1
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Gaschignard G, Millet M, Bruley A, Benzerara K, Dezi M, Skouri-Panet F, Duprat E, Callebaut I. AlphaFold2-guided description of CoBaHMA, a novel family of bacterial domains within the heavy-metal-associated superfamily. Proteins 2024; 92:776-794. [PMID: 38258321 DOI: 10.1002/prot.26668] [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: 09/28/2023] [Revised: 12/22/2023] [Accepted: 01/01/2024] [Indexed: 01/24/2024]
Abstract
Three-dimensional (3D) structure information, now available at the proteome scale, may facilitate the detection of remote evolutionary relationships in protein superfamilies. Here, we illustrate this with the identification of a novel family of protein domains related to the ferredoxin-like superfold, by combining (i) transitive sequence similarity searches, (ii) clustering approaches, and (iii) the use of AlphaFold2 3D structure models. Domains of this family were initially identified in relation with the intracellular biomineralization of calcium carbonates by Cyanobacteria. They are part of the large heavy-metal-associated (HMA) superfamily, departing from the latter by specific sequence and structural features. In particular, most of them share conserved basic amino acids (hence their name CoBaHMA for Conserved Basic residues HMA), forming a positively charged surface, which is likely to interact with anionic partners. CoBaHMA domains are found in diverse modular organizations in bacteria, existing in the form of monodomain proteins or as part of larger proteins, some of which are membrane proteins involved in transport or lipid metabolism. This suggests that the CoBaHMA domains may exert a regulatory function, involving interactions with anionic lipids. This hypothesis might have a particular resonance in the context of the compartmentalization observed for cyanobacterial intracellular calcium carbonates.
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Affiliation(s)
- Geoffroy Gaschignard
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Maxime Millet
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Apolline Bruley
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Karim Benzerara
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Manuela Dezi
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Feriel Skouri-Panet
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Elodie Duprat
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
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2
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Gao L, Lam KH, Liu S, Przykopanski A, Lübke J, Qi R, Krüger M, Nowakowska MB, Selby K, Douillard FP, Dorner MB, Perry K, Lindström M, Dorner BG, Rummel A, Jin R. Crystal structures of OrfX1, OrfX2 and the OrfX1-OrfX3 complex from the orfX gene cluster of botulinum neurotoxin E1. FEBS Lett 2023; 597:524-537. [PMID: 36653893 PMCID: PMC10019085 DOI: 10.1002/1873-3468.14576] [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: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 01/20/2023]
Abstract
Botulinum neurotoxins (BoNTs) are among the most lethal toxins known to humans, comprising seven established serotypes termed BoNT/A-G encoded in two types of gene clusters (ha and orfX) in BoNT-producing clostridia. The ha cluster encodes four non-toxic neurotoxin-associated proteins (NAPs) that assemble with BoNTs to protect and enhance their oral toxicity. However, the structure and function of the orfX-type NAPs remain largely unknown. Here, we report the crystal structures for OrfX1, OrfX2, and an OrfX1-OrfX3 complex, which are encoded in the orfX cluster of a BoNT/E1-producing Clostridium botulinum strain associated with human foodborne botulism. These structures lay the foundation for future studies on the potential roles of OrfX proteins in oral intoxication and pathogenesis of BoNTs.
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Affiliation(s)
- Linfeng Gao
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA
| | - Kwok-ho Lam
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA
| | - Shun Liu
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA
| | - Adina Przykopanski
- Institute of Toxicology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Johanna Lübke
- Institute of Toxicology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Ruifeng Qi
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA
| | - Maren Krüger
- Biological Toxins, Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Seestrasse 10, 13353 Berlin, Germany
| | - Maria B. Nowakowska
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, P. O. Box 66, 00014 University of Helsinki, Finland
| | - Katja Selby
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, P. O. Box 66, 00014 University of Helsinki, Finland
| | - François P. Douillard
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, P. O. Box 66, 00014 University of Helsinki, Finland
| | - Martin B. Dorner
- Biological Toxins, Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Seestrasse 10, 13353 Berlin, Germany
| | - Kay Perry
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Miia Lindström
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, P. O. Box 66, 00014 University of Helsinki, Finland
| | - Brigitte G. Dorner
- Biological Toxins, Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Seestrasse 10, 13353 Berlin, Germany
| | - Andreas Rummel
- Institute of Toxicology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Rongsheng Jin
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA
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3
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Stepinac E, Landrein N, Skwarzyńska D, Wójcik P, Lesigang J, Lučić I, He CY, Bonhivers M, Robinson DR, Dong G. Structural studies of the shortest extended synaptotagmin with only two C2 domains from Trypanosoma brucei. iScience 2021; 24:102422. [PMID: 33997700 PMCID: PMC8093936 DOI: 10.1016/j.isci.2021.102422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/03/2021] [Accepted: 04/08/2021] [Indexed: 11/25/2022] Open
Abstract
Extended synaptotagmins (E-Syts) localize at membrane contact sites between the endoplasmic reticulum (ER) and the plasma membrane to mediate inter-membrane lipid transfer and control plasma membrane lipid homeostasis. All known E-Syts contain an N-terminal transmembrane (TM) hairpin, a central synaptotagmin-like mitochondrial lipid-binding protein (SMP) domain, and three or five C2 domains at their C termini. Here we report an uncharacterized E-Syt from the protist parasite Trypanosoma brucei, namely, TbE-Syt. TbE-Syt contains only two C2 domains (C2A and C2B), making it the shortest E-Syt known by now. We determined a 1.5-Å-resolution crystal structure of TbE-Syt-C2B and revealed that it binds lipids via both Ca2+- and PI(4,5)P2-dependent means. In contrast, TbE-Syt-C2A lacks the Ca2+-binding site but may still interact with lipids via a basic surface patch. Our studies suggest a mechanism for how TbE-Syt tethers the ER membrane tightly to the plasma membrane to transfer lipids between the two organelles. We identified a new type of extended synaptotagmin (E-Syt) in Trypanosoma brucei TbE-Syt is the shortest known E-Syt with only two C2 domains, C2A and C2B TbE-Syt-C2B binds lipids via both Ca2+- and PI(4,5)P2-dependent means Unlike all other known E-Syts, TbE-Syt-C2A and C2B are connected by a flexible loop
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Affiliation(s)
- Emma Stepinac
- Max Perutz Labs, Vienna Biocenter, Center for Medical Biochemistry, Medical University of Vienna, 1030 Vienna, Austria
| | - Nicolas Landrein
- University of Bordeaux, CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, 33000 Bordeaux, France
| | - Daria Skwarzyńska
- Max Perutz Labs, Vienna Biocenter, Center for Medical Biochemistry, Medical University of Vienna, 1030 Vienna, Austria.,Silesian University of Technology, Gliwice, Poland
| | - Patrycja Wójcik
- Max Perutz Labs, Vienna Biocenter, Center for Medical Biochemistry, Medical University of Vienna, 1030 Vienna, Austria.,Silesian University of Technology, Gliwice, Poland
| | - Johannes Lesigang
- Max Perutz Labs, Vienna Biocenter, Center for Medical Biochemistry, Medical University of Vienna, 1030 Vienna, Austria
| | - Iva Lučić
- Max Perutz Labs, Vienna Biocenter, Center for Medical Biochemistry, Medical University of Vienna, 1030 Vienna, Austria
| | - Cynthia Y He
- Department of Biological Sciences, Center for BioImaging Sciences, National University of Singapore, Singapore, Singapore
| | - Mélanie Bonhivers
- University of Bordeaux, CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, 33000 Bordeaux, France
| | - Derrick R Robinson
- University of Bordeaux, CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, 33000 Bordeaux, France
| | - Gang Dong
- Max Perutz Labs, Vienna Biocenter, Center for Medical Biochemistry, Medical University of Vienna, 1030 Vienna, Austria
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4
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Shah JS, Renthal R. Antennal Proteome of the Solenopsis invicta (Hymenoptera: Formicidae): Caste Differences in Olfactory Receptors and Chemosensory Support Proteins. JOURNAL OF INSECT SCIENCE (ONLINE) 2020; 20:5937575. [PMID: 33098433 PMCID: PMC7585320 DOI: 10.1093/jisesa/ieaa118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Indexed: 06/11/2023]
Abstract
Little is known about the expression pattern of odorant and pheromone transporters, receptors, and deactivation enzymes in the antennae of ants carrying out different tasks. In order to begin filling in this information gap, we compared the proteomes of the antennae of workers and males of the red fire ant, Solenopsis invicta Buren (Hymenoptera: Formicidae). Male ants do not perform any colony work, and their only activity is to leave the nest on a mating flight. Previous studies showed that male ants express fewer types of odorant receptors than workers. Thus, we expected to find large differences between male and worker antennae for expression of receptors, transporters, and deactivators of signaling chemicals. We found that the abundance of receptors was consistent with the expected caste-specific signaling complexity, but the numbers of different antenna-specific transporters and deactivating enzymes in males and workers were similar. It is possible that some of these proteins have antenna-specific functions that are unrelated to chemosensory reception. Alternatively, the similar complexity could be a vestige of ant progenitors that had more behaviorally active males. As the reduced behavior of male ants evolved, the selection process may have favored a complex repertoire of transporters and deactivating enzymes alongside a limited repertoire of odorant receptors.
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Affiliation(s)
- Jaee Shailesh Shah
- Department of Biology, University of Texas at San Antonio, San Antonio, TX
| | - Robert Renthal
- Department of Biology, University of Texas at San Antonio, San Antonio, TX
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5
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Pemberton JG, Kim YJ, Balla T. Integrated regulation of the phosphatidylinositol cycle and phosphoinositide-driven lipid transport at ER-PM contact sites. Traffic 2019; 21:200-219. [PMID: 31650663 DOI: 10.1111/tra.12709] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/02/2019] [Accepted: 10/16/2019] [Indexed: 12/20/2022]
Abstract
Among the structural phospholipids that form the bulk of eukaryotic cell membranes, phosphatidylinositol (PtdIns) is unique in that it also serves as the common precursor for low-abundance regulatory lipids, collectively referred to as polyphosphoinositides (PPIn). The metabolic turnover of PPIn species has received immense attention because of the essential functions of these lipids as universal regulators of membrane biology and their dysregulation in numerous human pathologies. The diverse functions of PPIn lipids occur, in part, by orchestrating the spatial organization and conformational dynamics of peripheral or integral membrane proteins within defined subcellular compartments. The emerging role of stable contact sites between adjacent membranes as specialized platforms for the coordinate control of ion exchange, cytoskeletal dynamics, and lipid transport has also revealed important new roles for PPIn species. In this review, we highlight the importance of membrane contact sites formed between the endoplasmic reticulum (ER) and plasma membrane (PM) for the integrated regulation of PPIn metabolism within the PM. Special emphasis will be placed on non-vesicular lipid transport during control of the PtdIns biosynthetic cycle as well as toward balancing the turnover of the signaling PPIn species that define PM identity.
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Affiliation(s)
- Joshua G Pemberton
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland
| | - Yeun Ju Kim
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland
| | - Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland
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6
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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: 12] [Impact Index Per Article: 2.4] [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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7
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Bian X, De Camilli P. In Vitro Assays to Measure the Membrane Tethering and Lipid Transport Activities of the Extended Synaptotagmins. Methods Mol Biol 2019; 1949:201-212. [PMID: 30790258 DOI: 10.1007/978-1-4939-9136-5_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
The three extended synaptotagmins (E-Syts) are endoplasmic reticulum (ER)-localized membrane proteins that mediate tethering of the ER to the plasma membrane (PM) via C2 domain-dependent interactions regulated by Ca2+ and/or PI(4,5)P2. The E-Syts also contains a Synaptotagmin-like Mitochondrial lipid-binding Protein (SMP) domain, a lipid-harboring module through which they mediate lipid transport between the two adjacent membranes. Here, we describe in vitro liposome-based methods to study the membrane tethering and lipid transport functions of E-Syt1. Its membrane tethering activity is monitored through a turbidity-based assay, and its lipid transport property is analyzed via fluorescence resonance energy transfer (FRET)-based assay. These in vitro methods have enabled us to gain insight into the mechanism of action and regulation of E-Syt1, such as the role of Ca2+ in releasing E-Syt1 from an autoinhibitory conformation. The same methods could be adapted to the study of other lipid transport proteins that function at membrane contact sites.
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Affiliation(s)
- Xin Bian
- Department of Neuroscience and Cell Biology, Howard Hughes Medical Institute, Program in Cellular Neuroscience, Neurodegeneration, and Repair, and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Pietro De Camilli
- Department of Neuroscience and Cell Biology, Howard Hughes Medical Institute, Program in Cellular Neuroscience, Neurodegeneration, and Repair, and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA.
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8
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Zhang H, Burrows J, Card GL, Attwood G, Wheeler TT, Arcus VL. The three dimensional structure of Bovine Salivary Protein 30b (BSP30b) and its interaction with specific rumen bacteria. PLoS One 2019; 14:e0206709. [PMID: 30978191 PMCID: PMC6461236 DOI: 10.1371/journal.pone.0206709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/26/2019] [Indexed: 11/18/2022] Open
Abstract
Bovine Salivary Protein 30b (BSP30b) is a member of the tubular lipid-binding (TULIP) superfamily that includes the human bactericidal/permeability-increasing proteins (BPI), lipopolysaccharide binding proteins (LBP) and palate, lung, and nasal epithelium carcinoma-associated proteins (PLUNC). BSP30b is most closely related to the PLUNC family and is predominantly found in bovine saliva. There are four BSP30 isoforms (BSP30a-d) and collectively, they are the most abundant protein component of bovine saliva. The PLUNC family members are proposed to be lipid binding proteins, although in most cases their lipid ligands are unknown. Here, we present the X-ray crystal structure of BSP30b at 2.0 Å resolution. We used a double methionine mutant and Se-Met SAD phasing to solve the structure. The structure adopts a curved cylindrical form with a hydrophobic channel formed by an α/β wrap, which is consistent with the TULIP superfamily. The structure of BSP30b in complex with oleic acid is also presented where the ligand is accommodated within the hydrophobic channel. The electron density for oleic acid suggests that the ligand is only partially occupied in the binding site implying that oleic acid may not be the preferred ligand. GFP-tagged BSP30b binds to the surface of olive oil droplets, as observed under fluorescent microscopy, and acts as a surfactant consistent with its association with decreased susceptibility to bloat in cattle. Bacteria extracted directly from bovine rumen contents indicate that the GFP_BSP30b fusion protein binds to a small number of selected bacterial species in vivo. These results suggest that BSP30b may bind to bacterial lipids from specific species and that this abundant protein may have important biological roles via interacting with rumen bacteria during feeding and rumination.
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Affiliation(s)
- Heng Zhang
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Judith Burrows
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Graeme L. Card
- Stanford Synchrotron Radiation Lightsource, Menlo Park, California, United States of America
| | - Graeme Attwood
- AgResearch Grasslands, Tennent Drive, Palmerston North, New Zealand
| | - Tom T. Wheeler
- Cawthron Research Institute, The Wood, Nelson, New Zealand
| | - Vickery L. Arcus
- School of Science, University of Waikato, Hamilton, New Zealand
- * E-mail:
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9
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AhYoung AP, Egea PF. Determining the Lipid-Binding Specificity of SMP Domains: An ERMES Subunit as a Case Study. Methods Mol Biol 2019; 1949:213-235. [PMID: 30790259 DOI: 10.1007/978-1-4939-9136-5_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Membrane contact sites between the endoplasmic reticulum (ER) and mitochondria function as a central hub for the exchange of phospholipids and calcium. The yeast Endoplasmic Reticulum-Mitochondrion Encounter Structure (ERMES) complex is composed of five subunits that tether the ER and mitochondria. Three ERMES subunits (i.e., Mdm12, Mmm1, and Mdm34) contain the synaptotagmin-like mitochondrial lipid-binding protein (SMP) domain. The SMP domain belongs to the tubular lipid-binding protein (TULIP) superfamily, which consists of ubiquitous lipid scavenging and transfer proteins. Herein, we describe the methods for expression and purification of recombinant Mdm12, a bona fide SMP-containing protein, together with the subsequent identification of its bound phospholipids by high-performance thin-layer chromatography (HPTLC) and the characterization of its lipid exchange and transfer functions using lipid displacement and liposome flotation in vitro assays with liposomes as model biological membranes. These methods can be applied to the study and characterization of novel lipid-binding and lipid-transfer proteins.
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Affiliation(s)
- Andrew P AhYoung
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Early Discovery Biochemistry, Genentech Inc., South San Francisco, CA, USA
| | - Pascal F Egea
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- The Molecular Biology Institute, University of California, Los Angeles, CA, USA.
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10
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Bülow S, Zeller L, Werner M, Toelge M, Holzinger J, Entzian C, Schubert T, Waldow F, Gisch N, Hammerschmidt S, Gessner A. Bactericidal/Permeability-Increasing Protein Is an Enhancer of Bacterial Lipoprotein Recognition. Front Immunol 2018; 9:2768. [PMID: 30581431 PMCID: PMC6293271 DOI: 10.3389/fimmu.2018.02768] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 11/12/2018] [Indexed: 12/12/2022] Open
Abstract
Adequate perception of immunologically important pathogen-associated molecular patterns like lipopolysaccharide and bacterial lipoproteins is essential for efficient innate and adaptive immune responses. In the context of Gram-negative infection, bactericidal/permeability-increasing protein (BPI) neutralizes endotoxic activity of lipopolysaccharides, and thus prohibits hyperactivation. So far, no immunological function of BPI has been described in Gram-positive infections. Here, we show a significant elevation of BPI in Gram-positive meningitis and, surprisingly, a positive correlation between BPI and pro-inflammatory markers like TNFα. To clarify the underlying mechanisms, we identify BPI ligands of Gram-positive origin, specifically bacterial lipopeptides and lipoteichoic acids, and determine essential structural motifs for this interaction. Importantly, the interaction of BPI with these newly defined ligands significantly enhances the immune response in peripheral blood mononuclear cells (PBMCs) mediated by Gram-positive bacteria, and thereby ensures their sensitive perception. In conclusion, we define BPI as an immune enhancing pattern recognition molecule in Gram-positive infections.
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Affiliation(s)
- Sigrid Bülow
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Lisa Zeller
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Maren Werner
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Martina Toelge
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Jonas Holzinger
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | | | | | - Franziska Waldow
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Nicolas Gisch
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Sven Hammerschmidt
- Department of Molecular Genetics and Infection Biology, Center for Functional Genomcis of Microbes, Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - André Gessner
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
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11
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Saurabh S, Vanaphan N, Wen W, Dauwalder B. High functional conservation of takeout family members in a courtship model system. PLoS One 2018; 13:e0204615. [PMID: 30261021 PMCID: PMC6160090 DOI: 10.1371/journal.pone.0204615] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 09/11/2018] [Indexed: 11/19/2022] Open
Abstract
takeout (to) is one of the male-specific genes expressed in the fat body that regulate male courtship behavior, and has been shown to act as a secreted protein in conjunction with courtship circuits. There are 23 takeout family members in Drosophila melanogaster, and homologues of this family are distributed across insect species. Sequence conservation among family members is low. Here we test the functional conservation of takeout family members by examining whether they can rescue the takeout courtship defect. We find that despite their sequence divergence takeout members from Aedes aegypti and Epiphas postvittana, as well as family members from D. melanogaster can substitute for takeout in courtship, demonstrating their functional conservation. Making use of the known E. postvittana Takeout structure, we used homology modeling and amphipathic helix analysis and found high overall structural conservation, including high conservation of the structure and amphipathic lining of an internal cavity that has been shown to accommodate hydrophobic ligands. Together these data suggest a high degree of structural conservation that likely underlies functional conservation in courtship. In addition, we have identified a role for a conserved exposed protein motif important for the protein’s role in courtship.
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Affiliation(s)
- Sumit Saurabh
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Nancy Vanaphan
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Walter Wen
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Brigitte Dauwalder
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
- * E-mail:
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12
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van Vliet AR, Sassano ML, Agostinis P. The Unfolded Protein Response and Membrane Contact Sites: Tethering as a Matter of Life and Death? ACTA ACUST UNITED AC 2018. [DOI: 10.1177/2515256418770512] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The endoplasmic reticulum (ER) is the most extensive organelle of the eukaryotic cell and constitutes the major site of protein and lipid synthesis and regulation of intracellular Ca2+ levels. To exert these functions properly, the ER network is shaped in structurally and functionally distinct domains that dynamically remodel in response to intrinsic and extrinsic cues. Moreover, the ER establishes a tight communication with virtually all organelles of the cell through specific subdomains called membrane contact sites. These contact sites allow preferential, nonvesicular channeling of key biological mediators including lipids and Ca2+ between organelles and are harnessed by the ER to interface with and coregulate a variety of organellar functions that are vital to maintain homeostasis. When ER homeostasis is lost, a condition that triggers the activation of an evolutionarily conserved pathway called the unfolded protein response (UPR), the ER undergoes rapid remodeling. These dynamic changes in ER morphology are functionally coupled to the modulation or formation of contact sites with key organelles, such as mitochondria and the plasma membrane, which critically regulate cell fate decisions of the ER-stressed cells. Certain components of the UPR have been shown to facilitate the formation of contact sites through various mechanisms including remodeling of the actin cytoskeleton. In this review, we discuss old and emerging evidence linking the UPR machinery to contact site formation in mammalian cells and discuss their important role in cellular homeostasis.
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Affiliation(s)
- Alexander R. van Vliet
- Cell Death Research & Therapy Laboratory, Department of Cellular and Molecular Medicine, KU Leuven-University of Leuven, Belgium
| | - Maria Livia Sassano
- Cell Death Research & Therapy Laboratory, Department of Cellular and Molecular Medicine, KU Leuven-University of Leuven, Belgium
| | - Patrizia Agostinis
- Cell Death Research & Therapy Laboratory, Department of Cellular and Molecular Medicine, KU Leuven-University of Leuven, Belgium
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13
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Kawano S, Tamura Y, Kojima R, Bala S, Asai E, Michel AH, Kornmann B, Riezman I, Riezman H, Sakae Y, Okamoto Y, Endo T. Structure-function insights into direct lipid transfer between membranes by Mmm1-Mdm12 of ERMES. J Cell Biol 2017; 217:959-974. [PMID: 29279306 PMCID: PMC5839780 DOI: 10.1083/jcb.201704119] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 11/06/2017] [Accepted: 12/01/2017] [Indexed: 12/26/2022] Open
Abstract
The ER–mitochondrial encounter structure (ERMES) physically links ER and mitochondrial membranes in yeast, but it is unclear whether ERMES directly facilitates lipid exchange between these organelles. Kawano et al. reveal by reconstitution experiments that a complex of Mmm1–Mdm12, two core subunits of ERMES, functions as a minimal unit for lipid transfer between membranes. The endoplasmic reticulum (ER)–mitochondrial encounter structure (ERMES) physically links the membranes of the ER and mitochondria in yeast. Although the ER and mitochondria cooperate to synthesize glycerophospholipids, whether ERMES directly facilitates the lipid exchange between the two organelles remains controversial. Here, we compared the x-ray structures of an ERMES subunit Mdm12 from Kluyveromyces lactis with that of Mdm12 from Saccharomyces cerevisiae and found that both Mdm12 proteins possess a hydrophobic pocket for phospholipid binding. However in vitro lipid transfer assays showed that Mdm12 alone or an Mmm1 (another ERMES subunit) fusion protein exhibited only a weak lipid transfer activity between liposomes. In contrast, Mdm12 in a complex with Mmm1 mediated efficient lipid transfer between liposomes. Mutations in Mmm1 or Mdm12 impaired the lipid transfer activities of the Mdm12–Mmm1 complex and furthermore caused defective phosphatidylserine transport from the ER to mitochondrial membranes via ERMES in vitro. Therefore, the Mmm1–Mdm12 complex functions as a minimal unit that mediates lipid transfer between membranes.
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Affiliation(s)
- Shin Kawano
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan.,Japan Science and Technology Agency/Core Research for Evolutional Science and Technology, Kyoto Sangyo University, Kyoto, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Japan.,Japan Science and Technology Agency/Core Research for Evolutional Science and Technology, Nagoya University, Nagoya, Japan
| | - Yasushi Tamura
- Japan Science and Technology Agency/Core Research for Evolutional Science and Technology, Nagoya University, Nagoya, Japan.,Research Center for Materials Science, Nagoya University, Nagoya, Japan.,Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata, Japan
| | - Rieko Kojima
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata, Japan
| | - Siqin Bala
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Eri Asai
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Agnès H Michel
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
| | | | - Isabelle Riezman
- Department of Biochemistry, National Centre of Competence in Research Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Howard Riezman
- Department of Biochemistry, National Centre of Competence in Research Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Yoshitake Sakae
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Yuko Okamoto
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Toshiya Endo
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan .,Japan Science and Technology Agency/Core Research for Evolutional Science and Technology, Kyoto Sangyo University, Kyoto, Japan.,Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Japan.,Japan Science and Technology Agency/Core Research for Evolutional Science and Technology, Nagoya University, Nagoya, Japan
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14
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Bian X, Saheki Y, De Camilli P. Ca 2+ releases E-Syt1 autoinhibition to couple ER-plasma membrane tethering with lipid transport. EMBO J 2017; 37:219-234. [PMID: 29222176 DOI: 10.15252/embj.201797359] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 11/08/2017] [Accepted: 11/10/2017] [Indexed: 11/09/2022] Open
Abstract
The extended synaptotagmins (E-Syts) are endoplasmic reticulum (ER) proteins that bind the plasma membrane (PM) via C2 domains and transport lipids between them via SMP domains. E-Syt1 tethers and transports lipids in a Ca2+-dependent manner, but the role of Ca2+ in this regulation is unclear. Of the five C2 domains of E-Syt1, only C2A and C2C contain Ca2+-binding sites. Using liposome-based assays, we show that Ca2+ binding to C2C promotes E-Syt1-mediated membrane tethering by releasing an inhibition that prevents C2E from interacting with PI(4,5)P2-rich membranes, as previously suggested by studies in semi-permeabilized cells. Importantly, Ca2+ binding to C2A enables lipid transport by releasing a charge-based autoinhibitory interaction between this domain and the SMP domain. Supporting these results, E-Syt1 constructs defective in Ca2+ binding in either C2A or C2C failed to rescue two defects in PM lipid homeostasis observed in E-Syts KO cells, delayed diacylglycerol clearance from the PM and impaired Ca2+-triggered phosphatidylserine scrambling. Thus, a main effect of Ca2+ on E-Syt1 is to reverse an autoinhibited state and to couple membrane tethering with lipid transport.
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Affiliation(s)
- Xin Bian
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA.,Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA.,Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
| | - Yasunori Saheki
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA .,Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA.,Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Pietro De Camilli
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA .,Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA.,Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA.,Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA
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15
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Gustafsson R, Berntsson RPA, Martínez-Carranza M, El Tekle G, Odegrip R, Johnson EA, Stenmark P. Crystal structures of OrfX2 and P47 from a Botulinum neurotoxin OrfX-type gene cluster. FEBS Lett 2017; 591:3781-3792. [PMID: 29067689 DOI: 10.1002/1873-3468.12889] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 10/17/2017] [Accepted: 10/18/2017] [Indexed: 11/08/2022]
Abstract
Botulinum neurotoxins are highly toxic substances and are all encoded together with one of two alternative gene clusters, the HA or the OrfX gene cluster. Very little is known about the function and structure of the proteins encoded in the OrfX gene cluster, which in addition to the toxin contains five proteins (OrfX1, OrfX2, OrfX3, P47, and NTNH). We here present the structures of OrfX2 and P47, solved to 2.1 and 1.8 Å, respectively. We show that they belong to the TULIP protein superfamily, which are often involved in lipid binding. OrfX1 and OrfX2 were both found to bind phosphatidylinositol lipids.
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Affiliation(s)
- Robert Gustafsson
- Department of Biochemistry and Biophysics, Stockholm University, Sweden
| | - Ronnie P-A Berntsson
- Department of Biochemistry and Biophysics, Stockholm University, Sweden.,Department of Medical Biochemistry and Biophysics, Umeå University, Sweden
| | | | - Geniver El Tekle
- Department of Biochemistry and Biophysics, Stockholm University, Sweden
| | - Richard Odegrip
- Department of Biochemistry and Biophysics, Stockholm University, Sweden
| | - Eric A Johnson
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, Sweden
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16
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The hypothetical protein P47 of Clostridium botulinum E1 strain Beluga has a structural topology similar to bactericidal/permeability-increasing protein. Toxicon 2017; 147:19-26. [PMID: 29042313 DOI: 10.1016/j.toxicon.2017.10.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/13/2017] [Indexed: 12/30/2022]
Abstract
Botulinum neurotoxins (BoNTs) are causative agents of the life-threatening disease botulism. They are naturally produced by species of the bacteria Clostridium botulinum as stable and non-covalent complexes, in which the BoNT molecule is assembled with several auxiliary non-toxic proteins. Some BoNT serotypes, represented by the well-studied BoNT serotype A (BoNT/A), are produced by Clostridium strains that carry the ha gene cluster, which encodes four neurotoxin-associated proteins (NTNHA, HA17, HA33, and HA70) that play an important role to deliver and protect BoNTs in the gastrointestinal tract during oral intoxication. In contrast, BoNT/E- and BoNT/F-producing strains carry a distinct gene cluster that encodes five proteins (NTNHA, P47, OrfX1, OrfX2, and OrfX3, termed the orfX cluster). The structures and functions of these proteins remain largely unknown. Here, we report the crystal structure of P47 resolved at 2.8 Å resolution. Surprisingly, P47 displays a structural topology that is similar to bactericidal/permeability-increasing (BPI) like proteins, which were previously identified only in eukaryotes. The similarity of a hydrophobic cleft of P47 with the phospholipid-binding groove of BPI suggests that P47 might be involved in lipid association to exert its function. Consistently, P47 associates and induces aggregation of asolectin-containing liposomes in a protein- and lipid-concentration dependent manner. These findings laid the foundation for future structural and functional studies of the potential roles of P47 and OrfX proteins in facilitating oral intoxication of BoNTs.
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17
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Muallem S, Chung WY, Jha A, Ahuja M. Lipids at membrane contact sites: cell signaling and ion transport. EMBO Rep 2017; 18:1893-1904. [PMID: 29030479 DOI: 10.15252/embr.201744331] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 06/10/2017] [Accepted: 09/21/2017] [Indexed: 12/14/2022] Open
Abstract
Communication between organelles is essential to coordinate cellular functions and the cell's response to physiological and pathological stimuli. Organellar communication occurs at membrane contact sites (MCSs), where the endoplasmic reticulum (ER) membrane is tethered to cellular organelle membranes by specific tether proteins and where lipid transfer proteins and cell signaling proteins are located. MCSs have many cellular functions and are the sites of lipid and ion transfer between organelles and generation of second messengers. This review discusses several aspects of MCSs in the context of lipid transfer, formation of lipid domains, generation of Ca2+ and cAMP second messengers, and regulation of ion transporters by lipids.
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Affiliation(s)
- Shmuel Muallem
- Epithelial Signaling and Transport Section, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA
| | - Woo Young Chung
- Epithelial Signaling and Transport Section, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA
| | - Archana Jha
- Epithelial Signaling and Transport Section, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA
| | - Malini Ahuja
- Epithelial Signaling and Transport Section, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA
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18
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Wong LH, Levine TP. Tubular lipid binding proteins (TULIPs) growing everywhere. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:1439-1449. [PMID: 28554774 PMCID: PMC5507252 DOI: 10.1016/j.bbamcr.2017.05.019] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/11/2017] [Accepted: 05/17/2017] [Indexed: 12/27/2022]
Abstract
Tubular lipid binding proteins (TULIPs) have become a focus of interest in the cell biology of lipid signalling, lipid traffic and membrane contact sites. Each tubular domain has an internal pocket with a hydrophobic lining that can bind a hydrophobic molecule such as a lipid. This allows TULIP proteins to carry lipids through the aqueous phase. TULIP domains were first found in a large family of extracellular proteins related to the bacterial permeability-inducing protein (BPI) and cholesterol ester transfer protein (CETP). Since then, the same fold and lipid transfer capacity have been found in SMP domains (so-called for their occurrence in synaptotagmin, mitochondrial and lipid binding proteins), which localise to intracellular membrane contact sites. Here the methods for identifying known TULIPs are described, and used to find previously unreported TULIPs, one in the silk polymer and another in prokaryotes illustrated by the E. coli protein YceB. The bacterial TULIP alters views on the likely evolution of the domain, suggesting its presence in the last universal common ancestor. The major function of TULIPs is to handle lipids, but we still do not know how they work in detail, or how many more remain to be discovered. This article is part of a Special Issue entitled: Membrane Contact Sites edited by Christian Ungermann and Benoit Kornmann. Proteins with the tubular lipid binding fold exist in a wider variety than is usually appreciated. TULIPs are found in prokaryotes, altering views on their evolution. It is not yet known whether TULIPs transfer lipids as tunnels or as shuttles. Tests have not yet been done to say if TULIPs with SMP domains (for example E-syts and ERMES components) tether contact sites. It is likely that more TULIPs remain to be discovered.
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Affiliation(s)
- Louise H Wong
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Tim P Levine
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK.
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19
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Abstract
Ca2+ influx across the plasma membrane is a key component of the receptor-evoked Ca2+ signaling that mediate numerous cell functions and reload the ER after partial or full ER Ca2+ store depletion. Ca2+ influx is activated in response to Ca2+ release from the ER, a concept developed by Jim Putney, and the channels mediating the influx are thus called store-operated Ca2+ influx channels, or SOCs. The molecular identity of the SOCs has been determined with the identification of the TRPC channels, STIM1 and the Orai channels. These channels are targeted to, operate and are regulated when at the ER/PM junctions. ER/PM junctions are a form of membrane contact sites (MCSs) that are present in all parts of the cells, where the ER makes contacts with cellular membranes and organelles. MCSs have many cellular functions, and are the sites of lipid and Ca2+ transport and delivery between organelles. This short review discusses aspects of MCSs in the context of Ca2+ transport.
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Affiliation(s)
- Woo Young Chung
- From the Epithelial Signaling and Transport Section, National Institute of Dental and Craniofacial Research, National Institute of Health, Bethesda MD 20892, United States
| | - Archana Jha
- From the Epithelial Signaling and Transport Section, National Institute of Dental and Craniofacial Research, National Institute of Health, Bethesda MD 20892, United States
| | - Malini Ahuja
- From the Epithelial Signaling and Transport Section, National Institute of Dental and Craniofacial Research, National Institute of Health, Bethesda MD 20892, United States
| | - Shmuel Muallem
- From the Epithelial Signaling and Transport Section, National Institute of Dental and Craniofacial Research, National Institute of Health, Bethesda MD 20892, United States.
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20
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Endoplasmic Reticulum - Plasma Membrane Crosstalk Mediated by the Extended Synaptotagmins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 997:83-93. [PMID: 28815523 DOI: 10.1007/978-981-10-4567-7_6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The endoplasmic reticulum (ER) possesses multiplicity of functions including protein synthesis, membrane lipid biogenesis, and Ca2+ storage and has broad localization throughout the cell. While the ER and most other membranous organelles are highly interconnected via vesicular traffic that relies on membrane budding and fusion reactions, the ER forms direct contacts with virtually all other membranous organelles, including the plasma membrane (PM), without membrane fusion. Growing evidence suggests that these contacts play major roles in cellular physiology, including the regulation of Ca2+ homeostasis and signaling and control of cellular lipid homeostasis. Extended synaptotagmins (E-Syts) are evolutionarily conserved family of ER-anchored proteins that tether the ER to the PM in PM PI(4,5)P2-dependent and cytosolic Ca2+-regulated manner. In addition, E-Syts possess a cytosolically exposed lipid-harboring module that confers the ability to transfer/exchange glycerolipids between the ER and the PM at E-Syts-mediated ER-PM contacts. In this chapter, the functions of ER-PM contacts and their role in non-vesicular lipid transport with special emphasis on the crosstalk between the two bilayers mediated by E-Syts will be discussed.
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21
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Tamura Y, Endo T. Role of Intra- and Inter-mitochondrial Membrane Contact Sites in Yeast Phospholipid Biogenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 997:121-133. [PMID: 28815526 DOI: 10.1007/978-981-10-4567-7_9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Eukaryotic cells exhibit intracellular compartments called organelles wherein various specialized enzymatic reactions occur. Despite the specificity of the characteristic functions of organelles, recent studies have shown that distinct organelles physically connect and communicate with each other to maintain the integrity of their functions. In yeast, multiple inter- and intramitochondrial membrane contact sites (MCSs) were identified to date and were proposed to be involved in phospholipid biogenesis. In the present article, we focus on inter- and intra-organellar MCSs involving mitochondria and their tethering factors, such as the ERMES (endoplasmic reticulum (ER)-mitochondria encounter structure) complex and EMC (conserved ER membrane protein complex) between mitochondria and the ER, vCLAMP (vacuole and mitochondria patch) between mitochondria and vacuoles, and the MICOS (mitochondrial contact site) complex between the mitochondrial outer and inner membranes (MOM and MIM). All of these membrane-tethering factors were proposed to be involved in phospholipid biogenesis. Furthermore, the existence of functional interconnections among multiple organelle contact sites is suggested. In the present article, we summarize the latest discoveries in regard to MCSs and MCS-forming factors involving mitochondria and discuss their molecular functions, with particular focus on phospholipid metabolism in yeast.
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Affiliation(s)
- Yasushi Tamura
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata, 990-8560, Japan.
| | - Toshiya Endo
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
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22
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Fernández-Murray JP, McMaster CR. Lipid synthesis and membrane contact sites: a crossroads for cellular physiology. J Lipid Res 2016; 57:1789-1805. [PMID: 27521373 DOI: 10.1194/jlr.r070920] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Indexed: 12/17/2022] Open
Abstract
Membrane contact sites (MCSs) are regions of close apposition between different organelles that contribute to the functional integration of compartmentalized cellular processes. In recent years, we have gained insight into the molecular architecture of several contact sites, as well as into the regulatory mechanisms that underlie their roles in cell physiology. We provide an overview of two selected topics where lipid metabolism intersects with MCSs and organelle dynamics. First, the role of phosphatidic acid phosphatase, Pah1, the yeast homolog of metazoan lipin, toward the synthesis of triacylglycerol is outlined in connection with the seipin complex, Fld1/Ldb16, and lipid droplet formation. Second, we recapitulate the different contact sites connecting mitochondria and the endomembrane system and emphasize their contribution to phospholipid synthesis and their coordinated regulation. A comprehensive view is emerging where the multiplicity of contact sites connecting different cellular compartments together with lipid transfer proteins functioning at more than one MCS allow for functional redundancy and cross-regulation.
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23
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Gallo A, Vannier C, Galli T. Endoplasmic Reticulum-Plasma Membrane Associations:Structures and Functions. Annu Rev Cell Dev Biol 2016; 32:279-301. [PMID: 27298092 DOI: 10.1146/annurev-cellbio-111315-125024] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Inside eukaryotic cells, membrane contact sites (MCSs), regions where two membrane-bound organelles are apposed at less than 30 nm, generate regions of important lipid and calcium exchange. This review principally focuses on the structure and the function of MCSs between the endoplasmic reticulum (ER) and the plasma membrane (PM). Here we describe how tethering structures form and maintain these junctions and, in some instances, participate in their function. We then discuss recent insights into the mechanisms by which specific classes of proteins mediate nonvesicular lipid exchange between the ER and PM and how such phenomena, already known to be crucial for maintaining organelle identity, are also emerging as regulators of cell growth and development.
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Affiliation(s)
- Alessandra Gallo
- Membrane Traffic in Health & Disease Group (INSERM ERL U950), F-75013 Paris, France;
| | - Christian Vannier
- Membrane Traffic in Health & Disease Group (INSERM ERL U950), F-75013 Paris, France;
| | - Thierry Galli
- Membrane Traffic in Health & Disease Group (INSERM ERL U950), F-75013 Paris, France;
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24
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Walton WG, Ahmad S, Little MR, Kim CS, Tyrrell J, Lin Q, Di YP, Tarran R, Redinbo MR. Structural Features Essential to the Antimicrobial Functions of Human SPLUNC1. Biochemistry 2016; 55:2979-91. [PMID: 27145151 PMCID: PMC4887393 DOI: 10.1021/acs.biochem.6b00271] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
SPLUNC1 is an abundantly secreted innate immune protein in the mammalian respiratory tract that exerts bacteriostatic and antibiofilm effects, binds to lipopolysaccharide (LPS), and acts as a fluid-spreading surfactant. Here, we unravel the structural elements essential for the surfactant and antimicrobial functions of human SPLUNC1 (short palate lung nasal epithelial clone 1). A unique α-helix (α4) that extends from the body of SPLUNC1 is required for the bacteriostatic, surfactant, and LPS binding activities of this protein. Indeed, we find that mutation of just four leucine residues within this helical motif to alanine is sufficient to significantly inhibit the fluid spreading abilities of SPLUNC1, as well as its bacteriostatic actions against Gram-negative pathogens Burkholderia cenocepacia and Pseudomonas aeruginosa. Conformational flexibility in the body of SPLUNC1 is also involved in the bacteriostatic, surfactant, and LPS binding functions of the protein as revealed by disulfide mutants introduced into SPLUNC1. In addition, SPLUNC1 exerts antibiofilm effects against Gram-negative bacteria, although α4 is not involved in this activity. Interestingly, though, the introduction of surface electrostatic mutations away from α4 based on the unique dolphin SPLUNC1 sequence, and confirmed by crystal structure, is shown to impart antibiofilm activity against Staphylococcus aureus, the first SPLUNC1-dependent effect against a Gram-positive bacterium reported to date. Together, these data pinpoint SPLUNC1 structural motifs required for the antimicrobial and surfactant actions of this protective human protein.
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Affiliation(s)
- William G. Walton
- Departments of Chemistry, Biochemistry and Microbiology, 4350 Genome Sciences Building, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - Saira Ahmad
- Marsico Lung Institute, Cystic Fibrosis/Pulmonary Research and Treatment Center, 7102 Marsico Hall, University of North Carolina, Chapel Hill, NC 27599-7248, USA
| | - Michael R. Little
- Departments of Chemistry, Biochemistry and Microbiology, 4350 Genome Sciences Building, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - Christine S.K. Kim
- Marsico Lung Institute, Cystic Fibrosis/Pulmonary Research and Treatment Center, 7102 Marsico Hall, University of North Carolina, Chapel Hill, NC 27599-7248, USA
| | - Jean Tyrrell
- Marsico Lung Institute, Cystic Fibrosis/Pulmonary Research and Treatment Center, 7102 Marsico Hall, University of North Carolina, Chapel Hill, NC 27599-7248, USA
| | - Qiao Lin
- Department of Environmental and Occupational Health, 331 Bridgeside Point Building, University of Pittsburgh, Pittsburgh, PA 15260
| | - Y. Peter Di
- Department of Environmental and Occupational Health, 331 Bridgeside Point Building, University of Pittsburgh, Pittsburgh, PA 15260
| | - Robert Tarran
- Marsico Lung Institute, Cystic Fibrosis/Pulmonary Research and Treatment Center, 7102 Marsico Hall, University of North Carolina, Chapel Hill, NC 27599-7248, USA
| | - Matthew R. Redinbo
- Departments of Chemistry, Biochemistry and Microbiology, 4350 Genome Sciences Building, University of North Carolina, Chapel Hill, NC 27599-3290, USA,Corresponding Author: 4350 Genome Sciences Building, University of North Carolina, Chapel Hill, NC 27599-3290, USA, 919-962-4581, 919-962-2388 fax,
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25
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Control of plasma membrane lipid homeostasis by the extended synaptotagmins. Nat Cell Biol 2016; 18:504-15. [PMID: 27065097 PMCID: PMC4848133 DOI: 10.1038/ncb3339] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 03/11/2016] [Indexed: 02/08/2023]
Abstract
Acute metabolic changes of plasma membrane (PM) lipids, such as those mediating signaling reactions, are rapidly compensated by homeostatic responses whose molecular basis is poorly understood. Here we show that the Extended-Synaptotagmins (E-Syts), ER proteins which function as PI(4,5)P2 and Ca2+-regulated tethers to the PM, participate in these responses. E-Syts transfer glycerolipids between bilayers in vitro and such transfer requires Ca2+ and their SMP domain, a lipid-harboring module. Genome edited cells lacking E-Syts do not exhibit abnormalities in the major glycerolipids at rest, but display enhanced and sustained accumulation of PM diacylglycerol (DAG) upon PI(4,5)P2 hydrolysis by PLC activation, which can be rescued by expression of E-Syt1, but not by mutant E-Syt1 lacking the SMP domain. The formation of E-Syts-dependent ER-PM tethers in response to stimuli that cleave PI(4,5)P2 and elevate Ca2+ may help reverse accumulation of DAG in the PM by transferring it to the ER for metabolic recycling.
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Extended synaptotagmins are Ca2+-dependent lipid transfer proteins at membrane contact sites. Proc Natl Acad Sci U S A 2016; 113:4362-7. [PMID: 27044075 DOI: 10.1073/pnas.1517259113] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Organelles are in constant communication with each other through exchange of proteins (mediated by trafficking vesicles) and lipids [mediated by both trafficking vesicles and lipid transfer proteins (LTPs)]. It has long been known that vesicle trafficking can be tightly regulated by the second messenger Ca(2+), allowing membrane protein transport to be adjusted according to physiological demands. However, it remains unclear whether LTP-mediated lipid transport can also be regulated by Ca(2+) In this work, we show that extended synaptotagmins (E-Syts), poorly understood membrane proteins at endoplasmic reticulum-plasma membrane contact sites, are Ca(2+)-dependent LTPs. Using both recombinant and endogenous mammalian proteins, we discovered that E-Syts transfer glycerophospholipids between membrane bilayers in the presence of Ca(2+) E-Syts use their lipid-accommodating synaptotagmin-like mitochondrial lipid binding protein (SMP) domains to transfer lipids. However, the SMP domains themselves cannot transport lipids unless the two membranes are tightly tethered by Ca(2+)-bound C2 domains. Strikingly, the Ca(2+)-regulated lipid transfer activity of E-Syts was fully recapitulated when the SMP domain was fused to the cytosolic domain of synaptotagmin-1, the Ca(2+)sensor in synaptic vesicle fusion, indicating that a common mechanism of membrane tethering governs the Ca(2+)regulation of lipid transfer and vesicle fusion. Finally, we showed that microsomal vesicles isolated from mammalian cells contained robust Ca(2+)-dependent lipid transfer activities, which were mediated by E-Syts. These findings established E-Syts as a novel class of LTPs and showed that LTP-mediated lipid trafficking, like vesicular transport, can be subject to tight Ca(2+)regulation.
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Walley KR, Francis GA, Opal SM, Stein EA, Russell JA, Boyd JH. The Central Role of Proprotein Convertase Subtilisin/Kexin Type 9 in Septic Pathogen Lipid Transport and Clearance. Am J Respir Crit Care Med 2016; 192:1275-86. [PMID: 26252194 DOI: 10.1164/rccm.201505-0876ci] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Microbial cell walls contain pathogenic lipids, including LPS in gram-negative bacteria, lipoteichoic acid in gram-positive bacteria, and phospholipomannan in fungi. These pathogen lipids are major ligands for innate immune receptors and figure prominently in triggering the septic inflammatory response. Alternatively, pathogen lipids can be cleared and inactivated, thus limiting the inflammatory response. Accordingly, biological mechanisms for sequestering and clearing pathogen lipids from the circulation have evolved. Pathogen lipids released into the circulation are initially bound by transfer proteins, notably LPS binding protein and phospholipid transfer protein, and incorporated into high-density lipoprotein particles. Next, LPS binding protein, phospholipid transfer protein, and other transfer proteins transfer these lipids to ApoB-containing lipoproteins, including low-density (LDL) and very-low-density lipoproteins and chylomicrons. Pathogen lipids within these lipoproteins and their remnants are then cleared from the circulation by the liver. Hepatic clearance involves the LDL receptor (LDLR) and possibly other receptors. Once absorbed by the liver, these lipids are then excreted in the bile. Recent evidence suggests pathogen lipid clearance can be modulated. Importantly, reduced proprotein convertase subtilisin/kexin type 9 activity increases recycling of the LDLR and thereby increases LDLR on the surface of hepatocytes, which increases clearance by the liver of pathogen lipids transported in LDL. Increased pathogen lipid clearance, which can be achieved by inhibiting proprotein convertase subtilisin/kexin type 9, may decrease the systemic inflammatory response to sepsis and improve clinical outcomes.
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Affiliation(s)
- Keith R Walley
- 1 Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gordon A Francis
- 1 Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven M Opal
- 2 Infectious Disease Division, Memorial Hospital of Rhode Island and Alpert Medical School of Brown University, Providence, Rhode Island; and
| | - Evan A Stein
- 3 Metabolic and Atherosclerosis Research Center, Cincinnati, Ohio
| | - James A Russell
- 1 Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada
| | - John H Boyd
- 1 Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada
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Wideman JG, Muñoz-Gómez SA. The evolution of ERMIONE in mitochondrial biogenesis and lipid homeostasis: An evolutionary view from comparative cell biology. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:900-912. [PMID: 26825688 DOI: 10.1016/j.bbalip.2016.01.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 01/19/2016] [Accepted: 01/25/2016] [Indexed: 12/17/2022]
Abstract
The ER-mitochondria organizing network (ERMIONE) in Saccharomyces cerevisiae is involved in maintaining mitochondrial morphology and lipid homeostasis. ERMES and MICOS are two scaffolding complexes of ERMIONE that contribute to these processes. ERMES is ancient but has been lost in several lineages including animals, plants, and SAR (stramenopiles, alveolates and rhizaria). On the other hand, MICOS is ancient and has remained present in all organisms bearing mitochondrial cristae. The ERMIONE precursor evolved in the α-proteobacterial ancestor of mitochondria which had the central subunit of MICOS, Mic60. The subsequent evolution of ERMIONE and its interactors in eukaryotes reflects the integrative co-evolution of mitochondria and their hosts and the adaptive paths that some lineages have followed in their specialization to certain environments. By approaching the ERMIONE from a perspective of comparative evolutionary cell biology, we hope to shed light on not only its evolutionary history, but also how ERMIONE components may function in organisms other than S. cerevisiae. This article is part of a Special Issue entitled: The cellular lipid landscape edited by Tim P. Levine and Anant K. Menon.
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Affiliation(s)
| | - Sergio A Muñoz-Gómez
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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The TULIP superfamily of eukaryotic lipid-binding proteins as a mediator of lipid sensing and transport. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:913-923. [PMID: 26825693 DOI: 10.1016/j.bbalip.2016.01.016] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 01/16/2016] [Accepted: 01/25/2016] [Indexed: 01/28/2023]
Abstract
The tubular lipid-binding (TULIP) superfamily has emerged in recent years as a major mediator of lipid sensing and transport in eukaryotes. It currently encompasses three protein families, SMP-like, BPI-like, and Takeout-like, which share a common fold. This fold consists of a long helix wrapped in a highly curved anti-parallel β-sheet, enclosing a central, lipophilic cavity. The SMP-like proteins, which include subunits of the ERMES complex and the extended synaptotagmins (E-Syts), appear to be mainly located at membrane contacts sites (MCSs) between organelles, mediating inter-organelle lipid exchange. The BPI-like proteins, which include the bactericidal/permeability-increasing protein (BPI), the LPS (lipopolysaccharide)-binding protein (LBP), the cholesteryl ester transfer protein (CETP), and the phospholipid transfer protein (PLTP), are either involved in innate immunity against bacteria through their ability to sense lipopolysaccharides, as is the case for BPI and LBP, or in lipid exchange between lipoprotein particles, as is the case for CETP and PLTP. The Takeout-like proteins, which are comprised of insect juvenile hormone-binding proteins and arthropod allergens, transport, where known, lipid hormones to target tissues during insect development. In all cases, the activity of these proteins is underpinned by their ability to bind large, hydrophobic ligands in their central cavity and segregate them away from the aqueous environment. Furthermore, where they are involved in lipid exchange, recent structural studies have highlighted their ability to establish lipophilic, tubular channels, either between organelles in the case of SMP domains or between lipoprotein particles in the case of CETP. Here, we review the current knowledge on the structure, versatile functions, and evolution of the TULIP superfamily. We propose a deep evolutionary split in this superfamily, predating the Last Eukaryotic Common Ancestor, between the SMP-like proteins, which act on lipids endogenous to the cell, and the BPI-like proteins (including the Takeout-like proteins of arthropods), which act on exogenous lipids. This article is part of a Special Issue entitled: The cellular lipid landscape edited by Tim P. Levine and Anant K. Menon.
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Reinisch KM, De Camilli P. SMP-domain proteins at membrane contact sites: Structure and function. Biochim Biophys Acta Mol Cell Biol Lipids 2015; 1861:924-927. [PMID: 26686281 DOI: 10.1016/j.bbalip.2015.12.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/01/2015] [Accepted: 12/07/2015] [Indexed: 01/28/2023]
Abstract
SMP-domains are found in proteins that localize to membrane contact sites. Elucidation of the properties of these proteins gives clues as to the molecular bases underlying processes that occur at such sites. Described here are recent discoveries concerning the structure, function, and regulation of the Extended-Synaptotagmin proteins and ERMES complex subunits, SMP-domain proteins at endoplasmic reticulum (ER)-plasma membrane and ER-mitochondrial contacts, respectively. They act as tethers contributing to the architecture of these sites and as lipid transporters that convey glycerolipids between apposed membranes. This article is part of a Special Issue entitled: The cellular lipid landscape edited by Tim P. Levine and Anant K. Menon.
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Affiliation(s)
- Karin M Reinisch
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.
| | - Pietro De Camilli
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; Department of Neurobiology, Howard Hughes Medical Institute, Kavli Institute for Neuroscience and Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT 06510, USA.
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Phillips MJ, Voeltz GK. Structure and function of ER membrane contact sites with other organelles. Nat Rev Mol Cell Biol 2015; 17:69-82. [PMID: 26627931 DOI: 10.1038/nrm.2015.8] [Citation(s) in RCA: 633] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The endoplasmic reticulum (ER) is the largest organelle in the cell, and its functions have been studied for decades. The past several years have provided novel insights into the existence of distinct domains between the ER and other organelles, known as membrane contact sites (MCSs). At these contact sites, organelle membranes are closely apposed and tethered, but do not fuse. Here, various protein complexes can work in concert to perform specialized functions such as binding, sensing and transferring molecules, as well as engaging in organelle biogenesis and dynamics. This Review describes the structure and functions of MCSs, primarily focusing on contacts of the ER with mitochondria and endosomes.
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Affiliation(s)
- Melissa J Phillips
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Gia K Voeltz
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
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Gautier T, Masson D, Lagrost L. The potential of cholesteryl ester transfer protein as a therapeutic target. Expert Opin Ther Targets 2015. [PMID: 26212254 DOI: 10.1517/14728222.2015.1073713] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Over recent decades, attempts to ascertain the pro-atherogenic nature of plasma cholesteryl ester transfer protein (CETP) and to establish the relevance of its pharmacological blockade as a promising high density lipoproteins-raising and anti-atherogenic therapy have been disappointing. AREAS COVERED The current review focuses on CETP as a multifaceted protein, on genetic variations at the CETP gene and on their possible consequences for cardiovascular risk in human populations. Specific attention is given to physiological modulation of endogenous CETP activity by the apoC1 inhibitor. Finally, the rationale behind the need for selection of patients to treat is discussed in the light of recent studies. EXPERT OPINION At this stage one can only speculate on the clinical outcome of pharmacological CETP inhibitors in high-risk populations, but recent advances give cause to adjust the expectations from now on. The CETP effect is probably largely influenced by the overall metabolic state, and whether CETP blockade may be relevant or not in promoting cholesterol disposal is still questioned. The possible need for a careful stratification of patients to treat with CETP inhibitors is outlined. Finally, manipulation of CETP activity should be considered with caution in the context of sepsis and infectious diseases.
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Affiliation(s)
- Thomas Gautier
- a 1 INSERM, LNC UMR866 , F-21000 Dijon, France.,b 2 University of Bourgogne Franche-Comté , F-21000 Dijon, France.,c 3 LipSTIC LabEx, Fondation de Coopération Scientifique Bourgogne-Franche Comté , F-21000 Dijon, France
| | - David Masson
- a 1 INSERM, LNC UMR866 , F-21000 Dijon, France.,b 2 University of Bourgogne Franche-Comté , F-21000 Dijon, France.,c 3 LipSTIC LabEx, Fondation de Coopération Scientifique Bourgogne-Franche Comté , F-21000 Dijon, France.,d 4 University Hospital of Dijon , F-21000 Dijon, France
| | - Laurent Lagrost
- a 1 INSERM, LNC UMR866 , F-21000 Dijon, France.,b 2 University of Bourgogne Franche-Comté , F-21000 Dijon, France.,c 3 LipSTIC LabEx, Fondation de Coopération Scientifique Bourgogne-Franche Comté , F-21000 Dijon, France.,d 4 University Hospital of Dijon , F-21000 Dijon, France.,e 5 UMR866, UFR Sciences de Santé, 7 boulevard Jeanne d'Arc , F-21000 Dijon, France
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Idevall-Hagren O, Lü A, Xie B, De Camilli P. Triggered Ca2+ influx is required for extended synaptotagmin 1-induced ER-plasma membrane tethering. EMBO J 2015. [PMID: 26202220 DOI: 10.15252/embj.201591565] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The extended synaptotagmins (E-Syts) are ER proteins that act as Ca(2+)-regulated tethers between the ER and the plasma membrane (PM) and have a putative role in lipid transport between the two membranes. Ca(2+) regulation of their tethering function, as well as the interplay of their different domains in such function, remains poorly understood. By exposing semi-intact cells to buffers of variable Ca(2+) concentrations, we found that binding of E-Syt1 to the PI(4,5)P2-rich PM critically requires its C2C and C2E domains and that the EC50 of such binding is in the low micromolar Ca(2+) range. Accordingly, E-Syt1 accumulation at ER-PM contact sites occurred only upon experimental manipulations known to achieve these levels of Ca(2+) via its influx from the extracellular medium, such as store-operated Ca(2+) entry in fibroblasts and membrane depolarization in β-cells. We also show that in spite of their very different physiological functions, membrane tethering by E-Syt1 (ER to PM) and by synaptotagmin (secretory vesicles to PM) undergo a similar regulation by plasma membrane lipids and cytosolic Ca(2+).
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Affiliation(s)
- Olof Idevall-Hagren
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT, USA
| | - Alice Lü
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT, USA
| | - Beichen Xie
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Pietro De Camilli
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT, USA
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Conserved SMP domains of the ERMES complex bind phospholipids and mediate tether assembly. Proc Natl Acad Sci U S A 2015; 112:E3179-88. [PMID: 26056272 DOI: 10.1073/pnas.1422363112] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Membrane contact sites (MCS) between organelles are proposed as nexuses for the exchange of lipids, small molecules, and other signals crucial to cellular function and homeostasis. Various protein complexes, such as the endoplasmic reticulum-mitochondrial encounter structure (ERMES), function as dynamic molecular tethers between organelles. Here, we report the reconstitution and characterization of subcomplexes formed by the cytoplasm-exposed synaptotagmin-like mitochondrial lipid-binding protein (SMP) domains present in three of the five ERMES subunits--the soluble protein Mdm12, the endoplasmic reticulum (ER)-resident membrane protein Mmm1, and the mitochondrial membrane protein Mdm34. SMP domains are conserved lipid-binding domains found exclusively in proteins at MCS. We show that the SMP domains of Mdm12 and Mmm1 associate into a tight heterotetramer with equimolecular stoichiometry. Our 17-Å-resolution EM structure of the complex reveals an elongated crescent-shaped particle in which two Mdm12 subunits occupy symmetric but distal positions at the opposite ends of a central ER-anchored Mmm1 homodimer. Rigid body fitting of homology models of these SMP domains in the density maps reveals a distinctive extended tubular structure likely traversed by a hydrophobic tunnel. Furthermore, these two SMP domains bind phospholipids and display a strong preference for phosphatidylcholines, a class of phospholipids whose exchange between the ER and mitochondria is essential. Last, we show that the three SMP-containing ERMES subunits form a ternary complex in which Mdm12 bridges Mmm1 to Mdm34. Our findings highlight roles for SMP domains in ERMES assembly and phospholipid binding and suggest a structure-based mechanism for the facilitated transport of phospholipids between organelles.
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Ning F, Wang C, Berry KZ, Kandasamy P, Liu H, Murphy RC, Voelker DR, Nho CW, Pan CH, Dai S, Niu L, Chu HW, Zhang G. Structural characterization of the pulmonary innate immune protein SPLUNC1 and identification of lipid ligands. FASEB J 2014; 28:5349-60. [PMID: 25223608 DOI: 10.1096/fj.14-259291] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The short palate, lung and nasal epithelial clone 1 (SPLUNC1) protein is a member of the palate, lung, and nasal epithelium clone (PLUNC) family, also known as bactericidal/permeability-increasing (BPI) fold-containing protein, family A, member 1 (BPIFA1). SPLUNC1 is an abundant protein in human airways, but its function remains poorly understood. The lipid ligands of SPLUNC1 as well as other PLUNC family members are largely unknown, although some reports provide evidence that lipopolysaccharide (LPS) could be a lipid ligand. Unlike previous hypotheses, we found significant structural differences between SPLUNC1 and BPI. Recombinant SPLUNC1 produced in HEK 293 cells harbored several molecular species of sphingomyelin and phosphatidylcholine as its ligands. Significantly, in vitro lipid-binding studies failed to demonstrate interactions between SPLUNC1 and LPS, lipoteichoic acid, or polymyxin B. Instead, one of the major and most important pulmonary surfactant phospholipids, dipalmitoylphosphatidylcholine (DPPC), bound to SPLUNC1 with high affinity and specificity. We found that SPLUNC1 could be the first protein receptor for DPPC. These discoveries provide insight into the specific determinants governing the interaction between SPLUNC1 and lipids and also shed light on novel functions that SPLUNC1 and other PLUNC family members perform in host defense.
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Affiliation(s)
- Fangkun Ning
- School of Life Sciences, University of Science and Technology of China, Hefei, China; Integrated Department of Immunology, National Jewish Health and University of Colorado Denver, Denver, Colorado, USA
| | - Chao Wang
- Integrated Department of Immunology, National Jewish Health and University of Colorado Denver, Denver, Colorado, USA
| | - Karin Zemski Berry
- Department of Pharmacology, University of Colorado Denver, Aurora, Colorado, USA
| | | | - Haolin Liu
- Integrated Department of Immunology, National Jewish Health and University of Colorado Denver, Denver, Colorado, USA
| | - Robert C Murphy
- Department of Pharmacology, University of Colorado Denver, Aurora, Colorado, USA
| | - Dennis R Voelker
- Department of Medicine, National Jewish Health, Denver, Colorado, USA; and
| | - Chu Won Nho
- Functional Food Center, Korea Institute of Science and Technology, GangNeung, Korea
| | - Choel-Ho Pan
- Functional Food Center, Korea Institute of Science and Technology, GangNeung, Korea
| | - Shaodong Dai
- Integrated Department of Immunology, National Jewish Health and University of Colorado Denver, Denver, Colorado, USA
| | - Liwen Niu
- School of Life Sciences, University of Science and Technology of China, Hefei, China;
| | - Hong-Wei Chu
- Integrated Department of Immunology, National Jewish Health and University of Colorado Denver, Denver, Colorado, USA; Department of Medicine, National Jewish Health, Denver, Colorado, USA; and
| | - Gongyi Zhang
- Integrated Department of Immunology, National Jewish Health and University of Colorado Denver, Denver, Colorado, USA
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Structure of a lipid-bound extended synaptotagmin indicates a role in lipid transfer. Nature 2014; 510:552-5. [PMID: 24847877 PMCID: PMC4135724 DOI: 10.1038/nature13269] [Citation(s) in RCA: 230] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 03/21/2014] [Indexed: 11/25/2022]
Abstract
Growing evidence suggests that close appositions between the endoplasmic reticulum (ER) and other membranes, including appositions with the plasma membrane (PM), mediate exchange of lipids between the two bilayers. The mechanisms of such exchange, which allows lipid transfer independently of vesicular transport, remain poorly understood. The presence of an SMP (synaptotagmin-like-mitochondrial-lipid binding protein) domain, a proposed lipid binding module, in several proteins localized at membrane contact sites raised the possibility that such domains may be implicated in lipid transport1,2. SMP-containing proteins include components of the ERMES complex, an ER-mitochondrial tether3, and the Extended-Synaptotagmins/tricalbins, which are ER-PM tethers4-6. Here we present at 2.44 Å resolution the crystal structure of a fragment of Extended-Synaptotagmin 2 (E-Syt2), including an SMP domain and two adjacent C2 domains. The SMP domain has a beta-barrel structure like protein modules in the TULIP superfamily. It dimerizes to form a ~90 Å long cylinder traversed by a channel lined entirely with hydrophobic residues, with the two C2A-C2B fragments forming arched structures flexibly linked to the SMP domain. Importantly, structural analysis complemented by mass spectrometry revealed the presence of glycerophospholipids in the E-Syt2 SMP channel, indicating a direct role for E-Syts in lipid transport. These findings provide strong evidence for a role of SMP domain containing proteins in the control of lipid transfer at membrane contact sites and have broad implication beyond the field of ER to PM appositions.
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Tamura Y, Sesaki H, Endo T. Phospholipid transport via mitochondria. Traffic 2014; 15:933-45. [PMID: 24954234 DOI: 10.1111/tra.12188] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 06/16/2014] [Accepted: 06/16/2014] [Indexed: 12/27/2022]
Abstract
In eukaryotic cells, complex membrane structures called organelles are highly developed to exert specialized functions. Mitochondria are one of such organelles consisting of the outer and inner membranes (OM and IM) with characteristic protein and phospholipid compositions. Maintaining proper phospholipid compositions of the membranes is crucial for mitochondrial integrity, thereby contributing to normal cell activities. As cellular locations for phospholipid synthesis are restricted to specific compartments such as the endoplasmic reticulum (ER) membrane and the mitochondrial inner membrane, newly synthesized phospholipids have to be transported and distributed properly from the ER or mitochondria to other cellular membranes. Although understanding of molecular mechanisms of phospholipid transport are much behind those of protein transport, recent studies using yeast as a model system began to provide intriguing insights into phospholipid exchange between the ER and mitochondria as well as between the mitochondrial OM and IM. In this review, we summarize the latest findings of phospholipid transport via mitochondria and discuss the implicated molecular mechanisms.
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Affiliation(s)
- Yasushi Tamura
- Research Center for Materials Science, Nagoya University, Nagoya, 464-8602, Japan
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Hönscher C, Ungermann C. A close-up view of membrane contact sites between the endoplasmic reticulum and the endolysosomal system: from yeast to man. Crit Rev Biochem Mol Biol 2014; 49:262-8. [PMID: 24382115 DOI: 10.3109/10409238.2013.875512] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Maintenance of organelle identity is crucial for the functionality of eukaryotic cells. Hence, transfer reactions between different compartments must be highly efficient and tightly regulated at the same time. Membrane contact sites (MCSs) represent an important route for inter-organelle transport and communication independent of vesicular trafficking. Due to extensive research, the mechanistic understanding of these sites increases constantly. However, how the formation and the versatile functions of MCSs are regulated is mainly unclear. Within this review, we focus on one well-known MCS, the nucleus-vacuole junction in yeast and discuss its analogy to endoplasmic reticulum-late endosome contacts in metazoan. Formation of the junction in yeast requires Vac8, a protein that is involved in various cellular processes at the yeast vacuole and a target of multiple posttranslational modifications. We discuss the possibility that dual functionality of proteins involved in contact formation is a common principle to coordinate inter-organelle transfer with organellar biogenesis.
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Affiliation(s)
- Carina Hönscher
- Department of Biology/Chemistry, Biochemistry Section, University of Osnabrück , Osnabrück , Germany
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Flinner N, Ellenrieder L, Stiller SB, Becker T, Schleiff E, Mirus O. Mdm10 is an ancient eukaryotic porin co-occurring with the ERMES complex. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:3314-3325. [PMID: 24135058 DOI: 10.1016/j.bbamcr.2013.10.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 09/20/2013] [Accepted: 10/07/2013] [Indexed: 12/17/2022]
Abstract
Mitochondrial β-barrel proteins fulfill central functions in the outer membrane like metabolite exchange catalyzed by the voltage-dependent anion channel (VDAC) and protein biogenesis by the central components of the preprotein translocase of the outer membrane (Tom40) or of the sorting and assembly machinery (Sam50). The mitochondrial division and morphology protein Mdm10 is another essential outer membrane protein with proposed β-barrel fold, which has so far only been found in Fungi. Mdm10 is part of the endoplasmic reticulum mitochondria encounter structure (ERMES), which tethers the ER to mitochondria and associates with the SAM complex. In here, we provide evidence that Mdm10 phylogenetically belongs to the VDAC/Tom40 superfamily. Contrary to Tom40 and VDAC, Mdm10 exposes long loops towards both sides of the membrane. Analyses of single loop deletion mutants of Mdm10 in the yeast Saccharomyces cerevisiae reveal that the loops are dispensable for Mdm10 function. Sequences similar to fungal Mdm10 can be found in species from Excavates to Fungi, but neither in Metazoa nor in plants. Strikingly, the presence of Mdm10 coincides with the appearance of the other ERMES components. Mdm10's presence in both unikonts and bikonts indicates an introduction at an early time point in eukaryotic evolution.
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Affiliation(s)
- Nadine Flinner
- JWGU Frankfurt am Main, Cluster of Excellence Macromolecular Complexes, Centre of Membrane Proteomics, Department of Biosciences, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Lars Ellenrieder
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, D-79104 Freiburg, Germany; Fakultät für Biologie, Universität Freiburg, D-79104 Freiburg, Germany
| | - Sebastian B Stiller
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, D-79104 Freiburg, Germany; Fakultät für Biologie, Universität Freiburg, D-79104 Freiburg, Germany
| | - Thomas Becker
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, D-79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Universität Freiburg, D-79104 Freiburg, Germany
| | - Enrico Schleiff
- JWGU Frankfurt am Main, Cluster of Excellence Macromolecular Complexes, Centre of Membrane Proteomics, Department of Biosciences, Max-von-Laue Str. 9, 60438 Frankfurt, Germany.
| | - Oliver Mirus
- JWGU Frankfurt am Main, Cluster of Excellence Macromolecular Complexes, Centre of Membrane Proteomics, Department of Biosciences, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
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