1
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Lourdes SR, Gurung R, Giri S, Mitchell CA, McGrath MJ. A new role for phosphoinositides in regulating mitochondrial dynamics. Adv Biol Regul 2024; 91:101001. [PMID: 38057188 DOI: 10.1016/j.jbior.2023.101001] [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: 11/17/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023]
Abstract
Phosphoinositides are a minor group of membrane-associated phospholipids that are transiently generated on the cytoplasmic leaflet of many organelle membranes and the plasma membrane. There are seven functionally distinct phosphoinositides, each derived via the reversible phosphorylation of phosphatidylinositol in various combinations on the inositol ring. Their generation and termination is tightly regulated by phosphatidylinositol-kinases and -phosphatases. These enzymes can function together in an integrated and coordinated manner, whereby the phosphoinositide product of one enzyme may subsequently serve as a substrate for another to generate a different phosphoinositide species. This regulatory mechanism not only enables the transient generation of phosphoinositides on membranes, but also more complex sequential or bidirectional conversion pathways, and phosphoinositides can also be transferred between organelles via membrane contacts. It is this capacity to fine-tune phosphoinositide signals that makes them ideal regulators of membrane organization and dynamics, through their recruitment of signalling, membrane altering and lipid transfer proteins. Research spanning several decades has provided extensive evidence that phosphoinositides are major gatekeepers of membrane organization, with roles in endocytosis, exocytosis, autophagy, lysosome dynamics, vesicular transport and secretion, cilia, inter-organelle membrane contact, endosome maturation and nuclear function. By contrast, there has been remarkably little known about the role of phosphoinositides at mitochondria - an enigmatic and major knowledge gap, with challenges in reliably detecting phosphoinositides at this site. Here we review recent significant breakthroughs in understanding the role of phosphoinositides in regulating mitochondrial dynamics and metabolic function.
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Affiliation(s)
- Sonia Raveena Lourdes
- Cancer Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Rajendra Gurung
- Cancer Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Saveen Giri
- Cancer Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Christina A Mitchell
- Cancer Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.
| | - Meagan J McGrath
- Cancer Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
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2
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Tang T, Hasan M, Capelluto DGS. Phafins Are More Than Phosphoinositide-Binding Proteins. Int J Mol Sci 2023; 24:ijms24098096. [PMID: 37175801 PMCID: PMC10178739 DOI: 10.3390/ijms24098096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Phafins are PH (Pleckstrin Homology) and FYVE (Fab1, YOTB, Vac1, and EEA1) domain-containing proteins. The Phafin protein family is classified into two groups based on their sequence homology and functional similarity: Phafin1 and Phafin2. This protein family is unique because both the PH and FYVE domains bind to phosphatidylinositol 3-phosphate [PtdIns(3)P], a phosphoinositide primarily found in endosomal and lysosomal membranes. Phafin proteins act as PtdIns(3)P effectors in apoptosis, endocytic cargo trafficking, and autophagy. Additionally, Phafin2 is recruited to macropinocytic compartments through coincidence detection of PtdIns(3)P and PtdIns(4)P. Membrane-associated Phafins serve as adaptor proteins that recruit other binding partners. In addition to the phosphoinositide-binding domains, Phafin proteins present a poly aspartic acid motif that regulates membrane binding specificity. In this review, we summarize the involvement of Phafins in several cellular pathways and their potential physiological functions while highlighting the similarities and differences between Phafin1 and Phafin2. Besides, we discuss research perspectives for Phafins.
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Affiliation(s)
- Tuoxian Tang
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mahmudul Hasan
- Protein Signaling Domains Laboratory, Department of Biological Sciences, Fralin Life Sciences Institute and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061, USA
| | - Daniel G S Capelluto
- Protein Signaling Domains Laboratory, Department of Biological Sciences, Fralin Life Sciences Institute and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061, USA
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3
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Nawrotek A, Dubois P, Zeghouf M, Cherfils J. Molecular principles of bidirectional signalling between membranes and small GTPases. FEBS Lett 2023; 597:778-793. [PMID: 36700390 DOI: 10.1002/1873-3468.14585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/23/2022] [Accepted: 12/30/2022] [Indexed: 01/27/2023]
Abstract
Most small GTPases actuate their functions on subcellular membranes, which are increasingly seen as integral components of small GTPase signalling. In this review, we used the highly studied regulation of Arf GTPases by their GEFs to categorize the molecular principles of membrane contributions to small GTPase signalling, which have been highlighted by integrated structural biology combining in vitro reconstitutions in artificial membranes and high-resolution structures. As an illustration of how this framework can be harnessed to better understand the cooperation between small GTPases, their regulators and membranes, we applied it to the activation of the small GTPase Rac1 by DOCK-ELMO, identifying novel contributions of membranes to Rac1 activation. We propose that these structure-based principles should be considered when interrogating the mechanisms whereby small GTPase systems ensure spatial and temporal control of cellular signalling on membranes.
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Affiliation(s)
- Agata Nawrotek
- CNRS, Ecole Normale Supérieure Paris-Saclay and Université Paris-Saclay, Gif-sur-Yvette, France
| | - Pavlina Dubois
- CNRS, Ecole Normale Supérieure Paris-Saclay and Université Paris-Saclay, Gif-sur-Yvette, France
| | - Mahel Zeghouf
- CNRS, Ecole Normale Supérieure Paris-Saclay and Université Paris-Saclay, Gif-sur-Yvette, France
| | - Jacqueline Cherfils
- CNRS, Ecole Normale Supérieure Paris-Saclay and Université Paris-Saclay, Gif-sur-Yvette, France
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4
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Rosenhouse-Dantsker A, Gazgalis D, Logothetis DE. PI(4,5)P 2 and Cholesterol: Synthesis, Regulation, and Functions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1422:3-59. [PMID: 36988876 DOI: 10.1007/978-3-031-21547-6_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) is the most abundant membrane phosphoinositide and cholesterol is an essential component of the plasma membrane (PM). Both lipids play key roles in a variety of cellular functions including as signaling molecules and major regulators of protein function. This chapter provides an overview of these two important lipids. Starting from a brief description of their structure, synthesis, and regulation, the chapter continues to describe the primary functions and signaling processes in which PI(4,5)P2 and cholesterol are involved. While PI(4,5)P2 and cholesterol can act independently, they often act in concert or affect each other's impact. The chapters in this volume on "Cholesterol and PI(4,5)P2 in Vital Biological Functions: From Coexistence to Crosstalk" focus on the emerging relationship between cholesterol and PI(4,5)P2 in a variety of biological systems and processes. In this chapter, the next section provides examples from the ion channel field demonstrating that PI(4,5)P2 and cholesterol can act via common mechanisms. The chapter ends with a discussion of future directions.
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Affiliation(s)
| | - Dimitris Gazgalis
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Bouvé College of Health Sciences, Northeastern University, Boston, MA, USA
| | - Diomedes E Logothetis
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Bouvé College of Health Sciences, Northeastern University, Boston, MA, USA
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5
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Alkafaas SS, Abdallah AM, Ghosh S, Loutfy SA, Elkafas SS, Abdel Fattah NF, Hessien M. Insight into the role of clathrin-mediated endocytosis inhibitors in SARS-CoV-2 infection. Rev Med Virol 2023; 33:e2403. [PMID: 36345157 PMCID: PMC9877911 DOI: 10.1002/rmv.2403] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 11/10/2022]
Abstract
Emergence of SARS-CoV-2 variants warrants sustainable efforts to upgrade both the diagnostic and therapeutic protocols. Understanding the details of cellular and molecular basis of the virus-host cell interaction is essential for developing variant-independent therapeutic options. The internalization of SARS-CoV-2, into lung epithelial cells, is mediated by endocytosis, especially clathrin-mediated endocytosis (CME). Although vaccination is the gold standard strategy against viral infection, selective inhibition of endocytic proteins, complexes, and associated adaptor proteins may present a variant-independent therapeutic strategy. Although clathrin and/or dynamins are the most important proteins involved in CME, other endocytic mechanisms are clathrin and/or dynamin independent and rely on other proteins. Moreover, endocytosis implicates some subcellular structures, like plasma membrane, actin and lysosomes. Also, physiological conditions, such as pH and ion concentrations, represent an additional factor that mediates these events. Accordingly, endocytosis related proteins are potential targets for small molecules that inhibit endocytosis-mediated viral entry. This review summarizes the potential of using small molecules, targeting key proteins, participating in clathrin-dependent and -independent endocytosis, as variant-independent antiviral drugs against SARS-CoV-2 infection. The review takes two approaches. The first outlines the potential role of endocytic inhibitors in preventing endocytosis-mediated viral entry and its mechanism of action, whereas in the second computational analysis was implemented to investigate the selectivity of common inhibitors against endocytic proteins in SARS-CoV-2 endocytosis. The analysis revealed that remdesivir, methyl-β-cyclodextrin, rottlerin, and Bis-T can effectively inhibit clathrin, HMG-CoA reductase, actin, and dynamin I GTPase and are more potent in inhibiting SARS-CoV-2 than chloroquine. CME inhibitors for SARS-CoV-2 infection remain understudied.
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Affiliation(s)
- Samar Sami Alkafaas
- Molecular Cell Biology UniteDivision of BiochemistryDepartment of ChemistryFaculty of ScienceTanta UniversityTantaEgypt
| | - Abanoub Mosaad Abdallah
- Narcotic Research DepartmentNational Center for Social and Criminological Research (NCSCR)GizaEgypt
| | - Soumya Ghosh
- Department of GeneticsFaculty of Natural and Agricultural SciencesUniversity of the Free StateBloemfonteinSouth Africa
| | - Samah A. Loutfy
- Virology and Immunology UnitCancer Biology DepartmentNational Cancer Institute (NCI)Cairo UniversityCairoEgypt
- Nanotechnology Research CenterBritish UniversityCairoEgypt
| | - Sara Samy Elkafas
- Production Engineering and Mechanical Design DepartmentFaculty of EngineeringMenofia UniversityMenofiaEgypt
| | - Nasra F. Abdel Fattah
- Virology and Immunology UnitCancer Biology DepartmentNational Cancer Institute (NCI)Cairo UniversityCairoEgypt
| | - Mohamed Hessien
- Molecular Cell Biology UniteDivision of BiochemistryDepartment of ChemistryFaculty of ScienceTanta UniversityTantaEgypt
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6
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Maltan L, Andova AM, Derler I. The Role of Lipids in CRAC Channel Function. Biomolecules 2022; 12:biom12030352. [PMID: 35327543 PMCID: PMC8944985 DOI: 10.3390/biom12030352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/12/2022] [Accepted: 02/20/2022] [Indexed: 11/28/2022] Open
Abstract
The composition and dynamics of the lipid membrane define the physical properties of the bilayer and consequently affect the function of the incorporated membrane transporters, which also applies for the prominent Ca2+ release-activated Ca2+ ion channel (CRAC). This channel is activated by receptor-induced Ca2+ store depletion of the endoplasmic reticulum (ER) and consists of two transmembrane proteins, STIM1 and Orai1. STIM1 is anchored in the ER membrane and senses changes in the ER luminal Ca2+ concentration. Orai1 is the Ca2+-selective, pore-forming CRAC channel component located in the plasma membrane (PM). Ca2+ store-depletion of the ER triggers activation of STIM1 proteins, which subsequently leads to a conformational change and oligomerization of STIM1 and its coupling to as well as activation of Orai1 channels at the ER-PM contact sites. Although STIM1 and Orai1 are sufficient for CRAC channel activation, their efficient activation and deactivation is fine-tuned by a variety of lipids and lipid- and/or ER-PM junction-dependent accessory proteins. The underlying mechanisms for lipid-mediated CRAC channel modulation as well as the still open questions, are presented in this review.
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7
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Braun L, Schoen I, Vogel V. PIP 2-induced membrane binding of the vinculin tail competes with its other binding partners. Biophys J 2021; 120:4608-4622. [PMID: 34411575 DOI: 10.1016/j.bpj.2021.08.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 06/14/2021] [Accepted: 08/11/2021] [Indexed: 01/09/2023] Open
Abstract
Vinculin plays a key role during the first phase of focal adhesion formation and interacts with the plasma membrane through specific binding of its tail domain to the lipid phosphatidylinositol 4,5-bisphosphate (PIP2). Our understanding of the PIP2-vinculin interaction has been hampered by contradictory biochemical and structural data. Here, we used a multiscale molecular dynamics simulation approach, in which unbiased coarse-grained molecular dynamics were used to generate starting structures for subsequent microsecond-long all-atom simulations. This allowed us to map the interaction of the vinculin tail with PIP2-enriched membranes in atomistic detail. In agreement with experimental data, we have shown that membrane binding is sterically incompatible with the intramolecular interaction between vinculin's head and tail domain. Our simulations further confirmed biochemical and structural results, which identified two positively charged surfaces, the basic collar and the basic ladder, as the main PIP2 interaction sites. By introducing a valency-disaggregated binding network analysis, we were able to map the protein-lipid interactions in unprecedented detail. In contrast to the basic collar, in which PIP2 is specifically recognized by an up to hexavalent binding pocket, the basic ladder forms a series of low-valency binding sites. Importantly, many of these PIP2 binding residues are also involved in maintaining vinculin in a closed, autoinhibited conformation. These findings led us to propose a molecular mechanism for the coupling between vinculin activation and membrane binding. Finally, our refined binding site suggests an allosteric relationship between PIP2 and F-actin binding that disfavors simultaneous interaction with both ligands, despite nonoverlapping binding sites.
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Affiliation(s)
- Lukas Braun
- Laboratory of Applied Mechanobiology, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.
| | - Ingmar Schoen
- School of Pharmacy and Biomolecular Sciences, Irish Centre for Vascular Biology, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Viola Vogel
- Laboratory of Applied Mechanobiology, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
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8
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Abstract
A large proportion of proteins are expected to interact with cellular membranes to carry out their physiological functions in processes such as membrane transport, morphogenesis, cytoskeletal organization, and signal transduction. The recruitment of proteins at the membrane-cytoplasm interface and their activities are precisely regulated by phosphoinositides, which are negatively charged phospholipids found on the cytoplasmic leaflet of cellular membranes and play critical roles in membrane homeostasis and cellular signaling. Thus, it is important to reveal which proteins interact with phosphoinositides and to elucidate the underlying mechanisms. Here, we present two standard in vitro methods, liposome co-sedimentation and co-flotation assays, to study lipid-protein interactions. Liposomes can mimic various biological membranes in these assays because their lipid compositions and concentrations can be varied. Thus, in addition to mechanisms of lipid-protein interactions, these methods provide information on the possible specificities of proteins toward certain lipids such as specific phosphoinositide species and can hence shed light on the roles of membrane interactions on the functions of membrane-associated proteins.
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9
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Gao YG, Zhai X, Boldyrev IA, Molotkovsky JG, Patel DJ, Malinina L, Brown RE. Ceramide-1-phosphate transfer protein (CPTP) regulation by phosphoinositides. J Biol Chem 2021; 296:100600. [PMID: 33781749 PMCID: PMC8091061 DOI: 10.1016/j.jbc.2021.100600] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/19/2021] [Accepted: 03/25/2021] [Indexed: 12/25/2022] Open
Abstract
Ceramide-1-phosphate transfer proteins (CPTPs) are members of the glycolipid transfer protein (GLTP) superfamily that shuttle ceramide-1-phosphate (C1P) between membranes. CPTPs regulate cellular sphingolipid homeostasis in ways that impact programmed cell death and inflammation. CPTP downregulation specifically alters C1P levels in the plasma and trans-Golgi membranes, stimulating proinflammatory eicosanoid production and autophagy-dependent inflammasome-mediated cytokine release. However, the mechanisms used by CPTP to target the trans-Golgi and plasma membrane are not well understood. Here, we monitored C1P intervesicular transfer using fluorescence energy transfer (FRET) and showed that certain phosphoinositides (phosphatidylinositol 4,5 bisphosphate (PI-(4,5)P2) and phosphatidylinositol 4-phosphate (PI-4P)) increased CPTP transfer activity, whereas others (phosphatidylinositol 3-phosphate (PI-3P) and PI) did not. PIPs that stimulated CPTP did not stimulate GLTP, another superfamily member. Short-chain PI-(4,5)P2, which is soluble and does not remain membrane-embedded, failed to activate CPTP. CPTP stimulation by physiologically relevant PI-(4,5)P2 levels surpassed that of phosphatidylserine (PS), the only known non-PIP stimulator of CPTP, despite PI-(4,5)P2 increasing membrane equilibrium binding affinity less effectively than PS. Functional mapping of mutations that led to altered FRET lipid transfer and assessment of CPTP membrane interaction by surface plasmon resonance indicated that di-arginine motifs located in the α-6 helix and the α3-α4 helix regulatory loop of the membrane-interaction region serve as PI-(4,5)P2 headgroup-specific interaction sites. Haddock modeling revealed specific interactions involving the PI-(4,5)P2 headgroup that left the acyl chains oriented favorably for membrane embedding. We propose that PI-(4,5)P2 interaction sites enhance CPTP activity by serving as preferred membrane targeting/docking sites that favorably orient the protein for function.
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Affiliation(s)
- Yong-Guang Gao
- Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | - Xiuhong Zhai
- Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | - Ivan A Boldyrev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Julian G Molotkovsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Lucy Malinina
- Hormel Institute, University of Minnesota, Austin, Minnesota, USA
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10
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Review of PIP2 in Cellular Signaling, Functions and Diseases. Int J Mol Sci 2020; 21:ijms21218342. [PMID: 33172190 PMCID: PMC7664428 DOI: 10.3390/ijms21218342] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/30/2020] [Accepted: 11/03/2020] [Indexed: 12/27/2022] Open
Abstract
Phosphoinositides play a crucial role in regulating many cellular functions, such as actin dynamics, signaling, intracellular trafficking, membrane dynamics, and cell-matrix adhesion. Central to this process is phosphatidylinositol bisphosphate (PIP2). The levels of PIP2 in the membrane are rapidly altered by the activity of phosphoinositide-directed kinases and phosphatases, and it binds to dozens of different intracellular proteins. Despite the vast literature dedicated to understanding the regulation of PIP2 in cells over past 30 years, much remains to be learned about its cellular functions. In this review, we focus on past and recent exciting results on different molecular mechanisms that regulate cellular functions by binding of specific proteins to PIP2 or by stabilizing phosphoinositide pools in different cellular compartments. Moreover, this review summarizes recent findings that implicate dysregulation of PIP2 in many diseases.
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11
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Maffucci T, Falasca M. Inositol Polyphosphate-Based Compounds as Inhibitors of Phosphoinositide 3-Kinase-Dependent Signaling. Int J Mol Sci 2020; 21:E7198. [PMID: 33003448 PMCID: PMC7582811 DOI: 10.3390/ijms21197198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/21/2020] [Accepted: 09/21/2020] [Indexed: 02/07/2023] Open
Abstract
Signaling pathways regulated by the phosphoinositide 3-kinase (PI3K) enzymes have a well-established role in cancer development and progression. Over the past 30 years, the therapeutic potential of targeting this pathway has been well recognized, and this has led to the development of a multitude of drugs, some of which have progressed into clinical trials, with few of them currently approved for use in specific cancer settings. While many inhibitors compete with ATP, hence preventing the catalytic activity of the kinases directly, a deep understanding of the mechanisms of PI3K-dependent activation of its downstream effectors led to the development of additional strategies to prevent the initiation of this signaling pathway. This review summarizes previously published studies that led to the identification of inositol polyphosphates as promising parent molecules to design novel inhibitors of PI3K-dependent signals. We focus our attention on the inhibition of protein-membrane interactions mediated by binding of pleckstrin homology domains and phosphoinositides that we proposed 20 years ago as a novel therapeutic strategy.
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Affiliation(s)
- Tania Maffucci
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Marco Falasca
- Metabolic Signalling Group, School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
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12
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Abstract
While the organization of inanimate systems such as gases or liquids is predominantly thermodynamically driven—a mixture of two gases will tend to mix until they reach equilibrium—biological systems frequently exhibit organization that is far from a well-mixed equilibrium. The anisotropies displayed by cells are evident in some of the dynamic processes that constitute life including cell development, movement, and division. These anisotropies operate at different length-scales, from the meso- to the nanoscale, and are proposed to reflect self-organization, a characteristic of living systems that is becoming accessible to reconstitution from purified components, and thus a more thorough understanding. Here, some examples of self-organization underlying cellular anisotropies at the cellular level are reviewed, with an emphasis on Rho-family GTPases operating at the plasma membrane. Given the technical challenges of studying these dynamic proteins, some of the successful approaches that are being employed to study their self-organization will also be considered.
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Affiliation(s)
- Derek McCusker
- Dynamics of Cell Growth and Division, European Institute of Chemistry and Biology, F-33607 Bordeaux, France; Institute of Biochemistry and Cellular Genetics, UMR 5095, University of Bordeaux and Centre National de la Recherche Scientifique, F-33000 Bordeaux, France
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13
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Redpath GMI, Betzler VM, Rossatti P, Rossy J. Membrane Heterogeneity Controls Cellular Endocytic Trafficking. Front Cell Dev Biol 2020; 8:757. [PMID: 32850860 PMCID: PMC7419583 DOI: 10.3389/fcell.2020.00757] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 07/20/2020] [Indexed: 12/21/2022] Open
Abstract
Endocytic trafficking relies on highly localized events in cell membranes. Endocytosis involves the gathering of protein (cargo/receptor) at distinct plasma membrane locations defined by specific lipid and protein compositions. Simultaneously, the molecular machinery that drives invagination and eventually scission of the endocytic vesicle assembles at the very same place on the inner leaflet of the membrane. It is membrane heterogeneity - the existence of specific lipid and protein domains in localized regions of membranes - that creates the distinct molecular identity required for an endocytic event to occur precisely when and where it is required rather than at some random location within the plasma membrane. Accumulating evidence leads us to believe that the trafficking fate of internalized proteins is sealed following endocytosis, as this distinct membrane identity is preserved through the endocytic pathway, upon fusion of endocytic vesicles with early and sorting endosomes. In fact, just like at the plasma membrane, multiple domains coexist at the surface of these endosomes, regulating local membrane tubulation, fission and sorting to recycling pathways or to the trans-Golgi network via late endosomes. From here, membrane heterogeneity ensures that fusion events between intracellular vesicles and larger compartments are spatially regulated to promote the transport of cargoes to their intracellular destination.
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Affiliation(s)
- Gregory M I Redpath
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.,The ANZAC Research Institute, Concord Repatriation General Hospital, Concord, NSW, Australia
| | - Verena M Betzler
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland.,Biotechnology Institute Thurgau (BITg) at the University of Konstanz, Kreuzlingen, Switzerland
| | - Pascal Rossatti
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland.,Biotechnology Institute Thurgau (BITg) at the University of Konstanz, Kreuzlingen, Switzerland
| | - Jérémie Rossy
- Biotechnology Institute Thurgau (BITg) at the University of Konstanz, Kreuzlingen, Switzerland.,Department of Biology, University of Konstanz, Konstanz, Germany
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14
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Wheeler S, Sillence DJ. Niemann-Pick type C disease: cellular pathology and pharmacotherapy. J Neurochem 2019; 153:674-692. [PMID: 31608980 DOI: 10.1111/jnc.14895] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/10/2019] [Accepted: 09/15/2019] [Indexed: 12/22/2022]
Abstract
Niemann-Pick type C disease (NPCD) was first described in 1914 and affects approximately 1 in 150 000 live births. It is characterized clinically by diverse symptoms affecting liver, spleen, motor control, and brain; premature death invariably results. Its molecular origins were traced, as late as 1997, to a protein of late endosomes and lysosomes which was named NPC1. Mutation or absence of this protein leads to accumulation of cholesterol in these organelles. In this review, we focus on the intracellular events that drive the pathology of this disease. We first introduce endocytosis, a much-studied area of dysfunction in NPCD cells, and survey the various ways in which this process malfunctions. We briefly consider autophagy before attempting to map the more complex pathways by which lysosomal cholesterol storage leads to protein misregulation, mitochondrial dysfunction, and cell death. We then briefly introduce the metabolic pathways of sphingolipids (as these emerge as key species for treatment) and critically examine the various treatment approaches that have been attempted to date.
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Affiliation(s)
- Simon Wheeler
- School of Pharmacy, De Montfort University, The Gateway, Leicester, UK
| | - Dan J Sillence
- School of Pharmacy, De Montfort University, The Gateway, Leicester, UK
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15
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Legrand A, Martinez D, Grélard A, Berbon M, Morvan E, Tawani A, Loquet A, Mongrand S, Habenstein B. Nanodomain Clustering of the Plant Protein Remorin by Solid-State NMR. Front Mol Biosci 2019; 6:107. [PMID: 31681795 PMCID: PMC6803476 DOI: 10.3389/fmolb.2019.00107] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/30/2019] [Indexed: 11/24/2022] Open
Abstract
Nanodomains are dynamic membrane subcompartments, enriched in specific lipid, and protein components that act as functional platforms to manage an abundance of cellular processes. The remorin protein of plants is a well-established nanodomain marker and widely serves as a paradigm to study nanodomain clustering. Located at the inner leaflet of the plasma membrane, remorins perform essential functions during signaling. Using deuterium and phosphorus solid-state NMR, we inquire on the molecular determinants of the lipid-protein and protein-protein interactions driving nanodomain clustering. By monitoring thermotropism properties, lipid acyl chain order and membrane thickness, we report the effects of phosphoinositides and sterols on the interaction of various remorin peptides and protein constructs with the membrane. We probed several critical residues involved in this interaction and the involvement of the coiled-coil homo-oligomerisation domain into the formation of remorin nanodomains. We trace the essential role of the pH in nanodomain clustering based on anionic lipids such as phosphoinositides. Our results reveal a complex interplay between specific remorin residues and domains, the environmental pH and their resulting effects on the lipid dynamics for phosphoinositide-enriched membranes.
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Affiliation(s)
- Anthony Legrand
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université Bordeaux, Institut Polytechnique Bordeaux, Pessac, France.,Laboratoire de Biogenèse Membranaire - UMR 5200 - CNRS, Université de Bordeaux, Villenave-d'Ornon, France
| | - Denis Martinez
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université Bordeaux, Institut Polytechnique Bordeaux, Pessac, France
| | - Axelle Grélard
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université Bordeaux, Institut Polytechnique Bordeaux, Pessac, France
| | - Melanie Berbon
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université Bordeaux, Institut Polytechnique Bordeaux, Pessac, France
| | - Estelle Morvan
- European Institute of Chemistry and Biology - UMS3033/US001, Pessac, France
| | - Arpita Tawani
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université Bordeaux, Institut Polytechnique Bordeaux, Pessac, France
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université Bordeaux, Institut Polytechnique Bordeaux, Pessac, France
| | - Sébastien Mongrand
- Laboratoire de Biogenèse Membranaire - UMR 5200 - CNRS, Université de Bordeaux, Villenave-d'Ornon, France
| | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université Bordeaux, Institut Polytechnique Bordeaux, Pessac, France
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16
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Nawrotek A, Benabdi S, Niyomchon S, Kryszke MH, Ginestier C, Cañeque T, Tepshi L, Mariani A, St Onge RP, Giaever G, Nislow C, Charafe-Jauffret E, Rodriguez R, Zeghouf M, Cherfils J. PH-domain-binding inhibitors of nucleotide exchange factor BRAG2 disrupt Arf GTPase signaling. Nat Chem Biol 2019; 15:358-366. [PMID: 30742123 DOI: 10.1038/s41589-019-0228-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 11/29/2018] [Indexed: 12/30/2022]
Abstract
Peripheral membrane proteins orchestrate many physiological and pathological processes, making regulation of their activities by small molecules highly desirable. However, they are often refractory to classical competitive inhibition. Here, we demonstrate that potent and selective inhibition of peripheral membrane proteins can be achieved by small molecules that target protein-membrane interactions by a noncompetitive mechanism. We show that the small molecule Bragsin inhibits BRAG2-mediated Arf GTPase activation in vitro in a manner that requires a membrane. In cells, Bragsin affects the trans-Golgi network in a BRAG2- and Arf-dependent manner. The crystal structure of the BRAG2-Bragsin complex and structure-activity relationship analysis reveal that Bragsin binds at the interface between the PH domain of BRAG2 and the lipid bilayer to render BRAG2 unable to activate lipidated Arf. Finally, Bragsin affects tumorsphere formation in breast cancer cell lines. Bragsin thus pioneers a novel class of drugs that function by altering protein-membrane interactions without disruption.
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Affiliation(s)
- Agata Nawrotek
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole normale supérieure Paris-Saclay, Cachan, France.,CNRS, Cachan, France
| | - Sarah Benabdi
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole normale supérieure Paris-Saclay, Cachan, France.,CNRS, Cachan, France
| | - Supaporn Niyomchon
- Institut Curie, PSL Research University, Chemical Cell Biology Group, Paris, France.,CNRS, Paris, France.,INSERM, Paris, France
| | - Marie-Hélène Kryszke
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole normale supérieure Paris-Saclay, Cachan, France.,CNRS, Cachan, France
| | - Christophe Ginestier
- Université Aix-Marseille, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Team, Marseille, France
| | - Tatiana Cañeque
- Institut Curie, PSL Research University, Chemical Cell Biology Group, Paris, France.,CNRS, Paris, France.,INSERM, Paris, France
| | - Livia Tepshi
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole normale supérieure Paris-Saclay, Cachan, France.,CNRS, Cachan, France
| | - Angelica Mariani
- Institut Curie, PSL Research University, Chemical Cell Biology Group, Paris, France.,CNRS, Paris, France.,INSERM, Paris, France
| | - Robert P St Onge
- Genome Technology Center, Stanford School of Medicine, Stanford, CA, USA
| | - Guri Giaever
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
| | - Corey Nislow
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
| | - Emmanuelle Charafe-Jauffret
- Université Aix-Marseille, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Team, Marseille, France
| | - Raphaël Rodriguez
- Institut Curie, PSL Research University, Chemical Cell Biology Group, Paris, France.,CNRS, Paris, France.,INSERM, Paris, France
| | - Mahel Zeghouf
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole normale supérieure Paris-Saclay, Cachan, France. .,CNRS, Cachan, France.
| | - Jacqueline Cherfils
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole normale supérieure Paris-Saclay, Cachan, France. .,CNRS, Cachan, France.
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17
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Wheeler S, Schmid R, Sillence DJ. Lipid⁻Protein Interactions in Niemann⁻Pick Type C Disease: Insights from Molecular Modeling. Int J Mol Sci 2019; 20:E717. [PMID: 30736449 PMCID: PMC6387118 DOI: 10.3390/ijms20030717] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 01/31/2019] [Accepted: 02/03/2019] [Indexed: 12/19/2022] Open
Abstract
The accumulation of lipids in the late endosomes and lysosomes of Niemann⁻Pick type C disease (NPCD) cells is a consequence of the dysfunction of one protein (usually NPC1) but induces dysfunction in many proteins. We used molecular docking to propose (a) that NPC1 exports not just cholesterol, but also sphingosine, (b) that the cholesterol sensitivity of big potassium channel (BK) can be traced to a previously unappreciated site on the channel's voltage sensor, (c) that transient receptor potential mucolipin 1 (TRPML1) inhibition by sphingomyelin is likely an indirect effect, and (d) that phosphoinositides are responsible for both the mislocalization of annexin A2 (AnxA2) and a soluble NSF (N-ethylmaleimide Sensitive Fusion) protein attachment receptor (SNARE) recycling defect. These results are set in the context of existing knowledge of NPCD to sketch an account of the endolysosomal pathology key to this disease.
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Affiliation(s)
- Simon Wheeler
- School of Pharmacy, De Montfort University, The Gateway, Leicester LE1 9BH, UK.
| | - Ralf Schmid
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 7RH, UK.
| | - Dan J Sillence
- School of Pharmacy, De Montfort University, The Gateway, Leicester LE1 9BH, UK.
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18
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Curthoys NM, Mlodzianoski MJ, Parent M, Butler MB, Raut P, Wallace J, Lilieholm J, Mehmood K, Maginnis MS, Waters H, Busse B, Zimmerberg J, Hess ST. Influenza Hemagglutinin Modulates Phosphatidylinositol 4,5-Bisphosphate Membrane Clustering. Biophys J 2019; 116:893-909. [PMID: 30773293 DOI: 10.1016/j.bpj.2019.01.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 01/07/2019] [Accepted: 01/15/2019] [Indexed: 12/13/2022] Open
Abstract
The lipid phosphatidylinositol 4,5-bisphosphate (PIP2) forms nanoscopic clusters in cell plasma membranes; however, the processes determining PIP2 mobility and thus its spatial patterns are not fully understood. Using super-resolution imaging of living cells, we find that PIP2 is tightly colocalized with and modulated by overexpression of the influenza viral protein hemagglutinin (HA). Within and near clusters, HA and PIP2 follow a similar spatial dependence, which can be described by an HA-dependent potential gradient; PIP2 molecules move as if they are attracted to the center of clusters by a radial force of 0.079 ± 0.002 pN in HAb2 cells. The measured clustering and dynamics of PIP2 are inconsistent with the unmodified forms of the raft, tether, and fence models. Rather, we found that the spatial PIP2 distributions and how they change in time are explained via a novel, to our knowledge, dynamic mechanism: a radial gradient of PIP2 binding sites that are themselves mobile. This model may be useful for understanding other biological membrane domains whose distributions display gradients in density while maintaining their mobility.
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Affiliation(s)
- Nikki M Curthoys
- Department of Physics and Astronomy, University of Maine, Orono, Maine
| | | | - Matthew Parent
- Department of Physics and Astronomy, University of Maine, Orono, Maine
| | - Michael B Butler
- Department of Physics and Astronomy, University of Maine, Orono, Maine
| | - Prakash Raut
- Department of Physics and Astronomy, University of Maine, Orono, Maine
| | - Jaqulin Wallace
- Department of Physics and Astronomy, University of Maine, Orono, Maine
| | | | - Kashif Mehmood
- Department of Physics and Astronomy, University of Maine, Orono, Maine; Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine
| | - Melissa S Maginnis
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine
| | - Hang Waters
- Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Brad Busse
- Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Joshua Zimmerberg
- Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Samuel T Hess
- Department of Physics and Astronomy, University of Maine, Orono, Maine.
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19
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Small GTPase peripheral binding to membranes: molecular determinants and supramolecular organization. Biochem Soc Trans 2018; 47:13-22. [PMID: 30559268 DOI: 10.1042/bst20170525] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/23/2018] [Accepted: 11/27/2018] [Indexed: 01/26/2023]
Abstract
Small GTPases regulate many aspects of cell logistics by alternating between an inactive, GDP-bound form and an active, GTP-bound form. This nucleotide switch is coupled to a cytosol/membrane cycle, such that GTP-bound small GTPases carry out their functions at the periphery of endomembranes. A global understanding of the molecular determinants of the interaction of small GTPases with membranes and of the resulting supramolecular organization is beginning to emerge from studies of model systems. Recent studies highlighted that small GTPases establish multiple interactions with membranes involving their lipid anchor, their lipididated hypervariable region and elements in their GTPase domain, which combine to determine the strength, specificity and orientation of their association with lipids. Thereby, membrane association potentiates small GTPase interactions with GEFs, GAPs and effectors through colocalization and positional matching. Furthermore, it leads to small GTPase nanoclustering and to lipid demixing, which drives the assembly of molecular platforms in which proteins and lipids co-operate in producing high-fidelity signals through feedback and feedforward loops. Although still fragmentary, these observations point to an integrated model of signaling by membrane-attached small GTPases that involves a diversity of direct and indirect interactions, which can inspire new therapeutic strategies to block their activities in diseases.
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20
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Cebecauer M, Amaro M, Jurkiewicz P, Sarmento MJ, Šachl R, Cwiklik L, Hof M. Membrane Lipid Nanodomains. Chem Rev 2018; 118:11259-11297. [PMID: 30362705 DOI: 10.1021/acs.chemrev.8b00322] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Lipid membranes can spontaneously organize their components into domains of different sizes and properties. The organization of membrane lipids into nanodomains might potentially play a role in vital functions of cells and organisms. Model membranes represent attractive systems to study lipid nanodomains, which cannot be directly addressed in living cells with the currently available methods. This review summarizes the knowledge on lipid nanodomains in model membranes and exposes how their specific character contrasts with large-scale phase separation. The overview on lipid nanodomains in membranes composed of diverse lipids (e.g., zwitterionic and anionic glycerophospholipids, ceramides, glycosphingolipids) and cholesterol aims to evidence the impact of chemical, electrostatic, and geometric properties of lipids on nanodomain formation. Furthermore, the effects of curvature, asymmetry, and ions on membrane nanodomains are shown to be highly relevant aspects that may also modulate lipid nanodomains in cellular membranes. Potential mechanisms responsible for the formation and dynamics of nanodomains are discussed with support from available theories and computational studies. A brief description of current fluorescence techniques and analytical tools that enabled progress in lipid nanodomain studies is also included. Further directions are proposed to successfully extend this research to cells.
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Affiliation(s)
- Marek Cebecauer
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Dolejškova 3 , 18223 Prague 8 , Czech Republic
| | - Mariana Amaro
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Dolejškova 3 , 18223 Prague 8 , Czech Republic
| | - Piotr Jurkiewicz
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Dolejškova 3 , 18223 Prague 8 , Czech Republic
| | - Maria João Sarmento
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Dolejškova 3 , 18223 Prague 8 , Czech Republic
| | - Radek Šachl
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Dolejškova 3 , 18223 Prague 8 , Czech Republic
| | - Lukasz Cwiklik
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Dolejškova 3 , 18223 Prague 8 , Czech Republic
| | - Martin Hof
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Dolejškova 3 , 18223 Prague 8 , Czech Republic
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21
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Raze D, Verwaerde C, Deloison G, Werkmeister E, Coupin B, Loyens M, Brodin P, Rouanet C, Locht C. Heparin-Binding Hemagglutinin Adhesin (HBHA) Is Involved in Intracytosolic Lipid Inclusions Formation in Mycobacteria. Front Microbiol 2018; 9:2258. [PMID: 30333800 PMCID: PMC6176652 DOI: 10.3389/fmicb.2018.02258] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 09/05/2018] [Indexed: 12/19/2022] Open
Abstract
The heparin-binding hemagglutinin adhesin (HBHA) is an important virulence factor of Mycobacterium tuberculosis. It is a surface-displayed protein that serves as an adhesin for non-phagocytic cells and is involved in extra-pulmonary dissemination of the tubercle bacillus. It is also an important latency antigen useful for the diagnosis of latently M. tuberculosis-infected individuals. Using fluorescence time-lapse microscopy on mycobacteria that produce HBHA-green fluorescent protein chimera, we show here that HBHA can be found at two different locations and dynamically alternates between the mycobacterial surface and the interior of the cell, where it participates in the formation of intracytosolic lipid inclusions (ILI). Compared to HBHA-producing mycobacteria, HBHA-deficient mutants contain significantly lower amounts of ILI when grown in vitro or within macrophages, and the sizes of their ILI are significantly smaller. Lipid-binding assays indicate that HBHA is able to specifically bind to phosphatidylinositol and in particular to 4,5 di-phosphorylated phosphatidylinositol, but not to neutral lipids, the main constituents of ILI. HBHA derivatives lacking the C-terminal methylated, lysine-rich repeat region fail to bind to these lipids and these derivatives also fail to complement the phenotype of HBHA-deficient mutants. These studies indicate that HBHA is a moonlighting protein that serves several functions depending on its location. When surface exposed, HBHA serves as an adhesin, and when intracellularly localized, it participates in the generation of ILI, possibly as a cargo to transport phospholipids from the plasma membrane to the ILI in the process of being formed.
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Affiliation(s)
- Dominique Raze
- CNRS UMR8204, INSERM U1019, Centre d'Infection et d'Immunité de Lille, Institut Pasteur de Lille, Université de Lille, Lille, France
| | - Claudie Verwaerde
- CNRS UMR8204, INSERM U1019, Centre d'Infection et d'Immunité de Lille, Institut Pasteur de Lille, Université de Lille, Lille, France
| | - Gaspard Deloison
- CNRS UMR8204, INSERM U1019, Centre d'Infection et d'Immunité de Lille, Institut Pasteur de Lille, Université de Lille, Lille, France
| | - Elisabeth Werkmeister
- CNRS UMR8204, INSERM U1019, Centre d'Infection et d'Immunité de Lille, Institut Pasteur de Lille, Université de Lille, Lille, France
| | - Baptiste Coupin
- CNRS UMR8204, INSERM U1019, Centre d'Infection et d'Immunité de Lille, Institut Pasteur de Lille, Université de Lille, Lille, France
| | - Marc Loyens
- CNRS UMR8204, INSERM U1019, Centre d'Infection et d'Immunité de Lille, Institut Pasteur de Lille, Université de Lille, Lille, France
| | - Priscille Brodin
- CNRS UMR8204, INSERM U1019, Centre d'Infection et d'Immunité de Lille, Institut Pasteur de Lille, Université de Lille, Lille, France
| | - Carine Rouanet
- CNRS UMR8204, INSERM U1019, Centre d'Infection et d'Immunité de Lille, Institut Pasteur de Lille, Université de Lille, Lille, France
| | - Camille Locht
- CNRS UMR8204, INSERM U1019, Centre d'Infection et d'Immunité de Lille, Institut Pasteur de Lille, Université de Lille, Lille, France
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22
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Remorino A, De Beco S, Cayrac F, Di Federico F, Cornilleau G, Gautreau A, Parrini MC, Masson JB, Dahan M, Coppey M. Gradients of Rac1 Nanoclusters Support Spatial Patterns of Rac1 Signaling. Cell Rep 2018; 21:1922-1935. [PMID: 29141223 DOI: 10.1016/j.celrep.2017.10.069] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 09/18/2017] [Accepted: 10/18/2017] [Indexed: 01/03/2023] Open
Abstract
Rac1 is a small RhoGTPase switch that orchestrates actin branching in space and time and protrusion/retraction cycles of the lamellipodia at the cell front during mesenchymal migration. Biosensor imaging has revealed a graded concentration of active GTP-loaded Rac1 in protruding regions of the cell. Here, using single-molecule imaging and super-resolution microscopy, we show an additional supramolecular organization of Rac1. We find that Rac1 partitions and is immobilized into nanoclusters of 50-100 molecules each. These nanoclusters assemble because of the interaction of the polybasic tail of Rac1 with the phosphoinositide lipids PIP2 and PIP3. The additional interactions with GEFs and possibly GAPs, downstream effectors, and other partners are responsible for an enrichment of Rac1 nanoclusters in protruding regions of the cell. Our results show that subcellular patterns of Rac1 activity are supported by gradients of signaling nanodomains of heterogeneous molecular composition, which presumably act as discrete signaling platforms.
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Affiliation(s)
- Amanda Remorino
- Laboratoire Physico-Chimie, Institut Curie, CNRS UMR168, Paris-Science Lettres, Universite Pierre et Marie Curie-Paris 6, 75005 Paris, France
| | - Simon De Beco
- Laboratoire Physico-Chimie, Institut Curie, CNRS UMR168, Paris-Science Lettres, Universite Pierre et Marie Curie-Paris 6, 75005 Paris, France
| | - Fanny Cayrac
- Laboratoire Physico-Chimie, Institut Curie, CNRS UMR168, Paris-Science Lettres, Universite Pierre et Marie Curie-Paris 6, 75005 Paris, France
| | - Fahima Di Federico
- Laboratoire Physico-Chimie, Institut Curie, CNRS UMR168, Paris-Science Lettres, Universite Pierre et Marie Curie-Paris 6, 75005 Paris, France
| | - Gaetan Cornilleau
- Laboratoire Physico-Chimie, Institut Curie, CNRS UMR168, Paris-Science Lettres, Universite Pierre et Marie Curie-Paris 6, 75005 Paris, France
| | - Alexis Gautreau
- Ecole Polytechnique, Université Paris-Saclay, CNRS UMR7654, 91120 Palaiseau, France
| | - Maria Carla Parrini
- Institut Curie, Centre de Recherche, Paris Sciences Lettres, ART Group, Inserm U830, Paris 75005, France
| | - Jean-Baptiste Masson
- Decision and Bayesian Computation, Institut Pasteur, 25 Rue du Docteur Roux, Paris, 75015, France; Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS, Paris, France
| | - Maxime Dahan
- Laboratoire Physico-Chimie, Institut Curie, CNRS UMR168, Paris-Science Lettres, Universite Pierre et Marie Curie-Paris 6, 75005 Paris, France
| | - Mathieu Coppey
- Laboratoire Physico-Chimie, Institut Curie, CNRS UMR168, Paris-Science Lettres, Universite Pierre et Marie Curie-Paris 6, 75005 Paris, France.
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23
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Nicolas WJ, Grison MS, Bayer EM. Shaping intercellular channels of plasmodesmata: the structure-to-function missing link. JOURNAL OF EXPERIMENTAL BOTANY 2017; 69:91-103. [PMID: 28992136 DOI: 10.1093/jxb/erx225] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Plasmodesmata (PD) are a hallmark of the plant kingdom and a cornerstone of plant biology and physiology, forming the conduits for the cell-to-cell transfer of proteins, RNA and various metabolites, including hormones. They connect the cytosols and endomembranes of cells, which allows enhanced cell-to-cell communication and synchronization. Because of their unique position as intercellular gateways, they are at the frontline of plant defence and signalling and constitute the battleground for virus replication and spreading. The membranous organization of PD is remarkable, where a tightly furled strand of endoplasmic reticulum comes into close apposition with the plasma membrane, the two connected by spoke-like elements. The role of these structural features is, to date, still not completely understood. Recent data on PD seem to point in an unexpected direction, establishing a close parallel between PD and membrane contact sites and defining plasmodesmal membranes as microdomains. However, the implications of this new viewpoint are not fully understood. Aided by available phylogenetic data, this review attempts to reassess the function of the different elements comprising the PD and the relevance of membrane lipid composition and biophysics in defining specialized microdomains of PD, critical for their function.
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Affiliation(s)
- William J Nicolas
- Laboratoire de Biogénèse Membranaire, UMR 5200 CNRS, University of Bordeaux, France
| | - Magali S Grison
- Laboratoire de Biogénèse Membranaire, UMR 5200 CNRS, University of Bordeaux, France
| | - Emmanuelle M Bayer
- Laboratoire de Biogénèse Membranaire, UMR 5200 CNRS, University of Bordeaux, France
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24
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Pyrpassopoulos S, Shuman H, Ostap EM. Adhesion force and attachment lifetime of the KIF16B-PX domain interaction with lipid membranes. Mol Biol Cell 2017; 28:3315-3322. [PMID: 28931594 PMCID: PMC5687032 DOI: 10.1091/mbc.e17-05-0324] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 08/28/2017] [Accepted: 09/13/2017] [Indexed: 11/21/2022] Open
Abstract
KIF16B is a motor that binds early endosomes and controls the recycling of receptors. It has a PX domain that binds PI(3)P, which has been proposed to mechanically link motor to cargo. We determined the strength of this bond and its lifetime under load, and found it to be a suitable mechanical linkage for the KIF16B motor under working conditions. KIF16B is a highly processive kinesin-3 family member that participates in the trafficking and tubulation of early endosomes along microtubules. KIF16B attaches to lipid cargoes via a PX motif at its C-terminus, which has nanomolar affinity for bilayers containing phosphatidylinositol-3-phosphate (PI[3]P). As the PX domain has been proposed to be a primary mechanical anchor for the KIF16B-cargo attachment, we measured the adhesion forces and detachment kinetics of the PX domain as it interacts with membranes containing 2% PI(3)P and 98% phosphatidylcholine. Using optical tweezers, we found that the adhesion strength of a single PX domain ranged between 19 and 54 pN at loading rates between 80 and 1500 pN/s. These forces are substantially larger than the interaction of the adhesion of a pleckstrin homology domain with phosphatidylinositol 4,5-bisphosphate. This increased adhesion is the result of the membrane insertion of hydrophobic residues adjacent to the PI(3)P binding site, in addition to electrostatic interactions with PI(3)P. Attachment lifetimes under load decrease monotonically with force, indicating slip-bond behavior. However, the lifetime of membrane attachment under load appears to be well matched to the duration of processive motility of the KIF16B motor, indicating the PX domain is a suitable mechanical anchor for intracellular transport.
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Affiliation(s)
- Serapion Pyrpassopoulos
- Pennsylvania Muscle Institute, Department of Physiology, and Center for Engineering Mechanobiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104
| | - Henry Shuman
- Pennsylvania Muscle Institute, Department of Physiology, and Center for Engineering Mechanobiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104
| | - E Michael Ostap
- Pennsylvania Muscle Institute, Department of Physiology, and Center for Engineering Mechanobiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104
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Multiple interactions between an Arf/GEF complex and charged lipids determine activation kinetics on the membrane. Proc Natl Acad Sci U S A 2017; 114:11416-11421. [PMID: 28923919 DOI: 10.1073/pnas.1707970114] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Lipidated small GTPases and their regulators need to bind to membranes to propagate actions in the cell, but an integrated understanding of how the lipid bilayer exerts its effect has remained elusive. Here we focused on ADP ribosylation factor (Arf) GTPases, which orchestrate a variety of regulatory functions in lipid and membrane trafficking, and their activation by the guanine-nucleotide exchange factor (GEF) Brag2, which controls integrin endocytosis and cell adhesion and is impaired in cancer and developmental diseases. Biochemical and structural data are available that showed the exceptional efficiency of Arf activation by Brag2 on membranes. We determined the high-resolution crystal structure of unbound Brag2 containing the GEF (Sec7) and membrane-binding (pleckstrin homology) domains, revealing that it has a constitutively active conformation. We used this structure to analyze the interaction of uncomplexed Brag2 and of the myristoylated Arf1/Brag2 complex with a phosphatidylinositol bisphosphate (PIP2) -containing lipid bilayer, using coarse-grained molecular dynamics. These simulations revealed that the system forms a close-packed, oriented interaction with the membrane, in which multiple PIP2 lipids bind the canonical lipid-binding site and unique peripheral sites of the PH domain, the Arf GTPase and, unexpectedly, the Sec7 domain. We cross-validated these predictions by reconstituting the binding and kinetics of Arf and Brag2 in artificial membranes. Our coarse-grained structural model thus suggests that the high efficiency of Brag2 requires interaction with multiple lipids and a well-defined orientation on the membrane, resulting in a local PIP2 enrichment, which has the potential to signal toward the Arf pathway.
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Shengjuler D, Sun S, Cremer PS, Cameron CE. PIP-on-a-chip: A Label-free Study of Protein-phosphoinositide Interactions. J Vis Exp 2017:55869. [PMID: 28784961 PMCID: PMC5613778 DOI: 10.3791/55869] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Numerous cellular proteins interact with membrane surfaces to affect essential cellular processes. These interactions can be directed towards a specific lipid component within a membrane, as in the case of phosphoinositides (PIPs), to ensure specific subcellular localization and/or activation. PIPs and cellular PIP-binding domains have been studied extensively to better understand their role in cellular physiology. We applied a pH modulation assay on supported lipid bilayers (SLBs) as a tool to study protein-PIP interactions. In these studies, pH sensitive ortho-Sulforhodamine B conjugated phosphatidylethanolamine is used to detect protein-PIP interactions. Upon binding of a protein to a PIP-containing membrane surface, the interfacial potential is modulated (i.e. change in local pH), shifting the protonation state of the probe. A case study of the successful usage of the pH modulation assay is presented by using phospholipase C delta1 Pleckstrin Homology (PLC-δ1 PH) domain and phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) interaction as an example. The apparent dissociation constant (Kd,app) for this interaction was 0.39 ± 0.05 µM, similar to Kd,app values obtained by others. As previously observed, the PLC-δ1 PH domain is PI(4,5)P2 specific, shows weaker binding towards phosphatidylinositol 4-phosphate, and no binding to pure phosphatidylcholine SLBs. The PIP-on-a-chip assay is advantageous over traditional PIP-binding assays, including but not limited to low sample volume and no ligand/receptor labeling requirements, the ability to test high- and low-affinity membrane interactions with both small and large molecules, and improved signal to noise ratio. Accordingly, the usage of the PIP-on-a-chip approach will facilitate the elucidation of mechanisms of a wide range of membrane interactions. Furthermore, this method could potentially be used in identifying therapeutics that modulate protein's capacity to interact with membranes.
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Affiliation(s)
- Djoshkun Shengjuler
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University;
| | - Simou Sun
- Department of Chemistry, The Pennsylvania State University
| | - Paul S Cremer
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University; Department of Chemistry, The Pennsylvania State University;
| | - Craig E Cameron
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University;
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Roux A, Loranger A, Lavoie JN, Marceau N. Keratin 8/18 regulation of insulin receptor signaling and trafficking in hepatocytes through a concerted phosphoinositide-dependent Akt and Rab5 modulation. FASEB J 2017; 31:3555-3573. [PMID: 28442548 DOI: 10.1096/fj.201700036r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 04/11/2017] [Indexed: 01/30/2023]
Abstract
Keratins (Ks) are epithelial cell intermediate filament (IF) proteins that are expressed as pairs in a differentiation-regulated manner. Hepatocyte IFs are made only of K8/K18 pairs, which means that a K8 loss in K8-null mice leads to degradation of K18. Functionally, there is accumulating evidence that IFs contribute to signaling platforms. Here, we investigate the role of K8/K18 IFs in the regulation of insulin receptor (IR) signaling and trafficking in hepatocytes. We find that the IR substrate 1 (IRS1)/PI3K/Akt signaling cascade-downstream of IR-displays prolonged activation in K8-null compared with wild-type hepatocytes. Assessment of the Akt/mammalian target of rapamycin complex 1-mediated feedback loop to IRS1/PI3K, in the absence or presence of drug inhibitors, further supports a preferential K8/K18 IF intervention at the surface membrane. In K8-null hepatocytes, IR trafficking vesicles that are labeled by Rab5/EEA1/phosphatidylinositol 3-phosphate accumulate at a juxtanuclear region via a microtubule-dependent process. Moreover, interference with phosphatidylinositol 4,5-biphosphate signaling aggravates IR/Rab5 accumulation. Overall, results uncover K8/K18 IF regulation of IR signaling via a concerted modulation of phosphatidylinositol 4,5-biphosphate-dependent IRS1/PI3K/Akt signaling and Rab5/phosphatidylinositol 3-phosphate/microtubule trafficking in hepatocytes.-Roux, A., Loranger, A., Lavoie, J. N., Marceau, N. Keratin 8/18 regulation of insulin receptor signaling and trafficking in hepatocytes through a concerted phosphoinositide-dependent Akt and Rab5 modulation.
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Affiliation(s)
- Alexandra Roux
- Centre de Recherche Sur le Cancer de l'Université Laval, Québec City, Quebec, Canada.,Centre de Recherche du Centre Hospitalier Universitaire de Québec-Université Laval, L'Hôtel-Dieu de Québec, Québec City, Quebec, Canada
| | - Anne Loranger
- Centre de Recherche Sur le Cancer de l'Université Laval, Québec City, Quebec, Canada.,Centre de Recherche du Centre Hospitalier Universitaire de Québec-Université Laval, L'Hôtel-Dieu de Québec, Québec City, Quebec, Canada
| | - Josée N Lavoie
- Centre de Recherche Sur le Cancer de l'Université Laval, Québec City, Quebec, Canada.,Centre de Recherche du Centre Hospitalier Universitaire de Québec-Université Laval, L'Hôtel-Dieu de Québec, Québec City, Quebec, Canada
| | - Normand Marceau
- Centre de Recherche Sur le Cancer de l'Université Laval, Québec City, Quebec, Canada; .,Centre de Recherche du Centre Hospitalier Universitaire de Québec-Université Laval, L'Hôtel-Dieu de Québec, Québec City, Quebec, Canada
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