1
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Kuo A, Hla T. Regulation of cellular and systemic sphingolipid homeostasis. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00742-y. [PMID: 38890457 DOI: 10.1038/s41580-024-00742-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2024] [Indexed: 06/20/2024]
Abstract
One hundred and fifty years ago, Johann Thudichum described sphingolipids as unusual "Sphinx-like" lipids from the brain. Today, we know that thousands of sphingolipid molecules mediate many essential functions in embryonic development and normal physiology. In addition, sphingolipid metabolism and signalling pathways are dysregulated in a wide range of pathologies, and therapeutic agents that target sphingolipids are now used to treat several human diseases. However, our understanding of sphingolipid regulation at cellular and organismal levels and their functions in developmental, physiological and pathological settings is rudimentary. In this Review, we discuss recent advances in sphingolipid pathways in different organelles, how secreted sphingolipid mediators modulate physiology and disease, progress in sphingolipid-targeted therapeutic and diagnostic research, and the trans-cellular sphingolipid metabolic networks between microbiota and mammals. Advances in sphingolipid biology have led to a deeper understanding of mammalian physiology and may lead to progress in the management of many diseases.
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Affiliation(s)
- Andrew Kuo
- Vascular Biology Program, Boston Children's Hospital, Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Timothy Hla
- Vascular Biology Program, Boston Children's Hospital, Department of Surgery, Harvard Medical School, Boston, MA, USA.
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2
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Castello-Serrano I, Heberle FA, Diaz-Rohrer B, Ippolito R, Shurer CR, Lujan P, Campelo F, Levental KR, Levental I. Partitioning to ordered membrane domains regulates the kinetics of secretory traffic. eLife 2024; 12:RP89306. [PMID: 38837189 PMCID: PMC11152573 DOI: 10.7554/elife.89306] [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: 06/06/2024] Open
Abstract
The organelles of eukaryotic cells maintain distinct protein and lipid compositions required for their specific functions. The mechanisms by which many of these components are sorted to their specific locations remain unknown. While some motifs mediating subcellular protein localization have been identified, many membrane proteins and most membrane lipids lack known sorting determinants. A putative mechanism for sorting of membrane components is based on membrane domains known as lipid rafts, which are laterally segregated nanoscopic assemblies of specific lipids and proteins. To assess the role of such domains in the secretory pathway, we applied a robust tool for synchronized secretory protein traffic (RUSH, Retention Using Selective Hooks) to protein constructs with defined affinity for raft phases. These constructs consist solely of single-pass transmembrane domains (TMDs) and, lacking other sorting determinants, constitute probes for membrane domain-mediated trafficking. We find that while raft affinity can be sufficient for steady-state PM localization, it is not sufficient for rapid exit from the endoplasmic reticulum (ER), which is instead mediated by a short cytosolic peptide motif. In contrast, we find that Golgi exit kinetics are highly dependent on raft affinity, with raft preferring probes exiting the Golgi ~2.5-fold faster than probes with minimal raft affinity. We rationalize these observations with a kinetic model of secretory trafficking, wherein Golgi export can be facilitated by protein association with raft domains. These observations support a role for raft-like membrane domains in the secretory pathway and establish an experimental paradigm for dissecting its underlying machinery.
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Affiliation(s)
- Ivan Castello-Serrano
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of VirginiaCharlottesvilleUnited States
| | | | | | - Rossana Ippolito
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of VirginiaCharlottesvilleUnited States
| | - Carolyn R Shurer
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of VirginiaCharlottesvilleUnited States
| | - Pablo Lujan
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Felix Campelo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Kandice R Levental
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of VirginiaCharlottesvilleUnited States
| | - Ilya Levental
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of VirginiaCharlottesvilleUnited States
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3
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Lathe RS, McFarlane HE, Kesten C, Wang L, Khan GA, Ebert B, Ramírez-Rodríguez EA, Zheng S, Noord N, Frandsen K, Bhalerao RP, Persson S. NKS1/ELMO4 is an integral protein of a pectin synthesis protein complex and maintains Golgi morphology and cell adhesion in Arabidopsis. Proc Natl Acad Sci U S A 2024; 121:e2321759121. [PMID: 38579009 PMCID: PMC11009649 DOI: 10.1073/pnas.2321759121] [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: 01/03/2024] [Accepted: 03/07/2024] [Indexed: 04/07/2024] Open
Abstract
Adjacent plant cells are connected by specialized cell wall regions, called middle lamellae, which influence critical agricultural characteristics, including fruit ripening and organ abscission. Middle lamellae are enriched in pectin polysaccharides, specifically homogalacturonan (HG). Here, we identify a plant-specific Arabidopsis DUF1068 protein, called NKS1/ELMO4, that is required for middle lamellae integrity and cell adhesion. NKS1 localizes to the Golgi apparatus and loss of NKS1 results in changes to Golgi structure and function. The nks1 mutants also display HG deficient phenotypes, including reduced seedling growth, changes to cell wall composition, and tissue integrity defects. These phenotypes are comparable to qua1 and qua2 mutants, which are defective in HG biosynthesis. Notably, genetic interactions indicate that NKS1 and the QUAs work in a common pathway. Protein interaction analyses and modeling corroborate that they work together in a stable protein complex with other pectin-related proteins. We propose that NKS1 is an integral part of a large pectin synthesis protein complex and that proper function of this complex is important to support Golgi structure and function.
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Affiliation(s)
- Rahul S. Lathe
- Copenhagen Plant Science Center, Department of Plant & Environmental Sciences, University of Copenhagen, Frederiksberg C1871, Denmark
- Max-Planck Institute for Molecular Plant Physiology, Potsdam14476, Germany
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, UmeåSE-90187, Sweden
| | - Heather E. McFarlane
- Department of Cell & Systems Biology, University of Toronto, Toronto, ONM5S 3G5, Canada
- School of Biosciences, University of Melbourne, Parkville, VIC3010, Australia
| | - Christopher Kesten
- Copenhagen Plant Science Center, Department of Plant & Environmental Sciences, University of Copenhagen, Frederiksberg C1871, Denmark
| | - Liu Wang
- Copenhagen Plant Science Center, Department of Plant & Environmental Sciences, University of Copenhagen, Frederiksberg C1871, Denmark
- School of Biosciences, University of Melbourne, Parkville, VIC3010, Australia
| | - Ghazanfar Abbas Khan
- School of Biosciences, University of Melbourne, Parkville, VIC3010, Australia
- Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC3086, Australia
| | - Berit Ebert
- School of Biosciences, University of Melbourne, Parkville, VIC3010, Australia
- Department of Biology and Biotechnology, Ruhr University Bochum, Bochum44780, Germany
| | | | - Shuai Zheng
- Copenhagen Plant Science Center, Department of Plant & Environmental Sciences, University of Copenhagen, Frederiksberg C1871, Denmark
| | - Niels Noord
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, UmeåSE-90187, Sweden
| | - Kristian Frandsen
- Copenhagen Plant Science Center, Department of Plant & Environmental Sciences, University of Copenhagen, Frederiksberg C1871, Denmark
| | - Rishikesh P. Bhalerao
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, UmeåSE-90187, Sweden
| | - Staffan Persson
- Copenhagen Plant Science Center, Department of Plant & Environmental Sciences, University of Copenhagen, Frederiksberg C1871, Denmark
- Max-Planck Institute for Molecular Plant Physiology, Potsdam14476, Germany
- School of Biosciences, University of Melbourne, Parkville, VIC3010, Australia
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, University of AdelaideJoint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai200240, China
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4
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Thomas M, Varlas S, Wilks TR, Fielden SDP, O'Reilly RK. Controlled node growth on the surface of polymersomes. Chem Sci 2024; 15:4396-4402. [PMID: 38516085 PMCID: PMC10952076 DOI: 10.1039/d3sc05915d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 02/16/2024] [Indexed: 03/23/2024] Open
Abstract
Incorporating nucleobases into synthetic polymers has proven to be a versatile method for controlling self-assembly. The formation of strong directional hydrogen bonds between complementary nucleobases provides a driving force that permits access to complex particle morphologies. Here, nucleobase pairing was used to direct the formation and lengthening of nodes on the outer surface of vesicles formed from polymers (polymersomes) functionalised with adenine in their membrane-forming domains. Insertion of a self-assembling short diblock copolymer containing thymine into the polymersome membranes caused an increase in steric crowding at the hydrophilic/hydrophobic interface, which was relieved by initial node formation and subsequent growth. Nano-objects were imaged by (cryo-)TEM, which permitted quantification of node coverage and length. The ability to control node growth on the surface of polymersomes provides a new platform to develop higher-order nanomaterials with tailorable properties.
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Affiliation(s)
- Marjolaine Thomas
- School of Chemistry, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Spyridon Varlas
- School of Chemistry, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Thomas R Wilks
- School of Chemistry, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Stephen D P Fielden
- School of Chemistry, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Rachel K O'Reilly
- School of Chemistry, University of Birmingham Edgbaston Birmingham B15 2TT UK
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5
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Lujan P, Garcia-Cabau C, Wakana Y, Vera Lillo J, Rodilla-Ramírez C, Sugiura H, Malhotra V, Salvatella X, Garcia-Parajo MF, Campelo F. Sorting of secretory proteins at the trans-Golgi network by human TGN46. eLife 2024; 12:RP91708. [PMID: 38466628 DOI: 10.7554/elife.91708] [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] [Indexed: 03/13/2024] Open
Abstract
Secretory proteins are sorted at the trans-Golgi network (TGN) for export into specific transport carriers. However, the molecular players involved in this fundamental process remain largely elusive. Here, we identified the human transmembrane protein TGN46 as a receptor for the export of secretory cargo protein PAUF in CARTS - a class of protein kinase D-dependent TGN-to-plasma membrane carriers. We show that TGN46 is necessary for cargo sorting and loading into nascent carriers at the TGN. By combining quantitative fluorescence microscopy and mutagenesis approaches, we further discovered that the lumenal domain of TGN46 encodes for its cargo sorting function. In summary, our results define a cellular function of TGN46 in sorting secretory proteins for export from the TGN.
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Affiliation(s)
- Pablo Lujan
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Carla Garcia-Cabau
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Yuichi Wakana
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Javier Vera Lillo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Carmen Rodilla-Ramírez
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Hideaki Sugiura
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Vivek Malhotra
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Maria F Garcia-Parajo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Felix Campelo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
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6
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Castello-Serrano I, Heberle FA, Diaz-Rohrer B, Ippolito R, Shurer CR, Lujan P, Campelo F, Levental KR, Levental I. Partitioning to ordered membrane domains regulates the kinetics of secretory traffic. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.18.537395. [PMID: 37131599 PMCID: PMC10153169 DOI: 10.1101/2023.04.18.537395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The organelles of eukaryotic cells maintain distinct protein and lipid compositions required for their specific functions. The mechanisms by which many of these components are sorted to their specific locations remain unknown. While some motifs mediating subcellular protein localization have been identified, many membrane proteins and most membrane lipids lack known sorting determinants. A putative mechanism for sorting of membrane components is based on membrane domains known as lipid rafts, which are laterally segregated nanoscopic assemblies of specific lipids and proteins. To assess the role of such domains in the secretory pathway, we applied a robust tool for synchronized secretory protein traffic (RUSH, Retention Using Selective Hooks) to protein constructs with defined affinity for raft phases. These constructs consist solely of single-pass transmembrane domains (TMDs) and, lacking other sorting determinants, constitute probes for membrane domain-mediated trafficking. We find that while raft affinity can be sufficient for steady-state PM localization, it is not sufficient for rapid exit from the endoplasmic reticulum (ER), which is instead mediated by a short cytosolic peptide motif. In contrast, we find that Golgi exit kinetics are highly dependent on raft affinity, with raft preferring probes exiting Golgi ~2.5-fold faster than probes with minimal raft affinity. We rationalize these observations with a kinetic model of secretory trafficking, wherein Golgi export can be facilitated by protein association with raft domains. These observations support a role for raft-like membrane domains in the secretory pathway and establish an experimental paradigm for dissecting its underlying machinery.
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7
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Yagi M, Hama M, Ichii S, Nakashima Y, Kanbayashi D, Kurata T, Yusa K, Komano J. S phingomyelin synthase 1 supports two steps of rubella virus life cycle. iScience 2023; 26:108267. [PMID: 38026182 PMCID: PMC10654604 DOI: 10.1016/j.isci.2023.108267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/23/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Our knowledge of the regulatory mechanisms that govern the replication of the rubella virus (RV) in human cells is limited. To gain insight into the host-pathogen interaction, we conducted a loss-of-function screening using the CRISPR-Cas9 system in the human placenta-derived JAR cells. We identified sphingomyelin synthase 1 (SGMS1 or SMS1) as a susceptibility factor for RV infection. Genetic knockout of SGMS1 rendered JAR cells resistant to infection by RV. The re-introduction of SGMS1 restored cellular susceptibility to RV infection. The restricted step of RV infection was post-endocytosis processes associated with the endosomal acidification. In the late phase of the RV replication cycle, the maintenance of viral persistence was disrupted, partly due to the attenuated viral gene expression. Our results shed light on the unique regulation of RV replication by a host factor during the early and late phases of viral life cycle.
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Affiliation(s)
- Mayuko Yagi
- Department of Microbiology and Infection Control, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki City, Osaka 569-1041, Japan
| | - Minami Hama
- Department of Microbiology and Infection Control, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki City, Osaka 569-1041, Japan
| | - Sayaka Ichii
- Department of Microbiology and Infection Control, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki City, Osaka 569-1041, Japan
| | - Yurie Nakashima
- Department of Microbiology and Infection Control, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki City, Osaka 569-1041, Japan
| | - Daiki Kanbayashi
- Osaka Institute of Public Health, Morinomiya Center, 1-3-69, Nakamichi, Higashinari-ku, Osaka 537-0025, Japan
| | - Takako Kurata
- Osaka Institute of Public Health, Morinomiya Center, 1-3-69, Nakamichi, Higashinari-ku, Osaka 537-0025, Japan
| | - Kosuke Yusa
- Stem Cell Genetics, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Jun Komano
- Department of Microbiology and Infection Control, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki City, Osaka 569-1041, Japan
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8
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Fasimoye R, Dong W, Nirujogi RS, Rawat ES, Iguchi M, Nyame K, Phung TK, Bagnoli E, Prescott AR, Alessi DR, Abu-Remaileh M. Golgi-IP, a tool for multimodal analysis of Golgi molecular content. Proc Natl Acad Sci U S A 2023; 120:e2219953120. [PMID: 37155866 PMCID: PMC10193996 DOI: 10.1073/pnas.2219953120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/05/2023] [Indexed: 05/10/2023] Open
Abstract
The Golgi is a membrane-bound organelle that is essential for protein and lipid biosynthesis. It represents a central trafficking hub that sorts proteins and lipids to various destinations or for secretion from the cell. The Golgi has emerged as a docking platform for cellular signaling pathways including LRRK2 kinase whose deregulation leads to Parkinson disease. Golgi dysfunction is associated with a broad spectrum of diseases including cancer, neurodegeneration, and cardiovascular diseases. To allow the study of the Golgi at high resolution, we report a rapid Golgi immunoprecipitation technique (Golgi-IP) to isolate intact Golgi mini-stacks for subsequent analysis of their content. By fusing the Golgi-resident protein TMEM115 to three tandem HA epitopes (GolgiTAG), we purified the Golgi using Golgi-IP with minimal contamination from other compartments. We then established an analysis pipeline using liquid chromatography coupled with mass spectrometry to characterize the human Golgi proteome, metabolome, and lipidome. Subcellular proteomics confirmed known Golgi proteins and identified proteins not previously associated with the Golgi. Metabolite profiling established the human Golgi metabolome and revealed the enrichment of uridine-diphosphate (UDP) sugars and their derivatives, which is consistent with their roles in protein and lipid glycosylation. Furthermore, targeted metabolomics validated SLC35A2 as the subcellular transporter for UDP-hexose. Finally, lipidomics analysis showed that phospholipids including phosphatidylcholine, phosphatidylinositol, and phosphatidylserine are the most abundant Golgi lipids and that glycosphingolipids are enriched in this compartment. Altogether, our work establishes a comprehensive molecular map of the human Golgi and provides a powerful method to study the Golgi with high precision in health and disease.
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Affiliation(s)
- Rotimi Fasimoye
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, United Kingdom
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Wentao Dong
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
- Department of Chemical Engineering, Stanford University, Stanford, CA94305
- Department of Genetics, Stanford University, Stanford, CA94305
- The Institute for Chemistry, Engineering & Medicine for Human Health, Stanford University, Stanford, CA94305
| | - Raja S. Nirujogi
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, United Kingdom
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Eshaan S. Rawat
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
- Department of Chemical Engineering, Stanford University, Stanford, CA94305
- Department of Genetics, Stanford University, Stanford, CA94305
- The Institute for Chemistry, Engineering & Medicine for Human Health, Stanford University, Stanford, CA94305
| | - Miharu Iguchi
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
- Department of Chemical Engineering, Stanford University, Stanford, CA94305
- Department of Genetics, Stanford University, Stanford, CA94305
- The Institute for Chemistry, Engineering & Medicine for Human Health, Stanford University, Stanford, CA94305
| | - Kwamina Nyame
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
- Department of Chemical Engineering, Stanford University, Stanford, CA94305
- Department of Genetics, Stanford University, Stanford, CA94305
- The Institute for Chemistry, Engineering & Medicine for Human Health, Stanford University, Stanford, CA94305
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
| | - Toan K. Phung
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, United Kingdom
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Enrico Bagnoli
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, United Kingdom
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Alan R. Prescott
- Dundee Imaging Facility, School of Life Sciences, University of Dundee, DundeeDD1 5EH, United Kingdom
| | - Dario R. Alessi
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, United Kingdom
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Monther Abu-Remaileh
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
- Department of Chemical Engineering, Stanford University, Stanford, CA94305
- Department of Genetics, Stanford University, Stanford, CA94305
- The Institute for Chemistry, Engineering & Medicine for Human Health, Stanford University, Stanford, CA94305
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9
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Gallen AF, Romero-Arias JR, Barrio RA, Hernandez-Machado A. Vesicle formation induced by thermal fluctuations. SOFT MATTER 2023; 19:2908-2918. [PMID: 37006200 DOI: 10.1039/d2sm01167k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The process of fission and vesicle formation depends on the geometry of the membrane that will split. For instance, a flat surface finds it difficult to form vesicles because of the lack of curved regions where to start the process. Here we show that vesicle formation can be promoted by temperature, by using a membrane phase field model with Gaussian curvature. We find a phase transition between fluctuating and vesiculation phases that depends on temperature, spontaneous curvature, and the ratio between bending and Gaussian moduli. We analysed the energy dynamical behaviour of these processes and found that the main driving ingredient is the Gaussian energy term, although the curvature energy term usually helps with the process as well. We also found that the chemical potential can be used to investigate the temperature of the system. Finally we address how temperature changes the condition for spontaneous vesiculation for all geometries, making it happen in a wider range of values of the Gaussian modulus.
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Affiliation(s)
- Andreu F Gallen
- Departament Fisica de la Materia Condensada, Universitat de Barcelona, E-08028 Barcelona, Spain.
| | - J Roberto Romero-Arias
- Instituto de Investigaciones en Matematicas Aplicadas y en Sistemas, Universidad Nacional Autonoma de Mexico, 01000 Ciudad de Mexico, Mexico
| | - Rafael A Barrio
- Instituto de Fisica, U.N.A.M., 01000, Ap. Postal 101000, Mexico D.F, Mexico
| | - Aurora Hernandez-Machado
- Departament Fisica de la Materia Condensada, Universitat de Barcelona, E-08028 Barcelona, Spain.
- Institute of Nanoscience and Nanotechnology (IN2UB), 08028 Barcelona, Spain
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10
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Dai D, He C, Wang S, Wang M, Guo N, Song P. Toward Personalized Interventions for Psoriasis Vulgaris: Molecular Subtyping of Patients by Using a Metabolomics Approach. Front Mol Biosci 2022; 9:945917. [PMID: 35928224 PMCID: PMC9343857 DOI: 10.3389/fmolb.2022.945917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/15/2022] [Indexed: 11/29/2022] Open
Abstract
Aim: Psoriasis vulgaris (PV) is a complicated autoimmune disease characterized by erythema of the skin and a lack of available cures. PV is associated with an increased risk of metabolic syndrome and cardiovascular disease, which are both mediated by the interaction between systemic inflammation and aberrant metabolism. However, whether there are differences in the lipid metabolism between different levels of severity of PV remains elusive. Hence, we explored the molecular evidence for the subtyping of PV according to alterations in lipid metabolism using serum metabolomics, with the idea that such subtyping may contribute to the development of personalized treatment. Methods: Patients with PV were recruited at a dermatology clinic and classified based on the presence of metabolic comorbidities and their Psoriasis Area and Severity Index (PASI) from January 2019 to November 2019. Age- and sex-matched healthy controls were recruited from the preventive health department of the same institution for comparison. We performed targeted metabolomic analyses of serum samples and determined the correlation between metabolite composition and PASI scores. Results: A total of 123 participants, 88 patients with PV and 35 healthy subjects, were enrolled in this study. The patients with PV were assigned to a “PVM group” (PV with metabolic comorbidities) or a “PV group” (PV without metabolic comorbidities) and further subdivided into a “mild PV” (MP, PASI <10) and a “severe PV” (SP, PASI ≥10) groups. Compared with the matched healthy controls, levels of 27 metabolites in the MP subgroup and 28 metabolites in the SP subgroup were found to be altered. Among these, SM (d16:0/17:1) and SM (d19:1/20:0) were positively correlated with the PASI in the MP subgroup, while Cer (d18:1/18:0), PC (18:0/22:4), and PC (20:0/22:4) were positively correlated with the PASI in the SP subgroup. In the PVM group, levels of 17 metabolites were increased, especially ceramides and phosphatidylcholine, compared with matched patients from the PV group. In addition, the correlation analysis indicated that Cer (d18:1/18:0) and SM (d16:1/16:1) were not only correlated with PASI but also has strongly positive correlations with biochemical indicators. Conclusion: The results of this study indicate that patients with PV at different severity levels have distinct metabolic profiles, and that metabolic disorders complicate the disease development. These findings will help us understand the pathological progression and establish strategies for the precision treatment of PV.
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Affiliation(s)
- Dan Dai
- Department of Dermatology, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chunyan He
- Department of Dermatology, Hubei Provincial Hospital of TCM, Wuhan, China
| | - Shuo Wang
- Department of Oncology, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Mei Wang
- Leiden University-European Center for Chinese Medicine and Natural Compounds, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
- SU BioMedicine, BioPartner Center 3, Leiden, Netherlands
- *Correspondence: Mei Wang, ; Na Guo, ; Ping Song,
| | - Na Guo
- Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, China
- *Correspondence: Mei Wang, ; Na Guo, ; Ping Song,
| | - Ping Song
- Department of Dermatology, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- *Correspondence: Mei Wang, ; Na Guo, ; Ping Song,
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11
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Ramazanov BR, Tran ML, von Blume J. Sending out molecules from the TGN. Curr Opin Cell Biol 2021; 71:55-62. [PMID: 33706234 PMCID: PMC8328904 DOI: 10.1016/j.ceb.2021.02.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/27/2021] [Accepted: 02/04/2021] [Indexed: 01/20/2023]
Abstract
The sorting of secreted cargo proteins and their export from the trans-Golgi network (TGN) remains an enigma in the field of membrane trafficking; although the sorting mechanisms of many transmembrane proteins have been well described. The sorting of secreted proteins at the TGN is crucial for the release of signaling factors, as well as extracellular matrix proteins. These proteins are required for cell-cell communication and integrity of an organism. Missecretion of these factors can cause diseases such as neurological disorders, autoimmune disease, or cancer. The major open question is how soluble proteins that are not associated with the membrane are packed into TGN derived transport carriers to facilitate their transport to the plasma membrane. Recent investigations have identified novel types of protein and lipid machinery that facilitate the packing of these molecules into a TGN derived vesicle. In addition, novel research has uncovered an exciting link between cargo sorting and export in which TGN structure and dynamics, as well as TGN/endoplasmic reticulum contact sites, play a significant role. Here, we have reviewed the progress made in our understanding of these processes.
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Affiliation(s)
- Bulat R Ramazanov
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Mai Ly Tran
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Julia von Blume
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.
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12
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The PKD-Dependent Biogenesis of TGN-to-Plasma Membrane Transport Carriers. Cells 2021; 10:cells10071618. [PMID: 34203456 PMCID: PMC8303525 DOI: 10.3390/cells10071618] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/14/2021] [Accepted: 06/24/2021] [Indexed: 01/30/2023] Open
Abstract
Membrane trafficking is essential for processing and transport of proteins and lipids and to establish cell compartmentation and tissue organization. Cells respond to their needs and control the quantity and quality of protein secretion accordingly. In this review, we focus on a particular membrane trafficking route from the trans-Golgi network (TGN) to the cell surface: protein kinase D (PKD)-dependent pathway for constitutive secretion mediated by carriers of the TGN to the cell surface (CARTS). Recent findings highlight the importance of lipid signaling by organelle membrane contact sites (MCSs) in this pathway. Finally, we discuss our current understanding of multiple signaling pathways for membrane trafficking regulation mediated by PKD, G protein-coupled receptors (GPCRs), growth factors, metabolites, and mechanosensors.
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13
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Lujan P, Campelo F. Should I stay or should I go? Golgi membrane spatial organization for protein sorting and retention. Arch Biochem Biophys 2021; 707:108921. [PMID: 34038703 DOI: 10.1016/j.abb.2021.108921] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/12/2021] [Accepted: 05/03/2021] [Indexed: 12/23/2022]
Abstract
The Golgi complex is the membrane-bound organelle that lies at the center of the secretory pathway. Its main functions are to maintain cellular lipid homeostasis, to orchestrate protein processing and maturation, and to mediate protein sorting and export. These functions are not independent of one another, and they all require that the membranes of the Golgi complex have a well-defined biochemical composition. Importantly, a finely-regulated spatiotemporal organization of the Golgi membrane components is essential for the correct performance of the organelle. In here, we review our current mechanistic and molecular understanding of how Golgi membranes are spatially organized in the lateral and axial directions to fulfill their functions. In particular, we highlight the current evidence and proposed models of intra-Golgi transport, as well as the known mechanisms for the retention of Golgi residents and for the sorting and export of transmembrane cargo proteins. Despite the controversies, conflicting evidence, clashes between models, and technical limitations, the field has moved forward and we have gained extensive knowledge in this fascinating topic. However, there are still many important questions that remain to be completely answered. We hope that this review will help boost future investigations on these issues.
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Affiliation(s)
- Pablo Lujan
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860, Barcelona, Spain.
| | - Felix Campelo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860, Barcelona, Spain.
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14
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Wakana Y, Hayashi K, Nemoto T, Watanabe C, Taoka M, Angulo-Capel J, Garcia-Parajo MF, Kumata H, Umemura T, Inoue H, Arasaki K, Campelo F, Tagaya M. The ER cholesterol sensor SCAP promotes CARTS biogenesis at ER-Golgi membrane contact sites. J Cell Biol 2021; 220:211521. [PMID: 33156328 PMCID: PMC7654440 DOI: 10.1083/jcb.202002150] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 09/15/2020] [Accepted: 10/12/2020] [Indexed: 12/13/2022] Open
Abstract
In response to cholesterol deprivation, SCAP escorts SREBP transcription factors from the endoplasmic reticulum to the Golgi complex for their proteolytic activation, leading to gene expression for cholesterol synthesis and uptake. Here, we show that in cholesterol-fed cells, ER-localized SCAP interacts through Sac1 phosphatidylinositol 4-phosphate (PI4P) phosphatase with a VAP-OSBP complex, which mediates counter-transport of ER cholesterol and Golgi PI4P at ER-Golgi membrane contact sites (MCSs). SCAP knockdown inhibited the turnover of PI4P, perhaps due to a cholesterol transport defect, and altered the subcellular distribution of the VAP-OSBP complex. As in the case of perturbation of lipid transfer complexes at ER-Golgi MCSs, SCAP knockdown inhibited the biogenesis of the trans-Golgi network-derived transport carriers CARTS, which was reversed by expression of wild-type SCAP or a Golgi transport-defective mutant, but not of cholesterol sensing-defective mutants. Altogether, our findings reveal a new role for SCAP under cholesterol-fed conditions in the facilitation of CARTS biogenesis via ER-Golgi MCSs, depending on the ER cholesterol.
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Affiliation(s)
- Yuichi Wakana
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Kaito Hayashi
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Takumi Nemoto
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Chiaki Watanabe
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Masato Taoka
- Faculty of Science, Department of Chemistry, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Jessica Angulo-Capel
- Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Maria F Garcia-Parajo
- Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Hidetoshi Kumata
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Tomonari Umemura
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Hiroki Inoue
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Kohei Arasaki
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Felix Campelo
- Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Mitsuo Tagaya
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
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15
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Anastasia I, Ilacqua N, Raimondi A, Lemieux P, Ghandehari-Alavijeh R, Faure G, Mekhedov SL, Williams KJ, Caicci F, Valle G, Giacomello M, Quiroga AD, Lehner R, Miksis MJ, Toth K, de Aguiar Vallim TQ, Koonin EV, Scorrano L, Pellegrini L. Mitochondria-rough-ER contacts in the liver regulate systemic lipid homeostasis. Cell Rep 2021; 34:108873. [PMID: 33730569 DOI: 10.1016/j.celrep.2021.108873] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/18/2020] [Accepted: 02/23/2021] [Indexed: 12/12/2022] Open
Abstract
Contacts between organelles create microdomains that play major roles in regulating key intracellular activities and signaling pathways, but whether they also regulate systemic functions remains unknown. Here, we report the ultrastructural organization and dynamics of the inter-organellar contact established by sheets of curved rough endoplasmic reticulum closely wrapped around the mitochondria (wrappER). To elucidate the in vivo function of this contact, mouse liver fractions enriched in wrappER-associated mitochondria are analyzed by transcriptomics, proteomics, and lipidomics. The biochemical signature of the wrappER points to a role in the biogenesis of very-low-density lipoproteins (VLDL). Altering wrappER-mitochondria contacts curtails VLDL secretion and increases hepatic fatty acids, lipid droplets, and neutral lipid content. Conversely, acute liver-specific ablation of Mttp, the most upstream regulator of VLDL biogenesis, recapitulates this hepatic dyslipidemia phenotype and promotes remodeling of the wrappER-mitochondria contact. The discovery that liver wrappER-mitochondria contacts participate in VLDL biology suggests an involvement of inter-organelle contacts in systemic lipid homeostasis.
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Affiliation(s)
- Irene Anastasia
- Graduate Program in Neuroscience, Faculty of Medicine, Laval University, Quebec, QC, Canada; Mitochondria Biology Laboratory, Brain Research Center, Quebec, QC, Canada
| | - Nicolò Ilacqua
- Graduate Program in Neuroscience, Faculty of Medicine, Laval University, Quebec, QC, Canada; Mitochondria Biology Laboratory, Brain Research Center, Quebec, QC, Canada
| | - Andrea Raimondi
- Experimental Imaging Center, San Raffaele Scientific Institute, Milan, Italy
| | - Philippe Lemieux
- Mitochondria Biology Laboratory, Brain Research Center, Quebec, QC, Canada
| | | | - Guilhem Faure
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; National Center for Biotechnology Information, NLM, NIH, Bethesda, MD, USA
| | - Sergei L Mekhedov
- National Center for Biotechnology Information, NLM, NIH, Bethesda, MD, USA
| | - Kevin J Williams
- Department of Biological Chemistry, Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | | | - Giorgio Valle
- Department of Biology, University of Padua, Padua, Italy
| | | | - Ariel D Quiroga
- Instituto de Fisiología Experimental, CONICET, UNR, Rosario, Argentina; Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Richard Lehner
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Michael J Miksis
- Department of Engineering Science and Applied Mathematics, Northwestern University, Evanston, IL, USA
| | - Katalin Toth
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Thomas Q de Aguiar Vallim
- Department of Biological Chemistry, Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Medicine, Division of Cardiology, UCLA, Los Angeles, CA, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, NLM, NIH, Bethesda, MD, USA
| | - Luca Scorrano
- Department of Biology, University of Padua, Padua, Italy
| | - Luca Pellegrini
- Mitochondria Biology Laboratory, Brain Research Center, Quebec, QC, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec, QC, Canada.
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16
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Lujan P, Angulo-Capel J, Chabanon M, Campelo F. Interorganelle communication and membrane shaping in the early secretory pathway. Curr Opin Cell Biol 2021; 71:95-102. [PMID: 33711785 DOI: 10.1016/j.ceb.2021.01.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/25/2021] [Accepted: 01/30/2021] [Indexed: 01/02/2023]
Abstract
Biomolecules in the secretory pathway use membrane trafficking for reaching their final intracellular destination or for secretion outside the cell. This highly dynamic and multipartite process involves different organelles that communicate to one another while maintaining their identity, shape, and function. Recent studies unraveled new mechanisms of interorganelle communication that help organize the early secretory pathway. We highlight how the spatial proximity between endoplasmic reticulum (ER) exit sites and early Golgi elements provides novel means of ER-Golgi communication for ER export. We also review recent findings on how membrane contact sites between the ER and the trans-Golgi membranes can sustain anterograde traffic out of the Golgi complex.
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Affiliation(s)
- Pablo Lujan
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Barcelona, Spain
| | - Jessica Angulo-Capel
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Barcelona, Spain
| | - Morgan Chabanon
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Barcelona, Spain; Universitat Politècnica de Catalunya-BarcelonaTech, E-08034, Barcelona, Spain
| | - Felix Campelo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Barcelona, Spain.
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17
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Raote I, Chabanon M, Walani N, Arroyo M, Garcia-Parajo MF, Malhotra V, Campelo F. A physical mechanism of TANGO1-mediated bulky cargo export. eLife 2020; 9:e59426. [PMID: 33169667 PMCID: PMC7704110 DOI: 10.7554/elife.59426] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/09/2020] [Indexed: 01/08/2023] Open
Abstract
The endoplasmic reticulum (ER)-resident protein TANGO1 assembles into a ring around ER exit sites (ERES), and links procollagens in the ER lumen to COPII machinery, tethers, and ER-Golgi intermediate compartment (ERGIC) in the cytoplasm (Raote et al., 2018). Here, we present a theoretical approach to investigate the physical mechanisms of TANGO1 ring assembly and how COPII polymerization, membrane tension, and force facilitate the formation of a transport intermediate for procollagen export. Our results indicate that a TANGO1 ring, by acting as a linactant, stabilizes the open neck of a nascent COPII bud. Elongation of such a bud into a transport intermediate commensurate with bulky procollagens is then facilitated by two complementary mechanisms: (i) by relieving membrane tension, possibly by TANGO1-mediated fusion of retrograde ERGIC membranes and (ii) by force application. Altogether, our theoretical approach identifies key biophysical events in TANGO1-driven procollagen export.
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Affiliation(s)
- Ishier Raote
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Morgan Chabanon
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Politècnica de Catalunya-BarcelonaTechBarcelonaSpain
| | - Nikhil Walani
- Universitat Politècnica de Catalunya-BarcelonaTechBarcelonaSpain
| | - Marino Arroyo
- Universitat Politècnica de Catalunya-BarcelonaTechBarcelonaSpain
- Institute for Bioengineering of Catalonia, The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Centre Internacional de Mètodes Numèrics en Enginyeria (CIMNE)BarcelonaSpain
| | - Maria F Garcia-Parajo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and TechnologyBarcelonaSpain
- ICREABarcelonaSpain
| | - Vivek Malhotra
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
- ICREABarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
| | - Felix Campelo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and TechnologyBarcelonaSpain
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18
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Bolmatov D, Carrillo JMY, Sumpter BG, Katsaras J, Lavrentovich MO. Double membrane formation in heterogeneous vesicles. SOFT MATTER 2020; 16:8806-8817. [PMID: 33026033 DOI: 10.1039/d0sm01167c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Lipids are capable of forming a variety of structures, including multi-lamellar vesicles. Layered lipid membranes are found in cell organelles, such as autophagosomes and mitochondria. Here, we present a mechanism for the formation of a double-walled vesicle (i.e., two lipid bilayers) from a unilamellar vesicle through the partitioning and phase separation of a small molecule. Using molecular dynamics simulations, we show that double membrane formation proceeds via a nucleation and growth process - i.e., after a critical concentration of the small molecules, a patch of double membrane nucleates and grows to cover the entire vesicle. We discuss the implications of this mechanism and theoretical approaches for understanding the evolution and formation of double membranes.
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Affiliation(s)
- Dima Bolmatov
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. and Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, USA. and Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Jan-Michael Y Carrillo
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. and Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Bobby G Sumpter
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. and Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - John Katsaras
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. and Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, USA. and Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Maxim O Lavrentovich
- Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, USA. and Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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19
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Sakai Y, Koyama-Honda I, Tachikawa M, Knorr RL, Mizushima N. Modeling Membrane Morphological Change during Autophagosome Formation. iScience 2020; 23:101466. [PMID: 32891055 PMCID: PMC7479497 DOI: 10.1016/j.isci.2020.101466] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/21/2020] [Accepted: 08/12/2020] [Indexed: 11/23/2022] Open
Abstract
Autophagy is an intracellular degradation process that is mediated by de novo formation of autophagosomes. Autophagosome formation involves dynamic morphological changes; a disk-shaped membrane cisterna grows, bends to become a cup-shaped structure, and finally develops into a spherical autophagosome. We have constructed a theoretical model that integrates the membrane morphological change and entropic partitioning of putative curvature generators, which we have used to investigate the autophagosome formation process quantitatively. We show that the membrane curvature and the distribution of the curvature generators stabilize disk- and cup-shaped intermediate structures during autophagosome formation, which is quantitatively consistent with in vivo observations. These results suggest that various autophagy proteins with membrane curvature-sensing properties control morphological change by stabilizing these intermediate structures. Our model provides a framework for understanding autophagosome formation.
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Affiliation(s)
- Yuji Sakai
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS) Program, RIKEN, Wako, Saitama 351-0198, Japan
| | - Ikuko Koyama-Honda
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masashi Tachikawa
- Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS) Program, RIKEN, Wako, Saitama 351-0198, Japan
- Institute for Frontier Life and Medical Sciences, Kyoto University, Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507 Japan
| | - Roland L. Knorr
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Max Planck Institute of Colloids and Interfaces, Department of Theory & Bio-Systems, 14424 Potsdam, Germany
- Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology, 14424 Potsdam, Germany
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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20
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Bassaganyas L, Popa SJ, Horlbeck M, Puri C, Stewart SE, Campelo F, Ashok A, Butnaru CM, Brouwers N, Heydari K, Ripoche J, Weissman J, Rubinsztein DC, Schekman R, Malhotra V, Moreau K, Villeneuve J. New factors for protein transport identified by a genome-wide CRISPRi screen in mammalian cells. J Cell Biol 2019; 218:3861-3879. [PMID: 31488582 PMCID: PMC6829651 DOI: 10.1083/jcb.201902028] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 06/16/2019] [Accepted: 08/12/2019] [Indexed: 12/11/2022] Open
Abstract
Protein and membrane trafficking pathways are critical for cell and tissue homeostasis. Traditional genetic and biochemical approaches have shed light on basic principles underlying these processes. However, the list of factors required for secretory pathway function remains incomplete, and mechanisms involved in their adaptation poorly understood. Here, we present a powerful strategy based on a pooled genome-wide CRISPRi screen that allowed the identification of new factors involved in protein transport. Two newly identified factors, TTC17 and CCDC157, localized along the secretory pathway and were found to interact with resident proteins of ER-Golgi membranes. In addition, we uncovered that upon TTC17 knockdown, the polarized organization of Golgi cisternae was altered, creating glycosylation defects, and that CCDC157 is an important factor for the fusion of transport carriers to Golgi membranes. In conclusion, our work identified and characterized new actors in the mechanisms of protein transport and secretion and opens stimulating perspectives for the use of our platform in physiological and pathological contexts.
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Affiliation(s)
- Laia Bassaganyas
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, and Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
| | - Stephanie J Popa
- University of Cambridge Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Max Horlbeck
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA
| | - Claudia Puri
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Sarah E Stewart
- University of Cambridge Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Felix Campelo
- Institut de Ciencies Fotoniques, Barcelona Institute of Science and Technology, Castelldefels, Spain
| | - Anupama Ashok
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Cristian M Butnaru
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Photonic Investigations, Center of Advanced Laser Technologies, National Institute for Laser, Plasma and Radiation Physics, Magurele, Romania
| | - Nathalie Brouwers
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Jean Ripoche
- Institut National de la Sante et de la Recherche Medicale U1026, Université de Bordeaux, Bordeaux, France
| | - Jonathan Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA
| | - David C Rubinsztein
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
- UK Dementia Research Institute, Cambridge, UK
| | - Randy Schekman
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA
| | - Vivek Malhotra
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Kevin Moreau
- University of Cambridge Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Julien Villeneuve
- University of Cambridge Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
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21
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Chabanon M, Rangamani P. Geometric coupling of helicoidal ramps and curvature-inducing proteins in organelle membranes. J R Soc Interface 2019; 16:20190354. [PMID: 31480932 DOI: 10.1098/rsif.2019.0354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Cellular membranes display an incredibly diverse range of shapes, both in the plasma membrane and at membrane bound organelles. These morphologies are intricately related to cellular functions, enabling and regulating fundamental membrane processes. However, the biophysical mechanisms at the origin of these complex geometries are not fully understood from the standpoint of membrane-protein coupling. In this study, we focused on a minimal model of helicoidal ramps representative of specialized endoplasmic reticulum compartments. Given a helicoidal membrane geometry, we asked what is the distribution of spontaneous curvature required to maintain this shape at mechanical equilibrium? Based on the Helfrich energy of elastic membranes with spontaneous curvature, we derived the shape equation for minimal surfaces, and applied it to helicoids. We showed the existence of switches in the sign of the spontaneous curvature associated with geometric variations of the membrane structures. Furthermore, for a prescribed gradient of spontaneous curvature along the exterior boundaries, we identified configurations of the helicoidal ramps that are confined between two infinitely large energy barriers. Overall our results suggest possible mechanisms for geometric control of helicoidal ramps in membrane organelles based on curvature-inducing proteins.
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Affiliation(s)
- Morgan Chabanon
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla CA, USA
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla CA, USA
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22
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Welch LG, Munro S. A tale of short tails, through thick and thin: investigating the sorting mechanisms of Golgi enzymes. FEBS Lett 2019; 593:2452-2465. [DOI: 10.1002/1873-3468.13553] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/18/2019] [Accepted: 07/19/2019] [Indexed: 01/28/2023]
Affiliation(s)
- Lawrence G. Welch
- MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge UK
| | - Sean Munro
- MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge UK
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23
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Jirsová D, Füssy Z, Richtová J, Gruber A, Oborník M. Morphology, Ultrastructure, and Mitochondrial Genome of the Marine Non-Photosynthetic Bicosoecid Cafileria marina Gen. et sp. nov. Microorganisms 2019; 7:microorganisms7080240. [PMID: 31387253 PMCID: PMC6723347 DOI: 10.3390/microorganisms7080240] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/25/2019] [Accepted: 08/01/2019] [Indexed: 12/16/2022] Open
Abstract
In this paper, we describe a novel bacteriophagous biflagellate, Cafileria marina with two smooth flagellae, isolated from material collected from a rock surface in the Kvernesfjorden (Norway). This flagellate was characterized by scanning and transmission electron microscopy, fluorescence, and light microscopy. The sequence of the small subunit ribosomal RNA gene (18S) was used as a molecular marker for determining the phylogenetic position of this organism. Apart from the nuclear ribosomal gene, the whole mitochondrial genome was sequenced, assembled, and annotated. Morphological observations show that the newly described flagellate shares key ultrastructural characters with representatives of the family Bicosoecida (Heterokonta). Intriguingly, mitochondria of C. marina frequently associate with its nucleus through an electron-dense disc at the boundary of the two compartments. The function of this association remains unclear. Phylogenetic analyses corroborate the morphological data and place C. marina with other sequence data of representatives from the family Bicosoecida. We describe C. marina as a new species from a new genus in this family.
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Affiliation(s)
- Dagmar Jirsová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Zoltán Füssy
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Jitka Richtová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Ansgar Gruber
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Miroslav Oborník
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic.
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic.
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24
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von Blume J, Hausser A. Lipid-dependent coupling of secretory cargo sorting and trafficking at the trans-Golgi network. FEBS Lett 2019; 593:2412-2427. [PMID: 31344259 PMCID: PMC8048779 DOI: 10.1002/1873-3468.13552] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/10/2019] [Accepted: 07/22/2019] [Indexed: 12/17/2022]
Abstract
In eukaryotic cells, the trans-Golgi network (TGN) serves as a platform for secretory cargo sorting and trafficking. In recent years, it has become evident that a complex network of lipid–lipid and lipid–protein interactions contributes to these key functions. This review addresses the role of lipids at the TGN with a particular emphasis on sphingolipids and diacylglycerol. We further highlight how these lipids couple secretory cargo sorting and trafficking for spatiotemporal coordination of protein transport to the plasma membrane.
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Affiliation(s)
- Julia von Blume
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA.,Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Angelika Hausser
- Institute of Cell Biology and Immunology, University of Stuttgart, Germany.,Stuttgart Research Center Systems Biology, University of Stuttgart, Germany
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25
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Deng Y, Pakdel M, Blank B, Sundberg EL, Burd CG, von Blume J. Activity of the SPCA1 Calcium Pump Couples Sphingomyelin Synthesis to Sorting of Secretory Proteins in the Trans-Golgi Network. Dev Cell 2018; 47:464-478.e8. [PMID: 30393074 PMCID: PMC6261503 DOI: 10.1016/j.devcel.2018.10.012] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 08/29/2018] [Accepted: 10/05/2018] [Indexed: 12/24/2022]
Abstract
How the principal functions of the Golgi apparatus-protein processing, lipid synthesis, and sorting of macromolecules-are integrated to constitute cargo-specific trafficking pathways originating from the trans-Golgi network (TGN) is unknown. Here, we show that the activity of the Golgi localized SPCA1 calcium pump couples sorting and export of secreted proteins to synthesis of new lipid in the TGN membrane. A secreted Ca2+-binding protein, Cab45, constitutes the core component of a Ca2+-dependent, oligomerization-driven sorting mechanism whereby secreted proteins bound to Cab45 are packaged into a TGN-derived vesicular carrier whose membrane is enriched in sphingomyelin, a lipid implicated in TGN-to-cell surface transport. SPCA1 activity is controlled by the sphingomyelin content of the TGN membrane, such that local sphingomyelin synthesis promotes Ca2+ flux into the lumen of the TGN, which drives secretory protein sorting and export, thereby establishing a protein- and lipid-specific secretion pathway.
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Affiliation(s)
- Yongqiang Deng
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Mehrshad Pakdel
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Birgit Blank
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Emma L Sundberg
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Christopher G Burd
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.
| | - Julia von Blume
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
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26
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Mamode Cassim A, Gouguet P, Gronnier J, Laurent N, Germain V, Grison M, Boutté Y, Gerbeau-Pissot P, Simon-Plas F, Mongrand S. Plant lipids: Key players of plasma membrane organization and function. Prog Lipid Res 2018; 73:1-27. [PMID: 30465788 DOI: 10.1016/j.plipres.2018.11.002] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/07/2018] [Accepted: 11/09/2018] [Indexed: 12/29/2022]
Abstract
The plasma membrane (PM) is the biological membrane that separates the interior of all cells from the outside. The PM is constituted of a huge diversity of proteins and lipids. In this review, we will update the diversity of molecular species of lipids found in plant PM. We will further discuss how lipids govern global properties of the plant PM, explaining that plant lipids are unevenly distributed and are able to organize PM in domains. From that observation, it emerges a complex picture showing a spatial and multiscale segregation of PM components. Finally, we will discuss how lipids are key players in the function of PM in plants, with a particular focus on plant-microbe interaction, transport and hormone signaling, abiotic stress responses, plasmodesmata function. The last chapter is dedicated to the methods that the plant membrane biology community needs to develop to get a comprehensive understanding of membrane organization in plants.
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Affiliation(s)
- Adiilah Mamode Cassim
- Laboratoire de Biogenèse Membranaire (LBM), CNRS, University of Bordeaux, UMR 5200, F-33882 Villenave d'Ornon, France
| | - Paul Gouguet
- Laboratoire de Biogenèse Membranaire (LBM), CNRS, University of Bordeaux, UMR 5200, F-33882 Villenave d'Ornon, France
| | - Julien Gronnier
- Laboratoire de Biogenèse Membranaire (LBM), CNRS, University of Bordeaux, UMR 5200, F-33882 Villenave d'Ornon, France
| | - Nelson Laurent
- Agroécologie, AgroSup Dijon, INRA, University of Bourgogne Franche-Comté, F-21000 Dijon, ERL 6003 CNRS, Dijon, France
| | - Véronique Germain
- Laboratoire de Biogenèse Membranaire (LBM), CNRS, University of Bordeaux, UMR 5200, F-33882 Villenave d'Ornon, France
| | - Magali Grison
- Laboratoire de Biogenèse Membranaire (LBM), CNRS, University of Bordeaux, UMR 5200, F-33882 Villenave d'Ornon, France
| | - Yohann Boutté
- Laboratoire de Biogenèse Membranaire (LBM), CNRS, University of Bordeaux, UMR 5200, F-33882 Villenave d'Ornon, France
| | - Patricia Gerbeau-Pissot
- Agroécologie, AgroSup Dijon, INRA, University of Bourgogne Franche-Comté, F-21000 Dijon, ERL 6003 CNRS, Dijon, France
| | - Françoise Simon-Plas
- Agroécologie, AgroSup Dijon, INRA, University of Bourgogne Franche-Comté, F-21000 Dijon, ERL 6003 CNRS, Dijon, France.
| | - Sébastien Mongrand
- Laboratoire de Biogenèse Membranaire (LBM), CNRS, University of Bordeaux, UMR 5200, F-33882 Villenave d'Ornon, France.
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27
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Mizushima N. A brief history of autophagy from cell biology to physiology and disease. Nat Cell Biol 2018; 20:521-527. [PMID: 29686264 DOI: 10.1038/s41556-018-0092-5] [Citation(s) in RCA: 459] [Impact Index Per Article: 76.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 03/20/2018] [Indexed: 02/06/2023]
Abstract
The field of autophagy research has developed rapidly since the first description of the process in the 1960s and the identification of autophagy genes in the 1990s. Autophagy is now increasingly studied at the level of organismal pathophysiology and is being connected to the medical sciences. This Historical Perspective describes a brief history of autophagy and discusses unanswered cell biological questions in the field.
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Affiliation(s)
- Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan.
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