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Ferreira JV, Ahmed Y, Heunis T, Jain A, Johnson E, Räschle M, Ernst R, Vanni S, Carvalho P. Pex30-dependent membrane contact sites maintain ER lipid homeostasis. J Cell Biol 2025; 224:e202409039. [PMID: 40407417 PMCID: PMC12101078 DOI: 10.1083/jcb.202409039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2024] [Revised: 01/28/2025] [Accepted: 03/12/2025] [Indexed: 05/26/2025] Open
Abstract
In eukaryotic cells, communication between organelles and the coordination of their activities depend on membrane contact sites (MCS). How MCS are regulated under the dynamic cellular environment remains poorly understood. Here, we investigate how Pex30, a membrane protein localized to the endoplasmic reticulum (ER), regulates multiple MCS in budding yeast. We show that Pex30 is critical for the integrity of ER MCS with peroxisomes and vacuoles. This requires the dysferlin (DysF) domain on the Pex30 cytosolic tail. This domain binds to phosphatidic acid (PA) both in vitro and in silico, and it is important for normal PA metabolism in vivo. The DysF domain is evolutionarily conserved and may play a general role in PA homeostasis across eukaryotes. We further show that the ER-vacuole MCS requires a Pex30 C-terminal domain of unknown function and that its activity is controlled by phosphorylation in response to metabolic cues. These findings provide new insights into the dynamic nature of MCS and their coordination with cellular metabolism.
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Affiliation(s)
| | - Yara Ahmed
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Tiaan Heunis
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Aamna Jain
- Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
- Preclinical Center for Molecular Signaling, Saarland University, Homburg, Germany
| | - Errin Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Markus Räschle
- Department of Molecular Genetics, TU Kaiserslautern, Kaiserslautern, Germany
| | - Robert Ernst
- Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
- Preclinical Center for Molecular Signaling, Saarland University, Homburg, Germany
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss National Center for Competence in Research Bio-inspired Materials, University of Fribourg, Fribourg, Switzerland
| | - Pedro Carvalho
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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2
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Yu X, Mousley CJ, Bankaitis VA, Iyer P. A budding yeast-centric view of oxysterol binding protein family function. Adv Biol Regul 2025; 95:101061. [PMID: 39613716 DOI: 10.1016/j.jbior.2024.101061] [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: 11/18/2024] [Accepted: 11/21/2024] [Indexed: 12/01/2024]
Abstract
The Trans Golgi Network (TGN)/endosomal system is a sorting center for cargo brought via the anterograde secretory pathway and the endocytic pathway that internalizes material from the plasma membrane. As many of the cargo that transit this central trafficking hub are components of key homeostatic signaling pathways, TGN/endosomes define a critical signaling hub for cellular growth control. A particularly interesting yet incompletely understood aspect of regulation of TGN/endosome function is control of this system by two families of lipid exchange/lipid transfer proteins. The phosphatidylinositol transfer proteins promote pro-trafficking phosphoinositide (i.e. phosphatidylinositol-4-phosphate) signaling pathways whereas proteins of the oxysterol binding protein family play reciprocal roles in antagonizing those arms of phosphoinositide signaling. The precise mechanisms for how these lipid binding proteins execute their functions remain to be resolved. Moreover, information regarding the coupling of individual members of the oxysterol binding protein family to specific biological activities is particularly sparse. Herein, we review what is being learned regarding functions of the oxysterol binding protein family in the yeast model system. Focus is primarily directed at a discussion of the Kes1/Osh4 protein for which the most information is available.
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Affiliation(s)
- Xiaohan Yu
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Carl J Mousley
- School of Biomedical Sciences, Curtin Health Innovation Research Institute (CHIRI), Faculty of Health Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Vytas A Bankaitis
- Department of Cell Biology and Genetics, Texas A&M Health Science Center, College Station, TX, 77843, USA; Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA.
| | - Prasanna Iyer
- Department of Cell Biology and Genetics, Texas A&M Health Science Center, College Station, TX, 77843, USA.
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3
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Hamaï A, Drin G. Specificity of lipid transfer proteins: An in vitro story. Biochimie 2024; 227:85-110. [PMID: 39304019 DOI: 10.1016/j.biochi.2024.09.007] [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: 06/04/2024] [Revised: 09/06/2024] [Accepted: 09/17/2024] [Indexed: 09/22/2024]
Abstract
Lipids, which are highly diverse, are finely distributed between organelle membranes and the plasma membrane (PM) of eukaryotic cells. As a result, each compartment has its own lipid composition and molecular identity, which is essential for the functional fate of many proteins. This distribution of lipids depends on two main processes: lipid synthesis, which takes place in different subcellular regions, and the transfer of these lipids between and across membranes. This review will discuss the proteins that carry lipids throughout the cytosol, called LTPs (Lipid Transfer Proteins). More than the modes of action or biological roles of these proteins, we will focus on the in vitro strategies employed during the last 60 years to address a critical question: What are the lipid ligands of these LTPs? We will describe the extent to which these strategies, combined with structural data and investigations in cells, have made it possible to discover proteins, namely ORPs, Sec14, PITPs, STARDs, Ups/PRELIs, START-like, SMP-domain containing proteins, and bridge-like LTPs, which compose some of the main eukaryotic LTP families, and their lipid ligands. We will see how these approaches have played a central role in cell biology, showing that LTPs can connect distant metabolic branches, modulate the composition of cell membranes, and even create new subcellular compartments.
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Affiliation(s)
- Amazigh Hamaï
- Université Côte d'Azur, CNRS and Inserm, Institut de Pharmacologie Moléculaire et Cellulaire, UMR 7275, 660 route des lucioles, 06560, Valbonne Sophia Antipolis, France
| | - Guillaume Drin
- Université Côte d'Azur, CNRS and Inserm, Institut de Pharmacologie Moléculaire et Cellulaire, UMR 7275, 660 route des lucioles, 06560, Valbonne Sophia Antipolis, France.
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4
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Samardak K, Bâcle J, Moriel-Carretero M. Behind the stoNE wall: A fervent activity for nuclear lipids. Biochimie 2024; 227:53-84. [PMID: 39111564 DOI: 10.1016/j.biochi.2024.08.002] [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: 04/09/2024] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 09/27/2024]
Abstract
The four main types of biomolecules are nucleic acids, proteins, carbohydrates and lipids. The knowledge about their respective interactions is as important as the individual understanding of each of them. However, while, for example, the interaction of proteins with the other three groups is extensively studied, that of nucleic acids and lipids is, in comparison, very poorly explored. An iconic paradigm of physical (and likely functional) proximity between DNA and lipids is the case of the genomic DNA in eukaryotes: enclosed within the nucleus by two concentric lipid bilayers, the wealth of implications of this interaction, for example in genome stability, remains underassessed. Nuclear lipid-related phenotypes have been observed for 50 years, yet in most cases kept as mere anecdotical descriptions. In this review, we will bring together the evidence connecting lipids with both the nuclear envelope and the nucleoplasm, and will make critical analyses of these descriptions. Our exploration establishes a scenario in which lipids irrefutably play a role in nuclear homeostasis.
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Affiliation(s)
- Kseniya Samardak
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM) UMR5237, Université de Montpellier, Centre National de La Recherche Scientifique, 34293 Montpellier Cedex 5, France
| | - Janélie Bâcle
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM) UMR5237, Université de Montpellier, Centre National de La Recherche Scientifique, 34293 Montpellier Cedex 5, France
| | - María Moriel-Carretero
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM) UMR5237, Université de Montpellier, Centre National de La Recherche Scientifique, 34293 Montpellier Cedex 5, France.
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5
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Manik MIN, Tasnin MN, Takuma T, Ushimaru T. The yeast VAPs Scs2 and Scs22 are required for NVJ integrity and micronucleophagy. Biochem Biophys Res Commun 2024; 734:150628. [PMID: 39232457 DOI: 10.1016/j.bbrc.2024.150628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Revised: 08/23/2024] [Accepted: 08/29/2024] [Indexed: 09/06/2024]
Abstract
Microautophagy degrades cargos in the vacuole by direct engulfment of the vacuolar membrane. Micronucleophagy selectively degrades a portion of the nucleus in budding yeast. The vacuole contacts the nucleus via the nucleus-vacuole junction (NVJ), and in micronucleophagy a portion of the nucleus containing nucleolar proteins is made to protrude into the vacuole at the NVJ, followed by abscission and degradation. Microautophagy and micronucleophagy are induced by inactivation of target of rapamycin complex 1 (TORC1) protein kinase after nutrient starvation. Here, we show that the VAMP-associated proteins (VAPs) Scs2 and its paralog Scs22 are required for NVJ integrity and micronucleophagic degradation of nucleolar proteins. On the other hand, nucleolar dynamics prerequisite for micronucleophagy were not impaired in VAP mutant cells. Finally, yeast VAPs were critical for viability during prolonged nutrient starvation. This study sheds light on the emerging role of VAP in adaptation in responses to nutrient starvation.
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Affiliation(s)
- Md Imran Nur Manik
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan
| | - Most Naoshia Tasnin
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan
| | - Tsuneyuki Takuma
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan
| | - Takashi Ushimaru
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan; Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan; Research Institute of Green Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan.
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6
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Yuan H, Yang H, Gao Y, Zhang J, Ren J, Liu X, Li Y, Li Z, Zhao B, Fan Z. Discovery of Novel Spiropiperidinyl-α-methylene-γ-butyrolactones as Antifungal and Antitoxin Agents Targeting Oxysterol Binding Protein. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:15474-15486. [PMID: 38949855 DOI: 10.1021/acs.jafc.4c02848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Corn ear rot and fumonisin caused by Fusarium verticillioides pose a serious threat to food security. To find more highly active fungicidal and antitoxic candidates with structure diversity based on naturally occurring lead xanthatin, a series of novel spiropiperidinyl-α-methylene-γ-butyrolactones were rationally designed and synthesized. The in vitro bioassay results indicated that compound 7c showed broad-spectrum in vitro activity with EC50 values falling from 3.51 to 24.10 μg/mL against Rhizoctonia solani and Alternaria solani, which was more active than the positive controls xanthatin and oxathiapiprolin. In addition, compound 7c also showed good antitoxic efficacy against fumonisin with a 48% inhibition rate even at a concentration of 20 μg/mL. Fluorescence quenching and the molecular docking validated both 7c and oxathiapiprolin targeting at FvoshC. RNA sequencing analysis discovered that FUM gene cluster and protein processing in endoplasmic reticulum were downregulated. Our studies have discovered spiropiperidinyl-α-methylene-γ-butyrolactone as a novel FvoshC target-based scaffold for fungicide lead with antitoxin activity.
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Affiliation(s)
- Haolin Yuan
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Hongwei Yang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Yang Gao
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Jin Zhang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Jinzhou Ren
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Xiaoyu Liu
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Yixiao Li
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Zhengming Li
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Bin Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding 071001, P. R. China
| | - Zhijin Fan
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
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7
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Laframboise SJ, Deneault LF, Denoncourt A, Downey M, Baetz K. Uncovering the Role of the Yeast Lysine Acetyltransferase NuA4 in the Regulation of Nuclear Shape and Lipid Metabolism. Mol Cell Biol 2024; 44:273-288. [PMID: 38961766 PMCID: PMC11253884 DOI: 10.1080/10985549.2024.2366206] [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: 10/16/2023] [Accepted: 05/19/2024] [Indexed: 07/05/2024] Open
Abstract
Here, we report a novel role for the yeast lysine acetyltransferase NuA4 in regulating phospholipid availability for organelle morphology. Disruption of the NuA4 complex results in 70% of cells displaying nuclear deformations and nearly 50% of cells exhibiting vacuolar fragmentation. Cells deficient in NuA4 also show severe defects in the formation of nuclear-vacuole junctions (NJV), as well as a decrease in piecemeal microautophagy of the nucleus (PMN). To determine the cause of these defects we focused on Pah1, an enzyme that converts phosphatidic acid into diacylglycerol, favoring accumulation of lipid droplets over phospholipids that are used for membrane expansion. NuA4 subunit Eaf1 was required for Pah1 localization to the inner nuclear membrane and artificially tethering of Pah1 to the nuclear membrane rescued nuclear deformation and vacuole fragmentation defects, but not defects related to the formation of NVJs. Mutation of a NuA4-dependent acetylation site on Pah1 also resulted in aberrant Pah1 localization and defects in nuclear morphology and NVJ. Our work suggests a critical role for NuA4 in organelle morphology that is partially mediated through the regulation of Pah1 subcellular localization.
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Affiliation(s)
- Sarah Jane Laframboise
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
| | - Lauren F. Deneault
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
| | - Alix Denoncourt
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael Downey
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Kristin Baetz
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
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8
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Prokisch S, Büttner S. Partitioning into ER membrane microdomains impacts autophagic protein turnover during cellular aging. Sci Rep 2024; 14:13653. [PMID: 38871812 DOI: 10.1038/s41598-024-64493-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 06/09/2024] [Indexed: 06/15/2024] Open
Abstract
Eukaryotic membranes are compartmentalized into distinct micro- and nanodomains that rearrange dynamically in response to external and internal cues. This lateral heterogeneity of the lipid bilayer and associated clustering of distinct membrane proteins contribute to the spatial organization of numerous cellular processes. Here, we show that membrane microdomains within the endoplasmic reticulum (ER) of yeast cells are reorganized during metabolic reprogramming and aging. Using biosensors with varying transmembrane domain length to map lipid bilayer thickness, we demonstrate that in young cells, microdomains of increased thickness mainly exist within the nuclear ER, while progressing cellular age drives the formation of numerous microdomains specifically in the cortical ER. Partitioning of biosensors with long transmembrane domains into these microdomains increased protein stability and prevented autophagic removal. In contrast, reporters with short transmembrane domains progressively accumulated at the membrane contact site between the nuclear ER and the vacuole, the so-called nucleus-vacuole junction (NVJ), and were subjected to turnover via selective microautophagy occurring specifically at these sites. Reporters with long transmembrane domains were excluded from the NVJ. Our data reveal age-dependent rearrangement of the lateral organization of the ER and establish transmembrane domain length as a determinant of membrane contact site localization and autophagic degradation.
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Affiliation(s)
- Simon Prokisch
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden.
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9
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Sun S, Zhao G, Jia M, Jiang Q, Li S, Wang H, Li W, Wang Y, Bian X, Zhao YG, Huang X, Yang G, Cai H, Pastor-Pareja JC, Ge L, Zhang C, Hu J. Stay in touch with the endoplasmic reticulum. SCIENCE CHINA. LIFE SCIENCES 2024; 67:230-257. [PMID: 38212460 DOI: 10.1007/s11427-023-2443-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 08/28/2023] [Indexed: 01/13/2024]
Abstract
The endoplasmic reticulum (ER), which is composed of a continuous network of tubules and sheets, forms the most widely distributed membrane system in eukaryotic cells. As a result, it engages a variety of organelles by establishing membrane contact sites (MCSs). These contacts regulate organelle positioning and remodeling, including fusion and fission, facilitate precise lipid exchange, and couple vital signaling events. Here, we systematically review recent advances and converging themes on ER-involved organellar contact. The molecular basis, cellular influence, and potential physiological functions for ER/nuclear envelope contacts with mitochondria, Golgi, endosomes, lysosomes, lipid droplets, autophagosomes, and plasma membrane are summarized.
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Affiliation(s)
- Sha Sun
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Gan Zhao
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Mingkang Jia
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Qing Jiang
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Shulin Li
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Haibin Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenjing Li
- Laboratory of Computational Biology & Machine Intelligence, School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunyun Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xin Bian
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Yan G Zhao
- Brain Research Center, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Xun Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Ge Yang
- Laboratory of Computational Biology & Machine Intelligence, School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Huaqing Cai
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jose C Pastor-Pareja
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Institute of Neurosciences, Consejo Superior de Investigaciones Cientfflcas-Universidad Miguel Hernandez, San Juan de Alicante, 03550, Spain.
| | - Liang Ge
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Chuanmao Zhang
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China.
| | - Junjie Hu
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China.
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10
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Olkkonen VM, Ikonen E. Getting to Grips with the Oxysterol-Binding Protein Family - a Forty Year Perspective. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2024; 7:25152564241273598. [PMID: 39210909 PMCID: PMC11359446 DOI: 10.1177/25152564241273598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Accepted: 07/08/2024] [Indexed: 09/04/2024]
Abstract
This review discusses how research around the oxysterol-binding protein family has evolved. We briefly summarize how this protein family, designated OSBP-related (ORP) or OSBP-like (OSBPL) proteins, was discovered, how protein domains highly conserved among family members between taxa paved the way for understanding their mechanisms of action, and how insights into protein structural and functional features help to understand their versatility as lipid transporters. We also discuss questions and future avenues of research opened by these findings. The investigations on oxysterol-binding protein family serve as a real-life example of the notion that science often advances as a collective effort of multiple lines of enquiry, including serendipitous routes. While original articles invariably explain the motivation of the research undertaken in rational terms, the actual paths to findings may be less intentional. Fortunately, this does not reduce the impact of the discoveries made. Besides hopefully providing a useful account of ORP family proteins, we aim to convey this message.
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Affiliation(s)
- Vesa M. Olkkonen
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Elina Ikonen
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
- Faculty of Medicine, Dept of Anatomy and Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
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11
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Kim H, Park J, Kim H, Ko N, Park J, Jang E, Yoon S, Diaz J, Lee C, Jun Y. Structures of Vac8-containing protein complexes reveal the underlying mechanism by which Vac8 regulates multiple cellular processes. Proc Natl Acad Sci U S A 2023; 120:e2211501120. [PMID: 37094131 PMCID: PMC10161063 DOI: 10.1073/pnas.2211501120] [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: 07/06/2022] [Accepted: 03/30/2023] [Indexed: 04/26/2023] Open
Abstract
Vac8, a yeast vacuolar protein with armadillo repeats, mediates various cellular processes by changing its binding partners; however, the mechanism by which Vac8 differentially regulates these processes remains poorly understood. Vac8 interacts with Nvj1 to form the nuclear-vacuole junction (NVJ) and with Atg13 to mediate cytoplasm-to-vacuole targeting (Cvt), a selective autophagy-like pathway that delivers cytoplasmic aminopeptidase I directly to the vacuole. In addition, Vac8 associates with Myo2, a yeast class V myosin, through its interaction with Vac17 for vacuolar inheritance from the mother cell to the emerging daughter cell during cell divisions. Here, we determined the X-ray crystal structure of the Vac8-Vac17 complex and found that its interaction interfaces are bipartite, unlike those of the Vac8-Nvj1 and Vac8-Atg13 complexes. When the key amino acids present in the interface between Vac8 and Vac17 were mutated, vacuole inheritance was severely impaired in vivo. Furthermore, binding of Vac17 to Vac8 prevented dimerization of Vac8, which is required for its interactions with Nvj1 and Atg13, by clamping the H1 helix to the ARM1 domain of Vac8 and thereby preventing exposure of the binding interface for Vac8 dimerization. Consistently, the binding affinity of Vac17-bound Vac8 for Nvj1 or Atg13 was markedly lower than that of free Vac8. Likewise, free Vac17 had no affinity for the Vac8-Nvj1 and Vac8-Atg13 complexes. These results provide insights into how vacuole inheritance and other Vac8-mediated processes, such as NVJ formation and Cvt, occur independently of one another.
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Affiliation(s)
- Hyejin Kim
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, South Korea
| | - Jihyeon Park
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
| | - Hyunwoo Kim
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, South Korea
| | - Naho Ko
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
| | - Jumi Park
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, South Korea
| | - Eunhong Jang
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
| | - So Young Yoon
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
| | - Joyce Anne R. Diaz
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
| | - Changwook Lee
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, South Korea
| | - Youngsoo Jun
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
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12
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Severance ZC, Nuñez JI, Le-McClain AT, Malinky CA, Bensen RC, Fogle RS, Manginelli GW, Sakers SH, Falcon EC, Bui RH, Snead KJ, Bourne CR, Burgett AWG. Structure-Activity Relationships of Ligand Binding to Oxysterol-Binding Protein (OSBP) and OSBP-Related Protein 4. J Med Chem 2023; 66:3866-3875. [PMID: 36916802 PMCID: PMC10786236 DOI: 10.1021/acs.jmedchem.2c01025] [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: 03/16/2023]
Abstract
Oxysterol-binding protein (OSBP) and OSBP-related protein 4 (ORP4) have emerged as potentially druggable targets in antiviral and precision cancer drug development. Multiple structurally diverse small molecules function through targeting the OSBP/ORP family of proteins, including the antiviral steroidal compounds OSW-1 and T-00127-HEV2. Here, the structure-activity relationships of oxysterols and related compound binding to human OSBP and ORP4 are characterized. Oxysterols with hydroxylation at various side chain positions (i.e., C-20, C-24, C-25, and C-27)─but not C-22─confer high affinity interactions with OSBP and ORP4. A library of 20(S)-hydroxycholesterol analogues with varying sterol side chains reveal that side chain length modifications are not well tolerated for OSBP and ORP4 interactions. This side chain requirement is contradicted by the high affinity binding of T-00127-HEV2, a steroidal compound lacking the side chain. The binding results, in combination with docking studies using homology models of OSBP and ORP4, suggest multiple modes of steroidal ligand binding to OSBP and ORP4.
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Affiliation(s)
- Zachary C Severance
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73117, United States
| | - Juan I Nuñez
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Anh T Le-McClain
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Cori A Malinky
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Ryan C Bensen
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Robert S Fogle
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73117, United States
| | - Gianni W Manginelli
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Sophia H Sakers
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Emily C Falcon
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73117, United States
| | - Richard Hoang Bui
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73117, United States
| | - Kevin J Snead
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Christina R Bourne
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Anthony W G Burgett
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73117, United States
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, United States
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13
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Wang Z, Ke Q, Tao K, Li Q, Xia Y, Bao J, Chen Q. Activity and Point Mutation G699V in PcoORP1 Confer Resistance to Oxathiapiprolin in Phytophthora colocasiae Field Isolates. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:14140-14147. [PMID: 36315898 DOI: 10.1021/acs.jafc.2c06707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The oxysterol-binding protein inhibitor oxathiapiprolin is a new fungicide for controlling oomycetes diseases. Besides, laboratory mutagenesis oxathiapiprolin-resistance among phytopathogenic oomycetes in the field remains unknown. Here, the sensitivity of 97 P. colocasiae isolates to oxathiapiprolin was examined that were collected between 2011 and 2016. We obtained a baseline sensitivity with a mean EC50 value of 5.2639 × 10-4 μg mL-1. We showed that 6/32 isolates collected in Fujian Province from 2019 to 2020 were resistant to oxathiapiprolin without a significant fitness penalty on sporulation, vegetative growth, and virulence of the field isolates. The oxathiapiprolin resistance field isolates contained the point mutation glycine to valine at 699 in PcoORP1. The point mutation G699V was verified to confer resistance of P. colocasiae to oxathiapiprolin using the CRISPR/Cas9 system. The mutation G699V decreased the binding affinity between oxathiapiprolin and PcoORP1. These results will improve our understanding of the mechanism of P. colocasiae resistance to oxathiapiprolin under field conditions.
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Affiliation(s)
- Zhixin Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou 570228, China
| | - Qihan Ke
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou 570228, China
| | - Kezhu Tao
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou 570228, China
| | - Qianqian Li
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou 570228, China
| | - Yeqiang Xia
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiandong Bao
- The Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Qinghe Chen
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou 570228, China
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14
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Kobayashi J, Arita M, Sakai S, Kojima H, Senda M, Senda T, Hanada K, Kato R. Ligand Recognition by the Lipid Transfer Domain of Human OSBP Is Important for Enterovirus Replication. ACS Infect Dis 2022; 8:1161-1170. [PMID: 35613096 DOI: 10.1021/acsinfecdis.2c00108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Oxysterol-binding protein (OSBP), which transports cholesterol and phosphatidylinositol 4-monophosphate (PtdIns[4]P) between different organelles, serves as a conserved host factor for the replication of various viruses, and OSBP inhibitors exhibit antiviral effects. Here, we determined the crystal structure of the lipid transfer domain of human OSBP in complex with endogenous cholesterol. The hydrocarbon tail and tetracyclic ring of cholesterol interact with the hydrophobic tunnel of OSBP, and the hydroxyl group of cholesterol forms a hydrogen bond network at the bottom of the tunnel. Systematic mutagenesis of the ligand-binding region revealed that M446W and L590W substitutions confer functional tolerance to an OSBP inhibitor, T-00127-HEV2. Employing the M446W variant as a functional replacement for the endogenous OSBP in the presence of T-00127-HEV2, we have identified previously unappreciated amino acid residues required for viral replication. The combined use of the inhibitor and the OSBP variant will be useful in elucidating the enigmatic in vivo functions of OSBP.
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Affiliation(s)
- Jun Kobayashi
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Minetaro Arita
- Department of Virology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Shota Sakai
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Hirotatsu Kojima
- Drug Discovery Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Miki Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Kentaro Hanada
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Ryuichi Kato
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
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15
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Quon E, Nenadic A, Zaman MF, Johansen J, Beh CT. ER-PM membrane contact site regulation by yeast ORPs and membrane stress pathways. PLoS Genet 2022; 18:e1010106. [PMID: 35239652 PMCID: PMC8923467 DOI: 10.1371/journal.pgen.1010106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/15/2022] [Accepted: 02/16/2022] [Indexed: 02/01/2023] Open
Abstract
In yeast, at least seven proteins (Ice2p, Ist2p, Scs2/22p, Tcb1-Tcb3p) affect cortical endoplasmic reticulum (ER) tethering and contact with the plasma membrane (PM). In Δ-super-tether (Δ-s-tether) cells that lack these tethers, cortical ER-PM association is all but gone. Yeast OSBP homologue (Osh) proteins are also implicated in membrane contact site (MCS) assembly, perhaps as subunits for multicomponent tethers, though their function at MCSs involves intermembrane lipid transfer. Paradoxically, when analyzed by fluorescence and electron microscopy, the elimination of the OSH gene family does not reduce cortical ER-PM association but dramatically increases it. In response to the inactivation of all Osh proteins, the yeast E-Syt (extended-synaptotagmin) homologue Tcb3p is post-transcriptionally upregulated thereby generating additional Tcb3p-dependent ER-PM MCSs for recruiting more cortical ER to the PM. Although the elimination of OSH genes and the deletion of ER-PM tether genes have divergent effects on cortical ER-PM association, both elicit the Environmental Stress Response (ESR). Through comparisons of transcriptomic profiles of cells lacking OSH genes or ER-PM tethers, changes in ESR expression are partially manifested through the induction of the HOG (high-osmolarity glycerol) PM stress pathway or the ER-specific UPR (unfolded protein response) pathway, respectively. Defects in either UPR or HOG pathways also increase ER-PM MCSs, and expression of extra “artificial ER-PM membrane staples” rescues growth of UPR mutants challenged with lethal ER stress. Transcriptome analysis of OSH and Δ-s-tether mutants also revealed dysregulation of inositol-dependent phospholipid gene expression, and the combined lethality of osh4Δ and Δ-s-tether mutations is suppressed by overexpression of the phosphatidic acid biosynthetic gene, DGK1. These findings establish that the Tcb3p tether is induced by ER and PM stresses and ER-PM MCSs augment responses to membrane stresses, which are integrated through the broader ESR pathway. Membrane contact sites (MCSs) between the two largest cellular membranes, the endoplasmic reticulum (ER) and the plasma membrane (PM), are regulatory interfaces for lipid synthesis and bidirectional transport. The yeast Osh protein family, which represents the seven yeast oxysterol-binding protein related proteins (ORPs), is implicated in MCS regulation and lipid transfer between membranes. Ironically, we find that when all Osh proteins eliminated, ER-PM association is not reduced but significantly increases. We hypothesized this increase is due to compensatory increases in levels of tether proteins that physically link the ER and PM. In fact, in response to inactivating Osh protein expression, amounts of the tether protein Tcb3 increase and more ER-PM MCSs are produced. By testing the genomic transcriptional responses to the elimination of OSH and ER-PM tether genes, we find these mutants disrupt phospholipid regulation and they elicit the Environmental Stress Response (ESR) pathway, which integrates many different responses needed for recovery after cellular stress. OSH and ER-PM tether genes affect specific stress response pathways that impact the PM and ER, respectively. Combining OSH and tether mutations results in cell lethality, but these cells survive by increased expression of a key phospholipid biosynthetic gene. Based on these results, we propose that OSH and ER-PM tether genes affect phospholipid regulation and protect the PM and ER through membrane stress responses integrated through the ESR pathway.
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Affiliation(s)
- Evan Quon
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Aleksa Nenadic
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Mohammad F. Zaman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jesper Johansen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Christopher T. Beh
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, Canada
- * E-mail:
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16
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Arora A, Taskinen JH, Olkkonen VM. Coordination of inter-organelle communication and lipid fluxes by OSBP-related proteins. Prog Lipid Res 2022; 86:101146. [PMID: 34999137 DOI: 10.1016/j.plipres.2022.101146] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/10/2021] [Accepted: 01/03/2022] [Indexed: 12/31/2022]
Abstract
Oxysterol-binding protein (OSBP) and OSBP-related proteins (ORPs) constitute one of the largest families of lipid-binding/transfer proteins (LTPs) in eukaryotes. The current view is that many of them mediate inter-organelle lipid transfer over membrane contact sites (MCS). The transfer occurs in several cases in a 'counter-current' fashion: A lipid such as cholesterol or phosphatidylserine (PS) is transferred against its concentration gradient driven by transport of a phosphoinositide in the opposite direction. In this way ORPs are envisioned to maintain the distinct organelle lipid compositions, with impacts on multiple organelle functions. However, the functions of ORPs extend beyond lipid homeostasis to regulation of processes such as cell survival, proliferation and migration. Important expanding areas of mammalian ORP research include their roles in viral and bacterial infections, cancers, and neuronal function. The yeast OSBP homologue (Osh) proteins execute multifaceted functions in sterol and glycerophospholipid homeostasis, post-Golgi vesicle transport, phosphatidylinositol-4-phosphate, sphingolipid and target of rapamycin (TOR) signalling, and cell cycle control. These observations identify ORPs as lipid transporters and coordinators of signals with an unforeseen variety of cellular processes. Understanding their activities not only enlightens the biology of the living cell but also allows their employment as targets of new therapeutic approaches for disease.
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Affiliation(s)
- Amita Arora
- Minerva Foundation Institute for Medical Research, and Department of Anatomy, Faculty of Medicine, University of Helsinki, Finland
| | - Juuso H Taskinen
- Minerva Foundation Institute for Medical Research, and Department of Anatomy, Faculty of Medicine, University of Helsinki, Finland
| | - Vesa M Olkkonen
- Minerva Foundation Institute for Medical Research, and Department of Anatomy, Faculty of Medicine, University of Helsinki, Finland.
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17
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Egea PF. Mechanisms of Non-Vesicular Exchange of Lipids at Membrane Contact Sites: Of Shuttles, Tunnels and, Funnels. Front Cell Dev Biol 2021; 9:784367. [PMID: 34912813 PMCID: PMC8667587 DOI: 10.3389/fcell.2021.784367] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
Eukaryotic cells are characterized by their exquisite compartmentalization resulting from a cornucopia of membrane-bound organelles. Each of these compartments hosts a flurry of biochemical reactions and supports biological functions such as genome storage, membrane protein and lipid biosynthesis/degradation and ATP synthesis, all essential to cellular life. Acting as hubs for the transfer of matter and signals between organelles and throughout the cell, membrane contacts sites (MCSs), sites of close apposition between membranes from different organelles, are essential to cellular homeostasis. One of the now well-acknowledged function of MCSs involves the non-vesicular trafficking of lipids; its characterization answered one long-standing question of eukaryotic cell biology revealing how some organelles receive and distribute their membrane lipids in absence of vesicular trafficking. The endoplasmic reticulum (ER) in synergy with the mitochondria, stands as the nexus for the biosynthesis and distribution of phospholipids (PLs) throughout the cell by contacting nearly all other organelle types. MCSs create and maintain lipid fluxes and gradients essential to the functional asymmetry and polarity of biological membranes throughout the cell. Membrane apposition is mediated by proteinaceous tethers some of which function as lipid transfer proteins (LTPs). We summarize here the current state of mechanistic knowledge of some of the major classes of LTPs and tethers based on the available atomic to near-atomic resolution structures of several "model" MCSs from yeast but also in Metazoans; we describe different models of lipid transfer at MCSs and analyze the determinants of their specificity and directionality. Each of these systems illustrate fundamental principles and mechanisms for the non-vesicular exchange of lipids between eukaryotic membrane-bound organelles essential to a wide range of cellular processes such as at PL biosynthesis and distribution, lipid storage, autophagy and organelle biogenesis.
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Affiliation(s)
- Pascal F. Egea
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
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18
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Venditti R, Wilson C, De Matteis MA. Regulation and physiology of membrane contact sites. Curr Opin Cell Biol 2021; 71:148-157. [PMID: 33932623 DOI: 10.1016/j.ceb.2021.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/14/2022]
Abstract
Membrane contact sites (MCSs) in addition to impacting the functions of membrane-limited organelles also have a role in the spatial and functional organization of cells, tissues and whole organisms. MCSs have been identified between all organelles and the identification of their molecular composition has progressed significantly in recent years. Equally important is how MCSs respond dynamically to physiological stimuli, how this is regulated, and the physiological roles of MCSs in tissues and at the organismal level, an area that still remains relatively unexplored. In the present review, we focus on the regulation of MCSs, considerations of their function at the organismal level, and how mutations of MCS components linked to genetic diseases might inform us about their physiological relevance.
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Affiliation(s)
- Rossella Venditti
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; Department of Molecular Medicine and Medical Biotechnology, University of Napoli Federico II-Medical School, Naples, Italy
| | - Cathal Wilson
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Maria Antonietta De Matteis
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; Department of Molecular Medicine and Medical Biotechnology, University of Napoli Federico II-Medical School, Naples, Italy.
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19
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Tong J, Tan L, Im YJ. Structure of human ORP3 ORD reveals conservation of a key function and ligand specificity in OSBP-related proteins. PLoS One 2021; 16:e0248781. [PMID: 33857182 PMCID: PMC8049286 DOI: 10.1371/journal.pone.0248781] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 03/04/2021] [Indexed: 11/19/2022] Open
Abstract
Human ORP3 belongs to the oxysterol-binding protein (OSBP) family of lipid transfer proteins and is involved in lipid trafficking and cell signaling. ORP3 localizes to the ER-PM interfaces and is implicated in lipid transport and focal adhesion dynamics. Here, we report the 2.6–2.7 Å structures of the ORD (OSBP-related domain) of human ORP3 in apo-form and in complex with phosphatidylinositol 4-phosphate. The ORP3 ORD displays a helix grip β-barrel fold with a deep hydrophobic pocket which is conserved in the OSBP gene family. ORP3 binds PI(4)P by the residues around tunnel entrance and in the hydrophobic pocket, whereas it lacks sterol binding due to the narrow hydrophobic tunnel. The heterologous expression of the ORDs of human ORP3 or OSBP1 rescued the lethality of seven ORP (yeast OSH1-OSH7) knockout in yeast. In contrast, the PI(4)P-binding site mutant of ORP3 did not complement the OSH knockout cells. The N-terminal PH domain and FFAT motif of ORP3 are involved in protein targeting but are not essential in yeast complementation. This observation suggests that the essential function conserved in the ORPs of yeast and human is mediated by PI(4)P-binding of the ORD domain. This study suggests that the non-vesicular PI(4)P transport is a conserved function of all ORPs in eukaryotes.
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Affiliation(s)
- Junsen Tong
- College of Pharmacy, Chonnam National University, Gwangju, Republic of Korea
| | - Lingchen Tan
- College of Pharmacy, Chonnam National University, Gwangju, Republic of Korea
| | - Young Jun Im
- College of Pharmacy, Chonnam National University, Gwangju, Republic of Korea
- * E-mail:
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20
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Dubois GA, Jaillais Y. Anionic phospholipid gradients: an uncharacterized frontier of the plant endomembrane network. PLANT PHYSIOLOGY 2021; 185:577-592. [PMID: 33793905 PMCID: PMC8133617 DOI: 10.1093/plphys/kiaa056] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 09/16/2020] [Indexed: 05/19/2023]
Abstract
Anionic phospholipids include phosphatidic acid (PA), phosphatidylserine (PS), phosphatidylinositol (PI), and its phosphorylated derivatives the phosphoinositides (e.g. phosphatidylinositol-4-phosphate [PI4P] and phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2]). Although anionic phospholipids are low-abundant lipids, they are particularly important for membrane functions. In particular, anionic lipids act as biochemical and biophysical landmarks that contribute to the establishment of membrane identity, signaling activities, and compartment morphodynamics. Each anionic lipid accumulates in different endomembranes according to a unique subcellular pattern, where they locally provide docking platforms for proteins. As such, they are mostly believed to act in the compartments in which they accumulate. However, mounting evidence throughout eukaryotes suggests that anionic lipids are not as compartment-specific as initially thought and that they are instead organized as concentration gradients across different organelles. In this update, we review the evidence for the existence of anionic lipid gradients in plants. We then discuss the possible implication of these gradients in lipid dynamics and homeostasis, and also in coordinating subcellular activities. Finally, we introduce the notion that anionic lipid gradients at the cellular scale may translate into gradients at the tissue level, which could have implications for plant development.
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Affiliation(s)
- Gwennogan A Dubois
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, F-69342, Lyon, France
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, F-69342, Lyon, France
- Author for communication:
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21
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Marlow B, Kuenze G, Li B, Sanders CR, Meiler J. Structural determinants of cholesterol recognition in helical integral membrane proteins. Biophys J 2021; 120:1592-1604. [PMID: 33640379 DOI: 10.1016/j.bpj.2021.02.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 01/12/2021] [Accepted: 02/08/2021] [Indexed: 12/20/2022] Open
Abstract
Cholesterol is an integral component of mammalian membranes. It has been shown to modulate membrane fluidity and dynamics and alter integral membrane protein function. However, understanding the molecular mechanisms of how cholesterol impacts protein function is complicated by limited and conflicting structural data. Because of the nature of the crystallization and cryo-EM structure determination, it is difficult to distinguish between specific and biologically relevant interactions and a nonspecific association. The only widely recognized search algorithm for cholesterol-integral-membrane-protein interaction sites is sequence based, i.e., searching for the so-called "Cholesterol Recognition/interaction Amino acid Consensus" motif. Although these motifs are present in numerous integral membrane proteins, there is inconclusive evidence to support their necessity or sufficiency for cholesterol binding. Here, we leverage the increasing number of experimental cholesterol-integral-membrane-protein structures to systematically analyze putative interaction sites based on their spatial arrangement and evolutionary conservation. This analysis creates three-dimensional representations of general cholesterol interaction sites that form clusters across multiple integral membrane protein classes. We also classify cholesterol-integral-membrane-protein interaction sites as either likely-specific or nonspecific. Information gleaned from our characterization will eventually enable a structure-based approach to predict and design cholesterol-integral-membrane-protein interaction sites.
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Affiliation(s)
- Brennica Marlow
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee
| | - Georg Kuenze
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Department of Chemistry, Vanderbilt University, Nashville, Tennessee; Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany
| | - Bian Li
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee
| | - Charles R Sanders
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee; Department of Chemistry, Vanderbilt University, Nashville, Tennessee; Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany.
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22
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Kohler V, Büttner S. Remodelling of Nucleus-Vacuole Junctions During Metabolic and Proteostatic Stress. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2021; 4:25152564211016608. [PMID: 34124572 PMCID: PMC7610967 DOI: 10.1177/25152564211016608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/21/2021] [Accepted: 04/21/2021] [Indexed: 12/18/2022]
Abstract
Cellular adaptation to stress and metabolic cues requires a coordinated response of different intracellular compartments, separated by semipermeable membranes. One way to facilitate interorganellar communication is via membrane contact sites, physical bridges between opposing organellar membranes formed by an array of tethering machineries. These contact sites are highly dynamic and establish an interconnected organellar network able to quickly respond to external and internal stress by changing size, abundance and molecular architecture. Here, we discuss recent work on nucleus-vacuole junctions, connecting yeast vacuoles with the nucleus. Appearing as small, single foci in mitotic cells, these contacts expand into one enlarged patch upon nutrient exhaustion and entry into quiescence or can be shaped into multiple large foci essential to sustain viability upon proteostatic stress at the nuclear envelope. We highlight the remarkable plasticity and rapid remodelling of these contact sites upon metabolic or proteostatic stress and their emerging importance for cellular fitness.
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Affiliation(s)
- Verena Kohler
- Department of Molecular Biosciences, The Wenner‐Gren Institute, Stockholm University, Stockholm, Sweden
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner‐Gren Institute, Stockholm University, Stockholm, Sweden
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
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Zheng Koh DH, Saheki Y. Regulation of Plasma Membrane Sterol Homeostasis by Nonvesicular Lipid Transport. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2021; 4:25152564211042451. [PMID: 37366378 PMCID: PMC10259818 DOI: 10.1177/25152564211042451] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Sterol contributes to the structural integrity of cellular membranes and plays an important role in the regulation of cell signaling in eukaryotes. It is either produced in the endoplasmic reticulum or taken up from the extracellular environment. In most eukaryotic cells, however, the majority of sterol is enriched in the plasma membrane. Thus, the transport of sterol between the plasma membrane and other organelles, including the endoplasmic reticulum, is crucial for maintaining sterol homeostasis. While vesicular transport that relies on membrane budding and fusion reactions plays an important role in bulk sterol transport, this mode of transport is slow and non-selective. Growing evidence suggests a critical role of nonvesicular transport mediated by evolutionarily conserved families of lipid transfer proteins in more rapid and selective delivery of sterol. Some lipid transfer proteins act primarily at the sites of contacts formed between the endoplasmic reticulum and other organelles or the plasma membrane without membrane fusion. In this review, we describe the similarities and differences of sterol biosynthesis and uptake in mammals and yeast and discuss the role of their lipid transfer proteins in maintaining plasma membrane sterol homeostasis.
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Affiliation(s)
- Dylan Hong Zheng Koh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Yasunori Saheki
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
- Institute of Resource Development and
Analysis, Kumamoto University, Kumamoto 860-0811, Japan
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24
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Plasma Membrane Protein Nce102 Modulates Morphology and Function of the Yeast Vacuole. Biomolecules 2020; 10:biom10111476. [PMID: 33114062 PMCID: PMC7690685 DOI: 10.3390/biom10111476] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/15/2020] [Accepted: 10/21/2020] [Indexed: 01/02/2023] Open
Abstract
Membrane proteins are targeted not only to specific membranes in the cell architecture, but also to distinct lateral microdomains within individual membranes to properly execute their biological functions. Yeast tetraspan protein Nce102 has been shown to migrate between such microdomains within the plasma membrane in response to an acute drop in sphingolipid levels. Combining microscopy and biochemistry methods, we show that upon gradual ageing of a yeast culture, when sphingolipid demand increases, Nce102 migrates from the plasma membrane to the vacuole. Instead of being targeted for degradation it localizes to V-ATPase-poor, i.e., ergosterol-enriched, domains of the vacuolar membrane, analogous to its plasma membrane localization. We discovered that, together with its homologue Fhn1, Nce102 modulates vacuolar morphology, dynamics, and physiology. Specifically, the fusing of vacuoles, accompanying a switch of fermenting yeast culture to respiration, is retarded in the strain missing both proteins. Furthermore, the absence of either causes an enlargement of ergosterol-rich vacuolar membrane domains, while the vacuoles themselves become smaller. Our results clearly show decreased stability of the V-ATPase in the absence of either Nce102 or Fhn1, a possible result of the disruption of normal microdomain morphology of the vacuolar membrane. Therefore, the functionality of the vacuole as a whole might be compromised in these cells.
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25
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Lord CL, Wente SR. Nuclear envelope-vacuole contacts mitigate nuclear pore complex assembly stress. J Cell Biol 2020; 219:211463. [PMID: 33053148 PMCID: PMC7563749 DOI: 10.1083/jcb.202001165] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 08/10/2020] [Accepted: 09/23/2020] [Indexed: 01/04/2023] Open
Abstract
The intricacy of nuclear pore complex (NPC) biogenesis imposes risks of failure that can cause defects in nuclear transport and nuclear envelope (NE) morphology; however, cellular mechanisms used to alleviate NPC assembly stress are not well defined. In the budding yeast Saccharomyces cerevisiae, we demonstrate that NVJ1- and MDM1-enriched NE-vacuole contacts increase when NPC assembly is compromised in several nup mutants, including nup116ΔGLFG cells. These interorganelle nucleus-vacuole junctions (NVJs) cooperate with lipid droplets to maintain viability and enhance NPC formation in assembly mutants. Additionally, NVJs function with ATG1 to remodel the NE and promote vacuole-dependent degradation of specific nucleoporins in nup116ΔGLFG cells. Importantly, NVJs significantly improve the physiology of NPC assembly mutants, despite having only negligible effects when NPC biogenesis is unperturbed. These results therefore define how NE-vacuole interorganelle contacts coordinate responses to mitigate deleterious cellular effects caused by disrupted NPC assembly.
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26
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Li X, Yang X, Zheng X, Bai M, Hu D. Review on Structures of Pesticide Targets. Int J Mol Sci 2020; 21:E7144. [PMID: 32998191 PMCID: PMC7582455 DOI: 10.3390/ijms21197144] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/23/2020] [Accepted: 09/25/2020] [Indexed: 12/12/2022] Open
Abstract
Molecular targets play important roles in agrochemical discovery. Numerous pesticides target the key proteins in pathogens, insect, or plants. Investigating ligand-binding pockets and/or active sites in the proteins' structures is usually the first step in designing new green pesticides. Thus, molecular target structures are extremely important for the discovery and development of such pesticides. In this manuscript, we present a review of the molecular target structures, including those of antiviral, fungicidal, bactericidal, insecticidal, herbicidal, and plant growth-regulator targets, currently used in agrochemical research. The data will be helpful in pesticide design and the discovery of new green pesticides.
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Affiliation(s)
- Xiangyang Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China;
| | - Xueqing Yang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China;
| | - Xiaodong Zheng
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China;
| | - Miao Bai
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China;
| | - Deyu Hu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China;
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27
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Delfosse V, Bourguet W, Drin G. Structural and Functional Specialization of OSBP-Related Proteins. ACTA ACUST UNITED AC 2020. [DOI: 10.1177/2515256420946627] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Lipids are precisely distributed in the eukaryotic cell where they help to define organelle identity and function, in addition to their structural role. Once synthesized, many lipids must be delivered to other compartments by non-vesicular routes, a process that is undertaken by proteins called Lipid Transfer Proteins (LTPs). OSBP and the closely-related ORP and Osh proteins constitute a major, evolutionarily conserved family of LTPs in eukaryotes. Most of these target one or more subcellular regions, and membrane contact sites in particular, where two organelle membranes are in close proximity. It was initially thought that such proteins were strictly dedicated to sterol sensing or transport. However, over the last decade, numerous studies have revealed that these proteins have many more functions, and we have expanded our understanding of their mechanisms. In particular, many of them are lipid exchangers that exploit PI(4)P or possibly other phosphoinositide gradients to directionally transfer sterol or PS between two compartments. Importantly, these transfer activities are tightly coupled to processes such as lipid metabolism, cellular signalling and vesicular trafficking. This review describes the molecular architecture of OSBP/ORP/Osh proteins, showing how their specific structural features and internal configurations impart unique cellular functions.
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Affiliation(s)
- Vanessa Delfosse
- Centre de Biochimie Structurale, Inserm, CNRS, Univ Montpellier, Montpellier, France
| | - William Bourguet
- Centre de Biochimie Structurale, Inserm, CNRS, Univ Montpellier, Montpellier, France
| | - Guillaume Drin
- CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d’Azur, Valbonne, France
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ORP/Osh mediate cross-talk between ER-plasma membrane contact site components and plasma membrane SNAREs. Cell Mol Life Sci 2020; 78:1689-1708. [PMID: 32734583 PMCID: PMC7904734 DOI: 10.1007/s00018-020-03604-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/06/2020] [Accepted: 07/17/2020] [Indexed: 02/07/2023]
Abstract
OSBP-homologous proteins (ORPs, Oshp) are lipid binding/transfer proteins. Several ORP/Oshp localize to membrane contacts between the endoplasmic reticulum (ER) and the plasma membrane, where they mediate lipid transfer or regulate lipid-modifying enzymes. A common way in which they target contacts is by binding to the ER proteins, VAP/Scs2p, while the second membrane is targeted by other interactions with lipids or proteins.We have studied the cross-talk of secretory SNARE proteins and their regulators with ORP/Oshp and VAPA/Scs2p at ER-plasma membrane contact sites in yeast and murine primary neurons. We show that Oshp-Scs2p interactions depend on intact secretory SNARE proteins, especially Sec9p. SNAP-25/Sec9p directly interact with ORP/Osh proteins and their disruption destabilized the ORP/Osh proteins, associated with dysfunction of VAPA/Scs2p. Deleting OSH1-3 in yeast or knocking down ORP2 in primary neurons reduced the oligomerization of VAPA/Scs2p and affected their multiple interactions with SNAREs. These observations reveal a novel cross-talk between the machineries of ER-plasma membrane contact sites and those driving exocytosis.
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29
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Lipp NF, Ikhlef S, Milanini J, Drin G. Lipid Exchangers: Cellular Functions and Mechanistic Links With Phosphoinositide Metabolism. Front Cell Dev Biol 2020; 8:663. [PMID: 32793602 PMCID: PMC7385082 DOI: 10.3389/fcell.2020.00663] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/01/2020] [Indexed: 12/28/2022] Open
Abstract
Lipids are amphiphilic molecules that self-assemble to form biological membranes. Thousands of lipid species coexist in the cell and, once combined, define organelle identity. Due to recent progress in lipidomic analysis, we now know how lipid composition is finely tuned in different subcellular regions. Along with lipid synthesis, remodeling and flip-flop, lipid transfer is one of the active processes that regulates this intracellular lipid distribution. It is mediated by Lipid Transfer Proteins (LTPs) that precisely move certain lipid species across the cytosol and between the organelles. A particular subset of LTPs from three families (Sec14, PITP, OSBP/ORP/Osh) act as lipid exchangers. A striking feature of these exchangers is that they use phosphatidylinositol or phosphoinositides (PIPs) as a lipid ligand and thereby have specific links with PIP metabolism and are thus able to both control the lipid composition of cellular membranes and their signaling capacity. As a result, they play pivotal roles in cellular processes such as vesicular trafficking and signal transduction at the plasma membrane. Recent data have shown that some PIPs are used as energy by lipid exchangers to generate lipid gradients between organelles. Here we describe the importance of lipid counter-exchange in the cell, its structural basis, and presumed links with pathologies.
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Affiliation(s)
- Nicolas-Frédéric Lipp
- Institut de Pharmacologie Moléculaire et Cellulaire, CNRS, Université Côte d'Azur, Valbonne, France
| | - Souade Ikhlef
- Institut de Pharmacologie Moléculaire et Cellulaire, CNRS, Université Côte d'Azur, Valbonne, France
| | - Julie Milanini
- Institut de Pharmacologie Moléculaire et Cellulaire, CNRS, Université Côte d'Azur, Valbonne, France
| | - Guillaume Drin
- Institut de Pharmacologie Moléculaire et Cellulaire, CNRS, Université Côte d'Azur, Valbonne, France
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30
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Péresse T, Kovacs D, Subra M, Bigay J, Tsai MC, Polidori J, Gautier R, Desrat S, Fleuriot L, Debayle D, Litaudon M, Pham VC, Bignon J, Antonny B, Roussi F, Mesmin B. Molecular and cellular dissection of the oxysterol-binding protein cycle through a fluorescent inhibitor. J Biol Chem 2020; 295:4277-4288. [PMID: 32075908 PMCID: PMC7105299 DOI: 10.1074/jbc.ra119.012012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/09/2020] [Indexed: 01/02/2023] Open
Abstract
ORPphilins are bioactive natural products that strongly and selectively inhibit the growth of some cancer cell lines and are proposed to target intracellular lipid-transfer proteins of the oxysterol-binding protein (OSBP) family. These conserved proteins exchange key lipids, such as cholesterol and phosphatidylinositol 4-phosphate (PI(4)P), between organelle membranes. Among ORPphilins, molecules of the schweinfurthin family interfere with intracellular lipid distribution and metabolism, but their functioning at the molecular level is poorly understood. We report here that cell line sensitivity to schweinfurthin G (SWG) is inversely proportional to cellular OSBP levels. By taking advantage of the intrinsic fluorescence of SWG, we followed its fate in cell cultures and show that its incorporation at the trans-Golgi network depends on cellular abundance of OSBP. Using in vitro membrane reconstitution systems and cellular imaging approaches, we also report that SWG inhibits specifically the lipid transfer activity of OSBP. As a consequence, post-Golgi trafficking, membrane cholesterol levels, and PI(4)P turnover were affected. Finally, using intermolecular FRET analysis, we demonstrate that SWG directly binds to the lipid-binding cavity of OSBP. Collectively these results describe SWG as a specific and intrinsically fluorescent pharmacological tool for dissecting OSBP properties at the cellular and molecular levels. Our findings indicate that SWG binds OSBP with nanomolar affinity, that this binding is sensitive to the membrane environment, and that SWG inhibits the OSBP-catalyzed lipid exchange cycle.
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Affiliation(s)
- Tiphaine Péresse
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - David Kovacs
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Mélody Subra
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Joëlle Bigay
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Meng-Chen Tsai
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Joël Polidori
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Romain Gautier
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Sandy Desrat
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Lucile Fleuriot
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Delphine Debayle
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Marc Litaudon
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Van-Cuong Pham
- Advanced Center for Bioorganic Chemistry of the Institute of Marine Biochemistry, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, 8404, Caugiay, Hanoi, Vietnam
| | - Jérôme Bignon
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Bruno Antonny
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Fanny Roussi
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France.
| | - Bruno Mesmin
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France.
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31
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Shin JJH, Liu P, Chan LJ, Ullah A, Pan J, Borchers CH, Burke JE, Stefan C, Smits GJ, Loewen CJR. pH Biosensing by PI4P Regulates Cargo Sorting at the TGN. Dev Cell 2020; 52:461-476.e4. [PMID: 31928972 DOI: 10.1016/j.devcel.2019.12.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/04/2019] [Accepted: 12/13/2019] [Indexed: 01/09/2023]
Abstract
Phosphoinositides, diacylglycerolpyrophosphate, ceramide-1-phosphate, and phosphatidic acid belong to a unique class of membrane signaling lipids that contain phosphomonoesters in their headgroups having pKa values in the physiological range. The phosphomonoester headgroup of phosphatidic acid enables this lipid to act as a pH biosensor as changes in its protonation state with intracellular pH regulate binding to effector proteins. Here, we demonstrate that binding of pleckstrin homology (PH) domains to phosphatidylinositol 4-phosphate (PI4P) in the yeast trans-Golgi network (TGN) is dependent on intracellular pH, indicating PI4P is a pH biosensor. pH biosensing by TGN PI4P in response to nutrient availability governs protein sorting at the TGN, likely by regulating sterol transfer to the TGN by Osh1, a member of the conserved oxysterol-binding protein (OSBP) family of lipid transfer proteins. Thus, pH biosensing by TGN PI4P allows for direct metabolic regulation of protein trafficking and cell growth.
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Affiliation(s)
- John J H Shin
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; MRC Laboratory for Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Peter Liu
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Leslie J Chan
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Azmat Ullah
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1018 XH Amsterdam, The Netherlands
| | - Jingxi Pan
- University of Victoria, Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada; Department of Biochemistry & Microbiology, University of Victoria, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada
| | - Christoph H Borchers
- University of Victoria, Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada; Department of Biochemistry & Microbiology, University of Victoria, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada
| | - John E Burke
- Department of Biochemistry & Microbiology, University of Victoria, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada
| | - Christopher Stefan
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Gertien J Smits
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1018 XH Amsterdam, The Netherlands
| | - Christopher J R Loewen
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.
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Moosavi B, Gao M, Zhu XL, Yang GF. The anti-cancer compound Schweinfurthin A targets Osh2 and disrupts lipid metabolism in the yeast model. Bioorg Chem 2019; 94:103471. [PMID: 31813476 DOI: 10.1016/j.bioorg.2019.103471] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 11/09/2019] [Accepted: 11/23/2019] [Indexed: 12/17/2022]
Abstract
Schweinfurthin A (Sch A) is a natural product with a selective and strong anti-cancer effect. Although it is known to target oxysterol binding proteins, the detailed mode of action is not well understood. Here, we provide strong evidence that yeast cells can be used as a eukaryotic model system to decipher the molecular modes of Sch A. We show that Sch A (100 µM) targets Osh2 (a yeast oxysterol binding protein homolog) genetically and taking advantage of computational chemistry indicate that the tetrahydro-2H-xanthene portion of Sch A forms H-bonds with residues Ser105, Val113, and Lys201, while its isoprenoid side chain is placed in a hydrophobic pocket lined by the side chains of Leu41, Leu45, Leu58, Met56, and Phe174 in Osh2. This model suggests that Sch A occupies the same binding pocket in Osh2 which is occupied by its natural substrate, ergosterol. Osh proteins transport sterol and PI(4)P in a cyclic manner between two membranes. Therefore, we suggest that Sch A interferes with this function of Osh2. In support of this hypothesis, we show that Sch A toxicity rate changes upon manipulating the enzymes that modify the levels of sterol and PI(4)P. This approach also informs how Sch A exerts its toxic effect in yeast cells. These enzymes include Coq1, Sac1, Plc1, Stt4, Pik1, and Mss4. We demonstrate that Coq1 an enzyme required for coenzyme Q synthesis (also involved in sterol metabolism indirectly), Sac1, and Stt4 the enzymes governing PI(4)P level modify Sch A toxicity and finally propose Sch A disrupts sterol/PI(4)P exchange between membranes by occupying the sterol/PI(4)P binding pocket in Osh2.
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Affiliation(s)
- Behrooz Moosavi
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, PR China.
| | - Mengqi Gao
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, PR China
| | - Xiao-Lei Zhu
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, PR China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, PR China.
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Olkkonen VM, Koponen A, Arora A. OSBP-related protein 2 (ORP2): Unraveling its functions in cellular lipid/carbohydrate metabolism, signaling and F-actin regulation. J Steroid Biochem Mol Biol 2019; 192:105298. [PMID: 30716465 DOI: 10.1016/j.jsbmb.2019.01.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/21/2019] [Accepted: 01/25/2019] [Indexed: 12/20/2022]
Abstract
Oxysterol-binding protein (OSBP)-related proteins (ORPs) constitute a family of intracellular lipid-binding/transport proteins (LTPs) in eukaryotes. They typically have a modular structure comprising a lipid-binding domain and membrane targeting determinants, being thus suited for function at membrane contact sites. Among the mammalian ORPs, ORP2/OSBPL2 is the only member that only exists as a 'short' variant lacking a membrane-targeting pleckstrin homology domain. ORP2 is expressed ubiquitously and has been assigned a multitude of functions. Its OSBP-related domain binds cholesterol, oxysterols, and phosphoinositides, and its overexpression enhances cellular cholesterol efflux. Consistently, the latest observations suggest a function of ORP2 in cholesterol transport to the plasma membrane (PM) in exchange for phosphatidylinositol 4,5-bisphosphate (PI4,5P2), with significant impacts on the concentrations of PM cholesterol and PI4,5P2. On the other hand, ORP2 localizes at the surface of cytoplasmic lipid droplets (LDs) and at endoplasmic-reticulum-LD contact sites, and its depletion modifies cellular triglyceride (TG) metabolism. Study in an adrenocortical cell line further suggested a function of ORP2 in the synthesis of steroid hormones. Our recent knock-out of ORP2 in human hepatoma cells revealed its function in hepatocellular PI3K/Akt signaling, glucose and triglyceride metabolism, as well as in actin cytoskeletal regulation, cell adhesion, migration and proliferation. ORP2 was shown to interact physically with F-actin regulators such as DIAPH1, ARHGAP12, SEPT9 and MLC12, as well as with IQGAP1 and the Cdc37-Hsp90 chaperone complex controlling the activity of Akt. Interestingly, mutations in OSBPL2 encoding ORP2 are associated with autosomal dominant non-syndromic hearing loss, and the protein was found to localize in cochlear hair cell stereocilia. The functions assigned to ORP2 suggest that this protein, in concert with other LTPs, controls the subcellular distribution of cholesterol in various cell types and steroid hormone synthesis in adrenocortical cells. However, it also impacts cellular TG and carbohydrate metabolism and F-actin-dependent functions, revealing a bewildering spectrum of activities.
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Affiliation(s)
- Vesa M Olkkonen
- Minerva Foundation Institute for Medical Research, Biomedicum 2U, FI-00290, Helsinki, Finland; Department of Anatomy, Faculty of Medicine, FI-00014, University of Helsinki, Finland.
| | - Annika Koponen
- Minerva Foundation Institute for Medical Research, Biomedicum 2U, FI-00290, Helsinki, Finland; Department of Anatomy, Faculty of Medicine, FI-00014, University of Helsinki, Finland
| | - Amita Arora
- Minerva Foundation Institute for Medical Research, Biomedicum 2U, FI-00290, Helsinki, Finland; Department of Anatomy, Faculty of Medicine, FI-00014, University of Helsinki, Finland
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Molecular Determinants of Cholesterol Binding to Soluble and Transmembrane Protein Domains. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1135:47-66. [PMID: 31098810 DOI: 10.1007/978-3-030-14265-0_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Cholesterol-protein interactions play a critical role in lipid metabolism and maintenance of cell integrity. To elucidate the molecular mechanisms underlying these interactions, a growing number of studies have focused on determining the crystal structures of a variety of proteins complexed with cholesterol. These include structures in which cholesterol binds to transmembrane domains, and structures in which cholesterol interacts with soluble ones. However, it remains unknown whether there are differences in the prerequisites for cholesterol binding to these two types of domains. Thus, to define the molecular determinants that characterize the binding of cholesterol to these two distinct protein domains, we employed the database of crystal structures of proteins complexed with cholesterol. Our analysis suggests that cholesterol may bind more strongly to soluble domains than to transmembrane domains. The interactions between cholesterol and the protein in both cases critically depends on hydrophobic and aromatic residues. In addition, cholesterol binding sites in both types of domains involve polar and/or charged residues. However, the percentage of appearance of the different types of polar/charged residues in cholesterol binding sites differs between soluble and transmembrane domains. No differences were observed in the conformational characteristics of the cholesterol molecules bound to soluble versus transmembrane protein domains suggesting that cholesterol is insensitive to the environment provided by the different protein domains.
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Nishimura T, Gecht M, Covino R, Hummer G, Surma MA, Klose C, Arai H, Kono N, Stefan CJ. Osh Proteins Control Nanoscale Lipid Organization Necessary for PI(4,5)P 2 Synthesis. Mol Cell 2019; 75:1043-1057.e8. [PMID: 31402097 PMCID: PMC6739424 DOI: 10.1016/j.molcel.2019.06.037] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/13/2019] [Accepted: 06/25/2019] [Indexed: 11/28/2022]
Abstract
The plasma membrane (PM) is composed of a complex lipid mixture that forms heterogeneous membrane environments. Yet, how small-scale lipid organization controls physiological events at the PM remains largely unknown. Here, we show that ORP-related Osh lipid exchange proteins are critical for the synthesis of phosphatidylinositol (4,5)-bisphosphate [PI(4,5)P2], a key regulator of dynamic events at the PM. In real-time assays, we find that unsaturated phosphatidylserine (PS) and sterols, both Osh protein ligands, synergistically stimulate phosphatidylinositol 4-phosphate 5-kinase (PIP5K) activity. Biophysical FRET analyses suggest an unconventional co-distribution of unsaturated PS and phosphatidylinositol 4-phosphate (PI4P) species in sterol-containing membrane bilayers. Moreover, using in vivo imaging approaches and molecular dynamics simulations, we show that Osh protein-mediated unsaturated PI4P and PS membrane lipid organization is sensed by the PIP5K specificity loop. Thus, ORP family members create a nanoscale membrane lipid environment that drives PIP5K activity and PI(4,5)P2 synthesis that ultimately controls global PM organization and dynamics. The Osh lipid exchange proteins are required to maintain PI(4,5)P2 levels in the PM Unsaturated PS and sterols synergistically stimulate PIP5K activity The specificity loop conserved in PIP5Ks serves as a lipid sensor A simulation model of the PIP5K specificity loop embedded in a lipid bilayer
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Affiliation(s)
- Taki Nishimura
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK.
| | - Michael Gecht
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Roberto Covino
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany; Institute for Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | | | | | - Hiroyuki Arai
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; AMED-CREST, Japan Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyodaku, Tokyo 100-0004, Japan
| | - Nozomu Kono
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; PRIME, Japan Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyodaku, Tokyo 100-0004, Japan
| | - Christopher J Stefan
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK.
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36
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Nishimura T, Stefan CJ. Specialized ER membrane domains for lipid metabolism and transport. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1865:158492. [PMID: 31349025 DOI: 10.1016/j.bbalip.2019.07.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 11/15/2022]
Abstract
The endoplasmic reticulum (ER) is a highly organized organelle that performs vital functions including de novo membrane lipid synthesis and transport. Accordingly, numerous lipid biosynthesis enzymes are localized in the ER membrane. However, it is now evident that lipid metabolism is sub-compartmentalized within the ER and that lipid biosynthetic enzymes engage with lipid transfer proteins (LTPs) to rapidly shuttle newly synthesized lipids from the ER to other organelles. As such, intimate relationships between lipid metabolism and lipid transfer pathways exist within the ER network. Notably, certain LTPs enhance the activities of lipid metabolizing enzymes; likewise, lipid metabolism can ensure the specificity of LTP transfer/exchange reactions. Yet, our understanding of these mutual relationships is still emerging. Here, we highlight past and recent key findings on specialized ER membrane domains involved in efficient lipid metabolism and transport and consider unresolved issues in the field.
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Affiliation(s)
- Taki Nishimura
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK.
| | - Christopher J Stefan
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK.
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37
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Heterologous expression and functional characterization of the ligand-binding domain of oxysterol-binding protein from Aspergillus oryzae. Braz J Microbiol 2019; 50:415-424. [PMID: 30848436 DOI: 10.1007/s42770-019-00060-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 11/06/2018] [Indexed: 01/03/2023] Open
Abstract
Oxysterol-binding proteins (OSBPs) comprise a family of sterol-binding proteins. In this study, we focused on AoOSBP1, one of the five OSBP proteins identified from the industrial fungus Aspergillus oryzae. The temporal expression pattern analysis showed that the expression of AoOSBP1, in both gene and protein levels, was stably expressed throughout the developmental stages, while was upregulated during the accelerated growth stage. The immunofluorescence observation revealed that AoOSBP1 protein was mainly distributed in the conidiophore, indicating its underlying role in spore formation. The ligand-binding domain of AoOSBP1, namely OSBP-related domain (ORD), was heterologously expressed in Escherichia coli and purified. The binding assay carried out using microscale thermophoresis showed that the recombinant AoORD protein exhibited binding affinity for ergosterol, and exhibited much higher affinity to oxysterols (25-hydroxycholesterol and 7-ketocholesterol) and phytosterols (β-sitosterol and stigmasterol). By contrast, MBP tag as the negative control showed no binding affinity for sterols. The present work demonstrates that AoORD domain in AoOSBP1 is capable of binding sterols, plays an underlying role in sterols transportation, and may participate in spore formation.
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38
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Qiu S, Zeng B. Advances in understanding of the oxysterol-binding protein homologous in yeast and filamentous fungi. Int Microbiol 2019; 22:169-179. [PMID: 30810998 DOI: 10.1007/s10123-019-00056-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/02/2019] [Accepted: 01/03/2019] [Indexed: 01/14/2023]
Abstract
Oxysterol-binding protein is an important non-vesicular trafficking protein involved in the transportation of lipids in eukaryotic cells. Oxysterol-binding protein is identified as oxysterol-binding protein-related proteins (ORPs) in mammals and oxysterol-binding protein homologue (Osh) in yeast. Research has described the function and structure of oxysterol-binding protein in mammals and yeast, but little information about the protein's structure and function in filamentous fungi has been reported. This article focuses on recent advances in the research of Osh proteins in yeast and filamentous fungi, such as Aspergillus oryzae, Aspergillus nidulans, and Candida albicans. Furthermore, we point out some problems in the field, summarizing the membrane contact sites (MCS) of Osh proteins in yeast, and consider the future of Osh protein development.
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Affiliation(s)
- Shangkun Qiu
- Jiangxi Province Key Laboratory Bioprocess Engineering, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Bin Zeng
- Jiangxi Province Key Laboratory Bioprocess Engineering, Jiangxi Science and Technology Normal University, Nanchang, 330013, China.
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39
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Tamura Y, Kawano S, Endo T. Organelle contact zones as sites for lipid transfer. J Biochem 2019; 165:115-123. [PMID: 30371789 DOI: 10.1093/jb/mvy088] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/26/2018] [Indexed: 01/06/2023] Open
Abstract
Since the 1950s, electron microscopic observations have suggested the existence of special regions where the distinct organelle membranes are closely apposed to each other, yet their molecular basis and functions have not been examined for a long time. Recent studies using yeast as a model organism identified multiple organelle-membrane tethering sites/factors, such as ERMES (ER-mitochondria encounter structure), NVJ (Nuclear-vacuole junction), vCLAMP (Vacuole and mitochondria patch) and MICOS (Mitochondrial contact site). Among them, ERMES is the best-characterized contact-site protein complex, which was found to function as not only an organelle-tethering factor but also a phospholipid transfer protein complex. In this review, we will discuss recent advances in the characterization of ERMES and other organelle contact zones, vCLAMP, NVJ and MICOS in yeast.
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Affiliation(s)
- Yasushi Tamura
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata, Japan
| | - Shin Kawano
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, Japan.,Research Center for Protein Dynamics, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, Japan
| | - Toshiya Endo
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, Japan.,Research Center for Protein Dynamics, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, Japan
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40
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Allosteric enhancement of ORP1-mediated cholesterol transport by PI(4,5)P 2/PI(3,4)P 2. Nat Commun 2019; 10:829. [PMID: 30783101 PMCID: PMC6381110 DOI: 10.1038/s41467-019-08791-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 01/22/2019] [Indexed: 12/01/2022] Open
Abstract
Phosphatidylinositol phosphates (PIPs) and cholesterol are known to regulate the function of late endosomes and lysosomes (LELs), and ORP1L specifically localizes to LELs. Here, we show in vitro that ORP1 is a PI(4,5)P2- or PI(3,4)P2-dependent cholesterol transporter, but cannot transport any PIPs. In cells, both ORP1L and PI(3,4)P2 are required for the efficient removal of cholesterol from LELs. Structures of the lipid-binding domain of ORP1 (ORP1-ORD) in complex with cholesterol or PI(4,5)P2 display open conformations essential for ORP function. PI(4,5)P2/PI(3,4)P2 can facilitate ORP1-mediated cholesterol transport by promoting membrane targeting and cholesterol extraction. Thus, our work unveils a distinct mechanism by which PIPs may allosterically enhance OSBP/ORPs-mediated transport of major lipid species such as cholesterol. Phosphatidylinositol phosphates (PIPs) and cholesterol are known to regulate the function of late endosomes and lysosomes (LELs). Here authors unveil a mechanism by which PI(4,5)P2/PI(3,4)P2 allosterically enhances ORP1-mediated cholesterol exit from LELs.
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41
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Wu Q, Zhao B, Fan Z, Guo X, Yang D, Zhang N, Yu B, Zhou S, Zhao J, Chen F. Discovery of Novel Piperidinylthiazole Derivatives As Broad-Spectrum Fungicidal Candidates. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:1360-1370. [PMID: 30640452 DOI: 10.1021/acs.jafc.8b06054] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Oxathiapiprolin is one of the best active fungicides discovered for oomycetes control. To develop a fungicide candidate with a broad spectrum of activity, 22 new piperidinylthiazole derivatives were designed and synthesized. Compound 5l showed the best activity against Pseudoperonospora cubensis (Berk. et Curt.) Rostov and Phytophthora infestans in vivo with 100% and 80% of inhibition, respectively, at 1 mg/L, and 72.87% of field efficacy against P. cubensis at 1 g ai/667 m2 validated these results. Compound 5i exhibited a broad spectrum of excellent activity against Sclerotinia sclerotiorum with EC50 = 0.30 mg/L (>10 times more active than oxathiapiprolin and azoxystrobin in vitro), good activity against Botrytis cinerea, Cercospora arachidicola, and Gibberella zeae with EC50 of 14.54, 5.57, and 14.03 mg/L in vitro and against P. cubensis and P. infestans with 60% and 30% inhibition rates, respectively, at 1 mg/L in vivo. Mode of action studies by RNA sequencing analysis discovered oxysterol-binding protein (OSBP), chitin synthase (CHS1), and (1,3)-β-glucan synthase (FKS2) as the potent target of 5i against S. sclerotiorum. Quenching studies validated that OSBP was the same target of both 5i and oxathiapiprolin; it was quenched by both of them. Our studies discovered isothiazole-containing piperidinylthiazole as an OSBP target-based novel lead for fungicide development.
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Affiliation(s)
- Qifan Wu
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry , Nankai University , Tianjin 300071 , P. R. China
| | - Bin Zhao
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry , Nankai University , Tianjin 300071 , P. R. China
| | - Zhijin Fan
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry , Nankai University , Tianjin 300071 , P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Nankai University , Tianjin 300071 , P. R. China
| | - Xiaofeng Guo
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry , Nankai University , Tianjin 300071 , P. R. China
| | - Dongyan Yang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry , Nankai University , Tianjin 300071 , P. R. China
| | - Nailou Zhang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry , Nankai University , Tianjin 300071 , P. R. China
| | - Bin Yu
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry , Nankai University , Tianjin 300071 , P. R. China
| | - Shuang Zhou
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry , Nankai University , Tianjin 300071 , P. R. China
| | - Jiabao Zhao
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry , Nankai University , Tianjin 300071 , P. R. China
| | - Fan Chen
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry , Nankai University , Tianjin 300071 , P. R. China
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42
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Tong J, Tan L, Chun C, Im YJ. Structural basis of human ORP1-Rab7 interaction for the late-endosome and lysosome targeting. PLoS One 2019; 14:e0211724. [PMID: 30721249 PMCID: PMC6363164 DOI: 10.1371/journal.pone.0211724] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 01/20/2019] [Indexed: 02/07/2023] Open
Abstract
Oxysterol-binding protein (OSBP) and OSBP-related proteins (ORPs) constitute a family of lipid transfer proteins conserved in eukaryotes. ORP1 transports cholesterol at the interface between the late endosomes/lysosomes (LELs) and the endoplasmic reticulum (ER). ORP1 is targeted to the endosomal membranes by forming a tripartite complex with the LE GTPase Rab7 and its effector RILP (Rab7-interacting lysosomal protein). Here, we determined the crystal structure of human ORP1 ANK domain in complex with the GTP-bound form of Rab7. ORP1 ANK binds to the helix α3 of Rab7 located away from the switching regions, which makes the interaction independent of the nucleotide-binding state of Rab7. Thus, the effector-interacting switch regions of Rab7 are accessible for RILP binding, allowing formation of the ORP1-Rab7-RILP complex. ORP1 ANK binds to Rab7 and the Rab7-RILP complex with similar micro-molar affinities, which is consistent with the independence binding of ORP1 and RILP to Rab7. The structural model of the ORP1-Rab7-RILP complex correlates with the recruitment of ORP1 at the LEL-ER interface and the role in lipid transport and regulation.
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Affiliation(s)
- Junsen Tong
- College of Pharmacy, Chonnam National University, Gwangju, Republic of Korea
| | - Lingchen Tan
- College of Pharmacy, Chonnam National University, Gwangju, Republic of Korea
| | - ChangJu Chun
- College of Pharmacy, Chonnam National University, Gwangju, Republic of Korea
| | - Young Jun Im
- College of Pharmacy, Chonnam National University, Gwangju, Republic of Korea
- * E-mail:
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43
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Lipids and lipid domains of the yeast vacuole. Biochem Soc Trans 2018; 46:1047-1054. [PMID: 30242116 DOI: 10.1042/bst20180120] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 07/30/2018] [Accepted: 08/01/2018] [Indexed: 11/17/2022]
Abstract
The membrane raft has been a focus of intensive research for the past two decades. Liquid-ordered domains form in artificial liposomes containing sterol and saturated lipids, but their presence in living cell membranes has been controversial. The yeast vacuole is exceptional in that micron-sized raft-like domains form in the stationary phase and under several other conditions. The sterol content of the vacuole in the log phase is much lower than that of liposomes showing liquid-ordered domains, suggesting that sterols may need to be supplied to the vacuole for the raft-like domain formation. We will discuss how lipids and lipid domains are organized in the vacuolar membrane and examine whether evidence is strong enough to conclude that the observed micron-sized domains are rafts.
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44
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Pietrangelo A, Ridgway ND. Bridging the molecular and biological functions of the oxysterol-binding protein family. Cell Mol Life Sci 2018; 75:3079-3098. [PMID: 29536114 PMCID: PMC11105248 DOI: 10.1007/s00018-018-2795-y] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/18/2018] [Accepted: 03/07/2018] [Indexed: 12/19/2022]
Abstract
Oxysterol-binding protein (OSBP) and OSBP-related proteins (ORPs) constitute a large eukaryotic gene family that transports and regulates the metabolism of sterols and phospholipids. The original classification of the family based on oxysterol-binding activity belies the complex dual lipid-binding specificity of the conserved OSBP homology domain (OHD). Additional protein- and membrane-interacting modules mediate the targeting of select OSBP/ORPs to membrane contact sites between organelles, thus positioning the OHD between opposing membranes for lipid transfer and metabolic regulation. This unique subcellular location, coupled with diverse ligand preferences and tissue distribution, has identified OSBP/ORPs as key arbiters of membrane composition and function. Here, we will review how molecular models of OSBP/ORP-mediated intracellular lipid transport and regulation at membrane contact sites relate to their emerging roles in cellular and organismal functions.
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Affiliation(s)
- Antonietta Pietrangelo
- Atlantic Research Center, C306 CRC Bldg, Department of Pediatrics, and Biochemistry and Molecular Biology, Dalhousie University, 5849 University Av., Halifax, NS, B3H4R2, Canada
| | - Neale D Ridgway
- Atlantic Research Center, C306 CRC Bldg, Department of Pediatrics, and Biochemistry and Molecular Biology, Dalhousie University, 5849 University Av., Halifax, NS, B3H4R2, Canada.
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45
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Antonny B, Bigay J, Mesmin B. The Oxysterol-Binding Protein Cycle: Burning Off PI(4)P to Transport Cholesterol. Annu Rev Biochem 2018; 87:809-837. [PMID: 29596003 DOI: 10.1146/annurev-biochem-061516-044924] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To maintain an asymmetric distribution of ions across membranes, protein pumps displace ions against their concentration gradient by using chemical energy. Here, we describe a functionally analogous but topologically opposite process that applies to the lipid transfer protein (LTP) oxysterol-binding protein (OSBP). This multidomain protein exchanges cholesterol for the phosphoinositide phosphatidylinositol 4-phosphate [PI(4)P] between two apposed membranes. Because of the subsequent hydrolysis of PI(4)P, this counterexchange is irreversible and contributes to the establishment of a cholesterol gradient along organelles of the secretory pathway. The facts that some natural anti-cancer molecules block OSBP and that many viruses hijack the OSBP cycle for the formation of intracellular replication organelles highlight the importance and potency of OSBP-mediated lipid exchange. The architecture of some LTPs is similar to that of OSBP, suggesting that the principles of the OSBP cycle-burning PI(4)P for the vectorial transfer of another lipid-might be general.
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Affiliation(s)
- Bruno Antonny
- Institut de Pharmacologie Moléculaire et Cellulaire, CNRS UMR 7275, Université Côte d'Azur, 06560 Valbonne, France;
| | - Joëlle Bigay
- Institut de Pharmacologie Moléculaire et Cellulaire, CNRS UMR 7275, Université Côte d'Azur, 06560 Valbonne, France;
| | - Bruno Mesmin
- Institut de Pharmacologie Moléculaire et Cellulaire, CNRS UMR 7275, Université Côte d'Azur, 06560 Valbonne, France;
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46
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Structural basis of sterol recognition and nonvesicular transport by lipid transfer proteins anchored at membrane contact sites. Proc Natl Acad Sci U S A 2018; 115:E856-E865. [PMID: 29339490 DOI: 10.1073/pnas.1719709115] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Membrane contact sites (MCSs) in eukaryotic cells are hotspots for lipid exchange, which is essential for many biological functions, including regulation of membrane properties and protein trafficking. Lipid transfer proteins anchored at membrane contact sites (LAMs) contain sterol-specific lipid transfer domains [StARkin domain (SD)] and multiple targeting modules to specific membrane organelles. Elucidating the structural mechanisms of targeting and ligand recognition by LAMs is important for understanding the interorganelle communication and exchange at MCSs. Here, we determined the crystal structures of the yeast Lam6 pleckstrin homology (PH)-like domain and the SDs of Lam2 and Lam4 in the apo form and in complex with ergosterol. The Lam6 PH-like domain displays a unique PH domain fold with a conserved N-terminal α-helix. The Lam6 PH-like domain lacks the basic surface for phosphoinositide binding, but contains hydrophobic patches on its surface, which are critical for targeting to endoplasmic reticulum (ER)-mitochondrial contacts. Structures of the LAM SDs display a helix-grip fold with a hydrophobic cavity and a flexible Ω1-loop as a lid. Ergosterol is bound to the pocket in a head-down orientation, with its hydrophobic acyl group located in the tunnel entrance. The Ω1-loop in an open conformation is essential for ergosterol binding by direct hydrophobic interaction. Structural comparison suggested that the sterol binding mode of the Lam2 SD2 is likely conserved among the sterol transfer proteins of the StARkin superfamily. Structural models of full-length Lam2 correlated with the sterol transport function at the membrane contact sites.
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47
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Smindak RJ, Heckle LA, Chittari SS, Hand MA, Hyatt DM, Mantus GE, Sanfelippo WA, Kozminski KG. Lipid-dependent regulation of exocytosis in S. cerevisiae by OSBP homolog (Osh) 4. J Cell Sci 2017; 130:3891-3906. [PMID: 28993464 DOI: 10.1242/jcs.205435] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 10/04/2017] [Indexed: 11/20/2022] Open
Abstract
Polarized exocytosis is an essential process in many organisms and cell types for correct cell division or functional specialization. Previous studies established that homologs of the oxysterol-binding protein (OSBP) in S. cerevisiae, which comprise the Osh protein family, are necessary for efficient polarized exocytosis by supporting a late post-Golgi step. We define this step as the docking of a specific sub-population of exocytic vesicles with the plasma membrane. In the absence of other Osh proteins, yeast Osh4p can support this process in a manner dependent upon two lipid ligands, PI4P and sterol. Osh6p, which binds PI4P and phosphatidylserine, is also sufficient to support polarized exocytosis, again in a lipid-dependent manner. These data suggest that Osh-mediated exocytosis depends upon lipid binding and exchange without a strict requirement for sterol. We propose a two-step mechanism for Osh protein-mediated regulation of polarized exocytosis by using Osh4p as a model. We describe a specific in vivo role for lipid binding by an OSBP-related protein (ORP) in the process of polarized exocytosis, guiding our understanding of where and how OSBP and ORPs may function in more complex organisms.
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Affiliation(s)
- Richard J Smindak
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Lindsay A Heckle
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Supraja S Chittari
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Marissa A Hand
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Dylan M Hyatt
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Grace E Mantus
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | | | - Keith G Kozminski
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA .,Department of Cell Biology, University of Virginia, Charlottesville, VA 22908, USA
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