1
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Miao X, Law MCY, Kumar J, Chng CP, Zeng Y, Tan YB, Wu J, Guo X, Huang L, Zhuang Y, Gao W, Huang C, Luo D, Zhao W. Saddle curvature association of nsP1 facilitates the replication complex assembly of Chikungunya virus in cells. Nat Commun 2025; 16:4282. [PMID: 40341088 PMCID: PMC12062417 DOI: 10.1038/s41467-025-59402-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2024] [Accepted: 04/22/2025] [Indexed: 05/10/2025] Open
Abstract
Positive-sense RNA viruses, including SARS-CoV-1 and -2, DENV, and CHIKV, replicate in curved membrane compartments within host cells. Non-structural proteins (nsPs) critically regulate these nanoscale membrane structures, yet their curvature-dependent assembly remains elusive due to the challenges of imaging nanoscale interaction on curved surfaces. Using vertically aligned nanostructures to generate pre-defined membrane curvatures, we here investigate the impact of curvature on nsPs assembly. Taking CHIKV as a model, we reveal that nsP1 preferentially binds and stabilizes on positively curved membranes, with stronger accumulation at radii ≤150 nm. This is driven by hydrophobic residues in the membrane association (MA) loops of individual nsP1. Molecular dynamics simulations further confirm the improved binding stability of nsP1 on curved membranes, particularly when it forms a dodecamer ring. Together, nsP1 supports a strong saddle curvature association, with flexible MA loops sensing a range of positive curvatures in the x-z plane while the rigid dodecamer stabilizing fixed negative curvature in the x-y plane - crucial for constraining the membrane spherule neck during replication progression. Moreover, CHIKV replication enriches on patterned nanoring structures, underscoring the curvature-guided assembly of the viral replication complex. Our findings highlight membrane curvature as a key regulator of viral nsPs organization, opening new avenues for studying membrane remodeling in viral replication.
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Affiliation(s)
- Xinwen Miao
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
| | - Michelle Cheok Yien Law
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Jatin Kumar
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore, Singapore
| | - Choon-Peng Chng
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore, Singapore
| | - Yongpeng Zeng
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
| | - Yaw Bia Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Jiawei Wu
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
- State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Xiangfu Guo
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
| | - Lizhen Huang
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
| | - Yinyin Zhuang
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
| | - Weibo Gao
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore, Singapore
- School of Physics and Mathematical Science, Nanyang Technological University, Singapore, Singapore
| | - Changjin Huang
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore, Singapore.
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore.
- National Centre for Infectious Diseases, Singapore, Singapore.
| | - Wenting Zhao
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore.
- Institute for Digital Molecular Analytics and Science, Nanyang Technological University, Singapore, Singapore.
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2
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Lu CH, Lee CE, Nakamoto ML, Cui B. Cellular Signaling at the Nano-Bio Interface: Spotlighting Membrane Curvature. Annu Rev Phys Chem 2025; 76:251-277. [PMID: 40258240 PMCID: PMC12043246 DOI: 10.1146/annurev-physchem-090722-021151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2025]
Abstract
No longer viewed as a passive consequence of cellular activities, membrane curvature-the physical shape of the cell membrane-is now recognized as an active constituent of biological processes. Nanoscale topographies on extracellular matrices or substrate surfaces impart well-defined membrane curvatures on the plasma membrane. This review examines biological events occurring at the nano-bio interface, the physical interface between the cell membrane and surface nanotopography, which activates intracellular signaling by recruiting curvature-sensing proteins. We encompass a wide range of biological processes at the nano-bio interface, including cell adhesion, endocytosis, glycocalyx redistribution, regulation of mechanosensitive ion channels, cell migration, and differentiation. Despite the diversity of processes, we call attention to the critical role of membrane curvature in each process. We particularly highlight studies that elucidate molecular mechanisms involving curvature-sensing proteins with the hope of providing comprehensive insights into this rapidly advancing area of research.
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Affiliation(s)
- Chih-Hao Lu
- Department of Chemistry, Stanford University, Stanford, California, USA;
- Wu-Tsai Neuroscience Institute and Sarafan ChEM-H Institute, Stanford University, Stanford, California, USA
| | - Christina E Lee
- Wu-Tsai Neuroscience Institute and Sarafan ChEM-H Institute, Stanford University, Stanford, California, USA
- Biophysics Program, Stanford University School of Medicine, Stanford, California, USA
| | - Melissa L Nakamoto
- Department of Chemistry, Stanford University, Stanford, California, USA;
- Wu-Tsai Neuroscience Institute and Sarafan ChEM-H Institute, Stanford University, Stanford, California, USA
| | - Bianxiao Cui
- Department of Chemistry, Stanford University, Stanford, California, USA;
- Wu-Tsai Neuroscience Institute and Sarafan ChEM-H Institute, Stanford University, Stanford, California, USA
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3
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Sun WW, Michalak DJ, Sochacki KA, Kunamaneni P, Alfonzo-Méndez MA, Arnold AM, Strub MP, Hinshaw JE, Taraska JW. Cryo-electron tomography pipeline for plasma membranes. Nat Commun 2025; 16:855. [PMID: 39833141 PMCID: PMC11747107 DOI: 10.1038/s41467-025-56045-z] [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: 06/11/2024] [Accepted: 01/03/2025] [Indexed: 01/22/2025] Open
Abstract
Cryo-electron tomography (cryoET) provides sub-nanometer protein structure within the dense cellular environment. Existing sample preparation methods are insufficient at accessing the plasma membrane and its associated proteins. Here, we present a correlative cryo-electron tomography pipeline optimally suited to image large ultra-thin areas of isolated basal and apical plasma membranes. The pipeline allows for angstrom-scale structure determination with subtomogram averaging and employs a genetically encodable rapid chemically-induced electron microscopy visible tag for marking specific proteins within the complex cellular environment. The pipeline provides efficient, distributable, low-cost sample preparation and enables targeted structural studies of identified proteins at the plasma membrane of mammalian cells.
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Affiliation(s)
- Willy W Sun
- National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, MD, USA
| | - Dennis J Michalak
- National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, MD, USA
| | - Kem A Sochacki
- National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, MD, USA.
| | - Prasanthi Kunamaneni
- National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, MD, USA
- National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD, USA
| | - Marco A Alfonzo-Méndez
- National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, MD, USA
| | - Andreas M Arnold
- National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, MD, USA
| | - Marie-Paule Strub
- National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, MD, USA
| | - Jenny E Hinshaw
- National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD, USA.
| | - Justin W Taraska
- National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, MD, USA.
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4
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Liu J, Ha T. Connecting single-molecule and superresolution microscopies to cell biology through theoretical modeling. Biophys J 2025; 124:15-24. [PMID: 39600094 PMCID: PMC11739872 DOI: 10.1016/j.bpj.2024.11.3308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2024] [Revised: 11/12/2024] [Accepted: 11/22/2024] [Indexed: 11/29/2024] Open
Abstract
Recent developments of single-molecule and superresolution microscopies reveal novel spatial-temporal features of various cellular processes with unprecedented details, and greatly facilitate the development of theoretical models. In this review, we synthesize our view of how to meaningfully integrate these experimental approaches with theoretical modeling to obtain deeper understanding of the physical mechanisms of cell biology.
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Affiliation(s)
- Jian Liu
- Department of Cell Biology, Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, Maryland.
| | - Taekjip Ha
- Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts; Department of Pediatrics, Harvard Medical School, Boston, Massachusetts.
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5
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Frey F, Schwarz US. Coat stiffening can explain invagination of clathrin-coated membranes. Phys Rev E 2024; 110:064403. [PMID: 39916158 DOI: 10.1103/physreve.110.064403] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Accepted: 11/14/2024] [Indexed: 05/07/2025]
Abstract
Clathrin-mediated endocytosis is the main pathway used by eukaryotic cells to take up extracellular material, but the dominant physical mechanisms driving this process are still elusive. Recently, several high-resolution imaging techniques have been used on different cell lines to measure the geometrical properties of clathrin-coated pits over their whole lifetime. Here, we first show that the combination of all datasets with the recently introduced cooperative curvature model defines a consensus pathway, which is characterized by a flat-to-curved transition at finite area, followed by linear growth and subsequent saturation of curvature. We then apply an energetic model for the composite of the plasma membrane and clathrin coat to this consensus pathway to show that the dominant mechanism for invagination could be coat stiffening, which might originate from cooperative interactions between the different clathrin molecules and progressively drives the system toward its intrinsic curvature. Our theory predicts that two length scales determine the invagination pathway, namely the patch size at which the flat-to-curved transition occurs and the final pit radius.
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Affiliation(s)
- Felix Frey
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Ulrich S Schwarz
- Heidelberg University, Institute for Theoretical Physics and BioQuant, 69120 Heidelberg, Germany
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6
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Hu D, Li T, Bian H, Liu H, Wang P, Wang Y, Sun J. Silk films with distinct surface topography modulate plasma membrane curvature to polarize macrophages. Mater Today Bio 2024; 28:101193. [PMID: 39221204 PMCID: PMC11364906 DOI: 10.1016/j.mtbio.2024.101193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 08/03/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024] Open
Abstract
The physical properties of a biomaterial play a vital role in modulating macrophage polarization. However, discerning the specific effects of individual parameters can be intricate due to their interdependencies, limiting the mechanism underlying a specific parameter on the polarization of macrophages. Here, we engineered silk fibroin (SF) films with tunable surface roughness while maintaining similar physical properties by combining casting and salting out techniques. We demonstrate that increased surface roughness in SF films promotes M2-like macrophage polarization, characterized by enhanced secretion of anti-inflammatory cytokines. Transcriptomic analysis unveils the modulation of genes associated with extracellular matrix-cell interactions, highlighting the role of surface topography in regulating cellular processes. Mechanistically, we show that surface roughness induces macrophage membrane curvature, facilitating integrin αv endocytosis and thereby inhibiting the integrin-NF-kB signaling pathway. In vivo implantation assays corroborate that rough SF films substantially mitigate early inflammatory responses. This work establishes a direct link between surface roughness and intracellular signaling in macrophages, adding to our understanding of the biomaterial surface effect at the material-cell interface and bringing insights into material design.
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Affiliation(s)
- Doudou Hu
- Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Tiandong Li
- Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Haixu Bian
- Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Haiyu Liu
- Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Pengwei Wang
- Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Yeyuan Wang
- Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Jingchen Sun
- Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
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7
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Johnson A. Mechanistic divergences of endocytic clathrin-coated vesicle formation in mammals, yeasts and plants. J Cell Sci 2024; 137:jcs261847. [PMID: 39161994 PMCID: PMC11361644 DOI: 10.1242/jcs.261847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024] Open
Abstract
Clathrin-coated vesicles (CCVs), generated by clathrin-mediated endocytosis (CME), are essential eukaryotic trafficking organelles that transport extracellular and plasma membrane-bound materials into the cell. In this Review, we explore mechanisms of CME in mammals, yeasts and plants, and highlight recent advances in the characterization of endocytosis in plants. Plants separated from mammals and yeast over 1.5 billion years ago, and plant cells have distinct biophysical parameters that can influence CME, such as extreme turgor pressure. Plants can therefore provide a wider perspective on fundamental processes in eukaryotic cells. We compare key mechanisms that drive CCV formation and explore what these mechanisms might reveal about the core principles of endocytosis across the tree of life. Fascinatingly, CME in plants appears to more closely resemble that in mammalian cells than that in yeasts, despite plants being evolutionarily further from mammals than yeast. Endocytic initiation appears to be highly conserved across these three systems, requiring similar protein domains and regulatory processes. Clathrin coat proteins and their honeycomb lattice structures are also highly conserved. However, major differences are found in membrane-bending mechanisms. Unlike in mammals or yeast, plant endocytosis occurs independently of actin, highlighting that mechanistic assumptions about CME across different systems should be made with caution.
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Affiliation(s)
- Alexander Johnson
- Division of Anatomy, Center for Anatomy & Cell Biology, Medical University of Vienna, Vienna 1090, Austria
- Medical Imaging Cluster (MIC), Medical University of Vienna, Vienna 1090, Austria
- Biosciences, University of Exeter, Exeter EX4 4QD, UK
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8
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Liu J. Roles of membrane mechanics-mediated feedback in membrane traffic. Curr Opin Cell Biol 2024; 89:102401. [PMID: 39018789 PMCID: PMC11297666 DOI: 10.1016/j.ceb.2024.102401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/23/2024] [Accepted: 06/26/2024] [Indexed: 07/19/2024]
Abstract
Synthesizing the recent progresses, we present our perspectives on how local modulations of membrane curvature, tension, and bending energy define the feedback controls over membrane traffic processes. We speculate the potential mechanisms of, and the control logic behind, the different membrane mechanics-mediated feedback in endocytosis and exo-endocytosis coupling. We elaborate the path forward with the open questions for theoretical considerations and the grand challenges for experimental validations.
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Affiliation(s)
- Jian Liu
- Department of Cell Biology, Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, United States.
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9
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Sun WW, Michalak DJ, Sochacki KA, Kunamaneni P, Alfonzo-Méndez MA, Arnold AM, Strub MP, Hinshaw JE, Taraska JW. Cryo-electron tomography pipeline for plasma membranes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.600657. [PMID: 39372776 PMCID: PMC11451596 DOI: 10.1101/2024.06.27.600657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
Cryo-electron tomography (cryoET) provides sub-nanometer protein structure within the dense cellular environment. Existing sample preparation methods are insufficient at accessing the plasma membrane and its associated proteins. Here, we present a correlative cryo-electron tomography pipeline optimally suited to image large ultra-thin areas of isolated basal and apical plasma membranes. The pipeline allows for angstrom-scale structure determination with sub-tomogram averaging and employs a genetically-encodable rapid chemically-induced electron microscopy visible tag for marking specific proteins within the complex cell environment. The pipeline provides fast, efficient, distributable, low-cost sample preparation and enables targeted structural studies of identified proteins at the plasma membrane of cells.
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Affiliation(s)
- Willy W. Sun
- National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland, USA
- These authors contributed equally
| | - Dennis J. Michalak
- National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland, USA
- These authors contributed equally
| | - Kem A. Sochacki
- National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland, USA
- These authors contributed equally
| | - Prasanthi Kunamaneni
- National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland, USA
- National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - Marco A. Alfonzo-Méndez
- National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland, USA
| | - Andreas M. Arnold
- National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland, USA
| | - Marie-Paule Strub
- National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland, USA
| | - Jenny E. Hinshaw
- National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - Justin W. Taraska
- National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland, USA
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10
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Zhuang Y, Guo X, Razorenova OV, Miles CE, Zhao W, Shi X. Coaching ribosome biogenesis from the nuclear periphery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.597078. [PMID: 38948754 PMCID: PMC11212990 DOI: 10.1101/2024.06.21.597078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Severe invagination of the nuclear envelope is a hallmark of cancers, aging, neurodegeneration, and infections. However, the outcomes of nuclear invagination remain unclear. This work identified a new function of nuclear invagination: regulating ribosome biogenesis. With expansion microscopy, we observed frequent physical contact between nuclear invaginations and nucleoli. Surprisingly, the higher the invagination curvature, the more ribosomal RNA and pre-ribosomes are made in the contacted nucleolus. By growing cells on nanopillars that generate nuclear invaginations with desired curvatures, we can increase and decrease ribosome biogenesis. Based on this causation, we repressed the ribosome levels in breast cancer and progeria cells by growing cells on low-curvature nanopillars, indicating that overactivated ribosome biogenesis can be rescued by reshaping nuclei. Mechanistically, high-curvature nuclear invaginations reduce heterochromatin and enrich nuclear pore complexes, which promote ribosome biogenesis. We anticipate that our findings will serve as a foundation for further studies on nuclear deformation.
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Affiliation(s)
- Yinyin Zhuang
- Department of Developmental and Cell Biology, University of California, Irvine; Irvine, CA 92697, United States
| | - Xiangfu Guo
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University; Singapore 637459, Singapore
| | - Olga V. Razorenova
- Department of Molecular Biology and Biochemistry, University of California, Irvine; Irvine, CA 92697, United States
| | - Christopher E. Miles
- Department of Mathematics, University of California, Irvine; Irvine, CA 92697, United States
| | - Wenting Zhao
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University; Singapore 637459, Singapore
| | - Xiaoyu Shi
- Department of Developmental and Cell Biology, University of California, Irvine; Irvine, CA 92697, United States
- Department of Chemistry, University of California, Irvine; Irvine, CA 92697, United States
- Department of Biomedical Engineering, University of California, Irvine; Irvine, CA 92697, United States
- Lead contact
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11
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Wei L, Guo X, Haimov E, Obashi K, Lee SH, Shin W, Sun M, Chan CY, Sheng J, Zhang Z, Mohseni A, Ghosh Dastidar S, Wu XS, Wang X, Han S, Arpino G, Shi B, Molakarimi M, Matthias J, Wurm CA, Gan L, Taraska JW, Kozlov MM, Wu LG. Clathrin mediates membrane fission and budding by constricting membrane pores. Cell Discov 2024; 10:62. [PMID: 38862506 PMCID: PMC11166961 DOI: 10.1038/s41421-024-00677-w] [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: 08/24/2023] [Accepted: 04/04/2024] [Indexed: 06/13/2024] Open
Abstract
Membrane budding, which underlies fundamental processes like endocytosis, intracellular trafficking, and viral infection, is thought to involve membrane coat-forming proteins, including the most observed clathrin, to form Ω-shape profiles and helix-forming proteins like dynamin to constrict Ω-profiles' pores and thus mediate fission. Challenging this fundamental concept, we report that polymerized clathrin is required for Ω-profiles' pore closure and that clathrin around Ω-profiles' base/pore region mediates pore constriction/closure in neuroendocrine chromaffin cells. Mathematical modeling suggests that clathrin polymerization at Ω-profiles' base/pore region generates forces from its intrinsically curved shape to constrict/close the pore. This new fission function may exert broader impacts than clathrin's well-known coat-forming function during clathrin (coat)-dependent endocytosis, because it underlies not only clathrin (coat)-dependent endocytosis, but also diverse endocytic modes, including ultrafast, fast, slow, bulk, and overshoot endocytosis previously considered clathrin (coat)-independent in chromaffin cells. It mediates kiss-and-run fusion (fusion pore closure) previously considered bona fide clathrin-independent, and limits the vesicular content release rate. Furthermore, analogous to results in chromaffin cells, we found that clathrin is essential for fast and slow endocytosis at hippocampal synapses where clathrin was previously considered dispensable, suggesting clathrin in mediating synaptic vesicle endocytosis and fission. These results suggest that clathrin and likely other intrinsically curved coat proteins are a new class of fission proteins underlying vesicle budding and fusion. The half-a-century concept and studies that attribute vesicle-coat contents' function to Ω-profile formation and classify budding as coat-protein (e.g., clathrin)-dependent or -independent may need to be re-defined and re-examined by considering clathrin's pivotal role in pore constriction/closure.
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Affiliation(s)
- Lisi Wei
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Xiaoli Guo
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Ehud Haimov
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Kazuki Obashi
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | - Sung Hoon Lee
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Chung-Ang University, Seoul, Republic of Korea
| | - Wonchul Shin
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Min Sun
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Chung Yu Chan
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Jiansong Sheng
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- 900 Clopper Rd, Suite, 130, Gaithersburg, MD, USA
| | - Zhen Zhang
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Center of Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Ammar Mohseni
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | | | - Xin-Sheng Wu
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Xin Wang
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Sue Han
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Gianvito Arpino
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Emme 3 Srl - Via Luigi Meraviglia, 31 - 20020, Lainate, MI, Italy
| | - Bo Shi
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Maryam Molakarimi
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | | | | | - Lin Gan
- Department of Neuroscience & Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Justin W Taraska
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | - Michael M Kozlov
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel.
| | - Ling-Gang Wu
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
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12
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Nawara TJ, Yuan J, Seeley LD, Sztul E, Mattheyses AL. Fluidic shear stress alters clathrin dynamics and vesicle formation in endothelial cells. Biophys J 2024:S0006-3495(24)00390-4. [PMID: 38853434 DOI: 10.1016/j.bpj.2024.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 04/26/2024] [Accepted: 06/06/2024] [Indexed: 06/11/2024] Open
Abstract
Endothelial cells (ECs) experience a variety of highly dynamic mechanical stresses. Among others, cyclic stretch and increased plasma membrane tension inhibit clathrin-mediated endocytosis (CME) in non-ECs. It remains elusive how ECs maintain CME in these biophysically unfavorable conditions. Previously, we have used simultaneous two-wavelength axial ratiometry (STAR) microscopy to show that endocytic dynamics are similar between statically cultured human umbilical vein endothelial cells (HUVECs) and fibroblast-like Cos-7 cells. Here, we asked whether biophysical stresses generated by blood flow influence CME. We used our data processing platform-DrSTAR-to examine if clathrin dynamics are altered in HUVECs after experiencing fluidic shear stress (FSS). We found that HUVECs cultivated under a physiological level of FSS had increased clathrin dynamics compared with static controls. FSS increased both clathrin-coated vesicle formation and nonproductive flat clathrin lattices by 2.3-fold and 1.9-fold, respectively. The curvature-positive events had significantly delayed curvature initiation relative to clathrin recruitment in flow-stimulated cells, highlighting a shift toward flat-to-curved clathrin transitions in vesicle formation. Overall, our findings indicate that clathrin dynamics and clathrin-coated vesicle formation can be modulated by the local physiological environment and represent an important regulatory mechanism.
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Affiliation(s)
- Tomasz J Nawara
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Jie Yuan
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Leslie D Seeley
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Elizabeth Sztul
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Alexa L Mattheyses
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama.
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13
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Jiang A, Kudo K, Gormal RS, Ellis S, Guo S, Wallis TP, Longfield SF, Robinson PJ, Johnson ME, Joensuu M, Meunier FA. Dynamin1 long- and short-tail isoforms exploit distinct recruitment and spatial patterns to form endocytic nanoclusters. Nat Commun 2024; 15:4060. [PMID: 38744819 PMCID: PMC11094030 DOI: 10.1038/s41467-024-47677-8] [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: 03/11/2023] [Accepted: 04/09/2024] [Indexed: 05/16/2024] Open
Abstract
Endocytosis requires a coordinated framework of molecular interactions that ultimately lead to the fission of nascent endocytic structures. How cytosolic proteins such as dynamin concentrate at discrete sites that are sparsely distributed across the plasma membrane remains poorly understood. Two dynamin-1 major splice variants differ by the length of their C-terminal proline-rich region (short-tail and long-tail). Using sptPALM in PC12 cells, neurons and MEF cells, we demonstrate that short-tail dynamin-1 isoforms ab and bb display an activity-dependent recruitment to the membrane, promptly followed by their concentration into nanoclusters. These nanoclusters are sensitive to both Calcineurin and dynamin GTPase inhibitors, and are larger, denser, and more numerous than that of long-tail isoform aa. Spatiotemporal modelling confirms that dynamin-1 isoforms perform distinct search patterns and undergo dimensional reduction to generate endocytic nanoclusters, with short-tail isoforms more robustly exploiting lateral trapping in the generation of nanoclusters compared to the long-tail isoform.
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Affiliation(s)
- Anmin Jiang
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Kye Kudo
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Rachel S Gormal
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Sevannah Ellis
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Sikao Guo
- Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
| | - Tristan P Wallis
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Shanley F Longfield
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Phillip J Robinson
- Cell Signalling Unit, Children's Medical Research Institute, The University of Sydney, Sydney, NSW, 2145, Australia
| | - Margaret E Johnson
- Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
| | - Merja Joensuu
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.
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14
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Johnson DH, Kou OH, Bouzos N, Zeno WF. Protein-membrane interactions: sensing and generating curvature. Trends Biochem Sci 2024; 49:401-416. [PMID: 38508884 PMCID: PMC11069444 DOI: 10.1016/j.tibs.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/22/2024]
Abstract
Biological membranes are integral cellular structures that can be curved into various geometries. These curved structures are abundant in cells as they are essential for various physiological processes. However, curved membranes are inherently unstable, especially on nanometer length scales. To stabilize curved membranes, cells can utilize proteins that sense and generate membrane curvature. In this review, we summarize recent research that has advanced our understanding of interactions between proteins and curved membrane surfaces, as well as work that has expanded our ability to study curvature sensing and generation. Additionally, we look at specific examples of cellular processes that require membrane curvature, such as neurotransmission, clathrin-mediated endocytosis (CME), and organelle biogenesis.
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Affiliation(s)
- David H Johnson
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Orianna H Kou
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA
| | - Nicoletta Bouzos
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Wade F Zeno
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA.
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15
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Hembrom PS, Deepthi M, Biswas G, Mappurath B, Babu A, Reeja N, Mano N, Grace T. Reference genes for qPCR expression in black tiger shrimp, Penaeus monodon. Mol Biol Rep 2024; 51:422. [PMID: 38485790 DOI: 10.1007/s11033-024-09409-5] [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: 12/02/2023] [Accepted: 03/01/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND Gene expression profiling via qPCR is an essential tool for unraveling the intricate molecular mechanisms underlying growth and development. Identifying and validating the most appropriate reference genes is essential for qPCR experiments. Nevertheless, there exists a deficiency in a thorough assessment of reference genes concerning the expression of the genes in the research in the context of the growth and development of the Black Tiger Shrimp, P. monodon. This popular marine crustacean is extensively raised for human consumption. In this study, we assessed the expression stability of seven reference genes (ACTB, 18S, EF-1α, AK, PK, cox1, and CLTC) in adult tissues (hepatopancreas, gills, and stomach) of small and large polymorphs of P. monodon. METHODS AND RESULTS The stability of gene expressions was assessed utilizing NormFinder, BestKeeper, and geNorm, and a comprehensive ranking of these genes was conducted through the online tool RefFinder. In the overall ranking, 18S and CLTC emerged as the most stable genes in the hepatopancreas and stomach, while CLTC and AK exhibited significant statistical reliability in the gills of adult P. monodon. The validation of these identified stable genes was carried out using a growth-associated gene, insr-1. CONCLUSION The results indicated that 18S and CLTC stand out as the most versatile reference genes for conducting qPCR analysis focused on the growth of P. monodon. This study represents the first comprehensive exploration that identifies and assesses reference genes for qPCR analysis in P. monodon, providing valuable tools for research involving similar crustaceans.
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Affiliation(s)
- Preety Sweta Hembrom
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Mottakunja Deepthi
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Gourav Biswas
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Bhagya Mappurath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Adon Babu
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Narchikundil Reeja
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Neeraja Mano
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Tony Grace
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India.
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16
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Nawara TJ, Sztul E, Mattheyses AL. Fluidic shear stress alters clathrin dynamics and vesicle formation in endothelial cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.02.572628. [PMID: 38260513 PMCID: PMC10802377 DOI: 10.1101/2024.01.02.572628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Endothelial cells (ECs) experience a variety of highly dynamic mechanical stresses. Among others, cyclic stretch and increased plasma membrane tension inhibit clathrin-mediated endocytosis (CME) in non-ECs cells. How ECs overcome such unfavorable, from biophysical perspective, conditions and maintain CME remains elusive. Previously, we have used simultaneous two-wavelength axial ratiometry (STAR) microscopy to show that endocytic dynamics are similar between statically cultured human umbilical vein endothelial cells (HUVECs) and fibroblast-like Cos-7 cells. Here we asked whether biophysical stresses generated by blood flow could favor one mechanism of clathrin-coated vesicle formation to overcome environment present in vasculature. We used our data processing platform - DrSTAR - to examine if clathrin dynamics are altered in HUVECs grown under fluidic sheer stress (FSS). Surprisingly, we found that FSS led to an increase in clathrin dynamics. In HUVECs grown under FSS we observed a 2.3-fold increase in clathrin-coated vesicle formation and a 1.9-fold increase in non-productive flat clathrin lattices compared to cells grown in static conditions. The curvature-positive events had significantly delayed curvature initiation in flow-stimulated cells, highlighting a shift toward flat-to-curved clathrin transitions in vesicle formation. Overall, our findings indicate that clathrin dynamics and CCV formation can be modulated by the local physiological environment and represents an important regulatory mechanism.
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Affiliation(s)
- Tomasz J. Nawara
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Elizabeth Sztul
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Alexa L. Mattheyses
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
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17
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Ledoux B, Zanin N, Yang J, Mercier V, Coster C, Dupont-Gillain C, Alsteens D, Morsomme P, Renard HF. Plasma membrane nanodeformations promote actin polymerization through CIP4/CDC42 recruitment and regulate type II IFN signaling. SCIENCE ADVANCES 2023; 9:eade1660. [PMID: 38091386 PMCID: PMC10848735 DOI: 10.1126/sciadv.ade1660] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/10/2023] [Indexed: 12/18/2023]
Abstract
In their environment, cells must cope with mechanical stresses constantly. Among these, nanoscale deformations of plasma membrane induced by substrate nanotopography are now largely accepted as a biophysical stimulus influencing cell behavior and function. However, the mechanotransduction cascades involved and their precise molecular effects on cellular physiology are still poorly understood. Here, using homemade fluorescent nanostructured cell culture surfaces, we explored the role of Bin/Amphiphysin/Rvs (BAR) domain proteins as mechanosensors of plasma membrane geometry. Our data reveal that distinct subsets of BAR proteins bind to plasma membrane deformations in a membrane curvature radius-dependent manner. Furthermore, we show that membrane curvature promotes the formation of dynamic actin structures mediated by the Rho GTPase CDC42, the F-BAR protein CIP4, and the presence of PI(4,5)P2. In addition, these actin-enriched nanodomains can serve as platforms to regulate receptor signaling as they appear to contain interferon-γ receptor (IFNγ-R) and to lead to the partial inhibition of IFNγ-induced JAK/STAT signaling.
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Affiliation(s)
- Benjamin Ledoux
- UCLouvain, Louvain Institute of Biomolecular Science and Technology, Group of Molecular Physiology, Croix du Sud 4-5 bte L7.07.14, Louvain-la-Neuve 1348, Belgium
- UCLouvain, Louvain Institute of Biomolecular Science and Technology, NanoBiophysics lab, Croix du Sud 4-5 bte L7.07.07, Louvain-la-Neuve 1348, Belgium
- UNamur, Morph-Im platform, Rue de Bruxelles 61, Namur 5000, Belgium
| | - Natacha Zanin
- UNamur, NAmur Research Institute for LIfe Sciences, Unité de Recherche en Biologie Cellulaire animale, Rue de Bruxelles 61, Namur 5000, Belgium
| | - Jinsung Yang
- Gyeongsang National University, Department of Biochemistry, College of Medicine, Department of Convergence Medical Sciences, Institute of Medical Science, Jinju 52727, South Korea
| | - Vincent Mercier
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Charlotte Coster
- UCLouvain, Louvain Institute of Biomolecular Science and Technology, Group of Molecular Physiology, Croix du Sud 4-5 bte L7.07.14, Louvain-la-Neuve 1348, Belgium
| | - Christine Dupont-Gillain
- UCLouvain, Institute of Condensed Matter and Nanosciences, Bio- and Soft Matter, Place Louis Pasteur 1 bte L4.01.10, Louvain-la-Neuve 1348, Belgium
| | - David Alsteens
- UCLouvain, Louvain Institute of Biomolecular Science and Technology, NanoBiophysics lab, Croix du Sud 4-5 bte L7.07.07, Louvain-la-Neuve 1348, Belgium
| | - Pierre Morsomme
- UCLouvain, Louvain Institute of Biomolecular Science and Technology, Group of Molecular Physiology, Croix du Sud 4-5 bte L7.07.14, Louvain-la-Neuve 1348, Belgium
| | - Henri-François Renard
- UNamur, Morph-Im platform, Rue de Bruxelles 61, Namur 5000, Belgium
- UNamur, NAmur Research Institute for LIfe Sciences, Unité de Recherche en Biologie Cellulaire animale, Rue de Bruxelles 61, Namur 5000, Belgium
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18
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Pedersen RT, Snoberger A, Pyrpassopoulos S, Safer D, Drubin DG, Ostap EM. Endocytic myosin-1 is a force-insensitive, power-generating motor. J Cell Biol 2023; 222:e202303095. [PMID: 37549220 PMCID: PMC10406613 DOI: 10.1083/jcb.202303095] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/17/2023] [Accepted: 07/24/2023] [Indexed: 08/09/2023] Open
Abstract
Myosins are required for clathrin-mediated endocytosis, but their precise molecular roles in this process are not known. This is, in part, because the biophysical properties of the relevant motors have not been investigated. Myosins have diverse mechanochemical activities, ranging from powerful contractility against mechanical loads to force-sensitive anchoring. To better understand the essential molecular contribution of myosin to endocytosis, we studied the in vitro force-dependent kinetics of the Saccharomyces cerevisiae endocytic type I myosin called Myo5, a motor whose role in clathrin-mediated endocytosis has been meticulously studied in vivo. We report that Myo5 is a low-duty-ratio motor that is activated ∼10-fold by phosphorylation and that its working stroke and actin-detachment kinetics are relatively force-insensitive. Strikingly, the in vitro mechanochemistry of Myo5 is more like that of cardiac myosin than that of slow anchoring myosin-1s found on endosomal membranes. We, therefore, propose that Myo5 generates power to augment actin assembly-based forces during endocytosis in cells.
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Affiliation(s)
- Ross T.A. Pedersen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Aaron Snoberger
- Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Serapion Pyrpassopoulos
- Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel Safer
- Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David G. Drubin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - E. Michael Ostap
- Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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19
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Wang X, Li Y, Liu A, Padilla R, Lee DM, Kim D, Mettlen M, Chen Z, Schmid SL, Danuser G. Endocytosis gated by emergent properties of membrane-clathrin interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.02.551737. [PMID: 37577632 PMCID: PMC10418234 DOI: 10.1101/2023.08.02.551737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Clathrin-mediated endocytosis (CME), the major cellular entry pathway, starts when clathrin assembles on the plasma membrane into clathrin-coated pits (CCPs). Two populations of CCPs are detected within the same cell: 'productive' CCPs that invaginate and pinch off, forming clathrin-coated vesicles (CCVs) [1, 2], and 'abortive' CCPs [3, 4, 5] that prematurely disassemble. The mechanisms of gating between these two populations and their relations to the functions of dozens of early-acting endocytic accessory proteins (EAPs) [5, 6, 7, 8, 9] have remained elusive. Here, we use experimentally-guided modeling to integrate the clathrin machinery and membrane mechanics in a single dynamical system. We show that the split between the two populations is an emergent property of this system, in which a switch between an Open state and a Closed state follows from the competition between the chemical energy of the clathrin basket and the mechanical energy of membrane bending. In silico experiments revealed an abrupt transition between the two states that acutely depends on the strength of the clathrin basket. This critical strength is lowered by membrane-bending EAPs [10, 11, 12]. Thus, CME is poised to be shifted between abortive and productive events by small changes in membrane curvature and/or coat stability. This model clarifies the workings of a putative endocytic checkpoint whose existence was previously proposed based on statistical analyses of the lifetime distributions of CCPs [4, 13]. Overall, a mechanistic framework is established to elucidate the diverse and redundant functions of EAPs in regulating CME progression.
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20
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Li R, Pang L. Comparing the effects of proteins with IDRs on membrane system in yeast, mammalian cells, and the model plant Arabidopsis. CURRENT OPINION IN PLANT BIOLOGY 2023; 74:102375. [PMID: 37172364 DOI: 10.1016/j.pbi.2023.102375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/26/2023] [Accepted: 04/07/2023] [Indexed: 05/14/2023]
Abstract
Membrane vesiculation is an energy-costing process. Previous studies paid much attention to proteins with curvature-inducing motifs. Recent publications reveal that the liquid-like protein assembly on membrane surfaces provides an efficient yet structure-independent mechanism for increasing the membrane curvature, which plays important roles in vesicle transport in many aspects. Intrinsically disordered regions (IDRs) within the proteins are highly potent drivers of membrane curvature by providing large hydrodynamic radii to generate steric pressure. Biomolecular condensates formed by phase separation can provide a reaction platform for sequential processes or generate a wetting surface to sequestrate cargos and trigger membrane remodeling. We review the latest progress in yeast and mammalian cells, focus on the mechanism of clathrin-mediated endocytosis (CME) and autophagy initiation, and compare with what we know in model plant Arabidopsis. The comparison may give important insights into the understanding of basic membrane trafficking mechanisms in plant cells.
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Affiliation(s)
- Ruixi Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Lei Pang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
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21
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Lu CH, Tsai CT, Jones Iv T, Chim V, Klausen LH, Zhang W, Li X, Jahed Z, Cui B. A NanoCurvS platform for quantitative and multiplex analysis of curvature-sensing proteins. Biomater Sci 2023; 11:5205-5217. [PMID: 37337788 PMCID: PMC10809791 DOI: 10.1039/d2bm01856j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
The cell membrane is characterized by a rich variety of topographical features such as local protrusions or invaginations. Curvature-sensing proteins, including the Bin/Amphiphysin/Rvs (BAR) or epsin N-terminal homology (ENTH) family proteins, sense the bending sharpness and the positive/negative sign of these topographical features to induce subsequent intracellular signaling. A number of assays have been developed to study curvature-sensing properties of proteins in vitro, but it is still challenging to probe low curvature regime with the diameter of curvature from hundreds of nanometers to micrometers. It is particularly difficult to generate negative membrane curvatures with well-defined curvature values in the low curvature regime. In this work, we develop a nanostructure-based curvature sensing (NanoCurvS) platform that enables quantitative and multiplex analysis of curvature-sensitive proteins in the low curvature regime, in both negative and positive directions. We use NanoCurvS to quantitatively measure the sensing range of a negative curvature-sensing protein IRSp53 (an I-BAR protein) and a positive curvature-sensing protein FBP17 (an F-BAR protein). We find that, in cell lysates, the I-BAR domain of IRSp53 is able to sense shallow negative curvatures with the diameter-of-curvature up to 1500 nm, a range much wider than previously expected. NanoCurvS is also used to probe the autoinhibition effect of IRSp53 and the phosphorylation effect of FBP17. Therefore, the NanoCurvS platform provides a robust, multiplex, and easy-to-use tool for quantitative analysis of both positive and negative curvature-sensing proteins.
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Affiliation(s)
- Chih-Hao Lu
- Department of Chemistry, Stanford University, Stanford, CA, USA.
| | - Ching-Ting Tsai
- Department of Chemistry, Stanford University, Stanford, CA, USA.
| | - Taylor Jones Iv
- Department of Chemistry, Stanford University, Stanford, CA, USA.
| | - Vincent Chim
- Department of Chemistry, Stanford University, Stanford, CA, USA.
| | - Lasse H Klausen
- Department of Chemistry, Stanford University, Stanford, CA, USA.
| | - Wei Zhang
- Department of Chemistry, Stanford University, Stanford, CA, USA.
| | - Xiao Li
- Department of Chemistry, Stanford University, Stanford, CA, USA.
| | - Zeinab Jahed
- Department of Chemistry, Stanford University, Stanford, CA, USA.
| | - Bianxiao Cui
- Department of Chemistry, Stanford University, Stanford, CA, USA.
- Wu-Tsai Neuroscience Institute and ChEM-H institute, Stanford University, Stanford, CA, USA
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22
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Azar B. Profile of David G. Drubin. Proc Natl Acad Sci U S A 2023; 120:e2308153120. [PMID: 37399409 PMCID: PMC10334723 DOI: 10.1073/pnas.2308153120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023] Open
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23
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Pedersen RTA, Snoberger A, Pyrpassopoulos S, Safer D, Drubin DG, Ostap EM. Endocytic myosin-1 is a force-insensitive, power-generating motor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.21.533689. [PMID: 36993306 PMCID: PMC10055380 DOI: 10.1101/2023.03.21.533689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Myosins are required for clathrin-mediated endocytosis, but their precise molecular roles in this process are not known. This is, in part, because the biophysical properties of the relevant motors have not been investigated. Myosins have diverse mechanochemical activities, ranging from powerful contractility against mechanical loads to force-sensitive anchoring. To better understand the essential molecular contribution of myosin to endocytosis, we studied the in vitro force-dependent kinetics of the Saccharomyces cerevisiae endocytic type I myosin called Myo5, a motor whose role in clathrin-mediated endocytosis has been meticulously studied in vivo. We report that Myo5 is a low-duty-ratio motor that is activated ∼10-fold by phosphorylation, and that its working stroke and actin-detachment kinetics are relatively force-insensitive. Strikingly, the in vitro mechanochemistry of Myo5 is more like that of cardiac myosin than like that of slow anchoring myosin-1s found on endosomal membranes. We therefore propose that Myo5 generates power to augment actin assembly-based forces during endocytosis in cells. Summary Pedersen, Snoberger et al. measure the force-sensitivity of the yeast endocytic the myosin-1 called Myo5 and find that it is more likely to generate power than to serve as a force-sensitive anchor in cells. Implications for Myo5's role in clathrin-mediated endocytosis are discussed.
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Affiliation(s)
- Ross TA Pedersen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
- Present address: Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218
- Equal Contribution
| | - Aaron Snoberger
- Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Equal Contribution
| | - Serapion Pyrpassopoulos
- Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Daniel Safer
- Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - David G Drubin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - E Michael Ostap
- Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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24
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Küey C, Sittewelle M, Larocque G, Hernández-González M, Royle SJ. Recruitment of clathrin to intracellular membranes is sufficient for vesicle formation. eLife 2022; 11:e78929. [PMID: 35852853 PMCID: PMC9337851 DOI: 10.7554/elife.78929] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
The formation of a clathrin-coated vesicle (CCV) is a major membrane remodeling process that is crucial for membrane traffic in cells. Besides clathrin, these vesicles contain at least 100 different proteins although it is unclear how many are essential for the formation of the vesicle. Here, we show that intracellular clathrin-coated formation can be induced in living cells using minimal machinery and that it can be achieved on various membranes, including the mitochondrial outer membrane. Chemical heterodimerization was used to inducibly attach a clathrin-binding fragment 'hook' to an 'anchor' protein targeted to a specific membrane. Endogenous clathrin assembled to form coated pits on the mitochondria, termed MitoPits, within seconds of induction. MitoPits are double-membraned invaginations that form preferentially on high curvature regions of the mitochondrion. Upon induction, all stages of CCV formation - initiation, invagination, and even fission - were faithfully reconstituted. We found no evidence for the functional involvement of accessory proteins in this process. In addition, fission of MitoPit-derived vesicles was independent of known scission factors including dynamins and dynamin-related protein 1 (Drp1), suggesting that the clathrin cage generates sufficient force to bud intracellular vesicles. Our results suggest that, following its recruitment, clathrin is sufficient for intracellular CCV formation.
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Affiliation(s)
- Cansu Küey
- Centre for Mechanochemical Cell Biology and Division of Biomedical Cell Biology, Warwick Medical School, University of WarwickCoventryUnited Kingdom
| | - Méghane Sittewelle
- Centre for Mechanochemical Cell Biology and Division of Biomedical Cell Biology, Warwick Medical School, University of WarwickCoventryUnited Kingdom
| | - Gabrielle Larocque
- Centre for Mechanochemical Cell Biology and Division of Biomedical Cell Biology, Warwick Medical School, University of WarwickCoventryUnited Kingdom
| | - Miguel Hernández-González
- Centre for Mechanochemical Cell Biology and Division of Biomedical Cell Biology, Warwick Medical School, University of WarwickCoventryUnited Kingdom
| | - Stephen J Royle
- Centre for Mechanochemical Cell Biology and Division of Biomedical Cell Biology, Warwick Medical School, University of WarwickCoventryUnited Kingdom
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Abstract
Cell biologists have long debated the role of clathrin in curving membranes during endocytosis. New findings from Cail et al. (2022. J. Cell Biol.https://doi.org/10.1083/jcb.202109013) take an innovative approach to directly demonstrate the indispensable functions of both clathrin and its adaptor network in shaping endocytic vesicles.
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