1
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Maleš P, Nikšić-Franjić I, Wang A, Pem B, Bakarić D. Optical and molecular features of negatively curved surfaces created by POPE lipids: A crucial role of the initial conditions. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 317:124462. [PMID: 38754204 DOI: 10.1016/j.saa.2024.124462] [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: 02/13/2024] [Revised: 05/10/2024] [Accepted: 05/11/2024] [Indexed: 05/18/2024]
Abstract
Membrane fusion is closely related to plasma membrane domains rich in cone-shaped phosphatidylethanolamine (PE) lipids that can reverse membrane curvature under certain conditions. The phase transition of PE-based lipid membranes from the lamellar fluid phase (Lα) to the inverse hexagonal phase (HII) is commonly taken as a general model in reconstructing the membrane fusion pathway, and whose structural features have been mostly described so far using structural and microscopic techniques. The aim of this paper is to decipher the optical and molecular features of Lβ → Lα and especially of Lα → HII transition of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) lipids at pH = 7.0 when they are initially prepared in the form of both multi- and unilamellar liposomes (MLVs and LUVs). The distinction between optical properties of MLS- and LUVs-derived HII phase, provided from turbidity-sensitive temperature-dependent UV-Vis spectra, was attributed to different formation mechanisms of HII phase. Most importantly, from FTIR spectroscopic data of POPE lipids in Lβ (15 °C), Lα (50 °C) and HII (85 °C) phases we identified the changes in molecular features of POPE lipids during phase transitions. Among the latter, by far the most significant is different hydration pattern of POPE lipids in MLVs- and LUVs-derived HII phase which extends from the polar-apolar interface all the way to the terminal amino group of the POPE lipid, along with the changes in the conformation of glycerol backbone as evidenced by the signature of α-methylene groups. Molecular dynamics simulations confirmed higher water penetration in HII phase and provided insight into hydrogen bonding patterns.
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Affiliation(s)
- Petra Maleš
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Ivana Nikšić-Franjić
- School of Science, Constructor University, Bremen GmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Anna Wang
- School of Chemistry, Australian Centre for Astrobiology, and ARC Centre of Excellence in Synthetic Biology, University of New South Wales Sydney, Bedegal Country, Sydney, NSW 2052, Australia
| | - Barbara Pem
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Danijela Bakarić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia.
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2
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Alimohamadi H, Luo EWC, Gupta S, de Anda J, Yang R, Mandal T, Wong GCL. Comparing Multifunctional Viral and Eukaryotic Proteins for Generating Scission Necks in Membranes. ACS NANO 2024; 18:15545-15556. [PMID: 38838261 DOI: 10.1021/acsnano.4c00277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Deterministic formation of membrane scission necks by protein machinery with multiplexed functions is critical in biology. A microbial example is M2 viroporin, a proton pump from the influenza A virus that is multiplexed with membrane remodeling activity to induce budding and scission in the host membrane during viral maturation. In comparison, the dynamin family constitutes a class of eukaryotic proteins implicated in mitochondrial fission, as well as various budding and endocytosis pathways. In the case of Dnm1, the mitochondrial fission protein in yeast, the membrane remodeling activity is multiplexed with mechanoenzyme activity to create fission necks. It is not clear why these functions are combined in these scission processes, which occur in drastically different compositions and solution conditions. In general, direct experimental access to changing neck sizes induced by individual proteins or peptide fragments is challenging due to the nanoscale dimensions and influence of thermal fluctuations. Here, we use a mechanical model to estimate the size of scission necks by leveraging small-angle X-ray scattering structural data of protein-lipid systems under different conditions. The influence of interfacial tension, lipid composition, and membrane budding morphology on the size of the induced scission necks is systematically investigated using our data and molecular dynamic simulations. We find that the M2 budding protein from the influenza A virus has robust pH-dependent membrane activity that induces nanoscopic necks within the range of spontaneous hemifission for a broad range of lipid compositions. In contrast, the sizes of scission necks generated by mitochondrial fission proteins strongly depend on lipid composition, which suggests a role for mechanical constriction.
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Affiliation(s)
- Haleh Alimohamadi
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90025, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Elizabeth Wei-Chia Luo
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90025, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Shivam Gupta
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Jaime de Anda
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90025, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Rena Yang
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90025, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Taraknath Mandal
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Gerard C L Wong
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90025, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
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3
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Lee CT, Rangamani P. Modeling the mechanochemical feedback for membrane-protein interactions using a continuum mesh model. Methods Enzymol 2024; 701:387-424. [PMID: 39025577 DOI: 10.1016/bs.mie.2024.03.016] [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] [Indexed: 07/20/2024]
Abstract
The Helfrich free energy is widely used to model the generation of membrane curvature due to different physical and chemical components. The governing equations resulting from the energy minimization procedure are a system of coupled higher order partial differential equations. Simulations of membrane deformation for obtaining quantitative comparisons against experimental observations require computational schemes that will allow us to solve these equations without restrictions to axisymmetric coordinates. Here, we describe one such tool that we developed in our group based on discrete differential geometry to solve these equations along with examples.
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Affiliation(s)
- Christopher T Lee
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, United States.
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, United States.
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4
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Tranfield EM, Fabig G, Kurth T, Müller-Reichert T. How to apply the broad toolbox of correlative light and electron microscopy to address a specific biological question. Methods Cell Biol 2024; 187:1-41. [PMID: 38705621 DOI: 10.1016/bs.mcb.2024.02.030] [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] [Indexed: 05/07/2024]
Abstract
Correlative light and electron microscopy (CLEM) is an approach that combines the strength of multiple imaging techniques to obtain complementary information about a given specimen. The "toolbox" for CLEM is broad, making it sometimes difficult to choose an appropriate approach for a given biological question. In this chapter, we provide experimental details for three CLEM approaches that can help the interested reader in designing a personalized CLEM strategy for obtaining ultrastructural data by using transmission electron microscopy (TEM). First, we describe chemical fixation of cells grown on a solid support (broadest approach). Second, we apply high-pressure freezing/freeze substitution to describe cellular ultrastructure (cryo-immobilization approach). Third, we give a protocol for a ultrastructural labeling by immuno-electron microscopy (immuno-EM approach). In addition, we also describe how to overlay fluorescence and electron microscopy images, an approach that is applicable to each of the reported different CLEM strategies. Here we provide step-by step descriptions prior to discussing possible technical problems and variations of these three general schemes to suit different models or different biological questions. This chapter is written for electron microscopists that are new to CLEM and unsure how to begin. Therefore, our protocols are meant to provide basic information with further references that should help the reader get started with applying a tailored strategy for a specific CLEM experiment.
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Affiliation(s)
- Erin M Tranfield
- Electron Microscopy Facility, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Gunar Fabig
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Thomas Kurth
- Core Facility Electron Microscopy and Histology Facility, Technology Platform, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Thomas Müller-Reichert
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
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5
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Narvaez-Ortiz HY, Lynch MJ, Liu SL, Fries A, Nolen BJ. Both Las17-binding sites on Arp2/3 complex are important for branching nucleation and assembly of functional endocytic actin networks in S. cerevisiae. J Biol Chem 2024; 300:105766. [PMID: 38367669 PMCID: PMC10944109 DOI: 10.1016/j.jbc.2024.105766] [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: 09/27/2023] [Revised: 02/07/2024] [Accepted: 02/12/2024] [Indexed: 02/19/2024] Open
Abstract
Arp2/3 complex nucleates branched actin filaments that drive membrane invagination during endocytosis and leading-edge protrusion in lamellipodia. Arp2/3 complex is maximally activated in vitro by binding of a WASP family protein to two sites-one on the Arp3 subunit and one spanning Arp2 and ARPC1-but the importance of each site in the regulation of force-producing actin networks is unclear. Here, we identify mutations in budding yeast Arp2/3 complex that decrease or block engagement of Las17, the budding yeast WASP, at each site. As in the mammalian system, both sites are required for maximal activation in vitro. Dimerization of Las17 partially restores activity of mutations at both CA-binding sites. Arp2/3 complexes defective at either site assemble force-producing actin networks in a bead motility assay, but their reduced activity hinders motility by decreasing actin assembly near the bead surface and by failing to suppress actin filament bundling within the networks. While even the most defective Las17-binding site mutants assembled actin filaments at endocytic sites, they showed significant internalization defects, potentially because they lack the proper architecture to drive plasma membrane remodeling. Together, our data indicate that both Las17-binding sites are important to assemble functional endocytic actin networks in budding yeast, but Arp2/3 complex retains some activity in vitro and in vivo even with a severe defect at either Las17-binding site.
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Affiliation(s)
- Heidy Y Narvaez-Ortiz
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Michael J Lynch
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Su-Ling Liu
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Adam Fries
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Brad J Nolen
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA.
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6
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McCafferty CL, Klumpe S, Amaro RE, Kukulski W, Collinson L, Engel BD. Integrating cellular electron microscopy with multimodal data to explore biology across space and time. Cell 2024; 187:563-584. [PMID: 38306982 DOI: 10.1016/j.cell.2024.01.005] [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: 12/04/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Biology spans a continuum of length and time scales. Individual experimental methods only glimpse discrete pieces of this spectrum but can be combined to construct a more holistic view. In this Review, we detail the latest advancements in volume electron microscopy (vEM) and cryo-electron tomography (cryo-ET), which together can visualize biological complexity across scales from the organization of cells in large tissues to the molecular details inside native cellular environments. In addition, we discuss emerging methodologies for integrating three-dimensional electron microscopy (3DEM) imaging with multimodal data, including fluorescence microscopy, mass spectrometry, single-particle analysis, and AI-based structure prediction. This multifaceted approach fills gaps in the biological continuum, providing functional context, spatial organization, molecular identity, and native interactions. We conclude with a perspective on incorporating diverse data into computational simulations that further bridge and extend length scales while integrating the dimension of time.
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Affiliation(s)
| | - Sven Klumpe
- Research Group CryoEM Technology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - Rommie E Amaro
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Wanda Kukulski
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.
| | - Lucy Collinson
- Electron Microscopy Science Technology Platform, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Benjamin D Engel
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.
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7
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Lin Z, Mao Z, Ma R. Inferring biophysical properties of membranes during endocytosis using machine learning. SOFT MATTER 2024; 20:651-660. [PMID: 38164011 DOI: 10.1039/d3sm01221b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Endocytosis is a fundamental cellular process in eukaryotic cells that facilitates the transport of molecules into the cell. With the help of fluorescence microscopy and electron tomography, researchers have accumulated extensive geometric data of membrane shapes during endocytosis. These data contain rich information about the mechanical properties of membranes, which are hard to access via experiments due to the small dimensions of the endocytic patch. In this study, we propose an approach that combines machine learning with the Helfrich theory of membranes to infer the mechanical properties of membranes during endocytosis from a dataset of membrane shapes extracted from electron tomography. Our results demonstrate that machine learning can output solutions that both match the experimental profile and satisfy the membrane shape equations derived from Helfrich theory. The learning results show that during the early stage of endocytosis, the inferred membrane tension is negative, indicating the presence of strong compressive forces at the boundary of the endocytic invagination. Our method presents a generic framework for extracting membrane information from super-resolution imaging.
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Affiliation(s)
- Zhiwei Lin
- Department of Physics, College of Physical Science and Technology, Xiamen University, Xiamen 361005, China.
| | - Zhiping Mao
- School of Mathematical Sciences, Fujian Provincial Key Laboratory of Mathematical Modeling and High-Performance Scientific Computing, Xiamen University, Xiamen 361005, China.
| | - Rui Ma
- Department of Physics, College of Physical Science and Technology, Xiamen University, Xiamen 361005, China.
- Fujian Provincial Key Laboratory for Soft Functional Materials Research, Research Institute for Biomimetics and Soft Matter, Xiamen University, Xiamen 361005, China
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8
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Alimohamadi H, Luo EWC, Gupta S, de Anda J, Yang R, Mandal T, Wong GCL. Comparing multifunctional viral and eukaryotic proteins for generating scission necks in membranes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.05.574447. [PMID: 38260291 PMCID: PMC10802413 DOI: 10.1101/2024.01.05.574447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Deterministic formation of membrane scission necks by protein machinery with multiplexed functions is critical in biology. A microbial example is the M2 viroporin, a proton pump from the influenza A virus which is multiplexed with membrane remodeling activity to induce budding and scission in the host membrane during viral maturation. In comparison, the dynamin family constitutes a class of eukaryotic proteins implicated in mitochondrial fission, as well as various budding and endocytosis pathways. In the case of Dnm1, the mitochondrial fission protein in yeast, the membrane remodeling activity is multiplexed with mechanoenzyme activity to create fission necks. It is not clear why these functions are combined in these scission processes, which occur in drastically different compositions and solution conditions. In general, direct experimental access to changing neck sizes induced by individual proteins or peptide fragments is challenging due to the nanoscale dimensions and influence of thermal fluctuations. Here, we use a mechanical model to estimate the size of scission necks by leveraging Small-Angle X-ray Scattering (SAXS) structural data of protein-lipid systems under different conditions. The influence of interfacial tension, lipid composition, and membrane budding morphology on the size of the induced scission necks is systematically investigated using our data and molecular dynamic simulations. We find that the M2 budding protein from the influenza A virus has robust pH-dependent membrane activity that induces nanoscopic necks within the range of spontaneous hemi-fission for a broad range of lipid compositions. In contrast, the sizes of scission necks generated by mitochondrial fission proteins strongly depend on lipid composition, which suggests a role for mechanical constriction.
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9
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Guan K, Liu K, Jiang Y, Bian J, Gao Y, Dong E, Li Z. Nanoparticles Internalization through HIP-55-Dependent Clathrin Endocytosis Pathway. NANO LETTERS 2023; 23:11477-11484. [PMID: 38084909 DOI: 10.1021/acs.nanolett.3c03074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
Nanoparticles are promising tools for biomedicine. Many nanoparticles are internalized to function. Clathrin-mediated endocytosis is one of the most important mechanisms for nanoparticle internalization. However, the regulatory mechanism of clathrin-mediated nanoparticle endocytosis is still unclear. Here, we report that the adapter protein HIP-55 regulates clathrin-mediated nanoparticle endocytosis. CdSe/ZnS quantum dots (QDs), a typical nanoparticle, enter cells through the HIP-55-dependent clathrin endocytosis pathway. Both pharmacological inhibitor and genetic intervention demonstrate that QDs enter cells through clathrin-mediated endocytosis. HIP-55 can interact with clathrin and promote clathrin-mediated QDs endocytosis. Furthermore, HIP-55 ΔADF which is defective in F-actin binding fails to promote QDs endocytosis, indicating HIP-55 promotes clathrin-mediated QDs endocytosis depending on interaction with F-actin. In vivo, HIP-55 knockout also inhibits endocytosis of QDs. These findings reveal that HIP-55 acts as an intrinsic regulator for clathrin-mediated nanoparticle endocytosis, providing new insight into the nanoparticle internalization and a new strategy for nanodrug enrichment in target cells.
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Affiliation(s)
- Kaihang Guan
- Department of Cardiology and Institute of Vascular Medicine, Peking University Third Hospital; Beijing Key Laboratory of Cardiovascular Receptors Research; Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides, Ministry of Health; State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University; Research Unit of Medical Science Research Management/Basic and Clinical Research of Metabolic Cardiovascular Diseases, Chinese Academy of Medical Sciences, Beijing 100191, China
| | - Kai Liu
- Department of Cardiology and Institute of Vascular Medicine, Peking University Third Hospital; Beijing Key Laboratory of Cardiovascular Receptors Research; Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides, Ministry of Health; State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University; Research Unit of Medical Science Research Management/Basic and Clinical Research of Metabolic Cardiovascular Diseases, Chinese Academy of Medical Sciences, Beijing 100191, China
| | - Yunqi Jiang
- Department of Cardiology and Institute of Vascular Medicine, Peking University Third Hospital; Beijing Key Laboratory of Cardiovascular Receptors Research; Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides, Ministry of Health; State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University; Research Unit of Medical Science Research Management/Basic and Clinical Research of Metabolic Cardiovascular Diseases, Chinese Academy of Medical Sciences, Beijing 100191, China
| | - Jingwei Bian
- Department of Cardiology and Institute of Vascular Medicine, Peking University Third Hospital; Beijing Key Laboratory of Cardiovascular Receptors Research; Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides, Ministry of Health; State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University; Research Unit of Medical Science Research Management/Basic and Clinical Research of Metabolic Cardiovascular Diseases, Chinese Academy of Medical Sciences, Beijing 100191, China
| | - Yang Gao
- Research Center for Cardiopulmonary Rehabilitation, University of Health and Rehabilitation Sciences Qingdao Hospital (Qingdao Municipal Hospital), School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao 266071, China
| | - Erdan Dong
- Department of Cardiology and Institute of Vascular Medicine, Peking University Third Hospital; Beijing Key Laboratory of Cardiovascular Receptors Research; Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides, Ministry of Health; State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University; Research Unit of Medical Science Research Management/Basic and Clinical Research of Metabolic Cardiovascular Diseases, Chinese Academy of Medical Sciences, Beijing 100191, China
- Research Center for Cardiopulmonary Rehabilitation, University of Health and Rehabilitation Sciences Qingdao Hospital (Qingdao Municipal Hospital), School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao 266071, China
- Haihe Laboratory of Cell Ecosystem, Beijing 100191, China
| | - Zijian Li
- Department of Cardiology and Institute of Vascular Medicine, Peking University Third Hospital; Beijing Key Laboratory of Cardiovascular Receptors Research; Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides, Ministry of Health; State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University; Research Unit of Medical Science Research Management/Basic and Clinical Research of Metabolic Cardiovascular Diseases, Chinese Academy of Medical Sciences, Beijing 100191, China
- Department of Pharmacy, Peking University Third Hospital, Beijing 100191, China
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10
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Klebl DP, Aspinall L, Muench SP. Time resolved applications for Cryo-EM; approaches, challenges and future directions. Curr Opin Struct Biol 2023; 83:102696. [PMID: 37716094 DOI: 10.1016/j.sbi.2023.102696] [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: 02/21/2023] [Revised: 06/14/2023] [Accepted: 08/14/2023] [Indexed: 09/18/2023]
Abstract
Developments within the cryo-EM field have allowed us to generate higher-resolution "static" structures and pull out different conformational states which exist at equilibrium within the sample. Moreover, to trap non-equilibrium states and determine conformations that are present after a defined period of time (typically in the ms time frame) new approaches have been developed for the application of time-resolved cryo-EM. Here we give an overview of these different approaches and the limitations and strengths of each whilst identifying some of the current challenges to achieve higher resolutions and trap states within faster time frames. Time-resolved applications may play an important role in the ever-expanding toolkit of cryo-EM and open up new possibilities in both single particle and tomographic studies.
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Affiliation(s)
- David P Klebl
- School of Biomedical Sciences, Astbury Centre for Structural Molecular Biology, University of Leeds, UK
| | - Louie Aspinall
- School of Molecular and Cellular Biology, University of Leeds, UK
| | - Stephen P Muench
- School of Biomedical Sciences, Astbury Centre for Structural Molecular Biology, University of Leeds, UK.
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11
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Prischich D, Camarero N, Encinar del Dedo J, Cambra-Pellejà M, Prat J, Nevola L, Martín-Quirós A, Rebollo E, Pastor L, Giralt E, Geli MI, Gorostiza P. Light-dependent inhibition of clathrin-mediated endocytosis in yeast unveils conserved functions of the AP2 complex. iScience 2023; 26:107899. [PMID: 37766990 PMCID: PMC10520943 DOI: 10.1016/j.isci.2023.107899] [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: 07/19/2023] [Revised: 08/04/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Clathrin-mediated endocytosis (CME) is an essential cellular process, conserved among eukaryotes. Yeast constitutes a powerful genetic model to dissect the complex endocytic machinery, yet there is a lack of specific pharmacological agents to interfere with CME in these organisms. TL2 is a light-regulated peptide inhibitor targeting the AP2-β-adaptin/β-arrestin interaction and that can photocontrol CME with high spatiotemporal precision in mammalian cells. Here, we study endocytic protein dynamics by live-cell imaging of the fluorescently tagged coat-associated protein Sla1-GFP, demonstrating that TL2 retains its inhibitory activity in S. cerevisiae spheroplasts. This is despite the β-adaptin/β-arrestin interaction not being conserved in yeast. Our data indicate that the AP2 α-adaptin is the functional target of activated TL2. We identified as interacting partners for the α-appendage, the Eps15 and epsin homologues Ede1 and Ent1. This demonstrates that endocytic cargo loading and sensing can be executed by conserved molecular interfaces, regardless of the proteins involved.
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Affiliation(s)
- Davia Prischich
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red – Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, Spain
| | - Núria Camarero
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red – Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, Spain
| | - Javier Encinar del Dedo
- Department of Cell Biology, Institute for Molecular Biology of Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Maria Cambra-Pellejà
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Judit Prat
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Laura Nevola
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Andrés Martín-Quirós
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Elena Rebollo
- Molecular Imaging Platform, Institute for Molecular Biology of Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Laura Pastor
- Department of Cell Biology, Institute for Molecular Biology of Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Ernest Giralt
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Inorganic and Organic Chemistry, University of Barcelona (UB), Barcelona, Spain
| | - María Isabel Geli
- Department of Cell Biology, Institute for Molecular Biology of Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Pau Gorostiza
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red – Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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12
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Ren Y, Yang J, Fujita B, Jin H, Zhang Y, Berro J. Force redistribution in clathrin-mediated endocytosis revealed by coiled-coil force sensors. SCIENCE ADVANCES 2023; 9:eadi1535. [PMID: 37831774 PMCID: PMC10575576 DOI: 10.1126/sciadv.adi1535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 09/13/2023] [Indexed: 10/15/2023]
Abstract
Forces are central to countless cellular processes, yet in vivo force measurement at the molecular scale remains difficult if not impossible. During clathrin-mediated endocytosis, forces produced by the actin cytoskeleton are transmitted to the plasma membrane by a multiprotein coat for membrane deformation. However, the magnitudes of these forces remain unknown. Here, we present new in vivo force sensors that induce protein condensation under force. We measured the forces on the fission yeast Huntingtin-Interacting Protein 1 Related (HIP1R) homolog End4p, a protein that links the membrane to the actin cytoskeleton. End4p is under ~19-piconewton force near the actin cytoskeleton, ~11 piconewtons near the clathrin lattice, and ~9 piconewtons near the plasma membrane. Our results demonstrate that forces are collected and redistributed across the endocytic machinery.
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Affiliation(s)
- Yuan Ren
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Nanobiology Institute, Yale University, West Haven, CT 06516, USA
| | - Jie Yang
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Barbara Fujita
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Nanobiology Institute, Yale University, West Haven, CT 06516, USA
| | - Huaizhou Jin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yongli Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Julien Berro
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Nanobiology Institute, Yale University, West Haven, CT 06516, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
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13
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Rutkowski DM, Vincenzetti V, Vavylonis D, Martin SG. Cdc42 mobility and membrane flows regulate fission yeast cell shape and survival. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.21.550042. [PMID: 37503115 PMCID: PMC10370159 DOI: 10.1101/2023.07.21.550042] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Local Cdc42 GTPase activation promotes polarized exocytosis, resulting in membrane flows that deplete low-mobility membrane-associated proteins from the growth region. To investigate the self-organizing properties of the Cdc42 secretion-polarization system under membrane flow, we developed a reaction-diffusion particle model. The model includes positive feedback activation of Cdc42, hydrolysis by GTPase-activating proteins (GAPs), and flow-induced displacement by exo/endocytosis. Simulations show how polarization relies on flow-induced depletion of low mobility GAPs. To probe the role of Cdc42 mobility in the fission yeast Schizosaccharomyces pombe, we changed its membrane binding properties by replacing its prenylation site with 1, 2 or 3 repeats of the Rit1 C terminal membrane binding domain (ritC), yielding alleles with progressively lower unbinding and diffusion rates. Concordant modelling predictions and experimental observations show that lower Cdc42 mobility results in lower Cdc42 activation level and wider patches. Indeed, while Cdc42-1ritC cells are viable and polarized, Cdc42-2ritC polarize poorly and Cdc42-3ritC is inviable. The model further predicts that GAP depletion increases Cdc42 activity at the expense of loss of polarization. Experiments confirm this prediction, as deletion of Cdc42 GAPs restores viability to Cdc42-3ritC cells. Our combined experimental and modelling studies demonstrate how membrane flows are an integral part of Cdc42-driven pattern formation.
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Affiliation(s)
| | | | | | - Sophie G. Martin
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
- Department of Molecular and Cellular Biology, University of Geneva, Quai Ernest-Ansermet 30, 1205 Geneva
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14
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Fessler F, Sharma V, Muller P, Stocco A. Entry of microparticles into giant lipid vesicles by optical tweezers. Phys Rev E 2023; 107:L052601. [PMID: 37328973 DOI: 10.1103/physreve.107.l052601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/20/2023] [Indexed: 06/18/2023]
Abstract
Entry of micro- or nanosized objects into cells or vesicles made of lipid membranes occurs in many processes such as entry of viruses into host cells, microplastics pollution, drug delivery, or biomedical imaging. Here we investigate the microparticle crossing of lipid membranes in giant unilamellar vesicles in the absence of strong binding interactions (e.g., streptavidin-biotin binding). In these conditions, we observe that organic and inorganic particles can always penetrate inside the vesicles provided an external piconewton force is applied and for relatively low membrane tensions. In the limit of vanishing adhesion, we identify the role of the membrane area reservoir and show that a force minimum exists when the particle size is comparable to the bendocapillary length.
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Affiliation(s)
- Florent Fessler
- Institut Charles Sadron, UPR No. 22, CNRS, 23 Rue du Loess, 67200 Strasbourg, France
| | - Vaibhav Sharma
- Institut Charles Sadron, UPR No. 22, CNRS, 23 Rue du Loess, 67200 Strasbourg, France
| | - Pierre Muller
- Institut Charles Sadron, UPR No. 22, CNRS, 23 Rue du Loess, 67200 Strasbourg, France
| | - Antonio Stocco
- Institut Charles Sadron, UPR No. 22, CNRS, 23 Rue du Loess, 67200 Strasbourg, France
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15
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Krishnan S, Klingauf J. The readily retrievable pool of synaptic vesicles. Biol Chem 2023; 404:385-397. [PMID: 36867726 DOI: 10.1515/hsz-2022-0298] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/16/2023] [Indexed: 03/05/2023]
Abstract
In the CNS communication between neurons occurs at synapses by secretion of neurotransmitter via exocytosis of synaptic vesicles (SVs) at the active zone. Given the limited number of SVs in presynaptic boutons a fast and efficient recycling of exocytosed membrane and proteins by triggered compensatory endocytosis is required to maintain neurotransmission. Thus, pre-synapses feature a unique tight coupling of exo- and endocytosis in time and space resulting in the reformation of SVs with uniform morphology and well-defined molecular composition. This rapid response requires early stages of endocytosis at the peri-active zone to be well choreographed to ensure reformation of SVs with high fidelity. The pre-synapse can address this challenge by a specialized membrane microcompartment, where a pre-sorted and pre-assembled readily retrievable pool (RRetP) of endocytic membrane patches is formed, consisting of the vesicle cargo, presumably bound within a nucleated Clathrin and adaptor complex. This review considers evidence for the RRetP microcompartment to be the primary organizer of presynaptic triggered compensatory endocytosis.
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Affiliation(s)
- Sai Krishnan
- Institute of Medical Physics and Biophysics, University of Münster, Robert-Koch Strasse 31, D-48149, Münster, Germany
| | - Jürgen Klingauf
- Institute of Medical Physics and Biophysics, University of Münster, Robert-Koch Strasse 31, D-48149, Münster, Germany.,Center for Soft Nanoscience, Busso-Peus Strasse 10, D-48149, Münster, Germany
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16
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Hummel DR, Kaksonen M. Spatio-temporal regulation of endocytic protein assembly by SH3 domains in yeast. Mol Biol Cell 2023; 34:ar19. [PMID: 36696224 PMCID: PMC10011730 DOI: 10.1091/mbc.e22-09-0406] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Clathrin-mediated endocytosis is a conserved eukaryotic membrane trafficking pathway that is driven by a sequentially assembled molecular machinery that contains over 60 different proteins. SH3 domains are the most abundant protein-protein interaction domain in this process, but the function of most SH3 domains in protein dynamics remains elusive. Using mutagenesis and live-cell fluorescence microscopy in the budding yeast Saccharomyces cerevisiae, we dissected SH3-mediated regulation of the endocytic pathway. Our data suggest that multiple SH3 domains regulate the actin nucleation-promoting Las17-Vrp1 complex, and that the network of SH3 interactions coordinates both Las17-Vrp1 assembly and dissociation. Furthermore, most endocytic SH3 domain proteins use the SH3 domain for their own recruitment, while a minority use the SH3 domain to recruit other proteins and not themselves. Our results provide a dynamic map of SH3 functions in yeast endocytosis and a framework for SH3 interaction network studies across biology.
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Affiliation(s)
- Daniel R Hummel
- Department of Biochemistry, University of Geneva, Department of Biochemistry, 1205 Genève, Switzerland
| | - Marko Kaksonen
- Department of Biochemistry, University of Geneva, Department of Biochemistry, 1205 Genève, Switzerland
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17
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A conformational switch in clathrin light chain regulates lattice structure and endocytosis at the plasma membrane of mammalian cells. Nat Commun 2023; 14:732. [PMID: 36759616 PMCID: PMC9911608 DOI: 10.1038/s41467-023-36304-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 01/25/2023] [Indexed: 02/11/2023] Open
Abstract
Conformational changes in endocytic proteins are regulators of clathrin-mediated endocytosis. Three clathrin heavy chains associated with clathrin light chains (CLC) assemble into triskelia that link into a geometric lattice that curves to drive endocytosis. Structural changes in CLC have been shown to regulate triskelia assembly in solution, yet the nature of these changes, and their effects on lattice growth, curvature, and endocytosis in cells are unknown. Here, we develop a new correlative fluorescence resonance energy transfer (FRET) and platinum replica electron microscopy method, named FRET-CLEM. With FRET-CLEM, we measure conformational changes in clathrin at thousands of individual morphologically distinct clathrin-coated structures. We discover that the N-terminus of CLC repositions away from the plasma membrane and triskelia vertex as coats curve. Preventing this conformational switch with chemical tools increases lattice sizes and inhibits endocytosis. Thus, a specific conformational switch in the light chain regulates lattice curvature and endocytosis in mammalian cells.
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18
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Moss FR, Lincoff J, Tucker M, Mohammed A, Grabe M, Frost A. Brominated lipid probes expose structural asymmetries in constricted membranes. Nat Struct Mol Biol 2023; 30:167-175. [PMID: 36624348 PMCID: PMC9935397 DOI: 10.1038/s41594-022-00898-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 11/11/2022] [Indexed: 01/11/2023]
Abstract
Lipids in biological membranes are thought to be functionally organized, but few experimental tools can probe nanoscale membrane structure. Using brominated lipids as contrast probes for cryo-EM and a model ESCRT-III membrane-remodeling system composed of human CHMP1B and IST1, we observed leaflet-level and protein-localized structural lipid patterns within highly constricted and thinned membrane nanotubes. These nanotubes differed markedly from protein-free, flat bilayers in leaflet thickness, lipid diffusion rates and lipid compositional and conformational asymmetries. Simulations and cryo-EM imaging of brominated stearoyl-docosahexanenoyl-phosphocholine showed how a pair of phenylalanine residues scored the outer leaflet with a helical hydrophobic defect where polyunsaturated docosahexaenoyl tails accumulated at the bilayer surface. Combining cryo-EM of halogenated lipids with molecular dynamics thus enables new characterizations of the composition and structure of membranes on molecular length scales.
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Affiliation(s)
- Frank R Moss
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Altos Labs, Redwood City, CA, USA
| | - James Lincoff
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Maxwell Tucker
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Arshad Mohammed
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- University of California Berkeley, Berkeley, CA, USA
- Altos Labs, Redwood City, CA, USA
| | - Michael Grabe
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
- Cardiovascular Research Institute, University of California San Francisco (UCSF), San Francisco, CA, USA.
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.
- Altos Labs, Redwood City, CA, USA.
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19
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Exocytosis of the silicified cell wall of diatoms involves extensive membrane disintegration. Nat Commun 2023; 14:480. [PMID: 36717559 PMCID: PMC9886994 DOI: 10.1038/s41467-023-36112-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 01/16/2023] [Indexed: 01/31/2023] Open
Abstract
Diatoms are unicellular algae characterized by silica cell walls. These silica elements are known to be formed intracellularly in membrane-bound silica deposition vesicles and exocytosed after completion. How diatoms maintain membrane homeostasis during the exocytosis of these large and rigid silica elements remains unknown. Here we study the membrane dynamics during cell wall formation and exocytosis in two model diatom species, using live-cell confocal microscopy, transmission electron microscopy and cryo-electron tomography. Our results show that during its formation, the mineral phase is in tight association with the silica deposition vesicle membranes, which form a precise mold of the delicate geometrical patterns. We find that during exocytosis, the distal silica deposition vesicle membrane and the plasma membrane gradually detach from the mineral and disintegrate in the extracellular space, without any noticeable endocytic retrieval or extracellular repurposing. We demonstrate that within the cell, the proximal silica deposition vesicle membrane becomes the new barrier between the cell and its environment, and assumes the role of a new plasma membrane. These results provide direct structural observations of diatom silica exocytosis, and point to an extraordinary mechanism in which membrane homeostasis is maintained by discarding, rather than recycling, significant membrane patches.
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20
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Wu YL, Hoess P, Tschanz A, Matti U, Mund M, Ries J. Maximum-likelihood model fitting for quantitative analysis of SMLM data. Nat Methods 2023; 20:139-148. [PMID: 36522500 PMCID: PMC9834062 DOI: 10.1038/s41592-022-01676-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 10/14/2022] [Indexed: 12/23/2022]
Abstract
Quantitative data analysis is important for any single-molecule localization microscopy (SMLM) workflow to extract biological insights from the coordinates of the single fluorophores. However, current approaches are restricted to simple geometries or require identical structures. Here, we present LocMoFit (Localization Model Fit), an open-source framework to fit an arbitrary model to localization coordinates. It extracts meaningful parameters from individual structures and can select the most suitable model. In addition to analyzing complex, heterogeneous and dynamic structures for in situ structural biology, we demonstrate how LocMoFit can assemble multi-protein distribution maps of six nuclear pore components, calculate single-particle averages without any assumption about geometry or symmetry, and perform a time-resolved reconstruction of the highly dynamic endocytic process from static snapshots. We provide extensive simulation and visualization routines to validate the robustness of LocMoFit and tutorials to enable any user to increase the information content they can extract from their SMLM data.
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Affiliation(s)
- Yu-Le Wu
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Philipp Hoess
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Aline Tschanz
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Ulf Matti
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Markus Mund
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Jonas Ries
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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21
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Mironov AA, Beznoussenko GV. Algorithm for Modern Electron Microscopic Examination of the Golgi Complex. Methods Mol Biol 2022; 2557:161-209. [PMID: 36512216 DOI: 10.1007/978-1-0716-2639-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The Golgi complex (GC) is an essential organelle of the eukaryotic exocytic pathway. It has a very complexed structure and thus localization of its resident proteins is not trivial. Fast development of microscopic methods generates a huge difficulty for Golgi researchers to select the best protocol to use. Modern methods of light microscopy, such as super-resolution light microscopy (SRLM) and electron microscopy (EM), open new possibilities in analysis of various biological structures at organelle, cell, and organ levels. Nowadays, new generation of EM methods became available for the study of the GC; these include three-dimensional EM (3DEM), correlative light-EM (CLEM), immune EM, and new estimators within stereology that allow realization of maximal goal of any morphological study, namely, to achieve a three-dimensional model of the sample with optimal level of resolution and quantitative determination of its chemical composition. Methods of 3DEM have partially overlapping capabilities. This requires a careful comparison of these methods, identification of their strengths and weaknesses, and formulation of recommendations for their application to cell or tissue samples. Here, we present an overview of 3DEM methods for the study of the GC and some basics for how the images are formed and how the image quality can be improved.
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22
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Zabeo D, Davies KM. Studying membrane modulation mechanisms by electron cryo-tomography. Curr Opin Struct Biol 2022; 77:102464. [PMID: 36174286 DOI: 10.1016/j.sbi.2022.102464] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/02/2022] [Accepted: 08/12/2022] [Indexed: 12/14/2022]
Abstract
Membrane modulation is a key part of cellular life. Critical to processes like energy production, cell division, trafficking, migration and even pathogen entry, defects in membrane modulation are often associated with diseases. Studying the molecular mechanisms of membrane modulation is challenging due to the highly dynamic nature of the oligomeric assemblies involved, which adopt multiple conformations depending on the precise event they are participating in. With the development of electron cryo-tomography and subtomogram averaging, many of these challenges are being resolved as it is now possible to observe complex macromolecular assemblies inside a cell at nanometre to sub-nanometre resolutions. Here, we review the different ways electron cryo-tomography is being used to help uncover the molecular mechanisms used by cells to shape their membranes.
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Affiliation(s)
- Davide Zabeo
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Karen M Davies
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
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23
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Jacobs KC, Gladfelter AS, Lew DJ. Targeted secretion: Myosin V delivers vesicles through formin condensates. Curr Biol 2022; 32:R1228-R1231. [PMID: 36347230 DOI: 10.1016/j.cub.2022.10.001] [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] [Indexed: 11/09/2022]
Abstract
Secretory vesicles are often delivered to very specific targets, like pre-synaptic terminals or cell tips, to focus exocytosis. New work suggests that a biomolecular condensate focuses actin filaments that deliver incoming vesicles through the condensate to the plasma membrane.
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Affiliation(s)
- Katherine C Jacobs
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Amy S Gladfelter
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Daniel J Lew
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27705, USA.
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24
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Yang C, Colosi P, Hugelier S, Zabezhinsky D, Lakadamyali M, Svitkina T. Actin polymerization promotes invagination of flat clathrin-coated lattices in mammalian cells by pushing at lattice edges. Nat Commun 2022; 13:6127. [PMID: 36253374 PMCID: PMC9576739 DOI: 10.1038/s41467-022-33852-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/05/2022] [Indexed: 12/24/2022] Open
Abstract
Clathrin-mediated endocytosis (CME) requires energy input from actin polymerization in mechanically challenging conditions. The roles of actin in CME are poorly understood due to inadequate knowledge of actin organization at clathrin-coated structures (CCSs). Using platinum replica electron microscopy of mammalian cells, we show that Arp2/3 complex-dependent branched actin networks, which often emerge from microtubule tips, assemble along the CCS perimeter, lack interaction with the apical clathrin lattice, and have barbed ends oriented toward the CCS. This structure is hardly compatible with the widely held "apical pulling" model describing actin functions in CME. Arp2/3 complex inhibition or epsin knockout produce large flat non-dynamic CCSs, which split into invaginating subdomains upon recovery from Arp2/3 inhibition. Moreover, epsin localization to CCSs depends on Arp2/3 activity. We propose an "edge pushing" model for CME, wherein branched actin polymerization promotes severing and invagination of flat CCSs in an epsin-dependent manner by pushing at the CCS boundary, thus releasing forces opposing the intrinsic curvature of clathrin lattices.
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Affiliation(s)
- Changsong Yang
- grid.25879.310000 0004 1936 8972Department of Biology, University of Pennsylvania, Philadelphia, PA USA
| | - Patricia Colosi
- grid.25879.310000 0004 1936 8972Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Siewert Hugelier
- grid.25879.310000 0004 1936 8972Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Daniel Zabezhinsky
- grid.25879.310000 0004 1936 8972Department of Biology, University of Pennsylvania, Philadelphia, PA USA
| | - Melike Lakadamyali
- grid.25879.310000 0004 1936 8972Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Tatyana Svitkina
- grid.25879.310000 0004 1936 8972Department of Biology, University of Pennsylvania, Philadelphia, PA USA
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25
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Cheng Z, Zhang X, Zhang Y, Li L, Chen P. Role of MMP-2 and CD147 in kidney fibrosis. Open Life Sci 2022; 17:1182-1190. [PMID: 36185410 PMCID: PMC9482425 DOI: 10.1515/biol-2022-0482] [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: 03/02/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 11/16/2022] Open
Abstract
Matrix metalloproteinase-2 (MMP-2) and cluster of differentiation 147 (CD147) both play important roles in the development of kidney fibrosis, and CD147 can induce the production and activation of MMP-2. In the early stage of kidney fibrosis, MMP-2 promotes extracellular matrix (ECM) production and accelerates the development of kidney fibrosis, while in the advanced stage, MMP-2 activity decreases, leading to reduced ECM degradation and making it difficult to alleviate kidney fibrosis. The reason for the decrease in MMP-2 activity in the advanced stage is still unclear. On the one hand, it may be related to hypoxia and endocytosis, which lead to changes in the expression of MMP-2-related active regulatory molecules; on the other hand, it may be related to insufficient CD147 function. At present, the specific process by which CD147 is involved in the regulation of MMP-2 activity is not completely clear, and further in-depth studies are needed to clarify the roles of both factors in the pathophysiology of kidney fibrosis.
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Affiliation(s)
- Zhengyuan Cheng
- Department of Internal Medicine, Ma'anshan People's Hospital Affiliated to Medical School of Southeast University, Hubei Road 45, Huashan District, Ma'anshan 243099, Anhui Province, China
| | - Xiaojuan Zhang
- Department of Nephrology, Jinling Hospital Affiliated to Nanjing University, Zhongshan East Road 305, Xuanwu District, Nanjing 210008, Jiangsu Province, China
| | - Yu Zhang
- Department of Pathology and Pathophysiology, Medical School, Southeast University, Dingjiaqiao 87, Gulou District, Nanjing 210009, Jiangsu Province, China
| | - Li Li
- Department of Pathology and Pathophysiology, Medical School, Southeast University, Dingjiaqiao 87, Gulou District, Nanjing 210009, Jiangsu Province, China
| | - Pingsheng Chen
- Department of Pathology and Pathophysiology, Medical School, Southeast University, Dingjiaqiao 87, Gulou District, Nanjing 210009, Jiangsu Province, China
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26
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Skruzny M. The endocytic protein machinery as an actin-driven membrane-remodeling machine. Eur J Cell Biol 2022; 101:151267. [PMID: 35970066 DOI: 10.1016/j.ejcb.2022.151267] [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: 06/02/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 12/14/2022] Open
Abstract
In clathrin-mediated endocytosis, a principal membrane trafficking route of all eukaryotic cells, forces are applied to invaginate the plasma membrane and form endocytic vesicles. These forces are provided by specific endocytic proteins and the polymerizing actin cytoskeleton. One of the best-studied endocytic systems is endocytosis in yeast, known for its simplicity, experimental amenability, and overall similarity to human endocytosis. Importantly, the yeast endocytic protein machinery generates and transmits tremendous force to bend the plasma membrane, making this system beneficial for mechanistic studies of cellular force-driven membrane reshaping. This review summarizes important protein players, molecular functions, applied forces, and open questions and perspectives of this robust, actin-powered membrane-remodeling protein machine.
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Affiliation(s)
- Michal Skruzny
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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27
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Menon D, Hummel D, Kaksonen M. Regulation of membrane scission in yeast endocytosisDepartment of Biochemistry and National Centre of Competence in Research, Chemical Biology, University of Geneva, Geneva, Switzerland. Mol Biol Cell 2022; 33:ar114. [PMID: 35976707 DOI: 10.1091/mbc.e21-07-0346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
During clathrin-mediated endocytosis, a flat plasma membrane is shaped into an invagination that undergoes scission to form a vesicle. In mammalian cells, the force that drives the transition from invagination to vesicle is primarily provided by the GTPase dynamin that acts in concert with crescent-shaped BAR domain proteins. In yeast cells, the mechanism of endocytic scission is unclear. The yeast BAR domain protein complex Rvs161/167 (Rvs) nevertheless plays an important role in this process: deletion of Rvs dramatically reduces scission efficiency. A mechanistic understanding of the influence of Rvs on scission however, remains incomplete. We used quantitative live-cell imaging and genetic manipulation to understand the recruitment and function of Rvs and other late-stage proteins at yeast endocytic sites. We found that arrival of Rvs at endocytic sites is timed by interaction of its BAR domain with specific membrane curvature. A second domain of Rvs167 - the SH3 domain - affects localization efficiency of Rvs. We show that Myo3, one of the two type-I myosins in Saccharomyces cerevisiae, has a role in recruiting Rvs167 via the SH3 domain. Removal of the SH3 domain also affects assembly and disassembly of actin and impedes membrane invagination. Our results indicate that both BAR and SH3 domains are important for the role of Rvs as a regulator of scission. We tested other proteins implicated in vesicle formation in Saccharomyces cerevisiae, and found that neither synaptojanins nor dynamin contribute directly to membrane scission. We propose that recruitment of Rvs BAR domains delays scission and allows invaginations to grow by stabilizing them. We also propose that vesicle formation is dependent on the force exerted by the actin network.
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Affiliation(s)
- Deepikaa Menon
- Department of Biochemistry and National Centre of Competence in Research, Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Daniel Hummel
- Department of Biochemistry and National Centre of Competence in Research, Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Marko Kaksonen
- Department of Biochemistry and National Centre of Competence in Research, Chemical Biology, University of Geneva, Geneva, Switzerland
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Mendes A, Heil HS, Coelho S, Leterrier C, Henriques R. Mapping molecular complexes with super-resolution microscopy and single-particle analysis. Open Biol 2022; 12:220079. [PMID: 35892200 PMCID: PMC9326279 DOI: 10.1098/rsob.220079] [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] [Indexed: 12/25/2022] Open
Abstract
Understanding the structure of supramolecular complexes provides insight into their functional capabilities and how they can be modulated in the context of disease. Super-resolution microscopy (SRM) excels in performing this task by resolving ultrastructural details at the nanoscale with molecular specificity. However, technical limitations, such as underlabelling, preclude its ability to provide complete structures. Single-particle analysis (SPA) overcomes this limitation by combining information from multiple images of identical structures and producing an averaged model, effectively enhancing the resolution and coverage of image reconstructions. This review highlights important studies using SRM-SPA, demonstrating how it broadens our knowledge by elucidating features of key biological structures with unprecedented detail.
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Affiliation(s)
| | | | - Simao Coelho
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Ricardo Henriques
- Instituto Gulbenkian de Ciência, Oeiras, Portugal,MRC Laboratory for Molecular Cell Biology, University College London, London, UK
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29
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Heiligenstein X, Lucas MS. One for All, All for One: A Close Look at In-Resin Fluorescence Protocols for CLEM. Front Cell Dev Biol 2022; 10:866472. [PMID: 35846358 PMCID: PMC9280628 DOI: 10.3389/fcell.2022.866472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
Sample preparation is the novel bottleneck for high throughput correlative light and electron microscopy (CLEM). Protocols suitable for both imaging methods must therefore balance the requirements of each technique. For fluorescence light microscopy, a structure of interest can be targeted using: 1) staining, which is often structure or tissue specific rather than protein specific, 2) dye-coupled proteins or antibodies, or 3) genetically encoded fluorescent proteins. Each of these three methods has its own advantages. For ultrastructural investigation by electron microscopy (EM) resin embedding remains a significant sample preparation approach, as it stabilizes the sample such that it withstands the vacuum conditions of the EM, and enables long-term storage. Traditionally, samples are treated with heavy metal salts prior to resin embedding, in order to increase imaging contrast for EM. This is particularly important for volume EM (vEM) techniques. Yet, commonly used contrasting agents (e.g., osmium tetroxide, uranyl acetate) tend to impair fluorescence. The discovery that fluorescence can be preserved in resin-embedded specimens after mild heavy metal staining was a game changer for CLEM. These so-called in-resin fluorescence protocols present a significant leap forward for CLEM approaches towards high precision localization of a fluorescent signal in (volume) EM data. Integrated microscopy approaches, combining LM and EM detection into a single instrument certainly require such an “all in one” sample preparation. Preserving, or adding, dedicated fluorescence prior to resin embedding requires a compromise, which often comes at the expense of EM imaging contrast and membrane visibility. Especially vEM can be strongly hampered by a lack of heavy metal contrasting. This review critically reflects upon the fundamental aspects of resin embedding with regard to 1) specimen fixation and the physics and chemistry underlying the preservation of protein structure with respect to fluorescence and antigenicity, 2) optimization of EM contrast for transmission or scanning EM, and 3) the choice of embedding resin. On this basis, various existing workflows employing in-resin fluorescence are described, highlighting their common features, discussing advantages and disadvantages of the respective approach, and finally concluding with promising future developments for in-resin CLEM.
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Affiliation(s)
| | - Miriam S. Lucas
- Scientific Center for Light and Electron Microscopy (ScopeM), ETH Zurich, Zurich, Switzerland
- *Correspondence: Miriam S. Lucas,
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30
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van den Dries K, Fransen J, Cambi A. Fluorescence CLEM in biology: historic developments and current super-resolution applications. FEBS Lett 2022; 596:2486-2496. [PMID: 35674424 DOI: 10.1002/1873-3468.14421] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/12/2022]
Abstract
Correlative light and electron microscopy (CLEM) is a powerful imaging approach that allows the direct correlation of information obtained on a light and an electron microscope. There is a growing interest in the application of CLEM in biology, mainly attributable to technical advances in field of fluorescence microscopy in the past two decades. In this review, we summarize the important developments in CLEM for biological applications, focusing on the combination of fluorescence microscopy and electron microscopy. We first provide a brief overview of the early days of fluorescence CLEM usage starting with the initial rise in the late 1970s and the subsequent optimization of CLEM workflows during the following two decades. Next, we describe how the engineering of fluorescent proteins and the development of super-resolution fluorescence microscopy have significantly renewed the interest in CLEM resulting in the present application of fluorescence CLEM in many different areas of cellular and molecular biology. Lastly, we present the promises and challenges for the future of fluorescence CLEM discussing novel workflows, probe development and quantification possibilities.
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Affiliation(s)
- Koen van den Dries
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | - Jack Fransen
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands.,Microscopic Imaging Center, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | - Alessandra Cambi
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
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31
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Li X, Wang C, Wang L, Huang R, Li WC, Wang X, Wong SSW, Cai Z, Leung KCF, Jin L. A glutathione-responsive silica-based nanosystem capped with in-situ polymerized cell-penetrating poly(disulfide)s for precisely modulating immuno-inflammatory responses. J Colloid Interface Sci 2022; 614:322-336. [PMID: 35104706 DOI: 10.1016/j.jcis.2022.01.091] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/14/2022] [Accepted: 01/15/2022] [Indexed: 01/02/2023]
Abstract
HYPOTHESIS Precise modulation of immuno-inflammatory response is crucial to control periodontal diseases and related systemic comorbidities. The present nanosystem with the controlled-release and cell-penetrating manner enhances the inflammation modulation effects of baicalein in human gingival epithelial cells (hGECs) for better oral healthcare. EXPERIMENTS We constructed a red-emissive mesoporous silica nanoparticle-based nanosystem with cell-penetrating poly(disulfide) (CPD) capping, through a facile in-situ polymerization approach. It was featured with a glutathione-responsive manner and instant cellular internalization capacity for precisely delivering baicalein intracellularly. Laboratory experiments assessed whether and how the nanosystem per se with the delivered baicalein could modulate immuno-inflammatory responses in hGECs. FINDINGS The in-situ polymerized CPD layer capped the nanoparticles and yet controlled the release of baicalein in a glutathione-responsive manner. The CPD coating could facilitate cellular internalization of the nanosystem via endocytosis and thiol-mediated approaches. Notably, the intracellularly released baicalein effectively downregulated the expression of pro-inflammatory cytokines through inhibiting the NF-κB signaling pathway. The nanosystem per se could modulate immuno-inflammatory responses by passivating the cellular response to interlukin-1β. This study highlights that the as-synthesized nanosystem may serve as a novel multi-functional vehicle to modulate innate host response via targeting the NF-κB pathway for precision healthcare.
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Affiliation(s)
- Xuan Li
- Faculty of Dentistry, The University of Hong Kong, 34 Hospital Road, Hong Kong Special Administrative Region, China
| | - Chuan Wang
- Faculty of Dentistry, The University of Hong Kong, 34 Hospital Road, Hong Kong Special Administrative Region, China
| | - Leilei Wang
- Faculty of Dentistry, The University of Hong Kong, 34 Hospital Road, Hong Kong Special Administrative Region, China
| | - Regina Huang
- Faculty of Dentistry, The University of Hong Kong, 34 Hospital Road, Hong Kong Special Administrative Region, China
| | - Wai-Chung Li
- Department of Chemistry, State Key Laboratory of Environmental and Biological Analysis, The Hong Kong Baptist University, Hong Kong Special Administrative Region, China
| | - Xinna Wang
- Tissue Engineering Laboratory, Department of Mechanical Engineering, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | | | - Zongwei Cai
- Department of Chemistry, State Key Laboratory of Environmental and Biological Analysis, The Hong Kong Baptist University, Hong Kong Special Administrative Region, China
| | - Ken Cham-Fai Leung
- Department of Chemistry, State Key Laboratory of Environmental and Biological Analysis, The Hong Kong Baptist University, Hong Kong Special Administrative Region, China.
| | - Lijian Jin
- Faculty of Dentistry, The University of Hong Kong, 34 Hospital Road, Hong Kong Special Administrative Region, China.
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32
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Zaccai NR, Kadlecova Z, Dickson VK, Korobchevskaya K, Kamenicky J, Kovtun O, Umasankar PK, Wrobel AG, Kaufman JGG, Gray SR, Qu K, Evans PR, Fritzsche M, Sroubek F, Höning S, Briggs JAG, Kelly BT, Owen DJ, Traub LM. FCHO controls AP2's initiating role in endocytosis through a PtdIns(4,5)P 2-dependent switch. SCIENCE ADVANCES 2022; 8:eabn2018. [PMID: 35486718 PMCID: PMC9054013 DOI: 10.1126/sciadv.abn2018] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
Clathrin-mediated endocytosis (CME) is the main mechanism by which mammalian cells control their cell surface proteome. Proper operation of the pivotal CME cargo adaptor AP2 requires membrane-localized Fer/Cip4 homology domain-only proteins (FCHO). Here, live-cell enhanced total internal reflection fluorescence-structured illumination microscopy shows that FCHO marks sites of clathrin-coated pit (CCP) initiation, which mature into uniform-sized CCPs comprising a central patch of AP2 and clathrin corralled by an FCHO/Epidermal growth factor potential receptor substrate number 15 (Eps15) ring. We dissect the network of interactions between the FCHO interdomain linker and AP2, which concentrates, orients, tethers, and partially destabilizes closed AP2 at the plasma membrane. AP2's subsequent membrane deposition drives its opening, which triggers FCHO displacement through steric competition with phosphatidylinositol 4,5-bisphosphate, clathrin, cargo, and CME accessory factors. FCHO can now relocate toward a CCP's outer edge to engage and activate further AP2s to drive CCP growth/maturation.
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Affiliation(s)
- Nathan R. Zaccai
- CIMR, University of Cambridge, Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Zuzana Kadlecova
- CIMR, University of Cambridge, Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | | | - Kseniya Korobchevskaya
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford OX3 7FY, UK
| | - Jan Kamenicky
- Czech Academy of Sciences, Institute of Information Theory and Automation, Pod Vodarenskou vezi 4, 182 08 Prague 8, Czech Republic
| | - Oleksiy Kovtun
- MRC LMB Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Perunthottathu K. Umasankar
- Intracellular Trafficking Laboratory, Transdisciplinary Biology Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Antoni G. Wrobel
- CIMR, University of Cambridge, Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | | | - Sally R. Gray
- CIMR, University of Cambridge, Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Kun Qu
- MRC LMB Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | | | - Marco Fritzsche
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford OX3 7FY, UK
- Rosalind Franklin Institute, Harwell Campus, Didcot, UK
| | - Filip Sroubek
- Czech Academy of Sciences, Institute of Information Theory and Automation, Pod Vodarenskou vezi 4, 182 08 Prague 8, Czech Republic
| | - Stefan Höning
- Institute for Biochemistry I, Medical Faculty, University of Cologne, Joseph-Stelzmann-Straße 52, 50931 Cologne, Germany
| | - John A. G. Briggs
- MRC LMB Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Bernard T. Kelly
- CIMR, University of Cambridge, Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - David J. Owen
- CIMR, University of Cambridge, Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Linton M. Traub
- Department of Cell Biology, University of Pittsburgh School of Medicine, 3500 Terrace Street, Pittsburgh, PA, USA
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Kozak M, Kaksonen M. Condensation of Ede1 promotes the initiation of endocytosis. eLife 2022; 11:72865. [PMID: 35412456 PMCID: PMC9064294 DOI: 10.7554/elife.72865] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 04/01/2022] [Indexed: 11/27/2022] Open
Abstract
Clathrin-mediated endocytosis is initiated by a network of weakly interacting proteins through a poorly understood mechanism. Ede1, the yeast homolog of mammalian Eps15, is an early-arriving endocytic protein and a key initiation factor. In the absence of Ede1, most other early endocytic proteins lose their punctate localization and endocytic uptake is decreased. We show that in yeast cells, cytosolic concentration of Ede1 is buffered at a critical level. Excess amounts of Ede1 form large condensates which recruit other endocytic proteins and exhibit properties of phase-separated liquid droplets. We demonstrate that the central region of Ede1, containing a coiled-coil and a prion-like region, is essential for both the condensate formation and the function of Ede1 in endocytosis. The functionality of Ede1 mutants lacking the central region can be partially rescued by an insertion of heterologous prion-like domains. Conversely, fusion of a heterologous lipid-binding domain with the central region of Ede1 can promote clustering into stable plasma membrane domains. We propose that the ability of Ede1 to form condensed networks supports the clustering of early endocytic proteins and promotes the initiation of endocytosis.
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Affiliation(s)
- Mateusz Kozak
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Marko Kaksonen
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
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34
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Chou YC. A physical mechanism underlying the torque generation of the bacterial flagellar motor. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2022; 45:34. [PMID: 35411441 DOI: 10.1140/epje/s10189-022-00188-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
This study proposes a physical mechanism underlying the torque generation of a bacterial flagellar motor (BFM), in which the torque for the rotation of the rotor can be generated from impulsive forces resulting from collisions between the randomly moving stator and rotor. The torque required for the rotation of the rotor may be generated through two coexisting mechanisms: mechanism (A), in which the stator collides with the rotor, whose rotation axis fluctuates asymmetrically, generating a torque in the direction of the rod, and mechanism (B), in which physical collisions between the stator and the asymmetric [Formula: see text]and [Formula: see text] generate the torque in the direction of the rod. Mechanism (A) might be related the bidirectional rotation and the tumbling of the motion of the cell. Mechanism (B) might be related to occurrence of the steps in the time traces of the rotational angle, backward stepping or switching of the rotational direction, and the knee-shaped [Formula: see text]-[Formula: see text] relation. The above-mentioned characteristics of the rotation of BFM are reproduced in a model device designed to confirm the applicability of the proposed concept to real BFM. Moreover, a prediction of the disappearance of the knee-shaped [Formula: see text]-[Formula: see text] relation of the actual BFM at a high temperature is proposed.
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Affiliation(s)
- Y C Chou
- Department of Physics, National TsingHua University, Hsinchu, Taiwan, Republic of China.
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35
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Kaplan C, Kenny SJ, Chen X, Schöneberg J, Sitarska E, Diz-Muñoz A, Akamatsu M, Xu K, Drubin DG. Load adaptation by endocytic actin networks. Mol Biol Cell 2022; 33:ar50. [PMID: 35389747 PMCID: PMC9265150 DOI: 10.1091/mbc.e21-11-0589] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Clathrin-mediated endocytosis (CME) robustness under elevated membrane tension is maintained by actin assembly-mediated force generation. However, whether more actin assembles at endocytic sites in response to increased load has not previously been investigated. Here actin network ultrastructure at CME sites was examined under low and high membrane tension. Actin and N-WASP spatial organization indicate that actin polymerization initiates at the base of clathrin-coated pits and that the network then grows away from the plasma membrane. Actin network height at individual CME sites was not coupled to coat shape, raising the possibility that local differences in mechanical load feed back on assembly. By manipulating membrane tension and Arp2/3 complex activity we tested the hypothesis that actin assembly at CME sites increases in response to elevated load. Indeed, in response to elevated membrane tension, actin grew higher, resulting in greater coverage of the clathrin coat, and CME slowed. When membrane tension was elevated and the Arp2/3 complex was inhibited, shallow clathrin-coated pits accumulated, indicating that this adaptive mechanism is especially crucial for coat curvature generation. We propose that actin assembly increases in response to increased load to ensure CME robustness over a range of plasma membrane tensions. [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text].
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Affiliation(s)
- Charlotte Kaplan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3220
| | - Sam J Kenny
- Department of Chemistry, University of California, Berkeley, CA 94720-3220
| | - Xuyan Chen
- Department of Chemistry, University of California, Berkeley, CA 94720-3220
| | - Johannes Schöneberg
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3220.,Center for Neural Circuits and Behavior, University of California, San Diego, CA 92093
| | - Ewa Sitarska
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg
| | - Alba Diz-Muñoz
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg
| | - Matthew Akamatsu
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3220
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, CA 94720-3220.,Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - David G Drubin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3220
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Tagliatti E, Cortese K. Imaging Endocytosis Dynamics in Health and Disease. MEMBRANES 2022; 12:membranes12040393. [PMID: 35448364 PMCID: PMC9028293 DOI: 10.3390/membranes12040393] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/16/2022] [Accepted: 03/29/2022] [Indexed: 02/06/2023]
Abstract
Endocytosis is a critical process for cell growth and viability. It mediates nutrient uptake, guarantees plasma membrane homeostasis, and generates intracellular signaling cascades. Moreover, it plays an important role in dead cell clearance and defense against external microbes. Finally, endocytosis is an important cellular route for the delivery of nanomedicines for therapeutic treatments. Thus, it is not surprising that both environmental and genetic perturbation of endocytosis have been associated with several human conditions such as cancer, neurological disorders, and virus infections, among others. Over the last decades, a lot of research has been focused on developing advanced imaging methods to monitor endocytosis events with high resolution in living cells and tissues. These include fluorescence imaging, electron microscopy, and correlative and super-resolution microscopy. In this review, we outline the major endocytic pathways and briefly discuss how defects in the molecular machinery of these pathways lead to disease. We then discuss the current imaging methodologies used to study endocytosis in different contexts, highlighting strengths and weaknesses.
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Affiliation(s)
- Erica Tagliatti
- Laboratory of Pharmacology and Brain Pathology, Humanitas Clinical and Research Center, Via Manzoni 56, 20089 Milano, Italy
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, University College London, London WC1E 6BT, UK
- Correspondence: (E.T.); (K.C.)
| | - Katia Cortese
- Cellular Electron Microscopy Laboratory, Department of Experimental Medicine (DIMES), Human Anatomy, Università di Genova, Via Antonio de Toni 14, 16132 Genova, Italy
- Correspondence: (E.T.); (K.C.)
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37
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Abouelezz A, Almeida-Souza L. The mammalian endocytic cytoskeleton. Eur J Cell Biol 2022; 101:151222. [DOI: 10.1016/j.ejcb.2022.151222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 12/27/2022] Open
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38
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Nickaeen M, Berro J, Pollard TD, Slepchenko BM. A model of actin-driven endocytosis explains differences of endocytic motility in budding and fission yeast. Mol Biol Cell 2022; 33:ar16. [PMID: 34910589 PMCID: PMC9250386 DOI: 10.1091/mbc.e21-07-0362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 11/23/2021] [Accepted: 12/10/2021] [Indexed: 11/15/2022] Open
Abstract
A comparative study (Sun et al., 2019) showed that the abundance of proteins at sites of endocytosis in fission and budding yeast is more similar in the two species than previously thought, yet membrane invaginations in fission yeast elongate twofold faster and are nearly twice as long as in budding yeast. Here we use a three-dimensional model of a motile endocytic invagination (Nickaeen et al., 2019) to investigate factors affecting elongation of the invaginations. We found that differences in turgor pressure in the two yeast species can largely explain the paradoxical differences observed experimentally in endocytic motility.
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Affiliation(s)
- Masoud Nickaeen
- Richard D. Berlin Center for Cell Analysis and Modeling, Department of Cell Biology, University of Connecticut Health Center, Farmington, CT 06030
| | - Julien Berro
- Department of Molecular Biophysics and Biochemistry, Yale University, and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06511, and
- Nanobiology Institute, Yale University, New Haven, CT 06520
| | - Thomas D. Pollard
- Department of Molecular Cellular and Developmental Biology, Yale University
- Department of Molecular Biophysics and Biochemistry, Yale University, and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06511, and
| | - Boris M. Slepchenko
- Richard D. Berlin Center for Cell Analysis and Modeling, Department of Cell Biology, University of Connecticut Health Center, Farmington, CT 06030
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39
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Reda B, Alphée M, Julien H, Olivia DR. Non-linear elastic properties of actin patches to partially rescue yeast endocytosis efficiency in the absence of the cross-linker Sac6. SOFT MATTER 2022; 18:1479-1488. [PMID: 35088793 DOI: 10.1039/d1sm01437d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Clathrin mediated endocytosis is an essential and complex cellular process involving more than 60 proteins. In yeast, successful endocytosis requires counteracting a large turgor pressure. To this end, yeasts assemble actin patches, which accumulate elastic energy during their assembly. We investigated the material properties of reconstituted actin patches from a wild-type (WT) strain and a mutant strain lacking the cross-linker Sac6 (sac6Δ), which has reduced endocytosis efficiency in live cells. We hypothesized that a change in the viscous properties of the actin patches, which would dissipate more mechanical energy, could explain this reduced efficiency. There was however no significant difference in the viscosity of both types of patches. However, we discovered a significantly different non-linear elastic response. While WT patches had a constant elastic modulus at different stress values, sac6Δ patches had a lower elastic modulus at low stress, before stiffening at higher ones, up to values similar to those of WT patches. To understand the consequences of this discovery, we performed, in vivo, a precise analysis of actin patch dynamics. Our analysis reveals that a small fraction of actin patches successfully complete endocytosis in sac6Δ cells, provided that those assemble an excess of actin at the membrane compared to WT. This observation indicates that the non-linear elastic properties of actin networks in sac6Δ cells contribute to rescue endocytosis, requiring nevertheless more actin material to build-up the necessary stored elastic energy.
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Affiliation(s)
- Belbahri Reda
- PMMH, CNRS, ESPCI Paris, Université PSL, Sorbonne Université, Université de Paris, Paris, France.
- Aix Marseille Univ, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Michelot Alphée
- Aix Marseille Univ, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Heuvingh Julien
- PMMH, CNRS, ESPCI Paris, Université PSL, Sorbonne Université, Université de Paris, Paris, France.
| | - du Roure Olivia
- PMMH, CNRS, ESPCI Paris, Université PSL, Sorbonne Université, Université de Paris, Paris, France.
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40
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Dahan N, Bykov YS, Boydston EA, Fadel A, Gazi Z, Hochberg-Laufer H, Martenson J, Denic V, Shav-Tal Y, Weissman JS, Aviram N, Zalckvar E, Schuldiner M. Peroxisome function relies on organelle-associated mRNA translation. SCIENCE ADVANCES 2022; 8:eabk2141. [PMID: 35020435 PMCID: PMC8754406 DOI: 10.1126/sciadv.abk2141] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 11/18/2021] [Indexed: 05/26/2023]
Abstract
Crucial metabolic functions of peroxisomes rely on a variety of peroxisomal membrane proteins (PMPs). While mRNA transcripts of PMPs were shown to be colocalized with peroxisomes, the process by which PMPs efficiently couple translation with targeting to the peroxisomal membrane remained elusive. Here, we combine quantitative electron microscopy with proximity-specific ribosome profiling and reveal that translation of specific PMPs occurs on the surface of peroxisomes in the yeast Saccharomyces cerevisiae. This places peroxisomes alongside chloroplasts, mitochondria, and the endoplasmic reticulum as organelles that use localized translation for ensuring correct insertion of hydrophobic proteins into their membranes. Moreover, the correct targeting of these transcripts to peroxisomes is crucial for peroxisomal and cellular function, emphasizing the importance of localized translation for cellular physiology.
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Affiliation(s)
- Noa Dahan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yury S. Bykov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Elizabeth A. Boydston
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, California Institute for Quantitative Biosciences, Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Amir Fadel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Zohar Gazi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Hodaya Hochberg-Laufer
- The Mina and Everard Goodman Faculty of Life Sciences, The Bar-Ilan Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat Gan 5290002, Israel
| | - James Martenson
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford St., Cambridge, MA 02138, USA
| | - Vlad Denic
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford St., Cambridge, MA 02138, USA
| | - Yaron Shav-Tal
- The Mina and Everard Goodman Faculty of Life Sciences, The Bar-Ilan Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Jonathan S. Weissman
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, California Institute for Quantitative Biosciences, Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Naama Aviram
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
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41
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Abstract
The cytoskeleton is a complex of detergent-insoluble components of the cytoplasm playing critical roles in cell motility, shape generation, and mechanical properties of a cell. Fibrillar polymers-actin filaments, microtubules, and intermediate filaments-are major constituents of the cytoskeleton, which constantly change their organization during cellular activities. The actin cytoskeleton is especially polymorphic, as actin filaments can form multiple higher-order assemblies performing different functions. Structural information about cytoskeleton organization is critical for understanding its functions and mechanisms underlying various forms of cellular activity. Because of the nanometer-scale thickness of cytoskeletal fibers, electron microscopy (EM) is a key tool to determine the structure of the cytoskeleton.This article describes application of rotary shadowing (or platinum replica ) EM (PREM) for visualization of the cytoskeleton . The procedure is applicable to thin cultured cells growing on glass coverslips and consists of detergent extraction (or mechanical "unroofing") of cells to expose their cytoskeleton , chemical fixation to provide stability, ethanol dehydration and critical point drying to preserve three-dimensionality, rotary shadowing with platinum to create contrast, and carbon coating to stabilize replicas. This technique provides easily interpretable three-dimensional images, in which individual cytoskeletal fibers are clearly resolved and individual proteins can be identified by immunogold labeling. More importantly, PREM is easily compatible with live cell imaging, so that one can correlate the dynamics of a cell or its components, e.g., expressed fluorescent proteins, with high-resolution structural organization of the cytoskeleton in the same cell.
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Affiliation(s)
- Tatyana Svitkina
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
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42
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Nair KS, Raj NB, Nampoothiri KM, Mohanan G, Acosta-Gutiérrez S, Bajaj H. Curved membrane structures induced by native lipids in giant vesicles. J Colloid Interface Sci 2021; 611:397-407. [PMID: 34963074 DOI: 10.1016/j.jcis.2021.12.098] [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: 11/23/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 10/19/2022]
Abstract
Native lipids in cell-membrane support crucial functions like intercell communication via their ability to deform into curved membrane structures. Cell membrane mimicking Giant unilamellar vesicles (GUV) is imperative in understanding native lipid's role in membrane transformation however remains challenging to assemble. We construct two giant vesicle models mimicking bacterial inner-membrane (IM) and outer-membrane (OM) under physiological conditions using single-step gel-assisted lipid swelling. IM vesicles composed of native bacterial lipids undergo small-scale membrane remodeling into bud and short-nanotube structures. In contrast, OM vesicles asymmetrically assembled from Lipopolysaccharide (LPS) and bacterial lipids underwent global membrane deformation under controlled osmotic stress. Remarkably, highly-curved structures mimicking cell-membrane architectures, including daughter vesicle networks interconnected by necks and nano-tubes ranging from micro to nanoscale, are generated in OM vesicles at osmotic stress comparable to that applied in IM vesicles. Further, we provide a quantitative description of the membrane structures by experimentally determining membrane elastic parameters, i.e., neck curvature and bending rigidity. We can conclude that a larger spontaneous curvature estimated from the neck curvature and softer membranes in OM vesicles is responsible for large-scale deformation compared to IM vesicles. Our findings will help comprehend the shape dynamics of complex native bacterial lipid membranes.
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Affiliation(s)
- Karthika S Nair
- Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum 695019, Kerala, India
| | - Neethu B Raj
- Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum 695019, Kerala, India
| | - K Madhavan Nampoothiri
- Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum 695019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, Ghaziabad 201002, India
| | - Gayathri Mohanan
- Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum 695019, Kerala, India
| | - Silvia Acosta-Gutiérrez
- Department of Chemistry, Institute of Structural and Molecular Biology, University College London, UK.
| | - Harsha Bajaj
- Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum 695019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, Ghaziabad 201002, India.
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43
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Bergeron-Sandoval LP, Kumar S, Heris HK, Chang CLA, Cornell CE, Keller SL, François P, Hendricks AG, Ehrlicher AJ, Pappu RV, Michnick SW. Endocytic proteins with prion-like domains form viscoelastic condensates that enable membrane remodeling. Proc Natl Acad Sci U S A 2021; 118:e2113789118. [PMID: 34887356 PMCID: PMC8685726 DOI: 10.1073/pnas.2113789118] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2021] [Indexed: 11/18/2022] Open
Abstract
Membrane invagination and vesicle formation are key steps in endocytosis and cellular trafficking. Here, we show that endocytic coat proteins with prion-like domains (PLDs) form hemispherical puncta in the budding yeast, Saccharomyces cerevisiae These puncta have the hallmarks of biomolecular condensates and organize proteins at the membrane for actin-dependent endocytosis. They also enable membrane remodeling to drive actin-independent endocytosis. The puncta, which we refer to as endocytic condensates, form and dissolve reversibly in response to changes in temperature and solution conditions. We find that endocytic condensates are organized around dynamic protein-protein interaction networks, which involve interactions among PLDs with high glutamine contents. The endocytic coat protein Sla1 is at the hub of the protein-protein interaction network. Using active rheology, we inferred the material properties of endocytic condensates. These experiments show that endocytic condensates are akin to viscoelastic materials. We use these characterizations to estimate the interfacial tension between endocytic condensates and their surroundings. We then adapt the physics of contact mechanics, specifically modifications of Hertz theory, to develop a quantitative framework for describing how interfacial tensions among condensates, the membrane, and the cytosol can deform the plasma membrane to enable actin-independent endocytosis.
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Affiliation(s)
| | - Sandeep Kumar
- Département de Biochimie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | | | - Catherine L A Chang
- Department of Chemistry, University of Washington, Seattle, Seattle, WA 98195-1700
| | - Caitlin E Cornell
- Department of Chemistry, University of Washington, Seattle, Seattle, WA 98195-1700
| | - Sarah L Keller
- Department of Chemistry, University of Washington, Seattle, Seattle, WA 98195-1700
| | - Paul François
- Ernest Rutherford Physics Building, McGill University, Montreal, QC H3A 2T8, Canada
| | - Adam G Hendricks
- Department of Bioengineering, McGill University, Montreal, QC H3A 0C3, Canada
| | - Allen J Ehrlicher
- Department of Bioengineering, McGill University, Montreal, QC H3A 0C3, Canada
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130;
| | - Stephen W Michnick
- Département de Biochimie, Université de Montréal, Montréal, QC H3C 3J7, Canada;
- Centre Robert-Cedergren, Bio-Informatique et Génomique, Université de Montréal, Montréal, QC H3C 3J7, Canada
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44
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Parlanti P, Cappello V. Microscopes, tools, probes, and protocols: A guide in the route of correlative microscopy for biomedical investigation. Micron 2021; 152:103182. [PMID: 34801960 DOI: 10.1016/j.micron.2021.103182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 11/12/2021] [Accepted: 11/14/2021] [Indexed: 12/11/2022]
Abstract
In the last decades, the advancements of microscopes technology, together with the development of new imaging approaches, are trying to address some biological questions that have been unresolved in the past: the need to combine in the same analysis temporal, functional and morphological information on the biological sample has become pressing. For this reason, the use of correlative microscopy, in which two or more imaging techniques are combined in the same analysis, is getting increasingly widespread. In fact, correlative microscopy can overcome limitations of a single imaging method, giving access to a larger amount of information from the same specimen. However, correlative microscopy can be challenging, and appropriate protocols for sample preparation and imaging methods must be selected. Here we review the state of the art of correlating electron microscopy with different imaging methods, focusing on sample preparation, tools, and labeling methods, with the aim to provide a comprehensive guide for those scientists who are approaching the field of correlative methods.
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Affiliation(s)
- Paola Parlanti
- Istituto Italiano di Tecnologia, Center for Materials Interfaces, Electron Crystallography, Viale Rinaldo Piaggio 34, I-56025, Pontedera (PI), Italy.
| | - Valentina Cappello
- Istituto Italiano di Tecnologia, Center for Materials Interfaces, Electron Crystallography, Viale Rinaldo Piaggio 34, I-56025, Pontedera (PI), Italy.
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45
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Auddya D, Zhang X, Gulati R, Vasan R, Garikipati K, Rangamani P, Rudraraju S. Biomembranes undergo complex, non-axisymmetric deformations governed by Kirchhoff-Love kinematicsand revealed by a three-dimensional computational framework. Proc Math Phys Eng Sci 2021; 477:20210246. [PMID: 35153593 PMCID: PMC8580429 DOI: 10.1098/rspa.2021.0246] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 10/11/2021] [Indexed: 01/10/2023] Open
Abstract
Biomembranes play a central role in various phenomena like locomotion of cells, cell-cell interactions, packaging and transport of nutrients, transmission of nerve impulses, and in maintaining organelle morphology and functionality. During these processes, the membranes undergo significant morphological changes through deformation, scission, and fusion. Modelling the underlying mechanics of such morphological changes has traditionally relied on reduced order axisymmetric representations of membrane geometry and deformation. Axisymmetric representations, while robust and extensively deployed, suffer from their inability to model-symmetry breaking deformations and structural bifurcations. To address this limitation, a three-dimensional computational mechanics framework for high fidelity modelling of biomembrane deformation is presented. The proposed framework brings together Kirchhoff–Love thin-shell kinematics, Helfrich-energy-based mechanics, and state-of-the-art numerical techniques for modelling deformation of surface geometries. Lipid bilayers are represented as spline-based surface discretizations immersed in a three-dimensional space; this enables modelling of a wide spectrum of membrane geometries, boundary conditions, and deformations that are physically admissible in a three-dimensional space. The mathematical basis of the framework and its numerical machinery are presented, and their utility is demonstrated by modelling three classical, yet non-trivial, membrane deformation problems: formation of tubular shapes and their lateral constriction, Piezo1-induced membrane footprint generation and gating response, and the budding of membranes by protein coats during endocytosis. For each problem, the full three-dimensional membrane deformation is captured, potential symmetry-breaking deformation paths identified, and various case studies of boundary and load conditions are presented. Using the endocytic vesicle budding as a case study, we also present a ‘phase diagram’ for its symmetric and broken-symmetry states.
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Affiliation(s)
- Debabrata Auddya
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Xiaoxuan Zhang
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rahul Gulati
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ritvik Vasan
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Krishna Garikipati
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Mathematics, University of Michigan, Ann Arbor, MI 48109, USA.,Michigan Institute for Computational Discovery and Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Shiva Rudraraju
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
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46
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Abstract
Cryo-electron tomography has stepped fully into the spotlight. Enthusiasm is high. Fortunately for us, this is an exciting time to be a cryotomographer, but there is still a way to go before declaring victory. Despite its potential, cryo-electron tomography possesses many inherent challenges. How do we image through thick cell samples, and possibly even tissue? How do we identify a protein of interest amidst the noisy, crowded environment of the cytoplasm? How do we target specific moments of a dynamic cellular process for tomographic imaging? In this review, we cover the history of cryo-electron tomography and how it came to be, roughly speaking, as well as the many approaches that have been developed to overcome its intrinsic limitations.
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Affiliation(s)
- Ryan K. Hylton
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Matthew T. Swulius
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
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47
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Gerganova V, Lamas I, Rutkowski DM, Vještica A, Castro DG, Vincenzetti V, Vavylonis D, Martin SG. Cell patterning by secretion-induced plasma membrane flows. SCIENCE ADVANCES 2021; 7:eabg6718. [PMID: 34533984 PMCID: PMC8448446 DOI: 10.1126/sciadv.abg6718] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 07/26/2021] [Indexed: 05/20/2023]
Abstract
Cells self-organize using reaction-diffusion and fluid-flow principles. Whether bulk membrane flows contribute to cell patterning has not been established. Here, using mathematical modeling, optogenetics, and synthetic probes, we show that polarized exocytosis causes lateral membrane flows away from regions of membrane insertion. Plasma membrane–associated proteins with sufficiently low diffusion and/or detachment rates couple to the flows and deplete from areas of exocytosis. In rod-shaped fission yeast cells, zones of Cdc42 GTPase activity driving polarized exocytosis are limited by GTPase activating proteins (GAPs). We show that membrane flows pattern the GAP Rga4 distribution and that coupling of a synthetic GAP to membrane flows is sufficient to establish the rod shape. Thus, membrane flows induced by Cdc42-dependent exocytosis form a negative feedback restricting the zone of Cdc42 activity.
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Affiliation(s)
- Veneta Gerganova
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Switzerland
| | - Iker Lamas
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Switzerland
| | | | - Aleksandar Vještica
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Switzerland
| | - Daniela Gallo Castro
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Switzerland
| | - Vincent Vincenzetti
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Switzerland
| | - Dimitrios Vavylonis
- Department of Physics, Lehigh University, Bethlehem, PA 18015, USA
- Corresponding author. (S.G.M.); (D.V.)
| | - Sophie G. Martin
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Switzerland
- Corresponding author. (S.G.M.); (D.V.)
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48
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Abella M, Andruck L, Malengo G, Skruzny M. Actin-generated force applied during endocytosis measured by Sla2-based FRET tension sensors. Dev Cell 2021; 56:2419-2426.e4. [PMID: 34473942 DOI: 10.1016/j.devcel.2021.08.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/27/2021] [Accepted: 08/11/2021] [Indexed: 11/17/2022]
Abstract
Mechanical forces are integral to many cellular processes, including clathrin-mediated endocytosis, a principal membrane trafficking route into the cell. During endocytosis, forces provided by endocytic proteins and the polymerizing actin cytoskeleton reshape the plasma membrane into a vesicle. Assessing force requirements of endocytic membrane remodeling is essential for understanding endocytosis. Here, we determined actin-generated force applied during endocytosis using FRET-based tension sensors inserted into the major force-transmitting protein Sla2 in yeast. We measured at least 8 pN force transmitted over Sla2 molecule, hence possibly more than 300-880 pN applied during endocytic vesicle formation. Importantly, decreasing cell turgor pressure and plasma membrane tension reduced force transmitted over the Sla2. The measurements in hypotonic conditions and mutants lacking BAR-domain membrane scaffolds then showed the limits of the endocytic force-transmitting machinery. Our study provides force values and force profiles critical for understanding the mechanics of endocytosis and potentially other key cellular membrane-remodeling processes.
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Affiliation(s)
- Marc Abella
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
| | - Lynell Andruck
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
| | - Gabriele Malengo
- Flow Cytometry and Imaging Facility, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
| | - Michal Skruzny
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany.
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49
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Yu Y, Yoshimura SH. Investigating the morphological dynamics of the plasma membrane by high-speed atomic force microscopy. J Cell Sci 2021; 134:272010. [PMID: 34468000 DOI: 10.1242/jcs.243584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Despite numerous recent developments in bioimaging techniques, nanoscale and live-cell imaging of the plasma membrane has been challenging because of the insufficient z-resolution of optical microscopes, as well as the lack of fluorescent probes to specifically label small membrane structures. High-speed atomic force microscopy (HS-AFM) is a powerful tool for visualising the dynamics of a specimen surface and is therefore suitable for observing plasma membrane dynamics. Recent developments in HS-AFM for live-cell imaging have enabled the visualisation of the plasma membrane and the network of cortical actin underneath the membrane in a living cell. Furthermore, correlative imaging with fluorescence microscopy allows for the direct visualisation of morphological changes of the plasma membrane together with the dynamic assembly or disassembly of proteins during the entire course of endocytosis in a living cell. Here, we review these recent advances in HS-AFM in order to analyse various cellular events occurring at the cell surface.
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Affiliation(s)
- Yiming Yu
- Graduate School of Biostudies, Kyoto University, Yoshida-konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shige H Yoshimura
- Graduate School of Biostudies, Kyoto University, Yoshida-konoe, Sakyo-ku, Kyoto 606-8501, Japan
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50
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Muriel O, Michon L, Kukulski W, Martin SG. Ultrastructural plasma membrane asymmetries in tension and curvature promote yeast cell fusion. J Cell Biol 2021; 220:212551. [PMID: 34382996 PMCID: PMC8366684 DOI: 10.1083/jcb.202103142] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 07/15/2021] [Accepted: 07/26/2021] [Indexed: 12/24/2022] Open
Abstract
Cell–cell fusion is central for sexual reproduction, and generally involves gametes of different shapes and sizes. In walled fission yeast Schizosaccharomyces pombe, the fusion of h+ and h− isogametes requires the fusion focus, an actin structure that concentrates glucanase-containing vesicles for cell wall digestion. Here, we present a quantitative correlative light and electron microscopy (CLEM) tomographic dataset of the fusion site, which reveals the fusion focus ultrastructure. Unexpectedly, gametes show marked asymmetries: a taut, convex plasma membrane of h− cells progressively protrudes into a more slack, wavy plasma membrane of h+ cells. Asymmetries are relaxed upon fusion, with observations of ramified fusion pores. h+ cells have a higher exo-/endocytosis ratio than h− cells, and local reduction in exocytosis strongly diminishes membrane waviness. Reciprocally, turgor pressure reduction specifically in h− cells impedes their protrusions into h+ cells and delays cell fusion. We hypothesize that asymmetric membrane conformations, due to differential turgor pressure and exocytosis/endocytosis ratios between mating types, favor cell–cell fusion.
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Affiliation(s)
- Olivia Muriel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Laetitia Michon
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Wanda Kukulski
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Sophie G Martin
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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