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Lolicato F, Nickel W, Haucke V, Ebner M. Phosphoinositide switches in cell physiology - From molecular mechanisms to disease. J Biol Chem 2024; 300:105757. [PMID: 38364889 PMCID: PMC10944118 DOI: 10.1016/j.jbc.2024.105757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/02/2024] [Accepted: 02/08/2024] [Indexed: 02/18/2024] Open
Abstract
Phosphoinositides are amphipathic lipid molecules derived from phosphatidylinositol that represent low abundance components of biological membranes. Rather than serving as mere structural elements of lipid bilayers, they represent molecular switches for a broad range of biological processes, including cell signaling, membrane dynamics and remodeling, and many other functions. Here, we focus on the molecular mechanisms that turn phosphoinositides into molecular switches and how the dysregulation of these processes can lead to disease.
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Affiliation(s)
- Fabio Lolicato
- Heidelberg University Biochemistry Center, Heidelberg, Germany; Department of Physics, University of Helsinki, Helsinki, Finland.
| | - Walter Nickel
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany; Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany; Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Ebner
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.
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2
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Weckerly CC, Rahn TA, Ehrlich M, Wills RC, Pemberton JG, Airola MV, Hammond GRV. Nir1-LNS2 is a novel phosphatidic acid biosensor that reveals mechanisms of lipid production. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.582557. [PMID: 38464273 PMCID: PMC10925316 DOI: 10.1101/2024.02.28.582557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Despite various roles of phosphatidic acid (PA) in cellular functions such as lipid homeostasis and vesicular trafficking, there is a lack of high-affinity tools to study PA in live cells. After analysis of the predicted structure of the LNS2 domain in the lipid transfer protein Nir1, we suspected that this domain could serve as a novel PA biosensor. We created a fluorescently tagged Nir1-LNS2 construct and then performed liposome binding assays as well as pharmacological and genetic manipulations of HEK293A cells to determine how specific lipids affect the interaction of Nir1-LNS2 with membranes. We found that Nir1-LNS2 bound to both PA and PIP2 in vitro. Interestingly, only PA was necessary and sufficient to localize Nir1-LNS2 to membranes in cells. Nir1-LNS2 also showed a heightened responsiveness to PA when compared to biosensors using the Spo20 PA binding domain (PABD). Nir1-LNS2's high sensitivity revealed a modest but discernible contribution of PLD to PA production downstream of muscarinic receptors, which has not been visualized with previous Spo20-based probes. In summary, Nir1-LNS2 emerges as a versatile and sensitive biosensor, offering researchers a new powerful tool for real-time investigation of PA dynamics in live cells.
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Affiliation(s)
- Claire C Weckerly
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Taylor A Rahn
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
| | - Max Ehrlich
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Rachel C Wills
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Joshua G Pemberton
- Section on Molecular Signal Transduction, Program for Developmental Neuroscience, Eunice Kennedy Shriver NICHD, National Institutes of Health, Bethesda, MD, USA
| | - Michael V Airola
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
| | - Gerald R V Hammond
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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3
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Numata M, Kandasamy P, Voelker DR. The anti-inflammatory and antiviral properties of anionic pulmonary surfactant phospholipids. Immunol Rev 2023; 317:166-186. [PMID: 37144896 PMCID: PMC10524216 DOI: 10.1111/imr.13207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/06/2023] [Accepted: 04/10/2023] [Indexed: 05/06/2023]
Abstract
The pulmonary surfactant system of the lung is a lipid and protein complex, which regulates the biophysical properties of the alveoli to prevent lung collapse and the innate immune system in the lung. Pulmonary surfactant is a lipoprotein complex consisting of 90% phospholipids and 10% protein, by weight. Two minor components of pulmonary surfactant phospholipids, phosphatidylglycerol (PG) and phosphatidylinositol (PI), exist at very high concentrations in the extracellular alveolar compartments. We have reported that one of the most dominant molecular species of PG, palmitoyl-oleoyl-phosphatidylglycerol (POPG) and PI inhibit inflammatory responses induced by multiple toll-like receptors (TLR2/1, TLR3, TLR4, and TLR2/6) by interacting with subsets of multiprotein receptor components. These lipids also exert potent antiviral effects against RSV and influenza A, in vitro, by inhibiting virus binding to host cells. POPG and PI inhibit these viral infections in vivo, in multiple animal models. Especially noteworthy, these lipids markedly attenuate SARS-CoV-2 infection including its variants. These lipids are natural compounds that already exist in the lung and, thus, are less likely to cause adverse immune responses by hosts. Collectively, these data demonstrate that POPG and PI have strong potential as novel therapeutics for applications as anti-inflammatory compounds and preventatives, as treatments for broad ranges of RNA respiratory viruses.
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Affiliation(s)
- Mari Numata
- Department of Medicine, National Jewish Health, Denver, CO 80206
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, CO 80206
| | - Pitchaimani Kandasamy
- Department of Medicine, National Jewish Health, Denver, CO 80206
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, CO 80206
| | - Dennis R. Voelker
- Department of Medicine, National Jewish Health, Denver, CO 80206
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, CO 80206
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4
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Lee JJ, Ramadesikan S, Black AF, Christoffer C, Pacheco AFP, Subramanian S, Hanna CB, Barth G, Stauffacher CV, Kihara D, Aguilar RC. Heterogeneity in Lowe Syndrome: Mutations Affecting the Phosphatase Domain of OCRL1 Differ in Impact on Enzymatic Activity and Severity of Cellular Phenotypes. Biomolecules 2023; 13:615. [PMID: 37189363 PMCID: PMC10135975 DOI: 10.3390/biom13040615] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/23/2023] [Accepted: 03/25/2023] [Indexed: 04/01/2023] Open
Abstract
Lowe Syndrome (LS) is a condition due to mutations in the OCRL1 gene, characterized by congenital cataracts, intellectual disability, and kidney malfunction. Unfortunately, patients succumb to renal failure after adolescence. This study is centered in investigating the biochemical and phenotypic impact of patient's OCRL1 variants (OCRL1VAR). Specifically, we tested the hypothesis that some OCRL1VAR are stabilized in a non-functional conformation by focusing on missense mutations affecting the phosphatase domain, but not changing residues involved in binding/catalysis. The pathogenic and conformational characteristics of the selected variants were evaluated in silico and our results revealed some OCRL1VAR to be benign, while others are pathogenic. Then we proceeded to monitor the enzymatic activity and function in kidney cells of the different OCRL1VAR. Based on their enzymatic activity and presence/absence of phenotypes, the variants segregated into two categories that also correlated with the severity of the condition they induce. Overall, these two groups mapped to opposite sides of the phosphatase domain. In summary, our findings highlight that not every mutation affecting the catalytic domain impairs OCRL1's enzymatic activity. Importantly, data support the inactive-conformation hypothesis. Finally, our results contribute to establishing the molecular and structural basis for the observed heterogeneity in severity/symptomatology displayed by patients.
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Affiliation(s)
- Jennifer J. Lee
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (J.J.L.); (A.F.B.); (A.F.P.P.); (S.S.); (C.B.H.); (G.B.); (C.V.S.); (D.K.)
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Swetha Ramadesikan
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (J.J.L.); (A.F.B.); (A.F.P.P.); (S.S.); (C.B.H.); (G.B.); (C.V.S.); (D.K.)
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Adrianna F. Black
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (J.J.L.); (A.F.B.); (A.F.P.P.); (S.S.); (C.B.H.); (G.B.); (C.V.S.); (D.K.)
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Charles Christoffer
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA;
| | - Andres F. Pacheco Pacheco
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (J.J.L.); (A.F.B.); (A.F.P.P.); (S.S.); (C.B.H.); (G.B.); (C.V.S.); (D.K.)
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Sneha Subramanian
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (J.J.L.); (A.F.B.); (A.F.P.P.); (S.S.); (C.B.H.); (G.B.); (C.V.S.); (D.K.)
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Claudia B. Hanna
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (J.J.L.); (A.F.B.); (A.F.P.P.); (S.S.); (C.B.H.); (G.B.); (C.V.S.); (D.K.)
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Gillian Barth
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (J.J.L.); (A.F.B.); (A.F.P.P.); (S.S.); (C.B.H.); (G.B.); (C.V.S.); (D.K.)
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Cynthia V. Stauffacher
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (J.J.L.); (A.F.B.); (A.F.P.P.); (S.S.); (C.B.H.); (G.B.); (C.V.S.); (D.K.)
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (J.J.L.); (A.F.B.); (A.F.P.P.); (S.S.); (C.B.H.); (G.B.); (C.V.S.); (D.K.)
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA;
| | - Ruben Claudio Aguilar
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (J.J.L.); (A.F.B.); (A.F.P.P.); (S.S.); (C.B.H.); (G.B.); (C.V.S.); (D.K.)
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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5
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Borges-Araújo L, Monteiro ME, Mil-Homens D, Bernardes N, Sarmento MJ, Coutinho A, Prieto M, Fernandes F. Impact of Ca 2+-Induced PI(4,5)P 2 Clusters on PH-YFP Organization and Protein-Protein Interactions. Biomolecules 2022; 12:912. [PMID: 35883468 PMCID: PMC9312469 DOI: 10.3390/biom12070912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 11/16/2022] Open
Abstract
Despite its low abundance, phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) is a key modulator of membrane-associated signaling events in eukaryotic cells. Temporal and spatial regulation of PI(4,5)P2 concentration can achieve localized increases in the levels of this lipid, which are crucial for the activation or recruitment of peripheral proteins to the plasma membrane. The recent observation of the dramatic impact of physiological divalent cation concentrations on PI(4,5)P2 clustering, suggests that protein anchoring to the plasma membrane through PI(4,5)P2 is likely not defined solely by a simple (monomeric PI(4,5)P2)/(protein bound PI(4,5)P2) equilibrium, but instead depends on complex protein interactions with PI(4,5)P2 clusters. The insertion of PI(4,5)P2-binding proteins within these clusters can putatively modulate protein-protein interactions in the membrane, but the relevance of such effects is largely unknown. In this work, we characterized the impact of Ca2+ on the organization and protein-protein interactions of PI(4,5)P2-binding proteins. We show that, in giant unilamellar vesicles presenting PI(4,5)P2, the membrane diffusion properties of pleckstrin homology (PH) domains tagged with a yellow fluorescent protein (YFP) are affected by the presence of Ca2+, suggesting direct interactions between the protein and PI(4,5)P2 clusters. Importantly, PH-YFP is found to dimerize in the membrane in the absence of Ca2+. This oligomerization is inhibited in the presence of physiological concentrations of the divalent cation. These results confirm that cation-dependent PI(4,5)P2 clustering promotes interactions between PI(4,5)P2-binding proteins and has the potential to dramatically influence the organization and downstream interactions of PI(4,5)P2-binding proteins in the plasma membrane.
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Affiliation(s)
- Luís Borges-Araújo
- IBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (L.B.-A.); (D.M.-H.); (N.B.); (A.C.); (M.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
| | - Marina E. Monteiro
- Centro de Química-Física Molecular and Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (M.E.M.); (M.J.S.)
| | - Dalila Mil-Homens
- IBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (L.B.-A.); (D.M.-H.); (N.B.); (A.C.); (M.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
| | - Nuno Bernardes
- IBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (L.B.-A.); (D.M.-H.); (N.B.); (A.C.); (M.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
| | - Maria J. Sarmento
- Centro de Química-Física Molecular and Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (M.E.M.); (M.J.S.)
- Instituto de Medicina Molecular, Faculty of Medicine, University of Lisbon, Avenida Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Ana Coutinho
- IBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (L.B.-A.); (D.M.-H.); (N.B.); (A.C.); (M.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
- Departamento de Química e Bioquímica, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Manuel Prieto
- IBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (L.B.-A.); (D.M.-H.); (N.B.); (A.C.); (M.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
| | - Fábio Fernandes
- IBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (L.B.-A.); (D.M.-H.); (N.B.); (A.C.); (M.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
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6
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Joliot A, Prochiantz A. Unconventional Secretion, Gate to Homeoprotein Intercellular Transfer. Front Cell Dev Biol 2022; 10:926421. [PMID: 35837333 PMCID: PMC9274163 DOI: 10.3389/fcell.2022.926421] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/07/2022] [Indexed: 11/24/2022] Open
Abstract
Unconventional secretion allows for the secretion of fully mature and biologically active proteins mostly present in the cytoplasm or nucleus. Besides extra vesicle-driven secretion, non-extravesicular pathways also exist that specifically rely on the ability of the secreted proteins to translocate directly across the plasma membrane. This is the case for several homeoproteins, a family of over 300 transcription factors characterized by the structure of their DNA-binding homeodomain. The latter highly conserved homeodomain is necessary and sufficient for secretion, a process that requires PI(4,5)P2 binding, as is the case for FGF2 and HIV Tat unconventional secretion. An important feature of homeoproteins is their ability to cross membranes in both directions and thus to transfer between cells. This confers to homeoproteins their paracrine activity, an essential facet of their physiological functions.
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Affiliation(s)
- Alain Joliot
- INSERM U932, Institut Curie Centre de Recherche, PSL Research University, Paris, France
- *Correspondence: Alain Joliot,
| | - Alain Prochiantz
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U1050, PSL Research University, Labex MemoLife, Paris, France
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7
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Numata M, Voelker DR. Anti-inflammatory and anti-viral actions of anionic pulmonary surfactant phospholipids. Biochim Biophys Acta Mol Cell Biol Lipids 2022; 1867:159139. [PMID: 35240310 PMCID: PMC9050941 DOI: 10.1016/j.bbalip.2022.159139] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 02/14/2022] [Accepted: 02/21/2022] [Indexed: 12/15/2022]
Abstract
Pulmonary surfactant is a mixture of lipids and proteins, consisting of 90% phospholipid, and 10% protein by weight, found predominantly in pulmonary alveoli of vertebrate lungs. Two minor components of pulmonary surfactant phospholipids, phosphatidylglycerol (PG) and phosphatidylinositol (PI), are present within the alveoli at very high concentrations, and exert anti-inflammatory effects by regulating multiple Toll like receptors (TLR2/1, TLR4, and TLR2/6) by antagonizing cognate ligand-dependent activation. POPG also attenuates LPS-induced lung injury in vivo. In addition, these lipids bind directly to RSV and influenza A viruses (IAVs) and block interaction between host cells and virions, and thereby prevent viral replication in vitro. POPG and PI also inhibit RSV and IAV infection in vivo, in mice and ferrets. The lipids markedly inhibit SARS-CoV-2 infection in vitro. These findings suggest that both POPG and PI have strong potential to be applied as both prophylaxis and post-infection treatments for problematic respiratory viral infections.
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Affiliation(s)
- Mari Numata
- Department of Medicine, National Jewish Health, Denver, CO 80206, United States of America; Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, CO 80206, United States of America.
| | - Dennis R Voelker
- Department of Medicine, National Jewish Health, Denver, CO 80206, United States of America; Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, CO 80206, United States of America.
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8
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Ventura R, Martínez-Ruiz I, Hernández-Alvarez MI. Phospholipid Membrane Transport and Associated Diseases. Biomedicines 2022; 10:biomedicines10051201. [PMID: 35625937 PMCID: PMC9138374 DOI: 10.3390/biomedicines10051201] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 11/16/2022] Open
Abstract
Phospholipids are the basic structure block of eukaryotic membranes, in both the outer and inner membranes, which delimit cell organelles. Phospholipids can also be damaged by oxidative stress produced by mitochondria, for instance, becoming oxidized phospholipids. These damaged phospholipids have been related to prevalent diseases such as atherosclerosis or non-alcoholic steatohepatitis (NASH) because they alter gene expression and induce cellular stress and apoptosis. One of the main sites of phospholipid synthesis is the endoplasmic reticulum (ER). ER association with other organelles through membrane contact sites (MCS) provides a close apposition for lipid transport. Additionally, an important advance in this small cytosolic gap are lipid transfer proteins (LTPs), which accelerate and modulate the distribution of phospholipids in other organelles. In this regard, LTPs can be established as an essential point within phospholipid circulation, as relevant data show impaired phospholipid transport when LTPs are defected. This review will focus on phospholipid function, metabolism, non-vesicular transport, and associated diseases.
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Affiliation(s)
- Raúl Ventura
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain; (R.V.); (I.M.-R.)
| | - Inma Martínez-Ruiz
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain; (R.V.); (I.M.-R.)
| | - María Isabel Hernández-Alvarez
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain; (R.V.); (I.M.-R.)
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28029 Madrid, Spain
- IBUB Universitat de Barcelona—Institut de Biomedicina de la Universitat de Barcelona, 08028 Barcelona, Spain
- Correspondence:
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9
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Borges-Araújo L, Souza PCT, Fernandes F, Melo MN. Improved Parameterization of Phosphatidylinositide Lipid Headgroups for the Martini 3 Coarse-Grain Force Field. J Chem Theory Comput 2021; 18:357-373. [PMID: 34962393 DOI: 10.1021/acs.jctc.1c00615] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phosphoinositides are a family of membrane phospholipids that play crucial roles in membrane regulatory events. As such, these lipids are often a key part of molecular dynamics simulation studies of biological membranes, in particular of those employing coarse-grain models because of the potential long times and sizes of the involved membrane processes. Version 3 of the widely used Martini coarse-grain force field has been recently published, greatly refining many aspects of biomolecular interactions. In order to properly use it for lipid membrane simulations with phosphoinositides, we put forth the Martini 3-specific parameterization of inositol, phosphatidylinositol, and seven physiologically relevant phosphorylated derivatives of phosphatidylinositol. Compared to parameterizations for earlier Martini versions, focus was put on a more accurate reproduction of the behavior seen in both atomistic simulations and experimental studies, including the signaling-relevant phosphoinositide interaction with divalent cations. The models that we develop improve upon the conformational dynamics of phosphoinositides in the Martini force field and provide stable topologies at typical Martini time steps. They are able to reproduce experimentally known protein-binding poses as well as phosphoinositide aggregation tendencies. The latter was tested both in the presence and absence of calcium and included correct behavior of PI(4,5)P2 calcium-induced clusters, which can be of relevance for regulation.
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Affiliation(s)
- Luís Borges-Araújo
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon 1049-001, Portugal.,Associate Laboratory i4HB─Institute for Health and Bioeconomy, at Instituto Superior Técnico, Universidade de Lisboa, Lisbon 1049-001, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras 2780-157, Portugal
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS & University of Lyon, 7 Passage du Vercors, Lyon F-69367, France
| | - Fábio Fernandes
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon 1049-001, Portugal.,Associate Laboratory i4HB─Institute for Health and Bioeconomy, at Instituto Superior Técnico, Universidade de Lisboa, Lisbon 1049-001, Portugal.,Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon 1049-001, Portugal
| | - Manuel N Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras 2780-157, Portugal
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10
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Sarmento MJ, Borges-Araújo L, Pinto SN, Bernardes N, Ricardo JC, Coutinho A, Prieto M, Fernandes F. Quantitative FRET Microscopy Reveals a Crucial Role of Cytoskeleton in Promoting PI(4,5)P 2 Confinement. Int J Mol Sci 2021; 22:11727. [PMID: 34769158 PMCID: PMC8583820 DOI: 10.3390/ijms222111727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/24/2021] [Accepted: 10/26/2021] [Indexed: 01/30/2023] Open
Abstract
Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) is an essential plasma membrane component involved in several cellular functions, including membrane trafficking and cytoskeleton organization. This function multiplicity is partially achieved through a dynamic spatiotemporal organization of PI(4,5)P2 within the membrane. Here, we use a Förster resonance energy transfer (FRET) approach to quantitatively assess the extent of PI(4,5)P2 confinement within the plasma membrane. This methodology relies on the rigorous evaluation of the dependence of absolute FRET efficiencies between pleckstrin homology domains (PHPLCδ) fused with fluorescent proteins and their average fluorescence intensity at the membrane. PI(4,5)P2 is found to be significantly compartmentalized at the plasma membrane of HeLa cells, and these clusters are not cholesterol-dependent, suggesting that membrane rafts are not involved in the formation of these nanodomains. On the other hand, upon inhibition of actin polymerization, compartmentalization of PI(4,5)P2 is almost entirely eliminated, showing that the cytoskeleton network is the critical component responsible for the formation of nanoscale PI(4,5)P2 domains in HeLa cells.
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Affiliation(s)
- Maria J. Sarmento
- Centro de Química-Física Molecular and Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
| | - Luís Borges-Araújo
- IBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (L.B.-A.); (S.N.P.); (N.B.); (J.C.R.); (A.C.); (M.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Sandra N. Pinto
- IBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (L.B.-A.); (S.N.P.); (N.B.); (J.C.R.); (A.C.); (M.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Nuno Bernardes
- IBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (L.B.-A.); (S.N.P.); (N.B.); (J.C.R.); (A.C.); (M.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Joana C. Ricardo
- IBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (L.B.-A.); (S.N.P.); (N.B.); (J.C.R.); (A.C.); (M.P.)
| | - Ana Coutinho
- IBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (L.B.-A.); (S.N.P.); (N.B.); (J.C.R.); (A.C.); (M.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Departamento de Química e Bioquímica, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Manuel Prieto
- IBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (L.B.-A.); (S.N.P.); (N.B.); (J.C.R.); (A.C.); (M.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Fábio Fernandes
- IBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (L.B.-A.); (S.N.P.); (N.B.); (J.C.R.); (A.C.); (M.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
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11
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Damian M, Louet M, Gomes AAS, M'Kadmi C, Denoyelle S, Cantel S, Mary S, Bisch PM, Fehrentz JA, Catoire LJ, Floquet N, Banères JL. Allosteric modulation of ghrelin receptor signaling by lipids. Nat Commun 2021; 12:3938. [PMID: 34168117 PMCID: PMC8225672 DOI: 10.1038/s41467-021-23756-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 05/07/2021] [Indexed: 02/05/2023] Open
Abstract
The membrane is an integral component of the G protein-coupled receptor signaling machinery. Here we demonstrate that lipids regulate the signaling efficacy and selectivity of the ghrelin receptor GHSR through specific interactions and bulk effects. We find that PIP2 shifts the conformational equilibrium of GHSR away from its inactive state, favoring basal and agonist-induced G protein activation. This occurs because of a preferential binding of PIP2 to specific intracellular sites in the receptor active state. Another lipid, GM3, also binds GHSR and favors G protein activation, but mostly in a ghrelin-dependent manner. Finally, we find that not only selective interactions but also the thickness of the bilayer reshapes the conformational repertoire of GHSR, with direct consequences on G protein selectivity. Taken together, this data illuminates the multifaceted role of the membrane components as allosteric modulators of how ghrelin signal could be propagated.
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Affiliation(s)
- Marjorie Damian
- IBMM, UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France
| | - Maxime Louet
- IBMM, UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France
| | - Antoniel Augusto Severo Gomes
- IBMM, UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France
- Laboratório de Física Biológica, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Céline M'Kadmi
- IBMM, UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France
| | - Séverine Denoyelle
- IBMM, UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France
| | - Sonia Cantel
- IBMM, UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France
| | - Sophie Mary
- IBMM, UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France
| | - Paulo M Bisch
- Laboratório de Física Biológica, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | - Laurent J Catoire
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (FRC 550), Paris, France
| | - Nicolas Floquet
- IBMM, UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France
| | - Jean-Louis Banères
- IBMM, UMR 5247, CNRS, Université de Montpellier, ENSCM, Montpellier, France.
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12
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Struyfs C, Cammue BPA, Thevissen K. Membrane-Interacting Antifungal Peptides. Front Cell Dev Biol 2021; 9:649875. [PMID: 33912564 PMCID: PMC8074791 DOI: 10.3389/fcell.2021.649875] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/09/2021] [Indexed: 12/17/2022] Open
Abstract
The incidence of invasive fungal infections is increasing worldwide, resulting in more than 1.6 million deaths every year. Due to growing antifungal drug resistance and the limited number of currently used antimycotics, there is a clear need for novel antifungal strategies. In this context, great potential is attributed to antimicrobial peptides (AMPs) that are part of the innate immune system of organisms. These peptides are known for their broad-spectrum activity that can be directed toward bacteria, fungi, viruses, and/or even cancer cells. Some AMPs act via rapid physical disruption of microbial cell membranes at high concentrations causing cell leakage and cell death. However, more complex mechanisms are also observed, such as interaction with specific lipids, production of reactive oxygen species, programmed cell death, and autophagy. This review summarizes the structure and mode of action of antifungal AMPs, thereby focusing on their interaction with fungal membranes.
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Affiliation(s)
- Caroline Struyfs
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Bruno P A Cammue
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Karin Thevissen
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
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