1
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Yin L, Yuan L, Li J, Jiang B. The liquid-liquid phase separation in programmed cell death. Cell Signal 2024; 120:111215. [PMID: 38740235 DOI: 10.1016/j.cellsig.2024.111215] [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: 03/25/2024] [Revised: 04/23/2024] [Accepted: 05/07/2024] [Indexed: 05/16/2024]
Abstract
In recent years, the physical phenomenon of liquid-liquid phase separation has been widely introduced into biological research. Membrane-free organelles have been found to exist in cells that were driven by liquid-liquid phase separation. Intermolecular multivalent interactions can drive liquid-liquid phase separation to form condensates that are independent of other substances in the environment and thus can play an effective role in regulating multiple biological processes in the cell. The way of cell death has also long been a focus in multiple research. In the face of various stresses, cell death-related mechanisms are crucial for maintaining cellular homeostasis and regulating cell fate. With the in-depth study of cell death pathways, it has been found that the process of cell death was also accompanied by the regulation of liquid-liquid phase separation and played a key role. Therefore, this review summarized the roles of liquid-liquid phase separation in various cell death pathways, and explored the regulation of cell fate by liquid-liquid phase separation, with the expectation that the exploration of the mechanism of liquid-liquid phase separation would provide new insights into the treatment of diseases caused by regulated cell death.
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Affiliation(s)
- Leijing Yin
- Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, PR China; Sepsis Translational Medicine Key Lab of Hunan Province, Central South University, Changsha, Hunan 410078, PR China; National Medicine Functional Experimental Teaching Center, Central South University, Changsha, Hunan 410078, PR China.
| | - Ludong Yuan
- Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, PR China; Sepsis Translational Medicine Key Lab of Hunan Province, Central South University, Changsha, Hunan 410078, PR China; National Medicine Functional Experimental Teaching Center, Central South University, Changsha, Hunan 410078, PR China
| | - Jing Li
- Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, PR China; Sepsis Translational Medicine Key Lab of Hunan Province, Central South University, Changsha, Hunan 410078, PR China; National Medicine Functional Experimental Teaching Center, Central South University, Changsha, Hunan 410078, PR China
| | - Bimei Jiang
- Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, PR China; Sepsis Translational Medicine Key Lab of Hunan Province, Central South University, Changsha, Hunan 410078, PR China; National Medicine Functional Experimental Teaching Center, Central South University, Changsha, Hunan 410078, PR China.
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2
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Zhao Z, Satarifard V, Lipowsky R, Dimova R. Membrane nanotubes transform into double-membrane sheets at condensate droplets. Proc Natl Acad Sci U S A 2024; 121:e2321579121. [PMID: 38900795 DOI: 10.1073/pnas.2321579121] [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: 12/12/2023] [Accepted: 05/15/2024] [Indexed: 06/22/2024] Open
Abstract
Cellular membranes exhibit a multitude of highly curved morphologies such as buds, nanotubes, cisterna-like sheets defining the outlines of organelles. Here, we mimic cell compartmentation using an aqueous two-phase system of dextran and poly(ethylene glycol) encapsulated in giant vesicles. Upon osmotic deflation, the vesicle membrane forms nanotubes, which undergo surprising morphological transformations at the liquid-liquid interfaces inside the vesicles. At these interfaces, the nanotubes transform into cisterna-like double-membrane sheets (DMS) connected to the mother vesicle via short membrane necks. Using super-resolution (stimulated emission depletion) microscopy and theoretical considerations, we construct a morphology diagram predicting the tube-to-sheet transformation, which is driven by a decrease in the free energy. Nanotube knots can prohibit the tube-to-sheet transformation by blocking water influx into the tubes. Because both nanotubes and DMSs are frequently formed by cellular membranes, understanding the formation and transformation between these membrane morphologies provides insight into the origin and evolution of cellular organelles.
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Affiliation(s)
- Ziliang Zhao
- Max Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany
- Leibniz Institute of Photonic Technology e.V., Jena 07745, Germany
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Jena 07743, Germany
| | - Vahid Satarifard
- Max Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany
- Yale Institute for Network Science, Yale University, New Haven, CT 06520
| | - Reinhard Lipowsky
- Max Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany
| | - Rumiana Dimova
- Max Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany
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3
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Campelo F, Lillo JV, von Blume J. Protein condensates in the the secretory pathway: Unraveling biophysical interactions and function. Biophys J 2024; 123:1531-1541. [PMID: 38698644 DOI: 10.1016/j.bpj.2024.04.031] [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: 01/19/2024] [Revised: 03/23/2024] [Accepted: 04/30/2024] [Indexed: 05/05/2024] Open
Abstract
The emergence of phase separation phenomena among macromolecules has identified biomolecular condensates as fundamental cellular organizers. These condensates concentrate specific components and accelerate biochemical reactions without relying on membrane boundaries. Although extensive studies have revealed a large variety of nuclear and cytosolic membraneless organelles, we are witnessing a surge in the exploration of protein condensates associated with the membranes of the secretory pathway, such as the endoplasmic reticulum and the Golgi apparatus. This review focuses on protein condensates in the secretory pathway and discusses their impact on the organization and functions of this cellular process. Moreover, we explore the modes of condensate-membrane association and the biophysical and cellular consequences of protein condensate interactions with secretory pathway membranes.
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Affiliation(s)
- Felix Campelo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels, Barcelona, Spain.
| | - Javier Vera Lillo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels, Barcelona, Spain
| | - Julia von Blume
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut.
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4
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Ziethen N, Zwicker D. Heterogeneous nucleation and growth of sessile chemically active droplets. J Chem Phys 2024; 160:224901. [PMID: 38856073 DOI: 10.1063/5.0207761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 05/19/2024] [Indexed: 06/11/2024] Open
Abstract
Droplets are essential for spatially controlling biomolecules in cells. To work properly, cells need to control the emergence and morphology of droplets. On the one hand, driven chemical reactions can affect droplets profoundly. For instance, reactions can control how droplets nucleate and how large they grow. On the other hand, droplets coexist with various organelles and other structures inside cells, which could affect their nucleation and morphology. To understand the interplay of these two aspects, we study a continuous field theory of active phase separation. Our numerical simulations reveal that reactions suppress nucleation while attractive walls enhance it. Intriguingly, these two effects are coupled, leading to shapes that deviate substantially from the spherical caps predicted for passive systems. These distortions result from anisotropic fluxes responding to the boundary conditions dictated by the Young-Dupré equation. Interestingly, an electrostatic analogy of chemical reactions confirms these effects. We thus demonstrate how driven chemical reactions affect the emergence and morphology of droplets, which could be crucial for understanding biological cells and improving technical applications, e.g., in chemical engineering.
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Affiliation(s)
- Noah Ziethen
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
| | - David Zwicker
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
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5
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Litschel T, Kelley CF, Cheng X, Babl L, Mizuno N, Case LB, Schwille P. Membrane-induced 2D phase separation of the focal adhesion protein talin. Nat Commun 2024; 15:4986. [PMID: 38862544 PMCID: PMC11166923 DOI: 10.1038/s41467-024-49222-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 05/22/2024] [Indexed: 06/13/2024] Open
Abstract
Focal adhesions form liquid-like assemblies around activated integrin receptors at the plasma membrane. How they achieve their flexible properties is not well understood. Here, we use recombinant focal adhesion proteins to reconstitute the core structural machinery in vitro. We observe liquid-liquid phase separation of the core focal adhesion proteins talin and vinculin for a spectrum of conditions and interaction partners. Intriguingly, we show that binding to PI(4,5)P2-containing membranes triggers phase separation of these proteins on the membrane surface, which in turn induces the enrichment of integrin in the clusters. We suggest a mechanism by which 2-dimensional biomolecular condensates assemble on membranes from soluble proteins in the cytoplasm: lipid-binding triggers protein activation and thus, liquid-liquid phase separation of these membrane-bound proteins. This could explain how early focal adhesions maintain a structured and force-resistant organization into the cytoplasm, while still being highly dynamic and able to quickly assemble and disassemble.
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Affiliation(s)
- Thomas Litschel
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany.
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.
| | - Charlotte F Kelley
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Xiaohang Cheng
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Leon Babl
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Naoko Mizuno
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
- Laboratory of Structural Cell Biology, National Institutes of Health, Bethesda, MD, USA
| | - Lindsay B Case
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany.
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6
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Sun H, Yang B, Li Q, Zhu X, Song E, Liu C, Song Y, Jiang G. Polystyrene nanoparticles trigger aberrant condensation of TDP-43 and amyotrophic lateral sclerosis-like symptoms. NATURE NANOTECHNOLOGY 2024:10.1038/s41565-024-01683-5. [PMID: 38849544 DOI: 10.1038/s41565-024-01683-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 04/23/2024] [Indexed: 06/09/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by the dysfunction and progressive death of cerebral and spinal motor neurons. Preliminary epidemiological research has hinted at a relationship between environmental risks and the escalation of ALS, but the underlying reasons remain mostly mysterious. Here we show that nanosize polystyrene plastics (PS) induce ALS-like symptoms and illustrate the related molecular mechanism. When exposed to PS, cells endure internal oxidative stress, which leads to the aggregation of TAR DNA-binding protein 43 kDa (TDP-43), triggering ALS-like characteristics. In addition, the oxidized heat shock protein 70 fails to escort TDP-43 back to the nucleus. The cytoplasmic accumulation of TDP-43 facilitates the formation of a complex between PS and TDP-43, enhancing the condensation and solidification of TDP-43. These findings are corroborated through in silico and in vivo assays. Altogether, our work illustrates a unique toxicological mechanism induced by nanoparticles and provides insights into the connection between environmental pollution and neurodegenerative disorders.
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Affiliation(s)
- Hang Sun
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Bingwei Yang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Qiong Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Xiaokang Zhu
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Erqun Song
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Yang Song
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, China.
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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7
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Liu Y, Gong XT, Wang KN, He S, Wang Y, Lin Q, Liu Z, Yu X, Liu B. Dual-targeted fluorescent probe for tracking polarity and phase transition processes during lipophagy. MATERIALS HORIZONS 2024. [PMID: 38842407 DOI: 10.1039/d4mh00190g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Eukaryotic cells regulate various cellular processes through membrane-bound and membrane-less organelles, enabling active signal communication and material exchange. Lysosomes and lipid droplets are representative organelles, contributing to cell lipophagy when their interaction and metabolism are disrupted. Our limited understanding of the interacting behaviours and physicochemical properties of different organelles during lipophagy hinders accurate diagnosis and treatment of related diseases. In this contribution, we report a fluorescent probe, PTZ, engineered for dual-targeting of lipid droplets and lysosomes. PTZ can track liquid-liquid phase separation and respond to polarity shifts through ratiometric fluorescence emission, elucidating the lipophagy process from the perspective of organelle behavior and physicochemical properties. Leveraging on the multifunctionality of PTZ, we have successfully tracked the polarity and dynamic changes of lysosomes and lipid droplets during lipophagy. Furthermore, an unknown homogeneous transition of lipid droplets and lysosomes was discovered, which provided a new perspective for understanding lipophagy processes. And this work is expected to serve as a reference for diagnosis and treatment of lipophagy-related diseases.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China.
| | - Xiao-Ting Gong
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore.
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou 350207, China
| | - Kang-Nan Wang
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China.
| | - Simeng He
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Yumeng Wang
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China.
| | - Qiaowen Lin
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China.
| | - Zhiqiang Liu
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China.
| | - Xiaoqiang Yu
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China.
| | - Bin Liu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore.
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou 350207, China
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8
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Li M, Hou Y, Zhou Y, Yang Z, Zhao H, Jian T, Yu Q, Zeng F, Liu X, Zhang Z, Zhao YG. LLPS of FXR proteins drives replication organelle clustering for β-coronaviral proliferation. J Cell Biol 2024; 223:e202309140. [PMID: 38587486 PMCID: PMC11001562 DOI: 10.1083/jcb.202309140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/16/2024] [Accepted: 02/26/2024] [Indexed: 04/09/2024] Open
Abstract
β-Coronaviruses remodel host endomembranes to form double-membrane vesicles (DMVs) as replication organelles (ROs) that provide a shielded microenvironment for viral RNA synthesis in infected cells. DMVs are clustered, but the molecular underpinnings and pathophysiological functions remain unknown. Here, we reveal that host fragile X-related (FXR) family proteins (FXR1/FXR2/FMR1) are required for DMV clustering induced by expression of viral non-structural proteins (Nsps) Nsp3 and Nsp4. Depleting FXRs results in DMV dispersion in the cytoplasm. FXR1/2 and FMR1 are recruited to DMV sites via specific interaction with Nsp3. FXRs form condensates driven by liquid-liquid phase separation, which is required for DMV clustering. FXR1 liquid droplets concentrate Nsp3 and Nsp3-decorated liposomes in vitro. FXR droplets facilitate recruitment of translation machinery for efficient translation surrounding DMVs. In cells depleted of FXRs, SARS-CoV-2 replication is significantly attenuated. Thus, SARS-CoV-2 exploits host FXR proteins to cluster viral DMVs via phase separation for efficient viral replication.
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Affiliation(s)
- Meng Li
- Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, School of Life Sciences, Southern University of Science and Technology, Shenzhen, P.R. China
| | - Yali Hou
- Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, School of Life Sciences, Southern University of Science and Technology, Shenzhen, P.R. China
| | - Yuzheng Zhou
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, P.R. China
| | - Zhenni Yang
- Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, School of Life Sciences, Southern University of Science and Technology, Shenzhen, P.R. China
| | - Hongyu Zhao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
| | - Tao Jian
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Kowloon, P.R. China
| | - Qianxi Yu
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, P.R. China
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, P.R. China
| | - Fuxing Zeng
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, P.R. China
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, P.R. China
| | - Xiaotian Liu
- Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, School of Life Sciences, Southern University of Science and Technology, Shenzhen, P.R. China
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, P.R. China
| | - Yan G. Zhao
- Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, School of Life Sciences, Southern University of Science and Technology, Shenzhen, P.R. China
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9
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Schvartzman C, Ibarboure E, Martin A, Garanger E, Mutschler A, Lecommandoux S. Protocells Featuring Membrane-Bound and Dynamic Membraneless Organelles. Biomacromolecules 2024. [PMID: 38828905 DOI: 10.1021/acs.biomac.4c00200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Living cells, especially eukaryotic ones, use multicompartmentalization to regulate intra- and extracellular activities, featuring membrane-bound and membraneless organelles. These structures govern numerous biological and chemical processes spatially and temporally. Synthetic cell models, primarily utilizing lipidic and polymeric vesicles, have been developed to carry out cascade reactions within their compartments. However, these reconstructions often segregate membrane-bound and membraneless organelles, neglecting their collaborative role in cellular regulation. To address this, we propose a structural design incorporating microfluidic-produced liposomes housing synthetic membrane-bound organelles made from self-assembled poly(ethylene glycol)-block-poly(trimethylene carbonate) nanovesicles and synthetic membraneless organelles formed via temperature-sensitive elastin-like polypeptide phase separation. This architecture mirrors natural cellular organization, facilitating a detailed examination of the interactions for a comprehensive understanding of cellular dynamics.
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Affiliation(s)
- Clémence Schvartzman
- Université of Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600 Pessac, France
| | - Emmanuel Ibarboure
- Université of Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600 Pessac, France
| | - Anouk Martin
- Université of Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600 Pessac, France
| | - Elisabeth Garanger
- Université of Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600 Pessac, France
| | - Angela Mutschler
- Université of Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600 Pessac, France
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10
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Zorbas C, Soenmez A, Léger J, De Vleeschouwer C, Lafontaine DL. Detecting material state changes in the nucleolus by label-free digital holographic microscopy. EMBO Rep 2024; 25:2786-2811. [PMID: 38654122 PMCID: PMC11169520 DOI: 10.1038/s44319-024-00134-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 03/04/2024] [Accepted: 03/20/2024] [Indexed: 04/25/2024] Open
Abstract
Ribosome biogenesis is initiated in the nucleolus, a multiphase biomolecular condensate formed by liquid-liquid phase separation. The nucleolus is a powerful disease biomarker and stress biosensor whose morphology reflects function. Here we have used digital holographic microscopy (DHM), a label-free quantitative phase contrast microscopy technique, to detect nucleoli in adherent and suspension human cells. We trained convolutional neural networks to detect and quantify nucleoli automatically on DHM images. Holograms containing cell optical thickness information allowed us to define a novel index which we used to distinguish nucleoli whose material state had been modulated optogenetically by blue-light-induced protein aggregation. Nucleoli whose function had been impacted by drug treatment or depletion of ribosomal proteins could also be distinguished. We explored the potential of the technology to detect other natural and pathological condensates, such as those formed upon overexpression of a mutant form of huntingtin, ataxin-3, or TDP-43, and also other cell assemblies (lipid droplets). We conclude that DHM is a powerful tool for quantitatively characterizing nucleoli and other cell assemblies, including their material state, without any staining.
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Affiliation(s)
- Christiane Zorbas
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Biopark campus, B-6041, Gosselies, Belgium
| | - Aynur Soenmez
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Biopark campus, B-6041, Gosselies, Belgium
| | - Jean Léger
- ICTEAM-ELEN, Fonds de la Recherche Scientifique (F.R.S./FNRS), UCLouvain, B-1348, Louvain-la-Neuve, Belgium
| | - Christophe De Vleeschouwer
- ICTEAM-ELEN, Fonds de la Recherche Scientifique (F.R.S./FNRS), UCLouvain, B-1348, Louvain-la-Neuve, Belgium
| | - Denis Lj Lafontaine
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Biopark campus, B-6041, Gosselies, Belgium.
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11
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Wang R, Su Y, Yang W, Zhang H, Wang J, Gao W. Enhanced precision and efficiency in metabolic regulation: Compartmentalized metabolic engineering. BIORESOURCE TECHNOLOGY 2024; 402:130786. [PMID: 38703958 DOI: 10.1016/j.biortech.2024.130786] [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: 02/27/2024] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 05/06/2024]
Abstract
Metabolic engineering has witnessed remarkable advancements, enabling successful large-scale, cost-effective and efficient production of numerous compounds. However, the predominant expression of heterologous genes in the cytoplasm poses limitations, such as low substrate concentration, metabolic competition and product toxicity. To overcome these challenges, compartmentalized metabolic engineering allows the spatial separation of metabolic pathways for the efficient and precise production of target compounds. Compartmentalized metabolic engineering and its common strategies are comprehensively described in this study, where various membranous compartments and membraneless compartments have been used for compartmentalization and constructive progress has been made. Additionally, the challenges and future directions are discussed in depth. This review is dedicated to providing compartmentalized, precise and efficient methods for metabolic production, and provides valuable guidance for further development in the field of metabolic engineering.
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Affiliation(s)
- Rubing Wang
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Yaowu Su
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Wenqi Yang
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Huanyu Zhang
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Juan Wang
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China.
| | - Wenyuan Gao
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China.
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12
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Batisse C, Lapaillerie D, Humbert N, Real E, Zhu R, Mély Y, Parissi V, Ruff M, Batisse J. Integrase-LEDGF/p75 complex triggers the formation of biomolecular condensates that modulate HIV-1 integration efficiency in vitro. J Biol Chem 2024; 300:107374. [PMID: 38762180 PMCID: PMC11208922 DOI: 10.1016/j.jbc.2024.107374] [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: 05/20/2023] [Revised: 04/27/2024] [Accepted: 05/04/2024] [Indexed: 05/20/2024] Open
Abstract
The pre-integration steps of the HIV-1 viral cycle are some of the most valuable targets of recent therapeutic innovations. HIV-1 integrase (IN) displays multiple functions, thanks to its considerable conformational flexibility. Recently, such flexible proteins have been characterized by their ability to form biomolecular condensates as a result of Liquid-Liquid-Phase-Separation (LLPS), allowing them to evolve in a restricted microenvironment within cells called membrane-less organelles (MLO). The LLPS context constitutes a more physiological approach to study the integration of molecular mechanisms performed by intasomes (complexes containing viral DNA, IN, and its cellular cofactor LEDGF/p75). We investigated here if such complexes can form LLPS in vitro and if IN enzymatic activities were affected by this LLPS environment. We observed that the LLPS formed by IN-LEDGF/p75 functional complexes modulate the in vitro IN activities. While the 3'-processing of viral DNA ends was drastically reduced inside LLPS, viral DNA strand transfer was strongly enhanced. These two catalytic IN activities appear thus tightly regulated by the environment encountered by intasomes.
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Affiliation(s)
- Claire Batisse
- Department of Integrated Structural Biology, Chromatin Stability and DNA Mobility, IGBMC, U-596 INSERM, UMR-7104 CNRS, University of Strasbourg, Illkirch Cedex, France; GDR CNRS 2194 "DYNAVIR" (Viral DNA Integration and Chromatin Dynamics Network), France
| | - Delphine Lapaillerie
- Fundamental Microbiology and Pathogenicity Laboratory (MFP), UMR-5234 CNRS-University of Bordeaux, Bordeaux, France; GDR CNRS 2194 "DYNAVIR" (Viral DNA Integration and Chromatin Dynamics Network), France
| | - Nicolas Humbert
- Laboratory of Bioimaging and Pathologies, CNRS UMR 7021, Faculty of Pharmacy, University of Strasbourg, Illkirch Cedex, France
| | - Eleonore Real
- Laboratory of Bioimaging and Pathologies, CNRS UMR 7021, Faculty of Pharmacy, University of Strasbourg, Illkirch Cedex, France
| | - Rui Zhu
- Department of Integrated Structural Biology, Chromatin Stability and DNA Mobility, IGBMC, U-596 INSERM, UMR-7104 CNRS, University of Strasbourg, Illkirch Cedex, France; GDR CNRS 2194 "DYNAVIR" (Viral DNA Integration and Chromatin Dynamics Network), France
| | - Yves Mély
- Laboratory of Bioimaging and Pathologies, CNRS UMR 7021, Faculty of Pharmacy, University of Strasbourg, Illkirch Cedex, France
| | - Vincent Parissi
- Fundamental Microbiology and Pathogenicity Laboratory (MFP), UMR-5234 CNRS-University of Bordeaux, Bordeaux, France; GDR CNRS 2194 "DYNAVIR" (Viral DNA Integration and Chromatin Dynamics Network), France.
| | - Marc Ruff
- Department of Integrated Structural Biology, Chromatin Stability and DNA Mobility, IGBMC, U-596 INSERM, UMR-7104 CNRS, University of Strasbourg, Illkirch Cedex, France; GDR CNRS 2194 "DYNAVIR" (Viral DNA Integration and Chromatin Dynamics Network), France.
| | - Julien Batisse
- Department of Integrated Structural Biology, Chromatin Stability and DNA Mobility, IGBMC, U-596 INSERM, UMR-7104 CNRS, University of Strasbourg, Illkirch Cedex, France; GDR CNRS 2194 "DYNAVIR" (Viral DNA Integration and Chromatin Dynamics Network), France.
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13
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Cui Q, Liu Z, Bai G. Friend or foe: The role of stress granule in neurodegenerative disease. Neuron 2024:S0896-6273(24)00286-1. [PMID: 38744273 DOI: 10.1016/j.neuron.2024.04.025] [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: 12/01/2023] [Revised: 03/12/2024] [Accepted: 04/19/2024] [Indexed: 05/16/2024]
Abstract
Stress granules (SGs) are dynamic membraneless organelles that form in response to cellular stress. SGs are predominantly composed of RNA and RNA-binding proteins that assemble through liquid-liquid phase separation. Although the formation of SGs is considered a transient and protective response to cellular stress, their dysregulation or persistence may contribute to various neurodegenerative diseases. This review aims to provide a comprehensive overview of SG physiology and pathology. It covers the formation, composition, regulation, and functions of SGs, along with their crosstalk with other membrane-bound and membraneless organelles. Furthermore, this review discusses the dual roles of SGs as both friends and foes in neurodegenerative diseases and explores potential therapeutic approaches targeting SGs. The challenges and future perspectives in this field are also highlighted. A more profound comprehension of the intricate relationship between SGs and neurodegenerative diseases could inspire the development of innovative therapeutic interventions against these devastating diseases.
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Affiliation(s)
- Qinqin Cui
- Department of Neurology of Second Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Nanhu Brain-Computer Interface Institute, Hangzhou 311100, China.
| | - Zongyu Liu
- Department of Neurology of Second Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Ge Bai
- Department of Neurology of Second Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Nanhu Brain-Computer Interface Institute, Hangzhou 311100, China; Liangzhu Laboratory, MOE Frontier Science Center for Brain Science and Brain-Machine Integration, State Key Laboratory of Brain-Machine Intelligence, Zhejiang University, Hangzhou 311121, China; NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University, Hangzhou 310058, China; Institute of Fundamental and Transdisciplinary Research, Zhejiang University, Hangzhou 310058, China.
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14
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Bai Y, Ning K. How does severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) achieve immune evasion?: A narrative review. Medicine (Baltimore) 2024; 103:e37780. [PMID: 38640329 PMCID: PMC11030025 DOI: 10.1097/md.0000000000037780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/30/2024] [Accepted: 03/12/2024] [Indexed: 04/21/2024] Open
Abstract
COVID-19 caused by the novel coronavirus, severe acute respiratory syndrome coronavirus 2, (SARS-CoV-2) is a highly contagious disease known for its significant lung damage. Although the impact of the COVID-19 pandemic on our daily lives has been limited, the virus has not vanished entirely and continues to undergo mutations. This calls for a concentrated focus on the matter of SARS-CoV-2 immune evasion. Drawing on observations of immune escape mechanisms in other viruses, some scholars have proposed that liquid-liquid phase separation might play a crucial role in SARS-CoV-2's ability to evade the immune system. Within the structure of SARS-CoV-2, the nucleocapsid protein plays a pivotal role in RNA replication and transcription. Concurrently, this protein can engage in phase separation with RNA. A thorough examination of the phase separation related to the nucleocapsid protein may unveil the mechanism by which SARS-CoV-2 accomplishes immune evasion. Moreover, this analysis may provide valuable insights for future development of innovative antiviral drugs or vaccines.
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Affiliation(s)
- Yahu Bai
- Department of Respiratory, The First Affiliated Hospital of Shandong First Medical University, Shandong Provincial Qianfoshan Hospital, Shandong Institute of Respiratory Diseases, Shandong Institute of Anesthesia and Respiratory Critical Medicine, Jinan, China
| | - Kang Ning
- Department of Respiratory, The First Affiliated Hospital of Shandong First Medical University, Shandong Provincial Qianfoshan Hospital, Shandong Institute of Respiratory Diseases, Shandong Institute of Anesthesia and Respiratory Critical Medicine, Jinan, China
- Department of Respiratory, Occupational Diseases Hospital of Shandong First Medical University, Shandong Province Hospital of Occupational Diseases, Jinan, China
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15
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Kang CY, Chang Y, Zieske K. Lipid Membrane Topographies Are Regulators for the Spatial Distribution of Liquid Protein Condensates. NANO LETTERS 2024; 24:4330-4335. [PMID: 38579181 PMCID: PMC11036382 DOI: 10.1021/acs.nanolett.3c04169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/07/2024]
Abstract
Liquid protein condensates play important roles in orchestrating subcellular organization and as biochemical reaction hubs. Recent studies have linked lipid membranes to proteins capable of forming liquid condensates, and shown that biophysical parameters, like protein enrichment and restricted diffusion at membranes, regulate condensate formation and size. However, the impact of membrane topography on liquid condensates remains poorly understood. Here, we devised a cell-free system to reconstitute liquid condensates on lipid membranes with microstructured topographies and demonstrated that lipid membrane topography is a significant biophysical regulator. Using membrane surfaces designed with microwells, we observed ordered condensate patterns. Furthermore, we demonstrate that membrane topographies influence the shape of liquid condensates. Finally, we show that capillary forces, mediated by membrane topographies, lead to the directed fusion of liquid condensates. Our results demonstrate that membrane topography is a potent biophysical regulator for the localization and shape of mesoscale liquid protein condensates.
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Affiliation(s)
- Chae Yeon Kang
- Biophysics, Max
Planck Institute for the Science of Light, 91058 Erlangen, Germany
| | - Yoohyun Chang
- Biophysics, Max
Planck Institute for the Science of Light, 91058 Erlangen, Germany
| | - Katja Zieske
- Biophysics, Max
Planck Institute for the Science of Light, 91058 Erlangen, Germany
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16
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Sekula M, Tworzydlo W, Bilinski SM. Balbiani body of basal insects is potentially involved in multiplication and selective elimination of mitochondria. Sci Rep 2024; 14:8263. [PMID: 38594333 PMCID: PMC11004008 DOI: 10.1038/s41598-024-58997-6] [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: 01/03/2024] [Accepted: 04/05/2024] [Indexed: 04/11/2024] Open
Abstract
Oocytes of both vertebrates and invertebrates often contain an intricate organelle assemblage, termed the Balbiani body (Bb). It has previously been suggested that this assemblage is involved in the delivery of organelles and macromolecules to the germ plasm, formation of oocyte reserve materials, and transfer of mitochondria to the next generation. To gain further insight into the function of the Bb, we performed a series of analyses and experiments, including computer-aided 3-dimensional reconstructions, detection of DNA (mtDNA) synthesis as well as immunolocalization studies. We showed that in orthopteran Meconema meridionale, the Bb comprises a network of mitochondria and perinuclear nuage aggregations. As oogenesis progresses, the network expands filling almost entire ooplasm, then partitions into several smaller entities, termed micro-networks, and ultimately into individual mitochondria. As in somatic cells, this process involves microfilaments and elements of endoplasmic reticulum. We showed also that at least some of the individual mitochondria are surrounded by phagophores and eliminated via mitophagy. These findings support the idea that the Bb is implicated in the multiplication and selective elimination of (defective) mitochondria and therefore may participate in the transfer of undamaged (healthy) mitochondria to the next generation.
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Affiliation(s)
- Malgorzata Sekula
- Department of Developmental Biology and Invertebrate Morphology, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University in Krakow, Gronostajowa 9, 30-387, Kraków, Poland.
| | - Waclaw Tworzydlo
- Department of Developmental Biology and Invertebrate Morphology, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University in Krakow, Gronostajowa 9, 30-387, Kraków, Poland
| | - Szczepan M Bilinski
- Department of Developmental Biology and Invertebrate Morphology, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University in Krakow, Gronostajowa 9, 30-387, Kraków, Poland.
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17
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Duran J, Poolsup S, Allers L, Lemus MR, Cheng Q, Pu J, Salemi M, Phinney B, Jia J. A mechanism that transduces lysosomal damage signals to stress granule formation for cell survival. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.587368. [PMID: 38617306 PMCID: PMC11014484 DOI: 10.1101/2024.03.29.587368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Lysosomal damage poses a significant threat to cell survival. Our previous work has reported that lysosomal damage induces stress granule (SG) formation. However, the importance of SG formation in determining cell fate and the precise mechanisms through which lysosomal damage triggers SG formation remains unclear. Here, we show that SG formation is initiated via a novel calcium-dependent pathway and plays a protective role in promoting cell survival in response to lysosomal damage. Mechanistically, we demonstrate that during lysosomal damage, ALIX, a calcium-activated protein, transduces lysosomal damage signals by sensing calcium leakage to induce SG formation by controlling the phosphorylation of eIF2α. ALIX modulates eIF2α phosphorylation by regulating the association between PKR and its activator PACT, with galectin-3 exerting a negative effect on this process. We also found this regulatory event of SG formation occur on damaged lysosomes. Collectively, these investigations reveal novel insights into the precise regulation of SG formation triggered by lysosomal damage, and shed light on the interaction between damaged lysosomes and SGs. Importantly, SG formation is significant for promoting cell survival in the physiological context of lysosomal damage inflicted by SARS-CoV-2 ORF3a, adenovirus infection, Malaria hemozoin, proteopathic tau as well as environmental hazard silica.
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Affiliation(s)
- Jacob Duran
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87106, USA
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM 87106, USA
| | - Suttinee Poolsup
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87106, USA
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM 87106, USA
| | - Lee Allers
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM 87106, USA
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87106, USA
| | - Monica Rosas Lemus
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM 87106, USA
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87106, USA
| | - Qiuying Cheng
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87106, USA
| | - Jing Pu
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87106, USA
| | - Michelle Salemi
- Proteomics Core Facility, University of California Davis Genome Center, University of California, Davis, CA 95616, USA
| | - Brett Phinney
- Proteomics Core Facility, University of California Davis Genome Center, University of California, Davis, CA 95616, USA
| | - Jingyue Jia
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87106, USA
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM 87106, USA
- Lead Contact
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18
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Lin W, Nagy PD. Co-opted cytosolic proteins form condensate substructures within membranous replication organelles of a positive-strand RNA virus. THE NEW PHYTOLOGIST 2024. [PMID: 38515267 DOI: 10.1111/nph.19691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/22/2024] [Indexed: 03/23/2024]
Abstract
Positive-strand RNA viruses co-opt organellar membranes for biogenesis of viral replication organelles (VROs). Tombusviruses also co-opt pro-viral cytosolic proteins to VROs. It is currently not known what type of molecular organization keeps co-opted proteins sequestered within membranous VROs. In this study, we employed tomato bushy stunt virus (TBSV) and carnation Italian ringspot virus (CIRV) - Nicotiana benthamiana pathosystems to identify biomolecular condensate formation in VROs. We show that TBSV p33 and the CIRV p36 replication proteins sequester glycolytic and fermentation enzymes in unique condensate substructures associated with membranous VROs. We find that p33 and p36 form droplets in vitro driven by intrinsically disordered region. The replication protein organizes partitioning of co-opted host proteins into droplets. VRO-associated condensates are critical for local adenosine triphosphate production to support energy for virus replication. We find that co-opted endoplasmic reticulum membranes and actin filaments form meshworks within and around VRO condensates, contributing to unique composition and structure. We propose that p33/p36 organize liquid-liquid phase separation of co-opted concentrated host proteins in condensate substructures within membranous VROs. Overall, we demonstrate that subverted membranes and condensate substructures co-exist and are critical for VRO functions. The replication proteins induce and connect the two substructures within VROs.
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Affiliation(s)
- Wenwu Lin
- Department of Plant Pathology, University of Kentucky, Lexington, KY, 40543, USA
| | - Peter D Nagy
- Department of Plant Pathology, University of Kentucky, Lexington, KY, 40543, USA
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19
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Ferreira A, Castanheira P, Escrevente C, Barral DC, Barona T. Membrane trafficking alterations in breast cancer progression. Front Cell Dev Biol 2024; 12:1350097. [PMID: 38533085 PMCID: PMC10963426 DOI: 10.3389/fcell.2024.1350097] [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: 12/05/2023] [Accepted: 02/12/2024] [Indexed: 03/28/2024] Open
Abstract
Breast cancer (BC) is the most common type of cancer in women, and remains one of the major causes of death in women worldwide. It is now well established that alterations in membrane trafficking are implicated in BC progression. Indeed, membrane trafficking pathways regulate BC cell proliferation, migration, invasion, and metastasis. The 22 members of the ADP-ribosylation factor (ARF) and the >60 members of the rat sarcoma (RAS)-related in brain (RAB) families of small GTP-binding proteins (GTPases), which belong to the RAS superfamily, are master regulators of membrane trafficking pathways. ARF-like (ARL) subfamily members are involved in various processes, including vesicle budding and cargo selection. Moreover, ARFs regulate cytoskeleton organization and signal transduction. RABs are key regulators of all steps of membrane trafficking. Interestingly, the activity and/or expression of some of these proteins is found dysregulated in BC. Here, we review how the processes regulated by ARFs and RABs are subverted in BC, including secretion/exocytosis, endocytosis/recycling, autophagy/lysosome trafficking, cytoskeleton dynamics, integrin-mediated signaling, among others. Thus, we provide a comprehensive overview of the roles played by ARF and RAB family members, as well as their regulators in BC progression, aiming to lay the foundation for future research in this field. This research should focus on further dissecting the molecular mechanisms regulated by ARFs and RABs that are subverted in BC, and exploring their use as therapeutic targets or prognostic markers.
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20
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Wei W, Liu Y, Shen Y, Yang T, Dong Y, Han Z, Wang Y, Liu Z, Chai Y, Zhang M, Wang H, Shen H, Shen Y, Chen M. In situ tissue profile of rat trigeminal nerve in trigeminal neuralgia using spatial transcriptome sequencing. Int J Surg 2024; 110:1463-1474. [PMID: 38270619 PMCID: PMC10942187 DOI: 10.1097/js9.0000000000001110] [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: 07/18/2023] [Accepted: 01/08/2024] [Indexed: 01/26/2024]
Abstract
BACKGROUND Trigeminal neuralgia (TN) is the most common neuropathic disorder in the maxillofacial region. The etiology and pathogenesis of TN have not been clearly determined to date, although there are many hypotheses. OBJECTIVE The goal of this study was to investigate the interactions between different types of cells in TN, particularly the impact and intrinsic mechanism of demyelination on the trigeminal ganglion, and to identify new important target genes and regulatory pathways in TN. METHODS TN rat models were prepared by trigeminal root compression, and trigeminal nerve tissues were isolated for spatial transcriptome sequencing. The gene expression matrix was reduced dimensionally by PCA and presented by UMAP. Gene function annotation was analyzed by Metascape. The progression of certain clusters and the developmental pseudotime were analyzed using the Monocle package. Modules of the gene coexpression network between different groups were analyzed based on weighted gene coexpression network analysis and assigned AddModuleScore values. The intercellular communication of genes in these networks via ligand-receptor interactions was analyzed using CellPhoneDB analysis. RESULTS The results suggested that the trigeminal ganglion could affect Schwann cell demyelination and remyelination responses through many ligand-receptor interactions, while the effect of Schwann cells on the trigeminal ganglion was much weaker. Additionally, ferroptosis may be involved in the demyelination of Schwann cells. CONCLUSIONS This study provides spatial transcriptomics sequencing data on TN, reveals new markers, and redefines the relationship between the ganglion and myelin sheath, providing a theoretical basis and supporting data for future mechanistic research and drug development.
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Affiliation(s)
- Wenbin Wei
- Department of Oral Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai
| | - Yuemin Liu
- Department of Oral Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai
| | | | - Tao Yang
- Department of Medical Cosmetology, Suzhou, Jiangsu, People’s Republic of China
| | - Yabing Dong
- Department of Oral Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai
| | - Zixiang Han
- Department of Oral Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai
| | - Yiwen Wang
- Department of Oral Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai
| | - Zhiyang Liu
- Department of Oral Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai
| | - Ying Chai
- Department of Oral Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai
| | - Mengjie Zhang
- Department of Oral Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai
| | - Hanshao Wang
- Department of Oral Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai
| | - Hao Shen
- Clinical Laboratory, Suzhou Ninth People’s Hospital
| | | | - Minjie Chen
- Department of Oral Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai
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21
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Kurusu R, Morishita H, Komatsu M. p62 bodies: cytosolic zoning by phase separation. J Biochem 2024; 175:141-146. [PMID: 37948628 DOI: 10.1093/jb/mvad089] [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: 09/07/2023] [Accepted: 10/25/2023] [Indexed: 11/12/2023] Open
Abstract
Cellular zoning or partitioning is critical in preventing macromolecules from random diffusion and orchestrating the spatiotemporal dynamics of biochemical reactions. Along with membranous organelles, membraneless organelles contribute to the precise regulation of biochemical reactions inside cells. In response to environmental cues, membraneless organelles rapidly form through liquid-liquid phase separation, sequester certain proteins and RNAs, mediate specific reactions and dissociate. Among membraneless organelles, ubiquitin-positive condensates, namely, p62 bodies, maintain cellular homeostasis through selective autophagy of themselves to contribute to intracellular quality control. p62 bodies also activate the anti-oxidative stress response regulated by the KEAP1-NRF2 system. In this review, we present an overview of recent advancements in cellular and molecular biology related to p62 bodies, highlighting their dynamic nature and functions.
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Affiliation(s)
- Reo Kurusu
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Hideaki Morishita
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
- Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Masaaki Komatsu
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
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22
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Jiang J, Hou X, Xu K, Ji K, Ji Z, Xi J, Wang X. Bacteria-targeted magnolol-loaded multifunctional nanocomplexes for antibacterial and anti-inflammatory treatment. Biomed Mater 2024; 19:025029. [PMID: 38290149 DOI: 10.1088/1748-605x/ad2406] [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: 08/15/2023] [Accepted: 01/30/2024] [Indexed: 02/01/2024]
Abstract
Natural plant-derived small molecules have shown great potential for their antimicrobial and anti-inflammatory properties. In this study, we successfully developed a nanocomplex consisting of magnolol (Mag), a surfactant with an 18 carbon hydrocarbon chain and multi-amine head groups (C18N3), and a peptide (cyclic 9-amino acid peptide (CARG)) with targeting capabilities forStaphylococcus aureus(S. aureus). The obtained Mag/C18N3/CARG nanocomplexes exhibited strong antibacterial activity againstS. aureus. Furthermore, they demonstrated anti-inflammatory effects by reducing the secretion of pro-inflammatory cytokines such as TNF-α, IL-6, and IL-1βfrom macrophage inflammatory cells. This was achieved through downregulating the activation of NF-κB, KEAP1, and NRF2 signaling pathways. In a murine skin infection model, the Mag/C18N3/CARG nanocomplexes effectively suppressed the growth ofS. aureusin the infected area and promoted wound healing. Additionally, in a mouse model of acute kidney injury (AKI), the nanocomplexes significantly reduced the levels of blood urea nitrogen and creatinine, leading to a decrease in mortality rate. These findings demonstrate the potential of combining natural plant-derived small molecules with C18N3/CARG assemblies as a novel approach for the development of effective and safe antibacterial agents.
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Affiliation(s)
- Jian Jiang
- Central Laboratory, Binhai County People's Hospital, Clinical Medical College of Yangzhou University, Yancheng 224000, People's Republic of China
- Institute of Translational Medicine, Yangzhou University, Yangzhou 225009, People's Republic of China
| | - Xuefeng Hou
- Central Laboratory, Binhai County People's Hospital, Clinical Medical College of Yangzhou University, Yancheng 224000, People's Republic of China
| | - Kangjie Xu
- Central Laboratory, Binhai County People's Hospital, Clinical Medical College of Yangzhou University, Yancheng 224000, People's Republic of China
| | - Kangkang Ji
- Central Laboratory, Binhai County People's Hospital, Clinical Medical College of Yangzhou University, Yancheng 224000, People's Republic of China
| | - Zhongkai Ji
- Department of Orthopaedics, Binhai County People's Hospital, Yancheng 224000, People's Republic of China
| | - Juqun Xi
- Central Laboratory, Binhai County People's Hospital, Clinical Medical College of Yangzhou University, Yancheng 224000, People's Republic of China
- Institute of Translational Medicine, Yangzhou University, Yangzhou 225009, People's Republic of China
| | - Xin Wang
- Department of Critical Care Medicine, Binhai County People's Hospital, Yancheng 224000, People's Republic of China
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23
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Li Q, Liu Y, Zhang X. Biomolecular condensates in plant RNA silencing: insights into formation, function, and stress responses. THE PLANT CELL 2024; 36:227-245. [PMID: 37772963 PMCID: PMC10827315 DOI: 10.1093/plcell/koad254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 09/14/2023] [Accepted: 09/14/2023] [Indexed: 09/30/2023]
Abstract
Biomolecular condensates are dynamic structures formed through diverse mechanisms, including liquid-liquid phase separation. These condensates have emerged as crucial regulators of cellular processes in eukaryotic cells, enabling the compartmentalization of specific biological reactions while allowing for dynamic exchange of molecules with the surrounding environment. RNA silencing, a conserved gene regulatory mechanism mediated by small RNAs (sRNAs), plays pivotal roles in various biological processes. Multiple types of biomolecular condensate, including dicing bodies, processing bodies, small interfering RNA bodies, and Cajal bodies, have been identified as key players in RNA silencing pathways. These biomolecular condensates provide spatial compartmentation for the biogenesis, loading, action, and turnover of small RNAs. Moreover, they actively respond to stresses, such as viral infections, and modulate RNA silencing activities during stress responses. This review summarizes recent advances in understanding of dicing bodies and other biomolecular condensates involved in RNA silencing. We explore their formation, roles in RNA silencing, and contributions to antiviral resistance responses. This comprehensive overview provides insights into the functional significance of biomolecular condensates in RNA silencing and expands our understanding of their roles in gene expression and stress responses in plants.
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Affiliation(s)
- Qi Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Yang Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoming Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
- HainanYazhou Bay Seed Lab, Sanya, China
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24
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An Y, Webb MA, Jacobs WM. Active learning of the thermodynamics-dynamics trade-off in protein condensates. SCIENCE ADVANCES 2024; 10:eadj2448. [PMID: 38181073 PMCID: PMC10775998 DOI: 10.1126/sciadv.adj2448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 12/04/2023] [Indexed: 01/07/2024]
Abstract
Phase-separated biomolecular condensates exhibit a wide range of dynamic properties, which depend on the sequences of the constituent proteins and RNAs. However, it is unclear to what extent condensate dynamics can be tuned without also changing the thermodynamic properties that govern phase separation. Using coarse-grained simulations of intrinsically disordered proteins, we show that the dynamics and thermodynamics of homopolymer condensates are strongly correlated, with increased condensate stability being coincident with low mobilities and high viscosities. We then apply an "active learning" strategy to identify heteropolymer sequences that break this correlation. This data-driven approach and accompanying analysis reveal how heterogeneous amino acid compositions and nonuniform sequence patterning map to a range of independently tunable dynamic and thermodynamic properties of biomolecular condensates. Our results highlight key molecular determinants governing the physical properties of biomolecular condensates and establish design rules for the development of stimuli-responsive biomaterials.
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Affiliation(s)
- Yaxin An
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Michael A. Webb
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - William M. Jacobs
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
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25
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Seizova S, Ferrel A, Boothroyd J, Tonkin CJ. Toxoplasma protein export and effector function. Nat Microbiol 2024; 9:17-28. [PMID: 38172621 DOI: 10.1038/s41564-023-01563-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 11/16/2023] [Indexed: 01/05/2024]
Abstract
Toxoplasma gondii is a single-celled eukaryotic parasite with a considerable host range that must invade the cells of warm-blooded hosts to survive and replicate. The challenges and opportunities that such a strategy represent have been met by the evolution of effectors that are delivered into host cells, counter host defences and co-opt host cell functions for their own purposes. These effectors are delivered in two waves using distinct machinery for each. In this Review, we focus on understanding the architecture of these protein-export systems and how their protein cargo is recognized and selected. We discuss the recent findings on the role that host manipulation has in latent Toxoplasma infections. We also discuss how these recent findings compare to protein export in the related Plasmodium spp. (the causative agent of malaria) and how this can inform our understanding of host manipulation in the larger Apicomplexa phylum and its evolution.
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Affiliation(s)
- Simona Seizova
- School of Life Sciences, The University of Dundee, Dundee, UK
| | - Abel Ferrel
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - John Boothroyd
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
| | - Christopher J Tonkin
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.
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26
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Deng Q, Jiang H, Hu J, Pan R. Identification of Auxiliary Organellar Targeting Signals for Plant Peroxisomes Using Bioinformatic Analysis of Large Protein Sequence Datasets Followed by Experimental Validation. Methods Mol Biol 2024; 2792:265-275. [PMID: 38861094 DOI: 10.1007/978-1-0716-3802-6_21] [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: 06/12/2024]
Abstract
Eukaryotic cells are compartmentalized by membrane-bounded organelles to ensure that specific biochemical reactions and cellular functions occur in a spatially restricted manner. The subcellular localization of proteins is largely determined by their intrinsic targeting signals, which are mainly constituted by short peptides. A complete organelle targeting signal may contain a core signal (CoreS) as well as auxiliary signals (AuxiS). However, the AuxiS is often not as well characterized as the CoreS. Peroxisomes house many key steps in photorespiration, besides other crucial functions in plants. Peroxisome targeting signal type 1 (PTS1), which is carried by most peroxisome matrix proteins, was initially recognized as a C-terminal tripeptide with a "canonical" consensus of [S/A]-[K/R]-[L/M]. Many studies have shown the existence of auxiliary targeting signals upstream of PTS1, but systematic characterizations are lacking. Here, we designed an analytical strategy to characterize the auxiliary targeting signals for plant peroxisomes using large datasets and statistics followed by experimental validations. This method may also be applied to deciphering the auxiliary targeting signals for other organelles, whose organellar targeting depends on a core peptide with assistance from a nearby auxiliary signal.
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Affiliation(s)
- Qianwen Deng
- College of Agriculture and Biotechnology & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
- Zhijiang Lab, Hangzhou, China
| | - Hangjin Jiang
- Center for Data Science, Zhejiang University, Hangzhou, China
| | - Jianping Hu
- Michigan State University-Department of Energy Plant Research Laboratory and Plant Biology Department, Michigan State University, East Lansing, MI, USA
| | - Ronghui Pan
- College of Agriculture and Biotechnology & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China.
- Zhijiang Lab, Hangzhou, China.
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27
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Hoffmann C, Milovanovic D. Dipping contacts - a novel type of contact site at the interface between membraneless organelles and membranes. J Cell Sci 2023; 136:jcs261413. [PMID: 38149872 PMCID: PMC10785658 DOI: 10.1242/jcs.261413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023] Open
Abstract
Liquid-liquid phase separation is a major mechanism for organizing macromolecules, particularly proteins with intrinsically disordered regions, in compartments not limited by a membrane or a scaffold. The cell can therefore be perceived as a complex emulsion containing many of these membraneless organelles, also referred to as biomolecular condensates, together with numerous membrane-bound organelles. It is currently unclear how such a complex concoction operates to allow for intracellular trafficking, signaling and metabolic processes to occur with high spatiotemporal precision. Based on experimental observations of synaptic vesicle condensates - a membraneless organelle that is in fact packed with membranes - we present here the framework of dipping contacts: a novel type of contact site between membraneless organelles and membranes. In this Hypothesis, we propose that our framework of dipping contacts can serve as a foundation to investigate the interface that couples the diffusion and material properties of condensates to biochemical processes occurring in membranes. The identity and regulation of this interface is especially critical in the case of neurodegenerative diseases, where aberrant inclusions of misfolded proteins and damaged organelles underlie cellular pathology.
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Affiliation(s)
- Christian Hoffmann
- Laboratory of Molecular Neuroscience, German Center for Neurodegenerative Diseases (DZNE), 10117 Berlin, Germany
- Whitman Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Dragomir Milovanovic
- Laboratory of Molecular Neuroscience, German Center for Neurodegenerative Diseases (DZNE), 10117 Berlin, Germany
- Whitman Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
- National Center for X-ray Tomography, Advanced Light Source, Berkeley, CA 94720, USA
- Einstein Center for Neuroscience, Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität Berlin and Berlin Institute of Health, 10117 Berlin, Germany
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28
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Chen Y, Wang Y, Wang T, Pei X, Zhang J, Liu Y. TRIM21 undergoes phase separation dependent CC domain to regulate autophagy. Biochem Biophys Res Commun 2023; 684:149101. [PMID: 37879251 DOI: 10.1016/j.bbrc.2023.10.033] [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: 09/18/2023] [Revised: 09/30/2023] [Accepted: 10/09/2023] [Indexed: 10/27/2023]
Abstract
Tripartite motif (TRIM) family proteins as E3-ligases participate in various biological processes. TRIM21, as the first autoantibody protein, has been found to be associated with autophagy. However, the role of TRIM21 engaging in autophagy is still unclear. In this study, TRIM21 forms significate puncta in the cytoplasm and undergoes liquid-liquid phase separation in vitro. Furthermore, we identify phase separation of the coiled-coil (CC) domain is essential for autophagosome to mediate autophagy-related protein recruited. These findings show that phase separation of the CC domain of TRIM21 promotes autophagosome to impact cell fate.
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Affiliation(s)
- Yatao Chen
- Department of Biochemistry, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | | | - Tan Wang
- Department of Biochemistry, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoying Pei
- Department of Biochemistry, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jun Zhang
- Department of Biochemistry, School of Life Sciences, Nanjing Normal University, Nanjing, China.
| | - Yan Liu
- Department of Biochemistry, School of Life Sciences, Nanjing Normal University, Nanjing, China.
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29
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Ramšak M, Ramirez DA, Hough LE, Shirts MR, Vidmar S, Eleršič Filipič K, Anderluh G, Jerala R. Programmable de novo designed coiled coil-mediated phase separation in mammalian cells. Nat Commun 2023; 14:7973. [PMID: 38042897 PMCID: PMC10693550 DOI: 10.1038/s41467-023-43742-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/17/2023] [Indexed: 12/04/2023] Open
Abstract
Membraneless liquid compartments based on phase-separating biopolymers have been observed in diverse cell types and attributed to weak multivalent interactions predominantly based on intrinsically disordered domains. The design of liquid-liquid phase separated (LLPS) condensates based on de novo designed tunable modules that interact in a well-understood, controllable manner could improve our understanding of this phenomenon and enable the introduction of new features. Here we report the construction of CC-LLPS in mammalian cells, based on designed coiled-coil (CC) dimer-forming modules, where the stability of CC pairs, their number, linkers, and sequential arrangement govern the transition between diffuse, liquid and immobile condensates and are corroborated by coarse-grained molecular simulations. Through modular design, we achieve multiple coexisting condensates, chemical regulation of LLPS, condensate fusion, formation from either one or two polypeptide components or LLPS regulation by a third polypeptide chain. These findings provide further insights into the principles underlying LLPS formation and a design platform for controlling biological processes.
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Affiliation(s)
- Maruša Ramšak
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- Interdisciplinary doctoral study of biomedicine, Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Dominique A Ramirez
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Loren E Hough
- Department of Physics and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Sara Vidmar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- Interdisciplinary doctoral study of biomedicine, Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Kristina Eleršič Filipič
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.
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30
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Wang YL, Feng LL, Shi J, Chen WY, Bie SY, Bai SM, Zeng GD, Wang RZ, Zheng J, Wan XB, Fan XJ. CiRS-7 Enhances the Liquid-liquid Phase Separation of miRISC and Promotes DNA Damage Repair. Nucleus 2023; 14:2293599. [PMID: 38105528 PMCID: PMC10730229 DOI: 10.1080/19491034.2023.2293599] [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: 01/17/2023] [Accepted: 12/07/2023] [Indexed: 12/19/2023] Open
Abstract
Noncoding RNAs have been found to play important roles in DNA damage repair, whereas the participation of circRNA remains undisclosed. Here, we characterized ciRS-7, a circRNA containing over 70 putative miR-7-binding sites, as an enhancer of miRISC condensation and DNA repair. Both in vivo and in vitro experiments confirmed the condensation of TNRC6B and AGO2, two core protein components of human miRISC. Moreover, overexpressing ciRS-7 largely increased the condensate number of TNRC6B and AGO2 in cells, while silencing ciRS-7 reduced it. Additionally, miR-7 overexpression also promoted miRISC condensation. Consistent with the previous report that AGO2 participated in RAD51-mediated DNA damage repair, the overexpression of ciRS-7 significantly promoted irradiation-induced DNA damage repair by enhancing RAD51 recruitment. Our results uncover a new role of circRNA in liquid-liquid phase separation and provide new insight into the regulatory mechanism of ciRS-7 on miRISC function and DNA repair.
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Affiliation(s)
- Yun-Long Wang
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, P.R. China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R.China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Li-Li Feng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, P.R. China
- Department of Radiology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, P.R. China
| | - Jie Shi
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Wan-Ying Chen
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, P.R. China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R.China
| | - Shu-Ying Bie
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Shao-Mei Bai
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Guang-Dong Zeng
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Rui-Zhi Wang
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Jian Zheng
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Xiang-Bo Wan
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, P.R. China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R.China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Xin-Juan Fan
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
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31
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Lu T, Javed S, Bonfio C, Spruijt E. Interfacing Coacervates with Membranes: From Artificial Organelles and Hybrid Protocells to Intracellular Delivery. SMALL METHODS 2023; 7:e2300294. [PMID: 37354057 DOI: 10.1002/smtd.202300294] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/30/2023] [Indexed: 06/26/2023]
Abstract
Compartmentalization is crucial for the functioning of cells. Membranes enclose and protect the cell, regulate the transport of molecules entering and exiting the cell, and organize cellular machinery in subcompartments. In addition, membraneless condensates, or coacervates, offer dynamic compartments that act as biomolecular storage centers, organizational hubs, or reaction crucibles. Emerging evidence shows that phase-separated membraneless bodies in the cell are involved in a wide range of functional interactions with cellular membranes, leading to transmembrane signaling, membrane remodeling, intracellular transport, and vesicle formation. Such functional and dynamic interplay between phase-separated droplets and membranes also offers many potential benefits to artificial cells, as shown by recent studies involving coacervates and liposomes. Depending on the relative sizes and interaction strength between coacervates and membranes, coacervates can serve as artificial membraneless organelles inside liposomes, as templates for membrane assembly and hybrid artificial cell formation, as membrane remodelers for tubulation and possibly division, and finally, as cargo containers for transport and delivery of biomolecules across membranes by endocytosis or direct membrane crossing. Here, recent experimental examples of each of these functions are reviewed and the underlying physicochemical principles and possible future applications are discussed.
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Affiliation(s)
- Tiemei Lu
- Institute for Molecules and Materials, Radboud University, Nijmegen, 6525 AJ, The Netherlands
| | - Sadaf Javed
- Institute for Molecules and Materials, Radboud University, Nijmegen, 6525 AJ, The Netherlands
| | - Claudia Bonfio
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, Université de Strasbourg, Strasbourg, 67083, France
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Nijmegen, 6525 AJ, The Netherlands
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32
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Li Q, Song Q, Guo W, Cao Y, Cui X, Chen D, Shum HC. Synthetic Membraneless Droplets for Synaptic-Like Clustering of Lipid Vesicles. Angew Chem Int Ed Engl 2023; 62:e202313096. [PMID: 37728515 DOI: 10.1002/anie.202313096] [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: 09/05/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 09/21/2023]
Abstract
In eukaryotic cells, the membraneless organelles (MLOs) formed via liquid-liquid phase separation (LLPS) are found to interact intimately with membranous organelles (MOs). One major mode is the clustering of MOs by MLOs, such as the formation of clusters of synaptic vesicles at nerve terminals mediated by the synapsin-rich MLOs. Aqueous droplets, including complex coacervates and aqueous two-phase systems, have been plausible MLO-mimics to emulate or elucidate biological processes. However, neither of them can cluster lipid vesicles (LVs) like MLOs. In this work, we develop a synthetic droplet assembled from a combination of two different interactions underlying the formation of these two droplets, namely, associative and segregative interactions, which we call segregative-associative (SA) droplets. The SA droplets cluster and disperse LVs recapitulating the key functional features of synapsin condensates, which can be attributed to the weak electrostatic interaction environment provided by SA droplets. This work suggests LLPS with combined segregative and associative interactions as a possible route for synaptic clustering of lipid vesicles and highlights SA droplets as plausible MLO-mimics and models for studying and mimicking related cellular dynamics.
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Affiliation(s)
- Qingchuan Li
- School of Chemistry & Chemical Engineering, National Engineering Research Center for Colloidal Materials, Shandong University, 27 Shanda Nanlu, Jinan, Shandong, P.R.China
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong (SAR), Hong Kong, China
| | - Qingchun Song
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Wei Guo
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong (SAR), Hong Kong, China
| | - Yang Cao
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xinyu Cui
- Department of Public Health, Mudanjiang Medical University, Mudanjiang, 157000, P. R. China
| | - Dairong Chen
- School of Chemistry & Chemical Engineering, National Engineering Research Center for Colloidal Materials, Shandong University, 27 Shanda Nanlu, Jinan, Shandong, P.R.China
| | - Ho Cheung Shum
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong (SAR), Hong Kong, China
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33
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Bussi C, Mangiarotti A, Vanhille-Campos C, Aylan B, Pellegrino E, Athanasiadi N, Fearns A, Rodgers A, Franzmann TM, Šarić A, Dimova R, Gutierrez MG. Stress granules plug and stabilize damaged endolysosomal membranes. Nature 2023; 623:1062-1069. [PMID: 37968398 PMCID: PMC10686833 DOI: 10.1038/s41586-023-06726-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 10/09/2023] [Indexed: 11/17/2023]
Abstract
Endomembrane damage represents a form of stress that is detrimental for eukaryotic cells1,2. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis3-7. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. Here, by combining in vitro and in cellulo studies with computational modelling we uncover a biological function for stress granules whereby these biomolecular condensates form rapidly at endomembrane damage sites and act as a plug that stabilizes the ruptured membrane. Functionally, we demonstrate that stress granule formation and membrane stabilization enable efficient repair of damaged endolysosomes, through both ESCRT (endosomal sorting complex required for transport)-dependent and independent mechanisms. We also show that blocking stress granule formation in human macrophages creates a permissive environment for Mycobacterium tuberculosis, a human pathogen that exploits endomembrane damage to survive within the host.
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Affiliation(s)
| | | | - Christian Vanhille-Campos
- Institute of Science and Technology Austria, Klosterneuburg, Austria
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, UK
| | | | | | | | | | | | - Titus M Franzmann
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Anđela Šarić
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Rumiana Dimova
- Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
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34
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Vale-Costa S, Etibor TA, Brás D, Sousa AL, Ferreira M, Martins GG, Mello VH, Amorim MJ. ATG9A regulates the dissociation of recycling endosomes from microtubules to form liquid influenza A virus inclusions. PLoS Biol 2023; 21:e3002290. [PMID: 37983294 PMCID: PMC10695400 DOI: 10.1371/journal.pbio.3002290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 12/04/2023] [Accepted: 10/13/2023] [Indexed: 11/22/2023] Open
Abstract
It is now established that many viruses that threaten public health establish condensates via phase transitions to complete their lifecycles, and knowledge on such processes may offer new strategies for antiviral therapy. In the case of influenza A virus (IAV), liquid condensates known as viral inclusions, concentrate the 8 distinct viral ribonucleoproteins (vRNPs) that form IAV genome and are viewed as sites dedicated to the assembly of the 8-partite genomic complex. Despite not being delimited by host membranes, IAV liquid inclusions accumulate host membranes inside as a result of vRNP binding to the recycling endocytic marker Rab11a, a driver of the biogenesis of these structures. We lack molecular understanding on how Rab11a-recycling endosomes condensate specifically near the endoplasmic reticulum (ER) exit sites upon IAV infection. We show here that liquid viral inclusions interact with the ER to fuse, divide, and slide. We uncover that, contrary to previous indications, the reported reduction in recycling endocytic activity is a regulated process rather than a competition for cellular resources involving a novel role for the host factor ATG9A. In infection, ATG9A mediates the removal of Rab11a-recycling endosomes carrying vRNPs from microtubules. We observe that the recycling endocytic usage of microtubules is rescued when ATG9A is depleted, which prevents condensation of Rab11a endosomes near the ER. The failure to produce viral inclusions accumulates vRNPs in the cytosol and reduces genome assembly and the release of infectious virions. We propose that the ER supports the dynamics of liquid IAV inclusions, with ATG9A facilitating their formation. This work advances our understanding on how epidemic and pandemic influenza genomes are formed. It also reveals the plasticity of recycling endosomes to undergo condensation in response to infection, disclosing new roles for ATG9A beyond its classical involvement in autophagy.
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Affiliation(s)
- Sílvia Vale-Costa
- Cell Biology of Viral Infection Lab (CBV), Instituto Gulbenkian de Ciência (IGC)—Fundação Calouste Gulbenkian, Oeiras, Portugal
| | - Temitope Akhigbe Etibor
- Cell Biology of Viral Infection Lab (CBV), Instituto Gulbenkian de Ciência (IGC)—Fundação Calouste Gulbenkian, Oeiras, Portugal
| | - Daniela Brás
- Cell Biology of Viral Infection Lab (CBV), Instituto Gulbenkian de Ciência (IGC)—Fundação Calouste Gulbenkian, Oeiras, Portugal
| | - Ana Laura Sousa
- Electron Microscopy Facility (EMF), Instituto Gulbenkian de Ciência (IGC)—Fundação Calouste Gulbenkian, Oeiras, Portugal
| | - Mariana Ferreira
- Advanced Imaging Facility (AIF), Instituto Gulbenkian de Ciência (IGC)—Fundação Calouste Gulbenkian, Oeiras, Portugal
| | - Gabriel G. Martins
- Advanced Imaging Facility (AIF), Instituto Gulbenkian de Ciência (IGC)—Fundação Calouste Gulbenkian, Oeiras, Portugal
| | - Victor Hugo Mello
- Living Physics, Instituto Gulbenkian de Ciência (IGC)—Fundação Calouste Gulbenkian, Oeiras, Portugal
| | - Maria João Amorim
- Cell Biology of Viral Infection Lab (CBV), Instituto Gulbenkian de Ciência (IGC)—Fundação Calouste Gulbenkian, Oeiras, Portugal
- Cell Biology of Viral Infection Lab (CBV), Católica Biomedical Research Centre (CBR), Católica Medical School—Universidade Católica Portuguesa, Lisboa, Portugal
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35
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Gallo R, Rai AK, McIntyre ABR, Meyer K, Pelkmans L. DYRK3 enables secretory trafficking by maintaining the liquid-like state of ER exit sites. Dev Cell 2023; 58:1880-1897.e11. [PMID: 37643612 DOI: 10.1016/j.devcel.2023.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 02/16/2023] [Accepted: 08/01/2023] [Indexed: 08/31/2023]
Abstract
The dual-specificity kinase DYRK3 controls the formation and dissolution of multiple biomolecular condensates, regulating processes including stress recovery and mitotic progression. Here, we report that DYRK3 functionally interacts with proteins associated with endoplasmic reticulum (ER) exit sites (ERESs) and that inhibition of DYRK3 perturbs the organization of the ERES-Golgi interface and secretory trafficking. DYRK3-mediated regulation of ERES depends on the N-terminal intrinsically disordered region (IDR) of the peripheral membrane protein SEC16A, which co-phase separates with ERES components to form liquid-like condensates on the surface of the ER. By modulating the liquid-like properties of ERES, we show that their physical state is essential for functional cargo trafficking through the early secretory pathway. Our findings support a mechanism whereby phosphorylation by DYRK3 and its reversal by serine-threonine phosphatases regulate the material properties of ERES to create a favorable physicochemical environment for directional membrane traffic in eukaryotic cells.
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Affiliation(s)
- Raffaella Gallo
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland
| | - Arpan Kumar Rai
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland.
| | - Alexa B R McIntyre
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland
| | - Katrina Meyer
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland
| | - Lucas Pelkmans
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland.
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36
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Tang Q, Mao X, Chen Z, Ma C, Tu Y, Zhu Q, Lu J, Wang Z, Zhang Q, Wu W. Liquid-liquid phase separation-related gene in gliomas: FABP5 is a potential prognostic marker. J Gene Med 2023; 25:e3517. [PMID: 37114595 DOI: 10.1002/jgm.3517] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/03/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
BACKGROUND The glioma is the most malignant human brain tumor. Early glioma detection and treatment are still difficult. New biomarkers are desperately required to aid in the evaluation of diagnosis and prognosis. METHODS The single cell sequencing dataset scRNA-6148 for glioblastoma was obtained from the Chinese Glioma Genome Atlas database. Data were gathered for the transcriptome sequencing project. Genes involved in liquid-liquid phase separation (LLPS) were taken out of the DrLLPS database. To find the modules connected to LLPS, the weighted co-expression network was analyzed. Differential expression analysis was used to identify the differentially expressed genes (DEGs) in gliomas. Pseudo-time series analysis, gene set enrichment analysis (GSEA) and immune cell infiltration analysis were used to investigate the role of important genes in the immunological microenvironment. We examined the function of key glioma genes using polymerase chain reaction (PCR) testing, CCK-8 assays, clone generation assays, transwell assays and wound healing assays. RESULTS FABP5 was identified as a key gene in glioblastoma by multiomics research. Pseudo-time series analysis showed that FABP5 was highly linked with the differentiation of many different types of cells. GSEA revealed that FABP5 was strongly linked to several hallmark pathways in glioblastoma. We looked at immune cell infiltration and discovered a significant link between FABP5, macrophages and T cell follicular helpers. The PCR experiment results demonstrated that FABP5 expression was elevated in glioma samples. Cell experiments showed that FABP5 knockdown dramatically decreased the viability, proliferation, invasion and migration of the LN229 and U87 glioma cell lines. CONCLUSIONS Our study provides a new biomarker, FABP5, for glioma diagnosis and treatment.
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Affiliation(s)
- Qikai Tang
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
| | - Xiaoman Mao
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
- Department of Neurosurgery, Pukou Branch of Jiangsu People's Hospital, Nanjing Pukou District Central Hospital, Nanjing, China
| | - Zhengxin Chen
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
| | - Chenfeng Ma
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
| | - Yiming Tu
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
| | - Qianmiao Zhu
- Department of Neurosurgery, Zhongda Hospital, Southeast University, Nanjing, Jiangsu, China
| | - Jiacheng Lu
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
| | - Zhen Wang
- Department of Orthopaedics, Jinling Hospital, Nanjing Medical University, Nanjing, China
| | - Qixiang Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
| | - Wei Wu
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
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37
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Wang Y, He S, Fang X. Emerging roles of phase separation in plant transcription and chromatin organization. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102387. [PMID: 37311366 DOI: 10.1016/j.pbi.2023.102387] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 06/15/2023]
Abstract
Transcription is a core step in gene expression. Regulation of transcription is achieved at the level of transcription machinery, local chromatin environment as well as higher-order chromatin organization. Our understanding of transcriptional regulation was advanced by recent introduction of transcription and chromatin-associated condensates, which typically arise via phase separation of proteins and nucleic acids. While studies from mammalian cells are unveiling the mechanisms of phase separation in transcription regulation, those in plants further broaden and deepen our understanding of this process. In this review, we discuss recent progress in plants how phase separation operates in RNA-mediated chromatin silencing, transcription activity, and chromatin compartmentalization.
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Affiliation(s)
- Yunhe Wang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Shengbo He
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China.
| | - Xiaofeng Fang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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38
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Prosdocimi F, Cortines JR, José MV, Farias ST. Decoding viruses: An alternative perspective on their history, origins and role in nature. Biosystems 2023; 231:104960. [PMID: 37437771 DOI: 10.1016/j.biosystems.2023.104960] [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: 05/18/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 07/14/2023]
Abstract
This article provides an alternative perspective on viruses, exploring their origins, ecology, and evolution. Viruses are recognized as the most prevalent biological entities on Earth, permeating nearly all environments and forming the virosphere-a significant biological layer. They play a crucial role in regulating bacterial populations within ecosystems and holobionts, influencing microbial communities and nutrient recycling. Viruses are also key drivers of molecular evolution, actively participating in the maintenance and regulation of ecosystems and cellular organisms. Many eukaryotic genomes contain genomic elements with viral origins, which contribute to organismal equilibrium and fitness. Viruses are involved in the generation of species-specific orphan genes, facilitating adaptation and the development of unique traits in biological lineages. They have been implicated in the formation of vital structures like the eukaryotic nucleus and the mammalian placenta. The presence of virus-specific genes absent in cellular organisms suggests that viruses may pre-date cellular life. Like progenotes, viruses are ribonucleoprotein entities with simpler capsid architectures compared to proteolipidic membranes. This article presents a comprehensive scenario describing major transitions in prebiotic evolution and proposes that viruses emerged prior to the Last Universal Common Ancestor (LUCA) during the progenote era. However, it is important to note that viruses do not form a monophyletic clade, and many viral taxonomic groups originated more recently as reductions of cellular structures. Thus, viral architecture should be seen as an ancient and evolutionarily stable strategy adopted by biological systems. The goal of this article is to reshape perceptions of viruses, highlighting their multifaceted significance in the complex tapestry of life and fostering a deeper understanding of their origins, ecological impact, and evolutionary dynamics.
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Affiliation(s)
- Francisco Prosdocimi
- Laboratório de Biologia Teórica e de Sistemas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Juliana Reis Cortines
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Brazil
| | - Marco V José
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, CDMX, Mexico
| | - Sávio Torres Farias
- Laboratório de Genética Evolutiva Paulo Leminsk, Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil; Network of Researchers on the Chemical Evolution of Life (NoRCEL), Leeds, LS7 3RB, UK
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39
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Dragwidge JM, Van Damme D. Protein phase separation in plant membrane biology: more than just a compartmentalization strategy. THE PLANT CELL 2023; 35:3162-3172. [PMID: 37352127 PMCID: PMC10473209 DOI: 10.1093/plcell/koad177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 06/14/2023] [Accepted: 06/20/2023] [Indexed: 06/25/2023]
Abstract
The formation of biomolecular condensates through phase separation is an important strategy to compartmentalize cellular functions. While it is now well established that condensates exist throughout eukaryotic cells, how condensates assemble and function on lipid membranes is only beginning to be understood. In this perspective, we highlight work from plant, animal, and yeast model systems showing that condensates assemble on many endomembrane surfaces to carry out diverse functions. In vesicle trafficking, condensation has reported roles in the formation of endocytic vesicles and autophagosomes and in the inactivation of secretory COPII vesicles. We briefly discuss how membranes and membrane lipids regulate the formation and function of membrane-associated condensates. This includes how membranes act as surfaces for condensate assembly, with lipids mediating the nucleation of condensates during endocytosis and other processes. Additionally, membrane-condensate interactions give rise to the biophysical property of "wetting", which has functional importance in shaping autophagosomal and vacuolar membranes. We also speculate on the existence of membrane-associated condensates during cell polarity in plants and discuss how condensation may help to establish functional plasma membrane domains. Lastly, we provide advice on relevant in vitro and in vivo approaches and techniques to study membrane-associated phase separation.
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Affiliation(s)
- Jonathan Michael Dragwidge
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
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40
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Xu C, Kim A, Corbin JM, Wang GG. Onco-condensates: formation, multi-component organization, and biological functions. Trends Cancer 2023; 9:738-751. [PMID: 37349246 PMCID: PMC10524369 DOI: 10.1016/j.trecan.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 06/24/2023]
Abstract
Numerous cellular processes occur in the context of condensates, a type of large, membrane-less biomolecular assembly generated through phase separation. These condensates function as a hub of diversified cellular events by concentrating the required components. Cancer frequently coopts biomolecular condensation mechanisms to promote survival and/or proliferation. Onco-condensates, which refer to those that have causal roles or are critically involved in tumorigenicity, operate to abnormally elevate biological output of a proliferative process, or to suppress a tumor-suppressive pathway, thereby promoting oncogenesis. Here, we summarize advances regarding how multi-component onco-condensates are established and organized to promote oncogenesis, with those related to chromatin and transcription deregulation used as showcases. A better understanding should enable development of new means of targeting onco-condensates as potential therapeutics.
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Affiliation(s)
- Chenxi Xu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Arum Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Joshua M Corbin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA; Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
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41
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Wang Y, Majd S. Charged Lipids Modulate the Phase Separation in Multicomponent Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:11371-11378. [PMID: 37485979 DOI: 10.1021/acs.langmuir.3c01199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Phase separation in lipid membranes controls the organization of membrane components and thus regulates membrane-mediated processes. Membrane phase behavior is influenced by the molecular properties of its components and their relative concentrations. Charged lipid species are among the most essential components of lipid membranes, and their impact on the membrane phase behavior is yet to be fully understood. Aiming to provide insight into this impact, this paper investigates how the presence and amount of anionic and cationic lipids affect the phase behavior of multicomponent membranes. Membranes of ternary composition DOPC:DPPC:Chol with two distinct molar ratios were used to test the hypothesis that inclusion of charged lipids with saturated tails, beyond a certain concentration, would impede phase separation in an otherwise phase-separating membrane. Fluorescence microscopy examination of electroformed giant liposomes revealed that when more than half of DOPC in the examined mixtures was replaced with DOPA or DOTAP, phase separation in liposomes was somewhat suppressed, and this effect increased with increasing charged lipid content. This effect depended on the membrane surface charge density as the half-maximal effect was observed at around 0.0072 C Å-2 in all examined cases. The phase-separation suppressing effect of DOPA was neutralized when oppositely charged lipid DOTAP was included in the mixture. Likewise, presence of divalent cation Ca2+ in the solution neutralized the impact of negatively charged DOPA. These results underline the detrimental influence of surface charge density on membrane phase behavior. More importantly, these findings suggest that the charged lipid content in membranes may be a regulator of their phase behavior and open new opportunities for the design of synthetic lipid membranes.
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Affiliation(s)
- Yifei Wang
- Department of Biomedical Engineering, University of Houston, 3551 Cullen Boulevard, Houston, Texas 77204, United States
| | - Sheereen Majd
- Department of Biomedical Engineering, University of Houston, 3551 Cullen Boulevard, Houston, Texas 77204, United States
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42
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Zhang X, Zheng R, Li Z, Ma J. Liquid-liquid Phase Separation in Viral Function. J Mol Biol 2023; 435:167955. [PMID: 36642156 DOI: 10.1016/j.jmb.2023.167955] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 01/04/2023] [Accepted: 01/07/2023] [Indexed: 01/15/2023]
Abstract
An emerging set of results suggests that liquid-liquid phase separation (LLPS) is the basis for the formation of membrane-less compartments in cells. Evidence is now mounting that various types of virus-induced membrane-less compartments and organelles are also assembled via LLPS. Specifically, viruses appear to use intracellular phase transitions to form subcellular microenvironments known as viral factories, inclusion bodies, or viroplasms. These compartments - collectively referred to as viral biomolecular condensates - can be used to concentrate replicase proteins, viral genomes, and host proteins that are required for virus replication. They can also be used to subvert or avoid the intracellular immune response. This review examines how certain DNA or RNA viruses drive the formation of viral condensates, the possible biological functions of those condensates, and the biophysical and biochemical basis for their assembly.
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Affiliation(s)
- Xiaoyue Zhang
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, China
| | - Run Zheng
- Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, China
| | - Zhengshuo Li
- Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, China
| | - Jian Ma
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, China.
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43
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Pokhrel P, Jonchhe S, Pan W, Mao H. Single-Molecular Dissection of Liquid-Liquid Phase Transitions. J Am Chem Soc 2023; 145:17143-17150. [PMID: 37494702 PMCID: PMC10528544 DOI: 10.1021/jacs.3c03812] [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: 07/28/2023]
Abstract
Interaction between peptides and nucleic acids is a ubiquitous process that drives many cellular functions, such as replications, transcriptions, and translations. Recently, this interaction has been found in liquid-liquid phase separation (LLPS), a process responsible for the formation of newly discovered membraneless organelles with a variety of biological functions inside cells. In this work, we studied the molecular interaction between the poly-l-lysine (PLL) peptide and nucleic acids during the early stage of an LLPS process at the single-molecule level using optical tweezers. By monitoring the mechanical tension of individual nucleic acid templates upon PLL addition, we revealed a multistage LLPS process mediated by the long-range interactions between nucleic acids and polyelectrolytes. By varying different types (ssDNA, ssRNA, and dsDNA) and sequences (A-, T-, G-, or U-rich) of nucleic acids, we pieced together transition diagrams of the PLL-nucleic acid condensates from which we concluded that the propensity to form rigid nucleic acid-PLL complexes reduces the condensate formation during the LLPS process. We anticipate that these results are instrumental in understanding the transition mechanism of LLPS condensates, which allows new strategies to interfere with the biological functions of LLPS condensates inside cells.
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Affiliation(s)
- Pravin Pokhrel
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - Sagun Jonchhe
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - Wei Pan
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
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44
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Yu Y, Yoshimura SH. Self-assembly of CIP4 drives actin-mediated asymmetric pit-closing in clathrin-mediated endocytosis. Nat Commun 2023; 14:4602. [PMID: 37528083 PMCID: PMC10393992 DOI: 10.1038/s41467-023-40390-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 07/23/2023] [Indexed: 08/03/2023] Open
Abstract
Clathrin-mediated endocytosis is pivotal to signal transduction pathways between the extracellular environment and the intracellular space. Evidence from live-cell imaging and super-resolution microscopy of mammalian cells suggests an asymmetric distribution of actin fibres near the clathrin-coated pit, which induces asymmetric pit-closing rather than radial constriction. However, detailed molecular mechanisms of this 'asymmetricity' remain elusive. Herein, we used high-speed atomic force microscopy to demonstrate that CIP4, a multi-domain protein with a classic F-BAR domain and intrinsically disordered regions, is necessary for asymmetric pit-closing. Strong self-assembly of CIP4 via intrinsically disordered regions, together with stereospecific interactions with the curved membrane and actin-regulating proteins, generates a small actin-rich environment near the pit, which deforms the membrane and closes the pit. Our results provide mechanistic insights into how disordered and structured domain collaboration promotes spatio-temporal actin polymerisation near the plasma membrane.
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Affiliation(s)
- Yiming Yu
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
| | - Shige H Yoshimura
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan.
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45
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Flynn AJ, Miller K, Codjoe JM, King MR, Haswell ES. Mechanosensitive ion channels MSL8, MSL9, and MSL10 have environmentally sensitive intrinsically disordered regions with distinct biophysical characteristics in vitro. PLANT DIRECT 2023; 7:e515. [PMID: 37547488 PMCID: PMC10400277 DOI: 10.1002/pld3.515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 08/08/2023]
Abstract
Intrinsically disordered protein regions (IDRs) are highly dynamic sequences that rapidly sample a collection of conformations over time. In the past several decades, IDRs have emerged as a major component of many proteomes, comprising ~30% of all eukaryotic protein sequences. Proteins with IDRs function in a wide range of biological pathways and are notably enriched in signaling cascades that respond to environmental stresses. Here, we identify and characterize intrinsic disorder in the soluble cytoplasmic N-terminal domains of MSL8, MSL9, and MSL10, three members of the MscS-like (MSL) family of mechanosensitive ion channels. In plants, MSL channels are proposed to mediate cell and organelle osmotic homeostasis. Bioinformatic tools unanimously predicted that the cytosolic N-termini of MSL channels are intrinsically disordered. We examined the N-terminus of MSL10 (MSL10N) as an exemplar of these IDRs and circular dichroism spectroscopy confirms its disorder. MSL10N adopted a predominately helical structure when exposed to the helix-inducing compound trifluoroethanol (TFE). Furthermore, in the presence of molecular crowding agents, MSL10N underwent structural changes and exhibited alterations to its homotypic interaction favorability. Lastly, interrogations of collective behavior via in vitro imaging of condensates indicated that MSL8N, MSL9N, and MSL10N have sharply differing propensities for self-assembly into condensates, both inherently and in response to salt, temperature, and molecular crowding. Taken together, these data establish the N-termini of MSL channels as intrinsically disordered regions with distinct biophysical properties and the potential to respond uniquely to changes in their physiochemical environment.
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Affiliation(s)
- Aidan J. Flynn
- Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
- NSF Center for Engineering Mechanobiology, Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
- Department of Biochemistry and BiophysicsWashington University in St. LouisSt. LouisMissouriUSA
| | - Kari Miller
- Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
- NSF Center for Engineering Mechanobiology, Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
| | - Jennette M. Codjoe
- Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
- NSF Center for Engineering Mechanobiology, Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
| | - Matthew R. King
- Department of Biomedical EngineeringWashington University in St. LouisSt. LouisMissouriUSA
| | - Elizabeth S. Haswell
- Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
- NSF Center for Engineering Mechanobiology, Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
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46
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Toledo PL, Gianotti AR, Vazquez DS, Ermácora MR. Protein nanocondensates: the next frontier. Biophys Rev 2023; 15:515-530. [PMID: 37681092 PMCID: PMC10480383 DOI: 10.1007/s12551-023-01105-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/21/2023] [Indexed: 09/09/2023] Open
Abstract
Over the past decade, myriads of studies have highlighted the central role of protein condensation in subcellular compartmentalization and spatiotemporal organization of biological processes. Conceptually, protein condensation stands at the highest level in protein structure hierarchy, accounting for the assembly of bodies ranging from thousands to billions of molecules and for densities ranging from dense liquids to solid materials. In size, protein condensates range from nanocondensates of hundreds of nanometers (mesoscopic clusters) to phase-separated micron-sized condensates. In this review, we focus on protein nanocondensation, a process that can occur in subsaturated solutions and can nucleate dense liquid phases, crystals, amorphous aggregates, and fibers. We discuss the nanocondensation of proteins in the light of general physical principles and examine the biophysical properties of several outstanding examples of nanocondensation. We conclude that protein nanocondensation cannot be fully explained by the conceptual framework of micron-scale biomolecular condensation. The evolution of nanocondensates through changes in density and order is currently under intense investigation, and this should lead to the development of a general theoretical framework, capable of encompassing the full range of sizes and densities found in protein condensates.
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Affiliation(s)
- Pamela L. Toledo
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Alejo R. Gianotti
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Diego S. Vazquez
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Mario R. Ermácora
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
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47
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Gao XK, Sheng ZK, Lu YH, Sun YT, Rao XS, Shi LJ, Cong XX, Chen X, Wu HB, Huang M, Zheng Q, Guo JS, Jiang LJ, Zheng LL, Zhou YT. VAPB-mediated ER-targeting stabilizes IRS-1 signalosomes to regulate insulin/IGF signaling. Cell Discov 2023; 9:83. [PMID: 37528084 PMCID: PMC10394085 DOI: 10.1038/s41421-023-00576-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 06/08/2023] [Indexed: 08/03/2023] Open
Abstract
The scaffold protein IRS-1 is an essential node in insulin/IGF signaling. It has long been recognized that the stability of IRS-1 is dependent on its endomembrane targeting. However, how IRS-1 targets the intracellular membrane, and what type of intracellular membrane is actually targeted, remains poorly understood. Here, we found that the phase separation-mediated IRS-1 puncta attached to endoplasmic reticulum (ER). VAPB, an ER-anchored protein that mediates tethers between ER and membranes of other organelles, was identified as a direct interacting partner of IRS-1. VAPB mainly binds active IRS-1 because IGF-1 enhanced the VAPB-IRS-1 association and replacing of the nine tyrosine residues of YXXM motifs disrupted the VAPB-IRS-1 association. We further delineated that the Y745 and Y746 residues in the FFAT-like motif of IRS-1 mediated the association with VAPB. Notably, VAPB targeted IRS-1 to the ER and subsequently maintained its stability. Consistently, ablation of VAPB in mice led to downregulation of IRS-1, suppression of insulin signaling, and glucose intolerance. The amyotrophic lateral sclerosis (ALS)-derived VAPB P56S mutant also impaired IRS-1 stability by interfering with the ER-tethering of IRS-1. Our findings thus revealed a previously unappreciated condensate-membrane contact (CMC), by which VAPB stabilizes the membraneless IRS-1 signalosome through targeting it to ER membrane.
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Affiliation(s)
- Xiu Kui Gao
- Department of Biochemistry and Department of Orthopaedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- International Institutes of Medicine, the Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, Zhejiang, China.
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Zu Kang Sheng
- Department of Biochemistry and Department of Orthopaedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ye Hong Lu
- Department of Biochemistry and Department of Orthopaedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yu Ting Sun
- Department of Biochemistry and Department of Orthopaedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xi Sheng Rao
- Department of Biochemistry and Department of Orthopaedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lin Jing Shi
- Department of Biochemistry and Department of Orthopaedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiao Xia Cong
- Department of Biochemistry and Department of Orthopaedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiao Chen
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Hao Bo Wu
- Department of Biochemistry and Department of Orthopaedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Man Huang
- Department of Biochemistry and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejinag, China
- Key Laboratory of Multiple Organ Failure (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang, China
| | - Qiang Zheng
- Department of Biochemistry and Department of Orthopaedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jian-Sheng Guo
- Department of Pathology of Sir Run Run Shaw Hospital, Center of Cryo-Electron Microscopy, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Liang Jun Jiang
- Department of Biochemistry and Department of Orthopaedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Li Ling Zheng
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Department of Biochemistry and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejinag, China.
- Key Laboratory of Multiple Organ Failure (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang, China.
| | - Yi Ting Zhou
- Department of Biochemistry and Department of Orthopaedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Key Laboratory of Multiple Organ Failure (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang, China.
- ZJU-UoE Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.
- Liangzhu Laboratory, Hangzhou, Zhejiang, China.
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48
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Li R, Pang L. Comparing the effects of proteins with IDRs on membrane system in yeast, mammalian cells, and the model plant Arabidopsis. CURRENT OPINION IN PLANT BIOLOGY 2023; 74:102375. [PMID: 37172364 DOI: 10.1016/j.pbi.2023.102375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/26/2023] [Accepted: 04/07/2023] [Indexed: 05/14/2023]
Abstract
Membrane vesiculation is an energy-costing process. Previous studies paid much attention to proteins with curvature-inducing motifs. Recent publications reveal that the liquid-like protein assembly on membrane surfaces provides an efficient yet structure-independent mechanism for increasing the membrane curvature, which plays important roles in vesicle transport in many aspects. Intrinsically disordered regions (IDRs) within the proteins are highly potent drivers of membrane curvature by providing large hydrodynamic radii to generate steric pressure. Biomolecular condensates formed by phase separation can provide a reaction platform for sequential processes or generate a wetting surface to sequestrate cargos and trigger membrane remodeling. We review the latest progress in yeast and mammalian cells, focus on the mechanism of clathrin-mediated endocytosis (CME) and autophagy initiation, and compare with what we know in model plant Arabidopsis. The comparison may give important insights into the understanding of basic membrane trafficking mechanisms in plant cells.
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Affiliation(s)
- Ruixi Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Lei Pang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
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49
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Erazo-Oliveras A, Muñoz-Vega M, Mlih M, Thiriveedi V, Salinas ML, Rivera-Rodríguez JM, Kim E, Wright RC, Wang X, Landrock KK, Goldsby JS, Mullens DA, Roper J, Karpac J, Chapkin RS. Mutant APC reshapes Wnt signaling plasma membrane nanodomains by altering cholesterol levels via oncogenic β-catenin. Nat Commun 2023; 14:4342. [PMID: 37468468 PMCID: PMC10356786 DOI: 10.1038/s41467-023-39640-w] [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: 11/29/2021] [Accepted: 06/21/2023] [Indexed: 07/21/2023] Open
Abstract
Although the role of the Wnt pathway in colon carcinogenesis has been described previously, it has been recently demonstrated that Wnt signaling originates from highly dynamic nano-assemblies at the plasma membrane. However, little is known regarding the role of oncogenic APC in reshaping Wnt nanodomains. This is noteworthy, because oncogenic APC does not act autonomously and requires activation of Wnt effectors upstream of APC to drive aberrant Wnt signaling. Here, we demonstrate the role of oncogenic APC in increasing plasma membrane free cholesterol and rigidity, thereby modulating Wnt signaling hubs. This results in an overactivation of Wnt signaling in the colon. Finally, using the Drosophila sterol auxotroph model, we demonstrate the unique ability of exogenous free cholesterol to disrupt plasma membrane homeostasis and drive Wnt signaling in a wildtype APC background. Collectively, these findings provide a link between oncogenic APC, loss of plasma membrane homeostasis and CRC development.
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Affiliation(s)
- Alfredo Erazo-Oliveras
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX, 77843, USA
- Department of Nutrition, Texas A&M University, College Station, TX, 77843, USA
- CPRIT Regional Center of Excellence in Cancer Research, Texas A&M University, College Station, TX, 77843, USA
| | - Mónica Muñoz-Vega
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX, 77843, USA
- Department of Nutrition, Texas A&M University, College Station, TX, 77843, USA
- CPRIT Regional Center of Excellence in Cancer Research, Texas A&M University, College Station, TX, 77843, USA
| | - Mohamed Mlih
- Department of Cell Biology and Genetics, Texas A&M University, School of Medicine, Bryan, TX, 77807, USA
| | - Venkataramana Thiriveedi
- Department of Medicine, Division of Gastroenterology, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Michael L Salinas
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX, 77843, USA
- Department of Nutrition, Texas A&M University, College Station, TX, 77843, USA
- CPRIT Regional Center of Excellence in Cancer Research, Texas A&M University, College Station, TX, 77843, USA
| | - Jaileen M Rivera-Rodríguez
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX, 77843, USA
- Department of Nutrition, Texas A&M University, College Station, TX, 77843, USA
- CPRIT Regional Center of Excellence in Cancer Research, Texas A&M University, College Station, TX, 77843, USA
| | - Eunjoo Kim
- Division of Pulmonary Sciences and Critical Care Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Denver, CO, 80045, USA
| | - Rachel C Wright
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX, 77843, USA
- Department of Nutrition, Texas A&M University, College Station, TX, 77843, USA
| | - Xiaoli Wang
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX, 77843, USA
- Department of Nutrition, Texas A&M University, College Station, TX, 77843, USA
| | - Kerstin K Landrock
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX, 77843, USA
- Department of Nutrition, Texas A&M University, College Station, TX, 77843, USA
| | - Jennifer S Goldsby
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX, 77843, USA
- Department of Nutrition, Texas A&M University, College Station, TX, 77843, USA
- CPRIT Regional Center of Excellence in Cancer Research, Texas A&M University, College Station, TX, 77843, USA
| | - Destiny A Mullens
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX, 77843, USA
- Department of Nutrition, Texas A&M University, College Station, TX, 77843, USA
- CPRIT Regional Center of Excellence in Cancer Research, Texas A&M University, College Station, TX, 77843, USA
| | - Jatin Roper
- Department of Medicine, Division of Gastroenterology, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Jason Karpac
- Department of Cell Biology and Genetics, Texas A&M University, School of Medicine, Bryan, TX, 77807, USA
| | - Robert S Chapkin
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX, 77843, USA.
- Department of Nutrition, Texas A&M University, College Station, TX, 77843, USA.
- CPRIT Regional Center of Excellence in Cancer Research, Texas A&M University, College Station, TX, 77843, USA.
- Center for Environmental Health Research, Texas A&M University, College Station, TX, 77843, USA.
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50
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Kang JE, Jun JH, Kwon JH, Lee JH, Hwang K, Kim S, Jeong N. Arabidopsis Transcription Regulatory Factor Domain/Domain Interaction Analysis Tool-Liquid/Liquid Phase Separation, Oligomerization, GO Analysis: A Toolkit for Interaction Data-Based Domain Analysis. Genes (Basel) 2023; 14:1476. [PMID: 37510380 PMCID: PMC10379056 DOI: 10.3390/genes14071476] [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: 06/05/2023] [Revised: 07/04/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Although a large number of databases are available for regulatory elements, a bottleneck has been created by the lack of bioinformatics tools to predict the interaction modes of regulatory elements. To reduce this gap, we developed the Arabidopsis Transcription Regulatory Factor Domain/Domain Interaction Analysis Tool-liquid/liquid phase separation (LLPS), oligomerization, GO analysis (ART FOUNDATION-LOG), a useful toolkit for protein-nucleic acid interaction (PNI) and protein-protein interaction (PPI) analysis based on domain-domain interactions (DDIs). LLPS, protein oligomerization, the structural properties of protein domains, and protein modifications are major components in the orchestration of the spatiotemporal dynamics of PPIs and PNIs. Our goal is to integrate PPI/PNI information into the development of a prediction model for identifying important genetic variants in peaches. Our program unified interdatabase relational keys based on protein domains to facilitate inference from the model species. A key advantage of this program lies in the integrated information of related features, such as protein oligomerization, LOG analysis, structural characterizations of domains (e.g., domain linkers, intrinsically disordered regions, DDIs, domain-motif (peptide) interactions, beta sheets, and transmembrane helices), and post-translational modification. We provided simple tests to demonstrate how to use this program, which can be applied to other eukaryotic organisms.
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Affiliation(s)
- Jee Eun Kang
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Wanju 55365, Republic of Korea
| | - Ji Hae Jun
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Wanju 55365, Republic of Korea
| | - Jung Hyun Kwon
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Wanju 55365, Republic of Korea
| | - Ju-Hyun Lee
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Wanju 55365, Republic of Korea
| | - Kidong Hwang
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Wanju 55365, Republic of Korea
| | - Sungjong Kim
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Wanju 55365, Republic of Korea
| | - Namhee Jeong
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Wanju 55365, Republic of Korea
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