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Kundu S, Rohokale R, Lin C, Chen S, Biswas S, Guo Z. Bifunctional glycosphingolipid (GSL) probes to investigate GSL-interacting proteins in cell membranes. J Lipid Res 2024; 65:100570. [PMID: 38795858 PMCID: PMC11261293 DOI: 10.1016/j.jlr.2024.100570] [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: 03/19/2024] [Revised: 05/03/2024] [Accepted: 05/04/2024] [Indexed: 05/28/2024] Open
Abstract
Glycosphingolipids (GSLs) are abundant glycolipids on cells and essential for cell recognition, adhesion, signal transduction, and so on. However, their lipid anchors are not long enough to cross the membrane bilayer. To transduce transmembrane signals, GSLs must interact with other membrane components, whereas such interactions are difficult to investigate. To overcome this difficulty, bifunctional derivatives of II3-β-N-acetyl-D-galactosamine-GA2 (GalNAc-GA2) and β-N-acetyl-D-glucosamine-ceramide (GlcNAc-Cer) were synthesized as probes to explore GSL-interacting membrane proteins in live cells. Both probes contain photoreactive diazirine in the lipid moiety, which can crosslink with proximal membrane proteins upon photoactivation, and clickable alkyne in the glycan to facilitate affinity tag addition for crosslinked protein pull-down and characterization. The synthesis is highlighted by the efficient assembly of simple glycolipid precursors followed by on-site lipid remodeling. These probes were employed to profile GSL-interacting membrane proteins in HEK293 cells. The GalNAc-GA2 probe revealed 312 distinct proteins, with GlcNAc-Cer probe-crosslinked proteins as controls, suggesting the potential influence of the glycan on GSL functions. Many of the proteins identified with the GalNAc-GA2 probe are associated with GSLs, and some have been validated as being specific to this probe. The versatile probe design and experimental protocols are anticipated to be widely applicable to GSL research.
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Affiliation(s)
- Sayan Kundu
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Rajendra Rohokale
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Chuwei Lin
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Sixue Chen
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, USA; Department of Biology, University of Mississippi, Oxford, MS, USA
| | - Shayak Biswas
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Zhongwu Guo
- Department of Chemistry, University of Florida, Gainesville, FL, USA.
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Wan Mohamad Noor WNI, Nguyen NTH, Cheong TH, Chek MF, Hakoshima T, Inaba T, Hanawa-Suetsugu K, Nishimura T, Suetsugu S. Small GTPase Cdc42, WASP, and scaffold proteins for higher-order assembly of the F-BAR domain protein. SCIENCE ADVANCES 2023; 9:eadf5143. [PMID: 37126564 PMCID: PMC10132759 DOI: 10.1126/sciadv.adf5143] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The higher-order assembly of Bin-amphiphysin-Rvs (BAR) domain proteins, including the FCH-BAR (F-BAR) domain proteins, into lattice on the membrane is essential for the formation of subcellular structures. However, the regulation of their ordered assembly has not been elucidated. Here, we show that the higher ordered assembly of growth-arrested specific 7 (GAS7), an F-BAR domain protein, is regulated by the multivalent scaffold proteins of Wiskott-Aldrich syndrome protein (WASP)/neural WASP, that commonly binds to the BAR domain superfamily proteins, together with WISH, Nck, the activated small guanosine triphosphatase Cdc42, and a membrane-anchored phagocytic receptor. The assembly kinetics by fluorescence resonance energy transfer monitoring indicated that the GAS7 assembly on liposomes started within seconds and was further increased by the presence of these proteins. The regulated GAS7 assembly was abolished by Wiskott-Aldrich syndrome mutations both in vitro and in cellular phagocytosis. Therefore, Cdc42 and the scaffold proteins that commonly bind to the BAR domain superfamily proteins promoted GAS7 assembly.
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Affiliation(s)
- Wan Nurul Izzati Wan Mohamad Noor
- Division of Biological Science, Graduate school of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Nhung Thi Hong Nguyen
- Division of Biological Science, Graduate school of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Theng Ho Cheong
- Division of Biological Science, Graduate school of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Min Fey Chek
- Division of Biological Science, Graduate school of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Toshio Hakoshima
- Division of Biological Science, Graduate school of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Takehiko Inaba
- Division of Biological Science, Graduate school of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Kyoko Hanawa-Suetsugu
- Division of Biological Science, Graduate school of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Tamako Nishimura
- Division of Biological Science, Graduate school of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Shiro Suetsugu
- Division of Biological Science, Graduate school of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
- Data Science Center, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
- Center for Digital Green-Innovation, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
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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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Zhu Y, Li S, Jaume A, Jani RA, Delevoye C, Raposo G, Marks MS. Type II phosphatidylinositol 4-kinases function sequentially in cargo delivery from early endosomes to melanosomes. J Biophys Biochem Cytol 2022; 221:213509. [PMID: 36169639 PMCID: PMC9524207 DOI: 10.1083/jcb.202110114] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 03/31/2022] [Accepted: 05/04/2022] [Indexed: 12/11/2022] Open
Abstract
Melanosomes are pigment cell-specific lysosome-related organelles in which melanin pigments are synthesized and stored. Melanosome maturation requires delivery of melanogenic cargoes via tubular transport carriers that emanate from early endosomes and that require BLOC-1 for their formation. Here we show that phosphatidylinositol-4-phosphate (PtdIns4P) and the type II PtdIns-4-kinases (PI4KIIα and PI4KIIβ) support BLOC-1-dependent tubule formation to regulate melanosome biogenesis. Depletion of either PI4KIIα or PI4KIIβ with shRNAs in melanocytes reduced melanin content and misrouted BLOC-1-dependent cargoes to late endosomes/lysosomes. Genetic epistasis, cell fractionation, and quantitative live-cell imaging analyses show that PI4KIIα and PI4KIIβ function sequentially and non-redundantly downstream of BLOC-1 during tubule elongation toward melanosomes by generating local pools of PtdIns4P. The data show that both type II PtdIns-4-kinases are necessary for efficient BLOC-1-dependent tubule elongation and subsequent melanosome contact and content delivery during melanosome biogenesis. The independent functions of PtdIns-4-kinases in tubule extension are downstream of likely redundant functions in BLOC-1-dependent tubule initiation.
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Affiliation(s)
- Yueyao Zhu
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA.,Department of Biology, University of Pennsylvania School of Arts and Sciences, Philadelphia, PA
| | - Shuixing Li
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA.,Department of Pathology and Laboratory Medicine and Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Alexa Jaume
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA.,Department of Pathology and Laboratory Medicine and Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Riddhi Atul Jani
- Institut Curie, PSL Research University, CNRS, UMR 144, Structure and Membrane Compartments, Paris, France
| | - Cédric Delevoye
- Institut Curie, PSL Research University, CNRS, UMR 144, Structure and Membrane Compartments, Paris, France
| | - Graça Raposo
- Institut Curie, PSL Research University, CNRS, UMR 144, Structure and Membrane Compartments, Paris, France
| | - Michael S Marks
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA.,Department of Pathology and Laboratory Medicine and Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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Nishimura T, Oyama T, Hu HT, Fujioka T, Hanawa-Suetsugu K, Ikeda K, Yamada S, Kawana H, Saigusa D, Ikeda H, Kurata R, Oono-Yakura K, Kitamata M, Kida K, Hikita T, Mizutani K, Yasuhara K, Mimori-Kiyosue Y, Oneyama C, Kurimoto K, Hosokawa Y, Aoki J, Takai Y, Arita M, Suetsugu S. Filopodium-derived vesicles produced by MIM enhance the migration of recipient cells. Dev Cell 2021; 56:842-859.e8. [PMID: 33756122 DOI: 10.1016/j.devcel.2021.02.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 12/31/2020] [Accepted: 02/23/2021] [Indexed: 12/19/2022]
Abstract
Extracellular vesicles (EVs) are classified as large EVs (l-EVs, or microvesicles) and small EVs (s-EVs, or exosomes). S-EVs are thought to be generated from endosomes through a process that mainly depends on the ESCRT protein complex, including ALG-2 interacting protein X (ALIX). However, the mechanisms of l-EV generation from the plasma membrane have not been identified. Membrane curvatures are generated by the bin-amphiphysin-rvs (BAR) family proteins, among which the inverse BAR (I-BAR) proteins are involved in filopodial protrusions. Here, we show that the I-BAR proteins, including missing in metastasis (MIM), generate l-EVs by scission of filopodia. Interestingly, MIM-containing l-EV production was promoted by in vivo equivalent external forces and by the suppression of ALIX, suggesting an alternative mechanism of vesicle formation to s-EVs. The MIM-dependent l-EVs contained lysophospholipids and proteins, including IRS4 and Rac1, which stimulated the migration of recipient cells through lamellipodia formation. Thus, these filopodia-dependent l-EVs, which we named as filopodia-derived vesicles (FDVs), modify cellular behavior.
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Affiliation(s)
- Tamako Nishimura
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Takuya Oyama
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Hooi Ting Hu
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Toshifumi Fujioka
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Kyoko Hanawa-Suetsugu
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Kazutaka Ikeda
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan; Kazusa DNA Research Institute, 2-6-7 Kazusa, kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Sohei Yamada
- Division of Materials Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Hiroki Kawana
- Laboratory of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Daisuke Saigusa
- Tohoku University Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Hiroki Ikeda
- Department of Embryology, Nara Medical University, Kashihara 634-0813, Nara, Japan
| | - Rie Kurata
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Kayoko Oono-Yakura
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Manabu Kitamata
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Kazuki Kida
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Tomoya Hikita
- Division of Cancer Cell Regulation, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya 464-8681, Japan
| | - Kiyohito Mizutani
- Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, Kobe 650-0047, Japan
| | - Kazuma Yasuhara
- Division of Materials Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Yuko Mimori-Kiyosue
- Laboratory for Molecular and Cellular Dynamics, RIKEN Center for Biosystems Dynamics Research, Minatojima-minaminachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Chitose Oneyama
- Division of Cancer Cell Regulation, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya 464-8681, Japan
| | - Kazuki Kurimoto
- Department of Embryology, Nara Medical University, Kashihara 634-0813, Nara, Japan
| | - Yoichiroh Hosokawa
- Division of Materials Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Junken Aoki
- Laboratory of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Yoshimi Takai
- Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, Kobe 650-0047, Japan
| | - Makoto Arita
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan; Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-0011, Japan
| | - Shiro Suetsugu
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan; Data Science Center, Nara Institute of Science and Technology, Ikoma 630-0192, Japan.
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The state of F-BAR domains as membrane-bound oligomeric platforms. Trends Cell Biol 2021; 31:644-655. [PMID: 33888395 DOI: 10.1016/j.tcb.2021.03.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/16/2022]
Abstract
Fes/Cip4 homology Bin/amphiphysin/Rvs (F-BAR) domains, like all BAR domains, are dimeric units that oligomerize and bind membranes. F-BAR domains are generally coupled to additional domains that function in protein binding or have enzymatic activity. Because of their crescent shape and ability to oligomerize, F-BAR domains have been traditionally viewed as membrane-deformation modules. However, multiple independent studies have provided no evidence that certain F-BAR domains are able to tubulate membrane. Instead, a growing body of literature featuring structural, biochemical, biophysical, and microscopy-based studies supports the idea that the F-BAR domain family can be unified only by their ability to form oligomeric assemblies on membranes to provide platforms for molecular assembly.
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