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Margheritis E, Kappelhoff S, Danial J, Gehle N, Kohl W, Kurre R, González Montoro A, Cosentino K. Gasdermin D cysteine residues synergistically control its palmitoylation-mediated membrane targeting and assembly. EMBO J 2024:10.1038/s44318-024-00190-6. [PMID: 39143238 DOI: 10.1038/s44318-024-00190-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 07/15/2024] [Accepted: 07/17/2024] [Indexed: 08/16/2024] Open
Abstract
Gasdermin D (GSDMD) executes the cell death program of pyroptosis by assembling into oligomers that permeabilize the plasma membrane. Here, by single-molecule imaging, we elucidate the yet unclear mechanism of Gasdermin D pore assembly and the role of cysteine residues in GSDMD oligomerization. We show that GSDMD preassembles at the membrane into dimeric and trimeric building blocks that can either be inserted into the membrane, or further assemble into higher-order oligomers prior to insertion into the membrane. The GSDMD residues Cys39, Cys57, and Cys192 are the only relevant cysteines involved in GSDMD oligomerization. S-palmitoylation of Cys192, combined with the presence of negatively-charged lipids, controls GSDMD membrane targeting. Simultaneous Cys39/57/192-to-alanine (Ala) mutations, but not Ala mutations of Cys192 or the Cys39/57 pair individually, completely abolish GSDMD insertion into artificial membranes as well as into the plasma membrane. Finally, either Cys192 or the Cys39/Cys57 pair are sufficient to enable formation of GSDMD dimers/trimers, but they are all required for functional higher-order oligomer formation. Overall, our study unveils a cooperative role of Cys192 palmitoylation-mediated membrane binding and Cys39/57/192-mediated oligomerization in GSDMD pore assembly. This study supports a model in which Gasdermin D oligomerization relies on a two-step mechanism mediated by specific cysteine residues.
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Affiliation(s)
- Eleonora Margheritis
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Shirin Kappelhoff
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - John Danial
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge, UK
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, UK
| | - Nadine Gehle
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Wladislaw Kohl
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Rainer Kurre
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Ayelén González Montoro
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Katia Cosentino
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany.
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Danial JSH, Jenner A, Garcia-Saez AJ, Cosentino K. Real-Time Growth Kinetics Analysis of Macromolecular Assemblies in Cells with Single Molecule Resolution. J Phys Chem A 2023; 127:3490-3496. [PMID: 37023388 DOI: 10.1021/acs.jpca.3c00368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
Single molecule fluorescence microscopy has the unique advantage to provide real-time information on the spatiotemporal assembly of individual protein complexes in cellular membranes. This includes the assembly of proteins into oligomer species of numerous copy numbers. However, there is a need for improved tracing analysis of the real-time growth kinetics of these assemblies in cells with single molecule resolution. Here, we present an automated analysis software to accurately measure the real-time kinetics of assembly of individual high-order oligomer complexes. Our software comes with a simple Graphical User Interface (GUI), is available as a source code and an executable, and can analyze a full data set of several hundred to thousand molecules in less than 2 minutes. Importantly, this software is suitable for the analysis of intracellular protein oligomers, whose stoichiometry is usually more difficult to quantify due to variability in signal detection in the different areas of the cell. We validated our method with simulated ground-truth data and time-lapse images of diffraction-limited oligomeric assemblies of BAX and BAK proteins on mitochondria of cells undergoing apoptosis. Our approach provides the broad community of biologists with a fast, user-friendly tool to trace the compositional evolution of macromolecular assemblies, and potentially model their growth for a deeper understanding of the structural and biophysical mechanisms underlying their functions.
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Affiliation(s)
- John S H Danial
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 1TN, United Kingdom
| | - Andreas Jenner
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), 50931 Cologne, Germany
| | - Ana J Garcia-Saez
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), 50931 Cologne, Germany
| | - Katia Cosentino
- Department of Biology/Chemistry and Center of Cellular Nanoanalytics (CellNanOs), University of Osnabrück, 49076 Osnabrück, Germany
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Scalisi S, Pisignano D, Cella Zanacchi F. Single-molecule localization microscopy goes quantitative. Microsc Res Tech 2023; 86:494-504. [PMID: 36601697 DOI: 10.1002/jemt.24281] [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: 11/15/2022] [Revised: 12/10/2022] [Accepted: 12/12/2022] [Indexed: 01/06/2023]
Abstract
In the last few years, single-molecule localization (SMLM) techniques have been used to address biological questions in different research fields. More recently, super-resolution has also been proposed as a quantitative tool for quantifying protein copy numbers at the nanoscale level. In this scenario, quantitative approaches, mainly based on stepwise photobleaching and quantitative SMLM assisted by calibration standards, offer an exquisite tool for investigating protein complexes. This primer focuses on the basic concepts behind quantitative super-resolution microscopy, also providing strategies to overcome the technical hurdles that could limit their application.
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Affiliation(s)
- Silvia Scalisi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Dario Pisignano
- Dipartimento di Fisica "E. Fermi", Università di Pisa, Pisa, Italy
| | - Francesca Cella Zanacchi
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy
- Dipartimento di Fisica "E. Fermi", Università di Pisa, Pisa, Italy
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Margheritis E, Kappelhoff S, Cosentino K. Pore-Forming Proteins: From Pore Assembly to Structure by Quantitative Single-Molecule Imaging. Int J Mol Sci 2023; 24:ijms24054528. [PMID: 36901959 PMCID: PMC10003378 DOI: 10.3390/ijms24054528] [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: 01/05/2023] [Revised: 02/11/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
Pore-forming proteins (PFPs) play a central role in many biological processes related to infection, immunity, cancer, and neurodegeneration. A common feature of PFPs is their ability to form pores that disrupt the membrane permeability barrier and ion homeostasis and generally induce cell death. Some PFPs are part of the genetically encoded machinery of eukaryotic cells that are activated against infection by pathogens or in physiological programs to carry out regulated cell death. PFPs organize into supramolecular transmembrane complexes that perforate membranes through a multistep process involving membrane insertion, protein oligomerization, and finally pore formation. However, the exact mechanism of pore formation varies from PFP to PFP, resulting in different pore structures with different functionalities. Here, we review recent insights into the molecular mechanisms by which PFPs permeabilize membranes and recent methodological advances in their characterization in artificial and cellular membranes. In particular, we focus on single-molecule imaging techniques as powerful tools to unravel the molecular mechanistic details of pore assembly that are often obscured by ensemble measurements, and to determine pore structure and functionality. Uncovering the mechanistic elements of pore formation is critical for understanding the physiological role of PFPs and developing therapeutic approaches.
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Chumpen Ramirez S, Gómez-Sánchez R, Verlhac P, Hardenberg R, Margheritis E, Cosentino K, Reggiori F, Ungermann C. --Atg9 interactions via its transmembrane domains are required for phagophore expansion during autophagy. Autophagy 2022:1-20. [PMID: 36354155 DOI: 10.1080/15548627.2022.2136340] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
During macroautophagy/autophagy, precursor cisterna known as phagophores expand and sequester portions of the cytoplasm and/or organelles, and subsequently close resulting in double-membrane transport vesicles called autophagosomes. Autophagosomes fuse with lysosomes/vacuoles to allow the degradation and recycling of their cargoes. We previously showed that sequential binding of yeast Atg2 and Atg18 to Atg9, the only conserved transmembrane protein in autophagy, at the extremities of the phagophore mediates the establishment of membrane contact sites between the phagophore and the endoplasmic reticulum. As the Atg2-Atg18 complex transfers lipids between adjacent membranes in vitro, it has been postulated that this activity and the scramblase activity of the trimers formed by Atg9 are required for the phagophore expansion. Here, we present evidence that Atg9 indeed promotes Atg2-Atg18 complex-mediated lipid transfer in vitro, although this is not the only requirement for its function in vivo. In particular, we show that Atg9 function is dramatically compromised by a F627A mutation within the conserved interface between the transmembrane domains of the Atg9 monomers. Although Atg9F627A self-interacts and binds to the Atg2-Atg18 complex, the F627A mutation blocks the phagophore expansion and thus autophagy progression. This phenotype is conserved because the corresponding human ATG9A mutant severely impairs autophagy as well. Importantly, Atg9F627A has identical scramblase activity in vitro like Atg9, and as with the wild-type protein enhances Atg2-Atg18-mediated lipid transfer. Collectively, our data reveal that interactions of Atg9 trimers via their transmembrane segments play a key role in phagophore expansion beyond Atg9's role as a lipid scramblase.Abbreviations: BafA1: bafilomycin A1; Cvt: cytoplasm-to-vacuole targeting; Cryo-EM: cryo-electron microscopy; ER: endoplasmic reticulum; GFP: green fluorescent protein; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MCS: membrane contact site; NBD-PE: N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)-1,2-dihexadecanoyl-sn-glycero-3-phosphoethanolamine; PAS: phagophore assembly site; PE: phosphatidylethanolamine; prApe1: precursor Ape1; PtdIns3P: phosphatidylinositol-3-phosphate; SLB: supported lipid bilayer; SUV: small unilamellar vesicle; TMD: transmembrane domain; WT: wild type.
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Affiliation(s)
- Sabrina Chumpen Ramirez
- Osnabrück University, Department of Biology/Chemistry, Biochemistry section, Osnabrück, Germany
| | - Rubén Gómez-Sánchez
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Pauline Verlhac
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ralph Hardenberg
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Katia Cosentino
- Osnabrück University, Department of Biology/Chemistry, Osnabrück, Germany.,Center of Cellular Nanoanalytic Osnabrück (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Fulvio Reggiori
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Biomedicine, Aarhus University, Ole Worms Alle 4, 8000 Aarhus C, Aarhus, Denmark.,Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Aarhus C, Denmark
| | - Christian Ungermann
- Osnabrück University, Department of Biology/Chemistry, Biochemistry section, Osnabrück, Germany.,Center of Cellular Nanoanalytic Osnabrück (CellNanOs), Osnabrück University, Osnabrück, Germany
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Cosentino K, Hertlein V, Jenner A, Dellmann T, Gojkovic M, Peña-Blanco A, Dadsena S, Wajngarten N, Danial JSH, Thevathasan JV, Mund M, Ries J, Garcia-Saez AJ. The interplay between BAX and BAK tunes apoptotic pore growth to control mitochondrial-DNA-mediated inflammation. Mol Cell 2022; 82:933-949.e9. [PMID: 35120587 PMCID: PMC8901441 DOI: 10.1016/j.molcel.2022.01.008] [Citation(s) in RCA: 98] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 11/14/2021] [Accepted: 01/10/2022] [Indexed: 01/11/2023]
Abstract
BAX and BAK are key apoptosis regulators that mediate the decisive step of mitochondrial outer membrane permeabilization. However, the mechanism by which they assemble the apoptotic pore remains obscure. Here, we report that BAX and BAK present distinct oligomerization properties, with BAK organizing into smaller structures with faster kinetics than BAX. BAK recruits and accelerates BAX assembly into oligomers that continue to grow during apoptosis. As a result, BAX and BAK regulate each other as they co-assemble into the same apoptotic pores, which we visualize. The relative availability of BAX and BAK molecules thereby determines the growth rate of the apoptotic pore and the relative kinetics by which mitochondrial contents, most notably mtDNA, are released. This feature of BAX and BAK results in distinct activation kinetics of the cGAS/STING pathway with implications for mtDNA-mediated paracrine inflammatory signaling.
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Affiliation(s)
- Katia Cosentino
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany; Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), University of Osnabrück, 49076 Osnabrück, Germany
| | - Vanessa Hertlein
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Andreas Jenner
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany; Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Timo Dellmann
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Milos Gojkovic
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Aida Peña-Blanco
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Shashank Dadsena
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Noel Wajngarten
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - John S H Danial
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Jervis Vermal Thevathasan
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Markus Mund
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Jonas Ries
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Ana J Garcia-Saez
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany; Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany.
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