming increasingly evident that organelles do not act as autonomous discrete units but rather as interconnected hubs that engage in extensive communication through membrane contacts. In the last few years, our understanding of how these contacts coordinate organelle function has redefined our view of the cell. This review aims to present novel findings on the cellular interorganelle communication network and how its dysfunction may contribute to aging and neurodegeneration. The consequences of disturbed interorganellar communication are intimately linked with age-related pathologies. Given that both aging and neurodegenerative diseases are characterized by the concomitant failure of multiple cellular pathways, coordination of organelle communication and function could represent an emerging regulatory mechanism critical for long-term cellular homeostasis. We anticipate that defining the relationships between interorganelle communication, aging, and neurodegeneration will open new avenues for therapeutics.
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Affiliation(s)
- Maja Petkovic
- Department of Physiology, University of California at San Francisco, San Francisco, California 94158, USA
| | - Caitlin E O'Brien
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California 94158, USA
| | - Yuh Nung Jan
- Department of Physiology, University of California at San Francisco, San Francisco, California 94158, USA
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California 94158, USA
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158, USA
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29
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Siedlik MJ, Yang Z, Kadam PS, Eberwine J, Issadore D. Micro- and Nano-Devices for Studying Subcellular Biology. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2005793. [PMID: 33345457 PMCID: PMC8258219 DOI: 10.1002/smll.202005793] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/20/2020] [Indexed: 05/27/2023]
Abstract
Cells are complex machines whose behaviors arise from their internal collection of dynamically interacting organelles, supramolecular complexes, and cytoplasmic chemicals. The current understanding of the nature by which subcellular biology produces cell-level behaviors is limited by the technological hurdle of measuring the large number (>103 ) of small-sized (<1 μm) heterogeneous organelles and subcellular structures found within each cell. In this review, the emergence of a suite of micro- and nano-technologies for studying intracellular biology on the scale of organelles is described. Devices that use microfluidic and microelectronic components for 1) extracting and isolating subcellular structures from cells and lysate; 2) analyzing the physiology of individual organelles; and 3) recreating subcellular assembly and functions in vitro, are described. The authors envision that the continued development of single organelle technologies and analyses will serve as a foundation for organelle systems biology and will allow new insight into fundamental and clinically relevant biological questions.
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Affiliation(s)
- Michael J Siedlik
- Department of Bioengineering, 335 Skirkanich Hall, University of Pennsylvania, 210 South 33rd Street, Philadelphia, PA, 19104, USA
| | - Zijian Yang
- Department of Mechanical Engineering and Applied Science, 335 Skirkanich Hall, University of Pennsylvania, 210 South 33rd Street, Philadelphia, PA, 19104, USA
| | - Parnika S Kadam
- Systems Pharmacology and Translational Therapeutics, 38 John Morgan Building, University of Pennsylvania, 3620 Hamilton Walk, Philadelphia, PA, 19104, USA
| | - James Eberwine
- Systems Pharmacology and Translational Therapeutics, 38 John Morgan Building, University of Pennsylvania, 3620 Hamilton Walk, Philadelphia, PA, 19104, USA
| | - David Issadore
- Department of Bioengineering, 335 Skirkanich Hall, University of Pennsylvania, 210 South 33rd Street, Philadelphia, PA, 19104, USA
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Solnier J, Fladerer JP. Flavonoids: A complementary approach to conventional therapy of COVID-19? PHYTOCHEMISTRY REVIEWS : PROCEEDINGS OF THE PHYTOCHEMICAL SOCIETY OF EUROPE 2021; 20:773-795. [PMID: 32982616 PMCID: PMC7500502 DOI: 10.1007/s11101-020-09720-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 08/29/2020] [Indexed: 05/02/2023]
Abstract
COVID-19, the highly contagious novel disease caused by SARS-CoV-2, has become a major international concern as it has spread quickly all over the globe. However, scientific knowledge and therapeutic treatment options for this new coronavirus remain limited. Although previous outbreaks of human coronaviruses (CoVs) such as SARS and MERS stimulated research, there are, to date, no antiviral therapeutics available that specifically target these kinds of viruses. Natural compounds with a great diversity of chemical structures may provide an alternative approach for the discovery of new antivirals. In fact, numerous flavonoids were found to have antiviral effects against SARS-and MERS-CoV by mainly inhibiting the enzymes 3-chymotrypsin-like protease (3CLpro) and papain-like protease (PLpro). In this review, we specifically focused on the search for flavonoids, polyphenolic compounds, which are proven to be effective against human CoVs. We therefore summarized and analyzed the latest progress in research to identify flavonoids for antiviral therapy and proposed strategies for future work on medicinal plants against coronaviruses such as SARS-CoV-2. We discovered quercetin, herbacetin, and isobavachalcone as the most promising flavonoids with anti-CoV potential.
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Affiliation(s)
- Julia Solnier
- Institute of Pharmaceutical Sciences, Department of Pharmacognosy, University of Graz, Universitätsplatz 4, 8010 Graz, Austria
| | - Johannes-Paul Fladerer
- Institute of Pharmaceutical Sciences, Department of Pharmacognosy, University of Graz, Universitätsplatz 4, 8010 Graz, Austria
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31
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Benhammouda S, Vishwakarma A, Gatti P, Germain M. Mitochondria Endoplasmic Reticulum Contact Sites (MERCs): Proximity Ligation Assay as a Tool to Study Organelle Interaction. Front Cell Dev Biol 2021. [PMID: 34926468 DOI: 10.3389/fcell.2021.789959.ecollection2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023] Open
Abstract
Organelles cooperate with each other to regulate vital cellular homoeostatic functions. This occurs through the formation of close connections through membrane contact sites. Mitochondria-Endoplasmic-Reticulum (ER) contact sites (MERCS) are one of such contact sites that regulate numerous biological processes by controlling calcium and metabolic homeostasis. However, the extent to which contact sites shape cellular biology and the underlying mechanisms remain to be fully elucidated. A number of biochemical and imaging approaches have been established to address these questions, resulting in the identification of a number of molecular tethers between mitochondria and the ER. Among these techniques, fluorescence-based imaging is widely used, including analysing signal overlap between two organelles and more selective techniques such as in-situ proximity ligation assay (PLA). While these two techniques allow the detection of endogenous proteins, preventing some problems associated with techniques relying on overexpression (FRET, split fluorescence probes), they come with their own issues. In addition, proper image analysis is required to minimise potential artefacts associated with these methods. In this review, we discuss the protocols and outline the limitations of fluorescence-based approaches used to assess MERCs using endogenous proteins.
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Affiliation(s)
- Sara Benhammouda
- Groupe de Recherche en Signalisation Cellulaire and Département de Biologie Médicale, Université Du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
- Centre D'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Université du Québec à Montréal, Montréal, QC, Canada
| | - Anjali Vishwakarma
- Groupe de Recherche en Signalisation Cellulaire and Département de Biologie Médicale, Université Du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
- Centre D'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Université du Québec à Montréal, Montréal, QC, Canada
| | - Priya Gatti
- Groupe de Recherche en Signalisation Cellulaire and Département de Biologie Médicale, Université Du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
- Centre D'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Université du Québec à Montréal, Montréal, QC, Canada
| | - Marc Germain
- Groupe de Recherche en Signalisation Cellulaire and Département de Biologie Médicale, Université Du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
- Centre D'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Université du Québec à Montréal, Montréal, QC, Canada
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32
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Silva BSC, DiGiovanni L, Kumar R, Carmichael RE, Kim PK, Schrader M. Maintaining social contacts: The physiological relevance of organelle interactions. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118800. [PMID: 32712071 PMCID: PMC7377706 DOI: 10.1016/j.bbamcr.2020.118800] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/12/2020] [Accepted: 07/19/2020] [Indexed: 02/07/2023]
Abstract
Membrane-bound organelles in eukaryotic cells form an interactive network to coordinate and facilitate cellular functions. The formation of close contacts, termed "membrane contact sites" (MCSs), represents an intriguing strategy for organelle interaction and coordinated interplay. Emerging research is rapidly revealing new details of MCSs. They represent ubiquitous and diverse structures, which are important for many aspects of cell physiology and homeostasis. Here, we provide a comprehensive overview of the physiological relevance of organelle contacts. We focus on mitochondria, peroxisomes, the Golgi complex and the plasma membrane, and discuss the most recent findings on their interactions with other subcellular organelles and their multiple functions, including membrane contacts with the ER, lipid droplets and the endosomal/lysosomal compartment.
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Affiliation(s)
- Beatriz S C Silva
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter EX4 4QD, Devon, UK
| | - Laura DiGiovanni
- Program in Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Rechal Kumar
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter EX4 4QD, Devon, UK
| | - Ruth E Carmichael
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter EX4 4QD, Devon, UK.
| | - Peter K Kim
- Program in Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| | - Michael Schrader
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter EX4 4QD, Devon, UK.
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