1
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Dainiak N. Biology of Exfoliation of Plasma Membrane-Derived Vesicles and the Radiation Response: Historical Background, Applications in Biodosimetry and Cell-Free Therapeutics, and Quantal Mechanisms for Their Release and Function with Implications for Space Travel. Radiat Res 2024; 202:328-354. [PMID: 38981604 DOI: 10.1667/rade-24-00078.1] [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: 03/21/2024] [Accepted: 05/09/2024] [Indexed: 07/11/2024]
Abstract
This historical review of extracellular vesicles in the setting of exposure to ionizing radiation (IR) traces our understanding of how vesicles were initially examined and reported in the literature in the late 1970s (for secreted exosomes) and early 1980s (for plasma membrane-derived, exfoliated vesicles) to where we are now and where we may be headed in the next decade. An emphasis is placed on biophysical properties of extracellular vesicles, energy consumption and the role of vesiculation as an essential component of membrane turnover. The impact of intercellular signal trafficking by vesicle surface and intra-vesicular lipids, proteins, nucleic acids and metabolites is reviewed in the context of biomarkers for estimating individual radiation dose after exposure to radiation, pathogenesis of disease and development of cell-free therapeutics. Since vesicles express both growth stimulatory and inhibitory molecules, a hypothesis is proposed to consider superposition in a shared space and entanglement of molecules by energy sources that are external to human cells. Implications of this approach for travel in deep space are briefly discussed in the context of clinical disorders that have been observed after space travel.
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Affiliation(s)
- Nicholas Dainiak
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut 06520
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2
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Park J, Kim J, Park H, Kim T, Lee S. ESCRT-III: a versatile membrane remodeling machinery and its implications in cellular processes and diseases. Anim Cells Syst (Seoul) 2024; 28:367-380. [PMID: 39070887 PMCID: PMC11275535 DOI: 10.1080/19768354.2024.2380294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 07/03/2024] [Indexed: 07/30/2024] Open
Abstract
The endosomal sorting complexes required for transport (ESCRT) machinery is an evolutionarily conserved cytosolic protein complex that plays a crucial role in membrane remodeling and scission events across eukaryotes. Initially discovered for its function in multivesicular body (MVB) formation, the ESCRT complex has since been implicated in a wide range of membrane-associated processes, including endocytosis, exocytosis, cytokinesis, and autophagy. Recent advances have elucidated the ESCRT assembly pathway and highlighted the distinct functions of the various ESCRT complexes and their associated partners. Among the ESCRT complexes, ESCRT-III stands out as a critical player in membrane remodeling, with its subunits assembled into higher-order multimers capable of bending and severing membranes. This review focuses on the ESCRT-III complex, exploring its diverse functions in cellular processes beyond MVB biogenesis. We delve into the molecular mechanisms underlying ESCRT-III-mediated membrane remodeling and highlight its emerging roles in processes such as viral budding, autophagosome closure, and cytokinetic abscission. We also discuss the implications of ESCRT-III dysregulation in neurodegenerative diseases. The versatile membrane remodeling capabilities of ESCRT-III across diverse cellular processes underscore its importance in maintaining proper cellular function. Furthermore, we highlight the promising potential of ESCRT-III as a therapeutic target for neurodegenerative diseases, offering insights into the treatments of the diseases and the technical applications in related research fields.
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Affiliation(s)
- Jisoo Park
- Program in Biomedical Science & Engineering, Inha University, Incheon, Republic of Korea
| | - Jongyoon Kim
- Program in Biomedical Science & Engineering, Inha University, Incheon, Republic of Korea
| | - Hyungsun Park
- Program in Biomedical Science & Engineering, Inha University, Incheon, Republic of Korea
| | - Taewan Kim
- Program in Biomedical Science & Engineering, Inha University, Incheon, Republic of Korea
| | - Seongju Lee
- Program in Biomedical Science & Engineering, Inha University, Incheon, Republic of Korea
- Department of Anatomy, College of Medicine, Inha University, Incheon, Republic of Korea
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3
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Chandra M, Kendall AK, Ford MGJ, Jackson LP. VARP binds SNX27 to promote endosomal supercomplex formation on membranes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.11.603126. [PMID: 39026782 PMCID: PMC11257539 DOI: 10.1101/2024.07.11.603126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Multiple essential membrane trafficking pathways converge at endosomes to maintain cellular homeostasis by sorting critical transmembrane cargo proteins to the plasma membrane or the trans-Golgi network (TGN). The Retromer heterotrimer (VPS26/VPS35/VPS29 subunits) binds multiple sorting nexin (SNX) proteins on endosomal membranes, but molecular mechanisms regarding formation and regulation of metazoan SNX/Retromer complexes have been elusive. Here, we combine biochemical and biophysical approaches with AlphaFold2 Multimer modeling to identify a direct interaction between the VARP N-terminus and SNX27 PDZ domain. VARP and SNX27 interact with high nanomolar affinity using the binding pocket established for PDZ binding motif (PDZbm) cargo. Specific point mutations in VARP abrogate the interaction in vitro. We further establish a full biochemical reconstitution system using purified mammalian proteins to directly and systematically test whether multiple endosomal coat complexes are recruited to membranes to generate tubules. We successfully use purified coat components to demonstrate which combinations of Retromer with SNX27, ESCPE-1 (SNX2/SNX6), or both complexes can remodel membranes containing physiological cargo motifs and phospholipid composition. SNX27, alone and with Retromer, induces tubule formation in the presence of PI(3)P and PDZ cargo motifs. ESCPE-1 deforms membranes enriched with Folch I and CI-MPR cargo motifs, but surprisingly does not recruit Retromer. Finally, we find VARP is required to reconstitute a proposed endosomal "supercomplex" containing SNX27, ESCPE-1, and Retromer on PI(3)P-enriched membranes. These data suggest VARP functions as a key regulator in metazoans to promote cargo sorting out of endosomes.
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Affiliation(s)
- Mintu Chandra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Amy K Kendall
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Marijn G J Ford
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lauren P Jackson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
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4
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Swaminathan U, Pucadyil TJ. Reconstituting membrane fission using a high content and throughput assay. Biochem Soc Trans 2024; 52:1449-1457. [PMID: 38747723 DOI: 10.1042/bst20231325] [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: 03/13/2024] [Revised: 04/21/2024] [Accepted: 05/01/2024] [Indexed: 06/27/2024]
Abstract
Protein-mediated membrane fission has been analyzed both in bulk and at the single event resolution. Studies on membrane fission in vitro using tethers have provided fundamental insights into the process but are low in throughput. In recent years, supported membrane template (SMrT) have emerged as a facile and convenient assay system for membrane fission. SMrTs provide useful information on intermediates in the pathway to fission and are therefore high in content. They are also high in throughput because numerous fission events can be monitored in a single experiment. This review discusses the utility of SMrTs in providing insights into fission pathways and its adaptation to annotate membrane fission functions in proteins.
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Affiliation(s)
- Uma Swaminathan
- Indian Institute of Science Education and Research, Pune, India
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5
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Wei L, Guo X, Haimov E, Obashi K, Lee SH, Shin W, Sun M, Chan CY, Sheng J, Zhang Z, Mohseni A, Ghosh Dastidar S, Wu XS, Wang X, Han S, Arpino G, Shi B, Molakarimi M, Matthias J, Wurm CA, Gan L, Taraska JW, Kozlov MM, Wu LG. Clathrin mediates membrane fission and budding by constricting membrane pores. Cell Discov 2024; 10:62. [PMID: 38862506 PMCID: PMC11166961 DOI: 10.1038/s41421-024-00677-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 04/04/2024] [Indexed: 06/13/2024] Open
Abstract
Membrane budding, which underlies fundamental processes like endocytosis, intracellular trafficking, and viral infection, is thought to involve membrane coat-forming proteins, including the most observed clathrin, to form Ω-shape profiles and helix-forming proteins like dynamin to constrict Ω-profiles' pores and thus mediate fission. Challenging this fundamental concept, we report that polymerized clathrin is required for Ω-profiles' pore closure and that clathrin around Ω-profiles' base/pore region mediates pore constriction/closure in neuroendocrine chromaffin cells. Mathematical modeling suggests that clathrin polymerization at Ω-profiles' base/pore region generates forces from its intrinsically curved shape to constrict/close the pore. This new fission function may exert broader impacts than clathrin's well-known coat-forming function during clathrin (coat)-dependent endocytosis, because it underlies not only clathrin (coat)-dependent endocytosis, but also diverse endocytic modes, including ultrafast, fast, slow, bulk, and overshoot endocytosis previously considered clathrin (coat)-independent in chromaffin cells. It mediates kiss-and-run fusion (fusion pore closure) previously considered bona fide clathrin-independent, and limits the vesicular content release rate. Furthermore, analogous to results in chromaffin cells, we found that clathrin is essential for fast and slow endocytosis at hippocampal synapses where clathrin was previously considered dispensable, suggesting clathrin in mediating synaptic vesicle endocytosis and fission. These results suggest that clathrin and likely other intrinsically curved coat proteins are a new class of fission proteins underlying vesicle budding and fusion. The half-a-century concept and studies that attribute vesicle-coat contents' function to Ω-profile formation and classify budding as coat-protein (e.g., clathrin)-dependent or -independent may need to be re-defined and re-examined by considering clathrin's pivotal role in pore constriction/closure.
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Affiliation(s)
- Lisi Wei
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Xiaoli Guo
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Ehud Haimov
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Kazuki Obashi
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | - Sung Hoon Lee
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Chung-Ang University, Seoul, Republic of Korea
| | - Wonchul Shin
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Min Sun
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Chung Yu Chan
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Jiansong Sheng
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- 900 Clopper Rd, Suite, 130, Gaithersburg, MD, USA
| | - Zhen Zhang
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Center of Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Ammar Mohseni
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | | | - Xin-Sheng Wu
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Xin Wang
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Sue Han
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Gianvito Arpino
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Emme 3 Srl - Via Luigi Meraviglia, 31 - 20020, Lainate, MI, Italy
| | - Bo Shi
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Maryam Molakarimi
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | | | | | - Lin Gan
- Department of Neuroscience & Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Justin W Taraska
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | - Michael M Kozlov
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel.
| | - Ling-Gang Wu
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
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6
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Johnson DH, Kou OH, Bouzos N, Zeno WF. Protein-membrane interactions: sensing and generating curvature. Trends Biochem Sci 2024; 49:401-416. [PMID: 38508884 PMCID: PMC11069444 DOI: 10.1016/j.tibs.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/22/2024]
Abstract
Biological membranes are integral cellular structures that can be curved into various geometries. These curved structures are abundant in cells as they are essential for various physiological processes. However, curved membranes are inherently unstable, especially on nanometer length scales. To stabilize curved membranes, cells can utilize proteins that sense and generate membrane curvature. In this review, we summarize recent research that has advanced our understanding of interactions between proteins and curved membrane surfaces, as well as work that has expanded our ability to study curvature sensing and generation. Additionally, we look at specific examples of cellular processes that require membrane curvature, such as neurotransmission, clathrin-mediated endocytosis (CME), and organelle biogenesis.
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Affiliation(s)
- David H Johnson
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Orianna H Kou
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA
| | - Nicoletta Bouzos
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Wade F Zeno
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA.
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7
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Glatz JFC, Heather LC, Luiken JJFP. CD36 as a gatekeeper of myocardial lipid metabolism and therapeutic target for metabolic disease. Physiol Rev 2024; 104:727-764. [PMID: 37882731 DOI: 10.1152/physrev.00011.2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 10/02/2023] [Accepted: 10/22/2023] [Indexed: 10/27/2023] Open
Abstract
The multifunctional membrane glycoprotein CD36 is expressed in different types of cells and plays a key regulatory role in cellular lipid metabolism, especially in cardiac muscle. CD36 facilitates the cellular uptake of long-chain fatty acids, mediates lipid signaling, and regulates storage and oxidation of lipids in various tissues with active lipid metabolism. CD36 deficiency leads to marked impairments in peripheral lipid metabolism, which consequently impact on the cellular utilization of multiple different fuels because of the integrated nature of metabolism. The functional presence of CD36 at the plasma membrane is regulated by its reversible subcellular recycling from and to endosomes and is under the control of mechanical, hormonal, and nutritional factors. Aberrations in this dynamic role of CD36 are causally associated with various metabolic diseases, in particular insulin resistance, diabetic cardiomyopathy, and cardiac hypertrophy. Recent research in cardiac muscle has disclosed the endosomal proton pump vacuolar-type H+-ATPase (v-ATPase) as a key enzyme regulating subcellular CD36 recycling and being the site of interaction between various substrates to determine cellular substrate preference. In addition, evidence is accumulating that interventions targeting CD36 directly or modulating its subcellular recycling are effective for the treatment of metabolic diseases. In conclusion, subcellular CD36 localization is the major adaptive regulator of cellular uptake and metabolism of long-chain fatty acids and appears a suitable target for metabolic modulation therapy to mend failing hearts.
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Affiliation(s)
- Jan F C Glatz
- Department of Genetics & Cell Biology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Lisa C Heather
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, United Kingdom
| | - Joost J F P Luiken
- Department of Genetics & Cell Biology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
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8
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Yin W, Ma H, Qu Y, Wang S, Zhao R, Yang Y, Guo ZN. Targeted exosome-based nanoplatform for new-generation therapeutic strategies. Biomed Mater 2024; 19:032002. [PMID: 38471163 DOI: 10.1088/1748-605x/ad3310] [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: 09/11/2023] [Accepted: 03/12/2024] [Indexed: 03/14/2024]
Abstract
Exosomes, typically 30-150 nm in size, are lipid-bilayered small-membrane vesicles originating in endosomes. Exosome biogenesis is regulated by the coordination of various mechanisms whereby different cargoes (e.g. proteins, nucleic acids, and lipids) are sorted into exosomes. These components endow exosomes with bioregulatory functions related to signal transmission and intercellular communication. Exosomes exhibit substantial potential as drug-delivery nanoplatforms owing to their excellent biocompatibility and low immunogenicity. Proteins, miRNA, siRNA, mRNA, and drugs have been successfully loaded into exosomes, and these exosome-based delivery systems show satisfactory therapeutic effects in different disease models. To enable targeted drug delivery, genetic engineering and chemical modification of the lipid bilayer of exosomes are performed. Stimuli-responsive delivery nanoplatforms designed with appropriate modifications based on various stimuli allow precise control of on-demand drug delivery and can be utilized in clinical treatment. In this review, we summarize the general properties, isolation methods, characterization, biological functions, and the potential role of exosomes in therapeutic delivery systems. Moreover, the effective combination of the intrinsic advantages of exosomes and advanced bioengineering, materials science, and clinical translational technologies are required to accelerate the development of exosome-based delivery nanoplatforms.
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Affiliation(s)
- Wenjing Yin
- Stroke Center, Department of Neurology, The First Hospital of Jilin University, Chang Chun 130021, People's Republic of China
| | - Hongyin Ma
- Stroke Center, Department of Neurology, The First Hospital of Jilin University, Chang Chun 130021, People's Republic of China
| | - Yang Qu
- Stroke Center, Department of Neurology, The First Hospital of Jilin University, Chang Chun 130021, People's Republic of China
| | - Siji Wang
- Stroke Center, Department of Neurology, The First Hospital of Jilin University, Chang Chun 130021, People's Republic of China
| | - Ruoyu Zhao
- Stroke Center, Department of Neurology, The First Hospital of Jilin University, Chang Chun 130021, People's Republic of China
| | - Yi Yang
- Stroke Center, Department of Neurology, The First Hospital of Jilin University, Chang Chun 130021, People's Republic of China
| | - Zhen-Ni Guo
- Stroke Center, Department of Neurology, The First Hospital of Jilin University, Chang Chun 130021, People's Republic of China
- Neuroscience Research Center, Department of Neurology, The First Hospital of Jilin University, Chang Chun 130021, People's Republic of China
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9
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Thomas M, Varlas S, Wilks TR, Fielden SDP, O'Reilly RK. Controlled node growth on the surface of polymersomes. Chem Sci 2024; 15:4396-4402. [PMID: 38516085 PMCID: PMC10952076 DOI: 10.1039/d3sc05915d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 02/16/2024] [Indexed: 03/23/2024] Open
Abstract
Incorporating nucleobases into synthetic polymers has proven to be a versatile method for controlling self-assembly. The formation of strong directional hydrogen bonds between complementary nucleobases provides a driving force that permits access to complex particle morphologies. Here, nucleobase pairing was used to direct the formation and lengthening of nodes on the outer surface of vesicles formed from polymers (polymersomes) functionalised with adenine in their membrane-forming domains. Insertion of a self-assembling short diblock copolymer containing thymine into the polymersome membranes caused an increase in steric crowding at the hydrophilic/hydrophobic interface, which was relieved by initial node formation and subsequent growth. Nano-objects were imaged by (cryo-)TEM, which permitted quantification of node coverage and length. The ability to control node growth on the surface of polymersomes provides a new platform to develop higher-order nanomaterials with tailorable properties.
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Affiliation(s)
- Marjolaine Thomas
- School of Chemistry, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Spyridon Varlas
- School of Chemistry, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Thomas R Wilks
- School of Chemistry, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Stephen D P Fielden
- School of Chemistry, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Rachel K O'Reilly
- School of Chemistry, University of Birmingham Edgbaston Birmingham B15 2TT UK
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10
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Sambre P, Ho JCS, Parikh AN. Intravesicular Solute Delivery and Surface Area Regulation in Giant Unilamellar Vesicles Driven by Cycles of Osmotic Stresses. J Am Chem Soc 2024; 146:3250-3261. [PMID: 38266489 PMCID: PMC10859933 DOI: 10.1021/jacs.3c11679] [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: 10/19/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 01/26/2024]
Abstract
Phospholipid bilayers are dynamic cellular components that undergo constant changes in their topology, facilitating a broad diversity of physiological functions including endo- and exocytosis, cell division, and intracellular trafficking. These shape transformations consume energy, supplied invariably by the activity of proteins. Here, we show that cycles of oppositely directed osmotic stresses─unassisted by any protein activity─can induce well-defined remodeling of giant unilamellar vesicles, minimally recapitulating the phenomenologies of surface area homeostasis and macropinocytosis. We find that a stress cycle consisting of deflationary hypertonic stress followed by an inflationary hypotonic one prompts an elaborate sequence of membrane shape changes ultimately transporting molecular cargo from the outside into the intravesicular milieu. The initial osmotic deflation produces microscopic spherical invaginations. During the subsequent inflation, the first subpopulation contributes area to the swelling membrane, thereby providing a means for surface area regulation and tensional homeostasis. The second subpopulation vesiculates into the lumens of the mother vesicles, producing pinocytic vesicles. Remarkably, the gradients of solute concentrations between the GUV and the daughter pinocytic vesicles create cascades of water current, inducing pulsatory transient poration that enable solute exchange between the buds and the GUV interior. This results in an efficient water-flux-mediated delivery of molecular cargo across the membrane boundary. Our findings suggest a primitive physical mechanism for communication and transport across protocellular compartments driven only by osmotic stresses. They also suggest plausible physical routes for intravesicular, and possibly intracellular, delivery of ions, solutes, and molecular cargo stimulated simply by cycles of osmotic currents of water.
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Affiliation(s)
- Pallavi
D. Sambre
- Department
of Materials Science and Engineering, University
of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - James C. S. Ho
- Singapore
Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 59 Nanyang Drive, 636921 Singapore
- Institute
for Digital Molecular Analytics and Science, Nanyang Technological University, 60 Nanyang Drive, 637551Singapore
| | - Atul N. Parikh
- Department
of Materials Science and Engineering, University
of California, Davis, One Shields Avenue, Davis, California 95616, United States
- Singapore
Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 59 Nanyang Drive, 636921 Singapore
- Institute
for Digital Molecular Analytics and Science, Nanyang Technological University, 60 Nanyang Drive, 637551Singapore
- Department
of Biomedical Engineering, University of
California, Davis, One Shields Avenue, Davis, California 95616, United States
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11
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Noguchi H. Curvature sensing of curvature-inducing proteins with internal structure. Phys Rev E 2024; 109:024403. [PMID: 38491597 DOI: 10.1103/physreve.109.024403] [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: 09/04/2023] [Accepted: 01/15/2024] [Indexed: 03/18/2024]
Abstract
Many types of peripheral and transmembrane proteins can sense and generate membrane curvature. Laterally isotropic proteins and crescent proteins with twofold rotational symmetry, such as Bin/Amphiphysin/Rvs superfamily proteins, have been studied theoretically. However, proteins often have an asymmetric structure or a higher rotational symmetry. We studied theoretically the curvature sensing of proteins with asymmetric structures and structural deformations. First, we examined proteins consisting of two rodlike segments. When proteins have mirror symmetry, their sensing ability is similar to that of single-rod proteins; hence, with increasing protein density on a cylindrical membrane tube, a second- or first-order transition occurs at a middle or small tube radius, respectively. As asymmetry is introduced, this transition becomes a continuous change and metastable states appear at high protein densities. Protein with threefold, fivefold, or higher rotational symmetry has laterally isotropic bending energy. However, when a structural deformation is allowed, the protein can have a preferred orientation and stronger curvature sensing.
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Affiliation(s)
- Hiroshi Noguchi
- Institute for Solid State Physics, University of Tokyo, Kashiwa, Chiba 277-8581, Japan
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12
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Wu LG, Chan CY. Membrane transformations of fusion and budding. Nat Commun 2024; 15:21. [PMID: 38167896 PMCID: PMC10761761 DOI: 10.1038/s41467-023-44539-7] [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: 06/07/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024] Open
Abstract
Membrane fusion and budding mediate fundamental processes like intracellular trafficking, exocytosis, and endocytosis. Fusion is thought to open a nanometer-range pore that may subsequently close or dilate irreversibly, whereas budding transforms flat membranes into vesicles. Reviewing recent breakthroughs in real-time visualization of membrane transformations well exceeding this classical view, we synthesize a new model and describe its underlying mechanistic principles and functions. Fusion involves hemi-to-full fusion, pore expansion, constriction and/or closure while fusing vesicles may shrink, enlarge, or receive another vesicle fusion; endocytosis follows exocytosis primarily by closing Ω-shaped profiles pre-formed through the flat-to-Λ-to-Ω-shape transition or formed via fusion. Calcium/SNARE-dependent fusion machinery, cytoskeleton-dependent membrane tension, osmotic pressure, calcium/dynamin-dependent fission machinery, and actin/dynamin-dependent force machinery work together to generate fusion and budding modes differing in pore status, vesicle size, speed and quantity, controls release probability, synchronization and content release rates/amounts, and underlies exo-endocytosis coupling to maintain membrane homeostasis. These transformations, underlying mechanisms, and functions may be conserved for fusion and budding in general.
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Affiliation(s)
- Ling-Gang Wu
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
| | - Chung Yu Chan
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
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13
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Szatmári T, Balázs K, Csordás IB, Sáfrány G, Lumniczky K. Effect of radiotherapy on the DNA cargo and cellular uptake mechanisms of extracellular vesicles. Strahlenther Onkol 2023; 199:1191-1213. [PMID: 37347291 DOI: 10.1007/s00066-023-02098-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/01/2023] [Indexed: 06/23/2023]
Abstract
In the past decades, plenty of evidence has gathered pointing to the role of extracellular vesicles (EVs) secreted by irradiated cells in the development of radiation-induced non-targeted effects. EVs are complex natural structures composed of a phospholipid bilayer which are secreted by virtually all cells and carry bioactive molecules. They can travel certain distances in the body before being taken up by recipient cells. In this review we discuss the role and fate of EVs in tumor cells and highlight the importance of DNA specimens in EVs cargo in the context of radiotherapy. The effect of EVs depends on their cargo, which reflects physiological and pathological conditions of donor cell types, but also depends on the mode of EV uptake and mechanisms involved in the route of EV internalization. While the secretion and cargo of EVs from irradiated cells has been extensively studied in recent years, their uptake is much less understood. In this review, we will focus on recent knowledge regarding the EV uptake of cancer cells and the effect of radiation in this process.
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Affiliation(s)
- Tünde Szatmári
- Department of Radiobiology and Radiohygiene, Unit of Radiation Medicine, National Public Health Centre, 1097, Budapest, Hungary.
| | - Katalin Balázs
- Department of Radiobiology and Radiohygiene, Unit of Radiation Medicine, National Public Health Centre, 1097, Budapest, Hungary
| | - Ilona Barbara Csordás
- Department of Radiobiology and Radiohygiene, Unit of Radiation Medicine, National Public Health Centre, 1097, Budapest, Hungary
| | - Géza Sáfrány
- Department of Radiobiology and Radiohygiene, Unit of Radiation Medicine, National Public Health Centre, 1097, Budapest, Hungary
| | - Katalin Lumniczky
- Department of Radiobiology and Radiohygiene, Unit of Radiation Medicine, National Public Health Centre, 1097, Budapest, Hungary
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14
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Yuan F, Lee CT, Sangani A, Houser JR, Wang L, Lafer EM, Rangamani P, Stachowiak JC. The ins and outs of membrane bending by intrinsically disordered proteins. SCIENCE ADVANCES 2023; 9:eadg3485. [PMID: 37418523 PMCID: PMC10328403 DOI: 10.1126/sciadv.adg3485] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 06/07/2023] [Indexed: 07/09/2023]
Abstract
Membrane curvature is essential to diverse cellular functions. While classically attributed to structured domains, recent work illustrates that intrinsically disordered proteins are also potent drivers of membrane bending. Specifically, repulsive interactions among disordered domains drive convex bending, while attractive interactions drive concave bending, creating membrane-bound, liquid-like condensates. How might disordered domains that contain both repulsive and attractive domains affect curvature? Here, we examined chimeras that combined attractive and repulsive interactions. When the attractive domain was closer to the membrane, its condensation amplified steric pressure among repulsive domains, leading to convex curvature. In contrast, when the repulsive domain was closer to the membrane, attractive interactions dominated, resulting in concave curvature. Further, a transition from convex to concave curvature occurred with increasing ionic strength, which reduced repulsion while enhancing condensation. In agreement with a simple mechanical model, these results illustrate a set of design rules for membrane bending by disordered proteins.
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Affiliation(s)
- Feng Yuan
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Christopher T. Lee
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, USA
| | - Arjun Sangani
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Justin R. Houser
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Liping Wang
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Eileen M. Lafer
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, USA
| | - Jeanne C. Stachowiak
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
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15
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Jia W, Yuan J, Cheng B, Ling C. Targeting tumor-derived exosome-mediated premetastatic niche formation: The metastasis-preventive value of traditional Chinese medicine. Cancer Lett 2023:216261. [PMID: 37302563 DOI: 10.1016/j.canlet.2023.216261] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 06/13/2023]
Abstract
Tumor-derived exosome (TDE)-mediated premetastatic niche (PMN) formation is a potential mechanism underlying the organotropic metastasis of primary tumors. Traditional Chinese medicine (TCM) has shown considerable success in preventing and treating tumor metastasis. However, the underlying mechanisms remain elusive. In this review, we discussed PMN formation from the perspectives of TDE biogenesis, cargo sorting, and TDE recipient cell alterations, which are critical for metastatic outgrowth. We also reviewed the metastasis-preventive effects of TCM, which act by targeting the physicochemical materials and functional mediators of TDE biogenesis, regulating the cargo sorting machinery and secretory molecules in TDEs, and targeting the TDE-recipient cells involved in PMN formation.
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Affiliation(s)
- Wentao Jia
- Oncology Department of Traditional Chinese Medicine, The First Affiliated Hospital of Naval Medical University, Shanghai, 200433, China; Faculty of Traditional Chinese Medicine, Naval Medical University, Shanghai, 200043, China.
| | - Jiaying Yuan
- Oncology Department of Traditional Chinese Medicine, The First Affiliated Hospital of Naval Medical University, Shanghai, 200433, China; Faculty of Traditional Chinese Medicine, Naval Medical University, Shanghai, 200043, China.
| | - Binbin Cheng
- Oncology Department of Traditional Chinese Medicine, The First Affiliated Hospital of Naval Medical University, Shanghai, 200433, China; Faculty of Traditional Chinese Medicine, Naval Medical University, Shanghai, 200043, China.
| | - Changquan Ling
- Oncology Department of Traditional Chinese Medicine, The First Affiliated Hospital of Naval Medical University, Shanghai, 200433, China; Faculty of Traditional Chinese Medicine, Naval Medical University, Shanghai, 200043, China.
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16
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Lynch DL, Pavlova A, Fan Z, Gumbart JC. Understanding Virus Structure and Dynamics through Molecular Simulations. J Chem Theory Comput 2023. [PMID: 37192279 DOI: 10.1021/acs.jctc.3c00116] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Viral outbreaks remain a serious threat to human and animal populations and motivate the continued development of antiviral drugs and vaccines, which in turn benefits from a detailed understanding of both viral structure and dynamics. While great strides have been made in characterizing these systems experimentally, molecular simulations have proven to be an essential, complementary approach. In this work, we review the contributions of molecular simulations to the understanding of viral structure, functional dynamics, and processes related to the viral life cycle. Approaches ranging from coarse-grained to all-atom representations are discussed, including current efforts at modeling complete viral systems. Overall, this review demonstrates that computational virology plays an essential role in understanding these systems.
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Affiliation(s)
- Diane L Lynch
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Zixing Fan
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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17
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Yamaguchi M, Kashiwakura I. The Acute Radiation Syndrome-Mitigator Romiplostim and Secreted Extracellular Vesicles Improved Survival in Mice Acutely Exposed to Myelosuppressive Doses of Ionizing Radiation. Biomolecules 2023; 13:biom13050837. [PMID: 37238707 DOI: 10.3390/biom13050837] [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: 04/17/2023] [Revised: 05/02/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
In cases of accidental high-dose total-body irradiation (TBI), acute radiation syndrome (ARS) can cause death. We reported that the thrombopoietin receptor agonist romiplostim (RP) has the potential to completely rescue mice exposed to lethal TBI. Extracellular vesicles (EVs) are involved in cell-to-cell communication, and the mechanism of RP action may be related to EVs that reflect the radio-mitigative information. We investigated the radio-mitigative effects of EVs on mice with severe ARS. C57BL/6 mice exposed to lethal TBI were treated with RP, and the EVs were isolated from the serum and intraperitoneally injected into other mice with severe ARS. The 30-day survival rate of lethal TBI mice drastically improved by 50-100% with the administration of EVs in the sera collected weekly from the mice in which radiation damage was alleviated and mortality was avoided by the administration of RP. Four responsive miRNAs, namely, miR-144-5p, miR-3620-5p, miR-6354, and miR-7686-5p showed significant expression changes in an array analysis. In particular, miR-144-5p was expressed only in the EVs of RP-treated TBI mice. Specific EVs may exist in the circulating blood of mice that escaped mortality with an ARS mitigator, and their membrane surface and endogenous molecules may be the key to the survival of mice with severe ARS.
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Affiliation(s)
- Masaru Yamaguchi
- Graduate School of Health Sciences, Hirosaki University, 66-1 Hon-cho, Hirosaki 036-8564, Aomori, Japan
| | - Ikuo Kashiwakura
- Graduate School of Health Sciences, Hirosaki University, 66-1 Hon-cho, Hirosaki 036-8564, Aomori, Japan
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18
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Cortes-Galvez D, Dangerfield JA, Metzner C. Extracellular Vesicles and Their Membranes: Exosomes vs. Virus-Related Particles. MEMBRANES 2023; 13:397. [PMID: 37103824 PMCID: PMC10146078 DOI: 10.3390/membranes13040397] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 06/19/2023]
Abstract
Cells produce nanosized lipid membrane-enclosed vesicles which play important roles in intercellular communication. Interestingly, a certain type of extracellular vesicle, termed exosomes, share physical, chemical, and biological properties with enveloped virus particles. To date, most similarities have been discovered with lentiviral particles, however, other virus species also frequently interact with exosomes. In this review, we will take a closer look at the similarities and differences between exosomes and enveloped viral particles, with a focus on events taking place at the vesicle or virus membrane. Since these structures present an area with an opportunity for interaction with target cells, this is relevant for basic biology as well as any potential research or medical applications.
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Affiliation(s)
- Daniela Cortes-Galvez
- AG Histology and Embryology, Institute of Morphology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
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19
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Noguchi H. Membrane domain formation induced by binding/unbinding of curvature-inducing molecules on both membrane surfaces. SOFT MATTER 2023; 19:679-688. [PMID: 36597888 DOI: 10.1039/d2sm01536f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The domain formation of curvature-inducing molecules, such as peripheral or transmembrane proteins and conical surfactants, is studied in thermal equilibrium and nonequilibrium steady states using meshless membrane simulations. These molecules can bind to both surfaces of a bilayer membrane and also move to the opposite leaflet by a flip-flop. Under symmetric conditions for the two leaflets, the membrane domains form checkerboard patterns in addition to striped and spot patterns. The unbound membrane stabilizes the vertices of the checkerboard. Under asymmetric conditions, the domains form kagome-lattice and thread-like patterns. In the nonequilibrium steady states, a flow of the binding molecules between the upper and lower solutions can occur via flip-flop.
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Affiliation(s)
- Hiroshi Noguchi
- Institute for Solid State Physics, University of Tokyo, Kashiwa, Chiba 277-8581, Japan.
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20
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Woodward X, Javanainen M, Fábián B, Kelly CV. Nanoscale membrane curvature sorts lipid phases and alters lipid diffusion. Biophys J 2023:S0006-3495(23)00001-2. [PMID: 36604961 DOI: 10.1016/j.bpj.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/23/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
The precise spatiotemporal control of nanoscale membrane shape and composition is the result of a complex interplay of individual and collective molecular behaviors. Here, we employed single-molecule localization microscopy and computational simulations to observe single-lipid diffusion and sorting in model membranes with varying compositions, phases, temperatures, and curvatures. Supported lipid bilayers were created over 50-nm-radius nanoparticles to mimic the size of naturally occurring membrane buds, such as endocytic pits and the formation of viral envelopes. The curved membranes recruited liquid-disordered lipid phases while altering the diffusion and sorting of tracer lipids. Disorder-preferring fluorescent lipids sorted to and experienced faster diffusion on the nanoscale curvature only when embedded in a membrane capable of sustaining lipid phase separation at low temperatures. The curvature-induced sorting and faster diffusion even occurred when the sample temperature was above the miscibility temperature of the planar membrane, implying that the nanoscale curvature could induce phase separation in otherwise homogeneous membranes. Further confirmation and understanding of these results are provided by continuum and coarse-grained molecular dynamics simulations with explicit and spontaneous curvature-phase coupling, respectively. The curvature-induced membrane compositional heterogeneity and altered dynamics were achieved only with a coupling of the curvature with a lipid phase separation. These cross-validating results demonstrate the complex interplay of lipid phases, molecular diffusion, and nanoscale membrane curvature that are critical for membrane functionality.
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Affiliation(s)
- Xinxin Woodward
- Department of Physics and Astronomy, Wayne State University, Detroit, Michigan
| | - Matti Javanainen
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic; Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Balázs Fábián
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Christopher V Kelly
- Department of Physics and Astronomy, Wayne State University, Detroit, Michigan.
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21
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Muñoz-Hernández R, Rojas Á, Gato S, Gallego J, Gil-Gómez A, Castro MJ, Ampuero J, Romero-Gómez M. Extracellular Vesicles as Biomarkers in Liver Disease. Int J Mol Sci 2022; 23:ijms232416217. [PMID: 36555854 PMCID: PMC9786586 DOI: 10.3390/ijms232416217] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Extracellular vesicles (EVs) are membrane-derived vesicles released by a variety of cell types, including hepatocytes, hepatic stellate cells, and immune cells in normal and pathological conditions. Depending on their biogenesis, there is a complex repertoire of EVs that differ in size and origin. EVs can carry lipids, proteins, coding and non-coding RNAs, and mitochondrial DNA causing alterations to the recipient cells, functioning as intercellular mediators of cell-cell communication (auto-, para-, juxta-, or even endocrine). Nevertheless, many questions remain unanswered in relation to the function of EVs under physiological and pathological conditions. The development and optimization of methods for EV isolation are crucial for characterizing their biological functions, as well as their potential as a treatment option in the clinic. In this manuscript, we will comprehensively review the results from different studies that investigated the role of hepatic EVs during liver diseases, including non-alcoholic fatty liver disease, non-alcoholic steatohepatitis, alcoholic liver disease, fibrosis, and hepatocellular carcinoma. In general, the identification of patients with early-stage liver disease leads to better therapeutic interventions and optimal management. Although more light needs to be shed on the mechanisms of EVs, their use for early diagnosis, follow-up, and prognosis has come into the focus of research as a high-potential source of 'liquid biopsies', since they can be found in almost all biological fluids. The use of EVs as new targets or nanovectors in drug delivery systems for liver disease therapy is also summarized.
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Affiliation(s)
- Rocío Muñoz-Hernández
- SeLiver Group, Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital/CSIC/University of Seville, 41013 Seville, Spain
- CIBERehd, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence: (R.M.-H.); (M.R.-G.)
| | - Ángela Rojas
- SeLiver Group, Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital/CSIC/University of Seville, 41013 Seville, Spain
- CIBERehd, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Sheila Gato
- SeLiver Group, Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital/CSIC/University of Seville, 41013 Seville, Spain
- CIBERehd, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Javier Gallego
- SeLiver Group, Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital/CSIC/University of Seville, 41013 Seville, Spain
| | - Antonio Gil-Gómez
- SeLiver Group, Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital/CSIC/University of Seville, 41013 Seville, Spain
- CIBERehd, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - María José Castro
- Servicio de Citometría y Separación Celular, Instituto de Biomedicina de Sevilla Virgen del Rocio University Hospital/CSIC/University of Seville, 41013 Seville, Spain
| | - Javier Ampuero
- SeLiver Group, Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital/CSIC/University of Seville, 41013 Seville, Spain
- CIBERehd, Instituto de Salud Carlos III, 28029 Madrid, Spain
- UCM Digestive Diseases, Virgen del Rocío University Hospital, 41013 Seville, Spain
| | - Manuel Romero-Gómez
- SeLiver Group, Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital/CSIC/University of Seville, 41013 Seville, Spain
- CIBERehd, Instituto de Salud Carlos III, 28029 Madrid, Spain
- UCM Digestive Diseases, Virgen del Rocío University Hospital, 41013 Seville, Spain
- Correspondence: (R.M.-H.); (M.R.-G.)
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22
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Kita S, Shimomura I. Extracellular Vesicles as an Endocrine Mechanism Connecting Distant Cells. Mol Cells 2022; 45:771-780. [PMID: 36380729 PMCID: PMC9676990 DOI: 10.14348/molcells.2022.0110] [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: 07/05/2022] [Revised: 08/01/2022] [Accepted: 08/15/2022] [Indexed: 11/18/2022] Open
Abstract
The field of extracellular vesicles (EVs) has expanded tremendously over the last decade. The role of cell-to-cell communication in neighboring or distant cells has been increasingly ascribed to EVs generated by various cells. Initially, EVs were thought to a means of cellular debris or disposal system of unwanted cellular materials that provided an alternative to autolysis in lysosomes. Intercellular exchange of information has been considered to be achieved by well-known systems such as hormones, cytokines, and nervous networks. However, most research in this field has searched for and found evidence to support paracrine or endocrine roles of EV, which inevitably leads to a new concept that EVs are synthesized to achieve their paracrine or endocrine purposes. Here, we attempted to verify the endocrine role of EV production and their contents, such as RNAs and bioactive proteins, from the regulation of biogenesis, secretion, and action mechanisms while discussing the current technical limitations. It will also be important to discuss how blood EV concentrations are regulated as if EVs are humoral endocrine machinery.
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Affiliation(s)
- Shunbun Kita
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
- Adipose Management, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Iichiro Shimomura
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
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23
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Han QF, Li WJ, Hu KS, Gao J, Zhai WL, Yang JH, Zhang SJ. Exosome biogenesis: machinery, regulation, and therapeutic implications in cancer. Mol Cancer 2022; 21:207. [PMID: 36320056 PMCID: PMC9623991 DOI: 10.1186/s12943-022-01671-0] [Citation(s) in RCA: 149] [Impact Index Per Article: 74.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 10/13/2022] [Indexed: 12/14/2022] Open
Abstract
Exosomes are well-known key mediators of intercellular communication and contribute to various physiological and pathological processes. Their biogenesis involves four key steps, including cargo sorting, MVB formation and maturation, transport of MVBs, and MVB fusion with the plasma membrane. Each process is modulated through the competition or coordination of multiple mechanisms, whereby diverse repertoires of molecular cargos are sorted into distinct subpopulations of exosomes, resulting in the high heterogeneity of exosomes. Intriguingly, cancer cells exploit various strategies, such as aberrant gene expression, posttranslational modifications, and altered signaling pathways, to regulate the biogenesis, composition, and eventually functions of exosomes to promote cancer progression. Therefore, exosome biogenesis-targeted therapy is being actively explored. In this review, we systematically summarize recent progress in understanding the machinery of exosome biogenesis and how it is regulated in the context of cancer. In particular, we highlight pharmacological targeting of exosome biogenesis as a promising cancer therapeutic strategy.
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Affiliation(s)
- Qing-Fang Han
- grid.412633.10000 0004 1799 0733Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China ,grid.412633.10000 0004 1799 0733Henan Research Centre for Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Wen-Jia Li
- grid.412536.70000 0004 1791 7851Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation Medical Research Center, Sun Yat-Sen Memorial Hospital Sun Yat-Sen University, Guangzhou, 510120 China
| | - Kai-Shun Hu
- grid.412536.70000 0004 1791 7851Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation Medical Research Center, Sun Yat-Sen Memorial Hospital Sun Yat-Sen University, Guangzhou, 510120 China
| | - Jie Gao
- grid.412633.10000 0004 1799 0733Henan Research Centre for Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China ,Henan Diagnosis & Treatment League for Hepatopathy, Zhengzhou, 450052 Henan China
| | - Wen-Long Zhai
- grid.412633.10000 0004 1799 0733Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Jing-Hua Yang
- grid.412633.10000 0004 1799 0733Clinical Systems Biology Key Laboratories of Henan, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Shui-Jun Zhang
- grid.412633.10000 0004 1799 0733Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China ,grid.412633.10000 0004 1799 0733Henan Research Centre for Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China ,Henan Diagnosis & Treatment League for Hepatopathy, Zhengzhou, 450052 Henan China ,Henan Engineering & Research Center for Diagnosis and Treatment of Hepatobiliary and Pancreatic Surgical Diseases, Zhengzhou, 450052 Henan China
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24
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Strength in numbers: effect of protein crowding on the shape of cell membranes. Biochem Soc Trans 2022; 50:1257-1267. [PMID: 36214373 DOI: 10.1042/bst20210883] [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: 07/05/2022] [Revised: 09/16/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022]
Abstract
Continuous reshaping of the plasma membrane into pleomorphic shapes is critical for a plethora of cellular functions. How the cell carries out this enigmatic control of membrane remodeling has remained an active research field for decades and several molecular and biophysical mechanisms have shown to be involved in overcoming the energy barrier associated with membrane bending. The reported mechanisms behind membrane bending have been largely concerned with structural protein features, however, in the last decade, reports on the ability of densely packed proteins to bend membranes by protein-protein crowding, have challenged prevailing mechanistic views. Crowding has now been shown to generate spontaneous vesicle formation and tubular morphologies on cell- and model membranes, demonstrating crowding as a relevant player involved in the bending of membranes. Still, current research is largely based on unnatural overexpression of proteins in non-native domains, and together with efforts in modeling, this has led to questioning the in vivo impact of crowding. In this review, we examine this previously overlooked mechanism by summarizing recent advances in the understanding of protein-protein crowding and its prevalence in cellular membrane-shaping processes.
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25
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Lin C, Guo J, Jia R. Roles of Regulatory T Cell-Derived Extracellular Vesicles in Human Diseases. Int J Mol Sci 2022; 23:11206. [PMID: 36232505 PMCID: PMC9569925 DOI: 10.3390/ijms231911206] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/18/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Regulatory T (Treg) cells play crucial roles in maintaining immune self-tolerance and immune homeostasis, and closely associated with many human diseases. Recently, Treg cells-derived extracellular vesicles (Treg-EVs) have been demonstrated as a novel cell-contact independent inhibitory mechanism of Treg cells. Treg-EVs contain many specific biological molecules, which are delivered to target cells and modulate immune responses by inhibiting T cell proliferation, inducing T cell apoptosis, and changing the cytokine expression profiles of target cells. The abnormal quantity or function of Treg-EVs is associated with several types of human diseases or conditions, such as transplant rejection, inflammatory diseases, autoimmune diseases, and cancers. Treg-EVs are promising novel potential targets for disease diagnosis, therapy, and drug transport. Moreover, Treg-EVs possess distinct advantages over Treg cell-based immunotherapies. However, the therapeutic potential of Treg-EVs is limited by some factors, such as the standardized protocol for isolation and purification, large scale production, and drug loading efficiency. In this review, we systematically describe the structure, components, functions, and basic mechanisms of action of Treg-EVs and discuss the emerging roles in pathogenesis and the potential application of Treg-EVs in human diseases.
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Affiliation(s)
- Can Lin
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China
| | - Jihua Guo
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China
- Department of Endodontics, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China
| | - Rong Jia
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China
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26
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Illuminating membrane structural dynamics of fusion and endocytosis with advanced light imaging techniques. Biochem Soc Trans 2022; 50:1157-1167. [PMID: 35960003 PMCID: PMC9444071 DOI: 10.1042/bst20210263] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/24/2022] [Accepted: 07/27/2022] [Indexed: 11/17/2022]
Abstract
Visualization of cellular dynamics using fluorescent light microscopy has become a reliable and indispensable source of experimental evidence for biological studies. Over the past two decades, the development of super-resolution microscopy platforms coupled with innovations in protein and molecule labeling led to significant biological findings that were previously unobservable due to the barrier of the diffraction limit. As a result, the ability to image the dynamics of cellular processes is vastly enhanced. These imaging tools are extremely useful in cellular physiology for the study of vesicle fusion and endocytosis. In this review, we will explore the power of stimulated emission depletion (STED) and confocal microscopy in combination with various labeling techniques in real-time observation of the membrane transformation of fusion and endocytosis, as well as their underlying mechanisms. We will review how STED and confocal imaging are used to reveal fusion and endocytic membrane transformation processes in live cells, including hemi-fusion; hemi-fission; hemi-to-full fusion; fusion pore opening, expansion, constriction and closure; shrinking or enlargement of the Ω-shape membrane structure after vesicle fusion; sequential compound fusion; and the sequential endocytic membrane transformation from flat- to O-shape via the intermediate Λ- and Ω-shape transition. We will also discuss how the recent development of imaging techniques would impact future studies in the field.
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27
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Tamemoto N, Noguchi H. Excitable reaction-diffusion waves of curvature-inducing proteins on deformable membrane tubes. Phys Rev E 2022; 106:024403. [PMID: 36110014 DOI: 10.1103/physreve.106.024403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Living cells employ excitable reaction-diffusion waves for internal cellular functions, in which curvature-inducing proteins are often involved. However, the role of their mechanochemical coupling is not well understood. Here, we report the membrane deformation induced by the excitable reaction-diffusion waves of curvature-inducing proteins and the alternation in the waves due to the deformation, using a coarse-grained simulation of tubular membranes with a modified FitzHugh-Nagumo model. Protein-propagating waves deform tubular membranes and large deformations induce budding and erase waves. The wave speed and shape are determined by a combination of membrane deformation and spatial distribution of the curvature-inducing protein. Waves are also undulated in the azimuthal direction depending on the condition. Rotationally symmetric waves locally deform the tubes into a symmetric shape but maintain a straight shape on average. Our simulation method can be applied to other chemical reaction models and used to investigate various biomembrane phenomena.
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Affiliation(s)
- Naoki Tamemoto
- Institute for Solid State Physics, University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Hiroshi Noguchi
- Institute for Solid State Physics, University of Tokyo, Kashiwa, Chiba 277-8581, Japan
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28
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Noguchi H. Membrane shape deformation induced by curvature-inducing proteins consisting of chiral crescent binding and intrinsically disordered domains. J Chem Phys 2022; 157:034901. [DOI: 10.1063/5.0098249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Curvature-inducing proteins containing a bin/amphiphysin/Rvs domain often have intrinsically disordered domains. Recent experiments have shown that these disordered chains enhance curvature sensing and generation. Here, we report on the modification of protein–membrane interactions by disordered chains using meshless membrane simulations. The protein and bound membrane are modeled together as a chiral crescent protein rod with two excluded-volume chains. As the chain length increases, the repulsion between them reduces the cluster size of the proteins. It induces spindle-shaped vesicles and a transition between arc-shaped and circular protein assemblies in a disk-shaped vesicle. For flat membranes, an intermediate chain length induces many tubules owing to the repulsion between the protein assemblies, whereas longer chains promote perpendicular elongation of tubules. Moreover, protein rods with zero rod curvature and sufficiently long chains stabilize the spherical buds. For proteins with a negative rod curvature, an intermediate chain length induces a rugged membrane with branched protein assemblies, whereas longer chains induce the formation of tubules with periodic concave-ring structures.
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Affiliation(s)
- Hiroshi Noguchi
- Institute for Solid State Physics, University of Tokyo, Kashiwa, Chiba 277-8581, Japan
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29
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Budi YP, Lin LC, Chung CH, Chen LL, Jiang YF. Three-Dimensional Investigations of Virus-Associated Structures in the Nuclei with White Spot Syndrome Virus (WSSV) Infection in Red Swamp Crayfish ( Procambarus clarkii). Animals (Basel) 2022; 12:1730. [PMID: 35804629 PMCID: PMC9265099 DOI: 10.3390/ani12131730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/03/2022] [Accepted: 07/04/2022] [Indexed: 11/17/2022] Open
Abstract
White spot syndrome virus (WSSV) has been reported to cause severe economic loss in the shrimp industry. With WSSV being a large virus still under investigation, the 3D structure of its assembly remains unclear. The current study was planned to clarify the 3D structures of WSSV infections in the cell nucleus of red swamp crayfish (Procambarus clarkii). The samples from various tissues were prepared on the seventh day post-infection. The serial sections of the intestinal tissue were obtained for electron tomography after the ultrastructural screening. After 3D reconstruction, the WSSV-associated structures were further visualized, and the expressions of viral proteins were confirmed with immuno-gold labeling. While the pairs of sheet-like structures with unknown functions were observed in the nucleus, the immature virions could be recognized by the core units of nucleocapsids on a piece of the envelope. The maturation of the particle could include the elongation of core units and the filling of empty nucleocapsids with electron-dense materials. Our observations may bring to light a possible order of WSSV maturation in the cell nucleus of the crayfish, while more investigations remain necessary to visualize the detailed viral-host interactions.
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Affiliation(s)
- Yovita Permata Budi
- Graduate Institute of Molecular and Comparative Pathobiology, School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan;
- School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan; (L.-C.L.); (C.-H.C.)
| | - Li-Chi Lin
- School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan; (L.-C.L.); (C.-H.C.)
| | - Chang-Hsien Chung
- School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan; (L.-C.L.); (C.-H.C.)
| | - Li-Li Chen
- Institute of Marine Biology, National Taiwan Ocean University, Keelung City 20224, Taiwan;
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung City 20224, Taiwan
| | - Yi-Fan Jiang
- Graduate Institute of Molecular and Comparative Pathobiology, School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan;
- School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan; (L.-C.L.); (C.-H.C.)
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30
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Shin W, Zucker B, Kundu N, Lee SH, Shi B, Chan CY, Guo X, Harrison JT, Turechek JM, Hinshaw JE, Kozlov MM, Wu LG. Molecular mechanics underlying flat-to-round membrane budding in live secretory cells. Nat Commun 2022; 13:3697. [PMID: 35760780 PMCID: PMC9237132 DOI: 10.1038/s41467-022-31286-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 06/10/2022] [Indexed: 12/21/2022] Open
Abstract
Membrane budding entails forces to transform flat membrane into vesicles essential for cell survival. Accumulated studies have identified coat-proteins (e.g., clathrin) as potential budding factors. However, forces mediating many non-coated membrane buddings remain unclear. By visualizing proteins in mediating endocytic budding in live neuroendocrine cells, performing in vitro protein reconstitution and physical modeling, we discovered how non-coated-membrane budding is mediated: actin filaments and dynamin generate a pulling force transforming flat membrane into Λ-shape; subsequently, dynamin helices surround and constrict Λ-profile's base, transforming Λ- to Ω-profile, and then constrict Ω-profile's pore, converting Ω-profiles to vesicles. These mechanisms control budding speed, vesicle size and number, generating diverse endocytic modes differing in these parameters. Their impact is widespread beyond secretory cells, as the unexpectedly powerful functions of dynamin and actin, previously thought to mediate fission and overcome tension, respectively, may contribute to many dynamin/actin-dependent non-coated-membrane buddings, coated-membrane buddings, and other membrane remodeling processes.
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Affiliation(s)
- Wonchul Shin
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Ben Zucker
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, 69978, Ramat Aviv, Israel
| | - Nidhi Kundu
- Structural Cell Biology Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Sung Hoon Lee
- Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Bo Shi
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Chung Yu Chan
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Xiaoli Guo
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Jonathan T Harrison
- Structural Cell Biology Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | | | - Jenny E Hinshaw
- Structural Cell Biology Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.
| | - Michael M Kozlov
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, 69978, Ramat Aviv, Israel.
| | - Ling-Gang Wu
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
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31
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Tumor protein D54 binds intracellular nanovesicles via an extended amphipathic region. J Biol Chem 2022; 298:102136. [PMID: 35714773 PMCID: PMC9270247 DOI: 10.1016/j.jbc.2022.102136] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/22/2022] Open
Abstract
Tumor Protein D54 (TPD54) is an abundant cytosolic protein that belongs to the TPD52 family, a family of four proteins (TPD52, 53, 54 and 55) that are overexpressed in several cancer cells. Even though the functions of these proteins remain elusive, recent investigations indicate that TPD54 binds to very small cytosolic vesicles with a diameter of ca. 30 nm, half the size of classical (e.g. COPI and COPII) transport vesicles. Here, we investigated the mechanism of intracellular nanovesicle capture by TPD54. Bioinformatical analysis suggests that TPD54 contains a small coiled-coil followed by four amphipathic helices (AH1-4), which could fold upon binding to lipid membranes. Limited proteolysis, circular dichroism (CD) spectroscopy, tryptophan fluorescence, and cysteine mutagenesis coupled to covalent binding of a membrane sensitive probe showed that binding of TPD54 to small liposomes is accompanied by large structural changes in the amphipathic helix region. Furthermore, site-directed mutagenesis indicated that AH2 and AH3 have a predominant role in TPD54 binding to membranes both in cells and using model liposomes. We found that AH3 has the physicochemical features of an Amphipathic Lipid Packing Sensor (ALPS) motif, which, in other proteins, enables membrane binding in a curvature-dependent manner. Accordingly, we observed that binding of TPD54 to liposomes is very sensitive to membrane curvature and lipid unsaturation. We conclude that TPD54 recognizes nanovesicles through a combination of ALPS-dependent and -independent mechanisms.
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32
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Noguchi H, Tozzi C, Arroyo M. Binding of anisotropic curvature-inducing proteins onto membrane tubes. SOFT MATTER 2022; 18:3384-3394. [PMID: 35416229 DOI: 10.1039/d2sm00274d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Bin/Amphiphysin/Rvs superfamily proteins and other curvature-inducing proteins have anisotropic shapes and anisotropically bend biomembranes. Here, we report how the anisotropic proteins bind the membrane tube and are orientationally ordered using mean-field theory including an orientation-dependent excluded volume. The proteins exhibit a second-order or first-order nematic transition with increasing protein density depending on the radius of the membrane tube. The tube curvatures for the maximum protein binding and orientational order are different and varied by the protein density and rigidity. As the external force along the tube axis increases, a first-order transition from a large tube radius with low protein density to a small radius with high density occurs once, and subsequently, the protein orientation tilts to the tube-axis direction. When an isotropic bending energy is used for the proteins with an elliptic shape, the force-dependence curves become symmetric and the first-order transition occurs twice. This theory quantitatively reproduces the results of meshless membrane simulation for short proteins, whereas deviations are seen for long proteins owing to the formation of protein clusters.
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Affiliation(s)
- Hiroshi Noguchi
- Institute for Solid State Physics, University of Tokyo, Kashiwa, Chiba 277-8581, Japan.
| | - Caterina Tozzi
- Universitat Politèdcnica de Catalunya-BarcelonaTech, 08034 Barcelona, Spain
| | - Marino Arroyo
- Universitat Politèdcnica de Catalunya-BarcelonaTech, 08034 Barcelona, Spain
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), 08028 Barcelona, Spain
- Centre Internacional de Mètodes Numèrics en Enginyeria (CIMNE), 08034 Barcelona, Spain
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33
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Bernacchi S. Visualization of Retroviral Gag-Genomic RNA Cellular Interactions Leading to Genome Encapsidation and Viral Assembly: An Overview. Viruses 2022; 14:324. [PMID: 35215917 PMCID: PMC8876502 DOI: 10.3390/v14020324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/25/2022] [Accepted: 02/03/2022] [Indexed: 11/16/2022] Open
Abstract
Retroviruses must selectively recognize their unspliced RNA genome (gRNA) among abundant cellular and spliced viral RNAs to assemble into newly formed viral particles. Retroviral gRNA packaging is governed by Gag precursors that also orchestrate all the aspects of viral assembly. Retroviral life cycles, and especially the HIV-1 one, have been previously extensively analyzed by several methods, most of them based on molecular biology and biochemistry approaches. Despite these efforts, the spatio-temporal mechanisms leading to gRNA packaging and viral assembly are only partially understood. Nevertheless, in these last decades, progress in novel bioimaging microscopic approaches (as FFS, FRAP, TIRF, and wide-field microscopy) have allowed for the tracking of retroviral Gag and gRNA in living cells, thus providing important insights at high spatial and temporal resolution of the events regulating the late phases of the retroviral life cycle. Here, the implementation of these recent bioimaging tools based on highly performing strategies to label fluorescent macromolecules is described. This report also summarizes recent gains in the current understanding of the mechanisms employed by retroviral Gag polyproteins to regulate molecular mechanisms enabling gRNA packaging and the formation of retroviral particles, highlighting variations and similarities among the different retroviruses.
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Affiliation(s)
- Serena Bernacchi
- Architecture et Réactivité de l'ARN-UPR 9002, IBMC, CNRS, Université de Strasbourg, F-67000 Strasbourg, France
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34
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Noguchi H. Binding of curvature-inducing proteins onto tethered vesicles. SOFT MATTER 2021; 17:10469-10478. [PMID: 34749394 DOI: 10.1039/d1sm01360b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A tethered vesicle, which consists of a cylindrical membrane tube and a spherical vesicle, is produced by a mechanical force that is experimentally imposed by optical tweezers and a micropipette. This tethered vesicle is employed for examining the curvature sensing of curvature-inducing proteins. In this study, we clarify how the binding of proteins with a laterally isotropic spontaneous curvature senses and generates the membrane curvatures of the tethered vesicle using mean-field theory and meshless membrane simulation. The force-dependence curves of the protein density in the membrane tube and the tube curvature are reflection symmetric and point symmetric, respectively, from the force point, in which the tube has a sensing curvature. The bending rigidity and spontaneous curvature of the bound proteins can be estimated from these force-dependence curves. First-order transitions can occur between low and high protein densities in the tube at both low and high force amplitudes. The simulation results of the homogeneous phases agree very well with the theoretical predictions. In addition, beaded-necklace-like tubes with microphase separation are found in the simulation.
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Affiliation(s)
- Hiroshi Noguchi
- Institute for Solid State Physics, University of Tokyo, Kashiwa, Chiba 277-8581, Japan.
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35
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Rana R, Chauhan K, Gautam P, Kulkarni M, Banarjee R, Chugh P, Chhabra SS, Acharya R, Kalra SK, Gupta A, Jain S, Ganguly NK. Plasma-Derived Extracellular Vesicles Reveal Galectin-3 Binding Protein as Potential Biomarker for Early Detection of Glioma. Front Oncol 2021; 11:778754. [PMID: 34900729 PMCID: PMC8661035 DOI: 10.3389/fonc.2021.778754] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/01/2021] [Indexed: 12/11/2022] Open
Abstract
Gliomas are the most common type of the malignant brain tumor, which arise from glial cells. They make up about 40% of all primary brain tumors and around 70% of all primary malignant brain tumors. They can occur anywhere in the central nervous system (CNS) and have a poor prognosis. The average survival of glioma patients is approximately 6-15 months with poor aspects of life. In this edge, identification of proteins secreted by cancer cells is of special interest because it may provide a better understanding of tumor progression and provide early diagnosis of the diseases. Extracellular vesicles (EVs) were isolated from pooled plasma of healthy controls (n=03) and patients with different grades of glioma (Grade I or II or III, n=03 each). Nanoparticle tracking analysis, western blot, and flow cytometry were performed to determine the size, morphology, the concentration of glioma-derived vesicles and EV marker, CD63. Further, iTRAQ-based LC-MS/MS analysis of EV protein was performed to determine the differential protein abundance in extracellular vesicles across different glioma grades. We further verified galectin-3 binding protein (LGALS3BP) by ELISA in individual blood plasma and plasma-derived vesicles from control and glioma patients (n=40 each). Analysis by Max Quant identified 123 proteins from the pooled patient exosomes, out of which 34, 21, and 14 proteins were found to be differentially abundant by more than 1.3-fold in the different grades of glioma grade I, pilocytic astrocytoma; grade II, diffuse astrocytoma; grade III, anaplastic astrocytoma, respectively, in comparison with the control samples. A total of seven proteins-namely, CRP, SAA2, SERPINA3, SAA1, C4A, LV211, and KV112-showed differential abundance in all the three grades. LGALS3BP was seen to be upregulated across the different grades, and ELISA analysis from individual blood plasma and plasma-derived extracellular vesicles confirmed the increased expression of LGALS3BP in glioma patients (p<0.001). The present study provides LGALS3BP as a potential biomarker for early detection of glioma and improve survival outcome of the patient. The present study further provides the information of progression and monitoring the tumor grades (grade 1, grade II, grade III).
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Affiliation(s)
- Rashmi Rana
- Department of Research, Sir Ganga Ram Hospital, New Delhi, India
| | - Kirti Chauhan
- Department of Research, Sir Ganga Ram Hospital, New Delhi, India
| | - Poonam Gautam
- Laboratory of Molecular Oncology, National Institute of Pathology, Indian Council of Medical Research (ICMR), New Delhi, India
| | - Mahesh Kulkarni
- Biochemical Sciences Division, National Chemical Laboratory, Council of Scientific and Industrial Research (CSIR), Pune, India
| | - Reema Banarjee
- Biochemical Sciences Division, National Chemical Laboratory, Council of Scientific and Industrial Research (CSIR), Pune, India
| | - Parul Chugh
- Department of Research, Sir Ganga Ram Hospital, New Delhi, India
| | | | - Rajesh Acharya
- Department of Neurosurgery, Sir Ganga Ram Hospital, New Delhi, India
| | - Samir Kumar Kalra
- Department of Neurosurgery, Sir Ganga Ram Hospital, New Delhi, India
| | - Anshul Gupta
- Department of Neurosurgery, Sir Ganga Ram Hospital, New Delhi, India
| | - Sunila Jain
- Department of Histopathology, Sir Ganga Ram Hospital, New Delhi, India
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36
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Auddya D, Zhang X, Gulati R, Vasan R, Garikipati K, Rangamani P, Rudraraju S. Biomembranes undergo complex, non-axisymmetric deformations governed by Kirchhoff-Love kinematicsand revealed by a three-dimensional computational framework. Proc Math Phys Eng Sci 2021; 477:20210246. [PMID: 35153593 PMCID: PMC8580429 DOI: 10.1098/rspa.2021.0246] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 10/11/2021] [Indexed: 01/10/2023] Open
Abstract
Biomembranes play a central role in various phenomena like locomotion of cells, cell-cell interactions, packaging and transport of nutrients, transmission of nerve impulses, and in maintaining organelle morphology and functionality. During these processes, the membranes undergo significant morphological changes through deformation, scission, and fusion. Modelling the underlying mechanics of such morphological changes has traditionally relied on reduced order axisymmetric representations of membrane geometry and deformation. Axisymmetric representations, while robust and extensively deployed, suffer from their inability to model-symmetry breaking deformations and structural bifurcations. To address this limitation, a three-dimensional computational mechanics framework for high fidelity modelling of biomembrane deformation is presented. The proposed framework brings together Kirchhoff–Love thin-shell kinematics, Helfrich-energy-based mechanics, and state-of-the-art numerical techniques for modelling deformation of surface geometries. Lipid bilayers are represented as spline-based surface discretizations immersed in a three-dimensional space; this enables modelling of a wide spectrum of membrane geometries, boundary conditions, and deformations that are physically admissible in a three-dimensional space. The mathematical basis of the framework and its numerical machinery are presented, and their utility is demonstrated by modelling three classical, yet non-trivial, membrane deformation problems: formation of tubular shapes and their lateral constriction, Piezo1-induced membrane footprint generation and gating response, and the budding of membranes by protein coats during endocytosis. For each problem, the full three-dimensional membrane deformation is captured, potential symmetry-breaking deformation paths identified, and various case studies of boundary and load conditions are presented. Using the endocytic vesicle budding as a case study, we also present a ‘phase diagram’ for its symmetric and broken-symmetry states.
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Affiliation(s)
- Debabrata Auddya
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Xiaoxuan Zhang
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rahul Gulati
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ritvik Vasan
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Krishna Garikipati
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Mathematics, University of Michigan, Ann Arbor, MI 48109, USA.,Michigan Institute for Computational Discovery and Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Shiva Rudraraju
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
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37
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Farfan-Morales CN, Cordero-Rivera CD, Reyes-Ruiz JM, Hurtado-Monzón AM, Osuna-Ramos JF, González-González AM, De Jesús-González LA, Palacios-Rápalo SN, Del Ángel RM. Anti-flavivirus Properties of Lipid-Lowering Drugs. Front Physiol 2021; 12:749770. [PMID: 34690817 PMCID: PMC8529048 DOI: 10.3389/fphys.2021.749770] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/20/2021] [Indexed: 12/11/2022] Open
Abstract
Although Flaviviruses such as dengue (DENV) and zika (ZIKV) virus are important human pathogens, an effective vaccine or antiviral treatment against them is not available. Hence, the search for new strategies to control flavivirus infections is essential. Several studies have shown that the host lipid metabolism could be an antiviral target because cholesterol and other lipids are required during the replicative cycle of different Flaviviridae family members. FDA-approved drugs with hypolipidemic effects could be an alternative for treating flavivirus infections. However, a better understanding of the regulation between host lipid metabolism and signaling pathways triggered during these infections is required. The metabolic pathways related to lipid metabolism modified during DENV and ZIKV infection are analyzed in this review. Additionally, the role of lipid-lowering drugs as safe host-targeted antivirals is discussed.
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Affiliation(s)
- Carlos Noe Farfan-Morales
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies (CINVESTAV-IPN), Mexico City, Mexico
| | - Carlos Daniel Cordero-Rivera
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies (CINVESTAV-IPN), Mexico City, Mexico
| | - José Manuel Reyes-Ruiz
- Unidad Médica de Alta Especialidad, Hospital de Especialidades No. 14, Centro Médico Nacional "Adolfo Ruiz Cortines," Instituto Mexicano del Seguro Social, Heroica Veracruz, Mexico
| | - Arianna M Hurtado-Monzón
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies (CINVESTAV-IPN), Mexico City, Mexico
| | - Juan Fidel Osuna-Ramos
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies (CINVESTAV-IPN), Mexico City, Mexico
| | - Arely M González-González
- Laboratorio de Ingeniería Tisular y Medicina Traslacional, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Luis Adrián De Jesús-González
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies (CINVESTAV-IPN), Mexico City, Mexico
| | - Selvin Noé Palacios-Rápalo
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies (CINVESTAV-IPN), Mexico City, Mexico
| | - Rosa María Del Ángel
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies (CINVESTAV-IPN), Mexico City, Mexico
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38
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Booth A, Marklew CJ, Ciani B, Beales PA. The influence of phosphatidylserine localisation and lipid phase on membrane remodelling by the ESCRT-II/ESCRT-III complex. Faraday Discuss 2021; 232:188-202. [PMID: 34590635 DOI: 10.1039/d0fd00042f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The endosomal sorting complex required for transport (ESCRT) organises in supramolecular structures on the surface of lipid bilayers to drive membrane invagination and scission of intraluminal vesicles (ILVs), a process also controlled by membrane mechanics. However, ESCRT association with the membrane is also mediated by electrostatic interactions with anionic phospholipids. Phospholipid distribution within natural biomembranes is inhomogeneous due to, for example, the formation of lipid rafts and curvature-driven lipid sorting. Here, we have used phase-separated giant unilamellar vesicles (GUVs) to investigate the link between phosphatidylserine (PS)-rich lipid domains and ESCRT activity. We employ GUVs composed of phase separating lipid mixtures, where unsaturated DOPS and saturated DPPS lipids are incorporated individually or simultaneously to enhance PS localisation in liquid disordered (Ld) and/or liquid ordered (Lo) domains, respectively. PS partitioning between the coexisting phases is confirmed by a fluorescent Annexin V probe. Ultimately, we find that ILV generation promoted by ESCRTs is significantly enhanced when PS lipids localise within Ld domains. However, the ILVs that form are rich in Lo lipids. We interpret this surprising observation as preferential recruitment of the Lo phase beneath the ESCRT complex due to its increased rigidity, where the Ld phase is favoured in the neck of the resultant buds to facilitate the high membrane curvature in these regions of the membrane during the ILV formation process. Ld domains offer lower resistance to membrane bending, demonstrating a mechanism by which the composition and mechanics of membranes can be coupled to regulate the location and efficiency of ESCRT activity.
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Affiliation(s)
- Andrew Booth
- School of Chemistry, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Christopher J Marklew
- Department of Chemistry, Centre for Membrane Interactions and Dynamics, University of Sheffield, Sheffield S3 7HF, UK
| | - Barbara Ciani
- Department of Chemistry, Centre for Membrane Interactions and Dynamics, University of Sheffield, Sheffield S3 7HF, UK
| | - Paul A Beales
- School of Chemistry, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK. .,Bragg Centre for Materials Research, University of Leeds, Leeds, LS2 9JT, UK
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Abstract
Membrane bending is a ubiquitous cellular process that is required for membrane traffic, cell motility, organelle biogenesis, and cell division. Proteins that bind to membranes using specific structural features, such as wedge-like amphipathic helices and crescent-shaped scaffolds, are thought to be the primary drivers of membrane bending. However, many membrane-binding proteins have substantial regions of intrinsic disorder which lack a stable three-dimensional structure. Interestingly, many of these disordered domains have recently been found to form networks stabilized by weak, multivalent contacts, leading to assembly of protein liquid phases on membrane surfaces. Here we ask how membrane-associated protein liquids impact membrane curvature. We find that protein phase separation on the surfaces of synthetic and cell-derived membrane vesicles creates a substantial compressive stress in the plane of the membrane. This stress drives the membrane to bend inward, creating protein-lined membrane tubules. A simple mechanical model of this process accurately predicts the experimentally measured relationship between the rigidity of the membrane and the diameter of the membrane tubules. Discovery of this mechanism, which may be relevant to a broad range of cellular protrusions, illustrates that membrane remodeling is not exclusive to structured scaffolds but can also be driven by the rapidly emerging class of liquid-like protein networks that assemble at membranes.
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40
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Stotz HU, Brotherton D, Inal J. Communication is key: Extracellular vesicles as mediators of infection and defence during host-microbe interactions in animals and plants. FEMS Microbiol Rev 2021; 46:6358524. [PMID: 34448857 PMCID: PMC8767456 DOI: 10.1093/femsre/fuab044] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 08/23/2021] [Indexed: 12/12/2022] Open
Abstract
Extracellular vesicles (EVs) are now understood to be ubiquitous mediators of cellular communication. In this review, we suggest that EVs have evolved into a highly regulated system of communication with complex functions including export of wastes, toxins and nutrients, targeted delivery of immune effectors and vectors of RNA silencing. Eukaryotic EVs come in different shapes and sizes and have been classified according to their biogenesis and size distributions. Small EVs (or exosomes) are released through fusion of endosome-derived multivesicular bodies with the plasma membrane. Medium EVs (or microvesicles) bud off the plasma membrane as a form of exocytosis. Finally, large EVs (or apoptotic bodies) are produced as a result of the apoptotic process. This review considers EV secretion and uptake in four eukaryotic kingdoms, three of which produce cell walls. The impacts cell walls have on EVs in plants and fungi are discussed, as are roles of fungal EVs in virulence. Contributions of plant EVs to development and innate immunity are presented. Compelling cases are sporophytic self-incompatibility and cellular invasion by haustorium-forming filamentous pathogens. The involvement of EVs in all of these eukaryotic processes is reconciled considering their evolutionary history.
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Affiliation(s)
- Henrik U Stotz
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK
| | - Dominik Brotherton
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK
| | - Jameel Inal
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK.,School of Human Sciences, London Metropolitan University, London, N7 8DB, UK
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41
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Noguchi H. Vesicle budding induced by binding of curvature-inducing proteins. Phys Rev E 2021; 104:014410. [PMID: 34412221 DOI: 10.1103/physreve.104.014410] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/13/2021] [Indexed: 12/22/2022]
Abstract
Vesicle budding induced by protein binding that generates an isotropic spontaneous curvature is studied using a mean-field theory. Many spherical buds are formed via protein binding. As the binding chemical potential increases, the proteins first bind to the buds and then to the remainder of the vesicle. For a high spontaneous curvature and/or high bending rigidity of the bound membrane, it is found that a first-order transition occurs between a small number of large buds and a large number of small buds. These two states coexist around the transition point. The proposed scheme is simple and easily applicable to many interaction types, so we investigate the effects of interprotein interactions, the protein-insertion-induced changes in area, the variation of the saddle-splay modulus, and the area-difference-elasticity energy. The differences in the preferred curvatures for curvature sensing and generation are also clarified.
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Affiliation(s)
- Hiroshi Noguchi
- Institute for Solid State Physics, University of Tokyo, Kashiwa, Chiba 277-8581, Japan
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42
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Inamdar K, Tsai FC, Dibsy R, de Poret A, Manzi J, Merida P, Muller R, Lappalainen P, Roingeard P, Mak J, Bassereau P, Favard C, Muriaux D. Full assembly of HIV-1 particles requires assistance of the membrane curvature factor IRSp53. eLife 2021; 10:67321. [PMID: 34114563 PMCID: PMC8260224 DOI: 10.7554/elife.67321] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 06/10/2021] [Indexed: 01/07/2023] Open
Abstract
During HIV-1 particle formation, the requisite plasma membrane curvature is thought to be solely driven by the retroviral Gag protein. Here, we reveal that the cellular I-BAR protein IRSp53 is required for the progression of HIV-1 membrane curvature to complete particle assembly. siRNA-mediated knockdown of IRSp53 gene expression induces a decrease in viral particle production and a viral bud arrest at half completion. Single-molecule localization microscopy at the cell plasma membrane shows a preferential localization of IRSp53 around HIV-1 Gag assembly sites. In addition, we observe the presence of IRSp53 in purified HIV-1 particles. Finally, HIV-1 Gag protein preferentially localizes to curved membranes induced by IRSp53 I-BAR domain on giant unilamellar vesicles. Overall, our data reveal a strong interplay between IRSp53 I-BAR and Gag at membranes during virus assembly. This highlights IRSp53 as a crucial host factor in HIV-1 membrane curvature and its requirement for full HIV-1 particle assembly.
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Affiliation(s)
- Kaushik Inamdar
- Infectious disease Research Institute of Montpellier (IRIM), CNRS UMR 9004, University of Montpellier, Montpellier, France
| | - Feng-Ching Tsai
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Rayane Dibsy
- Infectious disease Research Institute of Montpellier (IRIM), CNRS UMR 9004, University of Montpellier, Montpellier, France
| | - Aurore de Poret
- Infectious disease Research Institute of Montpellier (IRIM), CNRS UMR 9004, University of Montpellier, Montpellier, France
| | - John Manzi
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Peggy Merida
- Infectious disease Research Institute of Montpellier (IRIM), CNRS UMR 9004, University of Montpellier, Montpellier, France
| | - Remi Muller
- CEMIPAI, CNRS UAR3725, University of Montpellier, Montpellier, France
| | - Pekka Lappalainen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | | | - Johnson Mak
- Institute for Glycomics, Griffith University, Brisbane, Australia
| | - Patricia Bassereau
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Cyril Favard
- Infectious disease Research Institute of Montpellier (IRIM), CNRS UMR 9004, University of Montpellier, Montpellier, France
| | - Delphine Muriaux
- Infectious disease Research Institute of Montpellier (IRIM), CNRS UMR 9004, University of Montpellier, Montpellier, France
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43
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Vanhille-Campos C, Šarić A. Modelling the dynamics of vesicle reshaping and scission under osmotic shocks. SOFT MATTER 2021; 17:3798-3806. [PMID: 33629089 DOI: 10.1039/d0sm02012e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We study the effects of osmotic shocks on lipid vesicles via coarse-grained molecular dynamics simulations by explicitly considering the solute in the system. We find that depending on their nature (hypo- or hypertonic) such shocks can lead to bursting events or engulfing of external material into inner compartments, among other morphology transformations. We characterize the dynamics of these processes and observe a separation of time scales between the osmotic shock absorption and the shape relaxation. Our work consequently provides an insight into the dynamics of compartmentalization in vesicular systems as a result of osmotic shocks, which can be of interest in the context of early proto-cell development and proto-cell compartmentalisation.
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Affiliation(s)
- Christian Vanhille-Campos
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London WC1E 6BT, UK.
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44
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Abstract
The sorting nexin (SNX) family of proteins deform the membrane to generate transport carriers in endosomal pathways. Here, we elucidate how a prototypic member, SNX1, acts in this process. Performing cryoelectron microscopy, we find that SNX1 assembles into a protein lattice that consists of helical rows of SNX1 dimers wrapped around tubular membranes in a crosslinked fashion. We also visualize the details of this structure, which provides a molecular understanding of how various parts of SNX1 contribute to its ability to deform the membrane. Moreover, we have compared the SNX1 structure with a previously elucidated structure of an endosomal coat complex formed by retromer coupled to a SNX, which reveals how the molecular organization of the SNX in this coat complex is affected by retromer. The comparison also suggests insight into intermediary stages of assembly that results in the formation of the retromer-SNX coat complex on the membrane.
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45
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Zamparo M, Valdembri D, Serini G, Kolokolov IV, Lebedev VV, Dall'Asta L, Gamba A. Optimality in Self-Organized Molecular Sorting. PHYSICAL REVIEW LETTERS 2021; 126:088101. [PMID: 33709726 DOI: 10.1103/physrevlett.126.088101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
We introduce a simple physical picture to explain the process of molecular sorting, whereby specific proteins are concentrated and distilled into submicrometric lipid vesicles in eukaryotic cells. To this purpose, we formulate a model based on the coupling of spontaneous molecular aggregation with vesicle nucleation. Its implications are studied by means of a phenomenological theory describing the diffusion of molecules toward multiple sorting centers that grow due to molecule absorption and are extracted when they reach a sufficiently large size. The predictions of the theory are compared with numerical simulations of a lattice-gas realization of the model and with experimental observations. The efficiency of the distillation process is found to be optimal for intermediate aggregation rates, where the density of sorted molecules is minimal and the process obeys simple scaling laws. Quantitative measures of endocytic sorting performed in primary endothelial cells are compatible with the hypothesis that these optimal conditions are realized in living cells.
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Affiliation(s)
- Marco Zamparo
- Institute of Condensed Matter Physics and Complex Systems, Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
- Italian Institute for Genomic Medicine c/o Candiolo Cancer Institute, Fondazione del Piemonte per l'Oncologia (FPO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Candiolo, 10060 Torino, Italy
| | - Donatella Valdembri
- Department of Oncology, University of Torino School of Medicine, Candiolo, 10060 Torino, Italy
- Candiolo Cancer Institute, Fondazione del Piemonte per l'Oncologia (FPO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Candiolo, 10060 Torino, Italy
| | - Guido Serini
- Department of Oncology, University of Torino School of Medicine, Candiolo, 10060 Torino, Italy
- Candiolo Cancer Institute, Fondazione del Piemonte per l'Oncologia (FPO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Candiolo, 10060 Torino, Italy
| | - Igor V Kolokolov
- L.D. Landau Institute for Theoretical Physics, 142432, Moscow Region, Chernogolovka, Ak. Semenova, 1-A, Russia
- National Research University Higher School of Economics, 101000, Myasnitskaya 20, Moscow, Russia
| | - Vladimir V Lebedev
- L.D. Landau Institute for Theoretical Physics, 142432, Moscow Region, Chernogolovka, Ak. Semenova, 1-A, Russia
- National Research University Higher School of Economics, 101000, Myasnitskaya 20, Moscow, Russia
| | - Luca Dall'Asta
- Institute of Condensed Matter Physics and Complex Systems, Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
- Italian Institute for Genomic Medicine c/o Candiolo Cancer Institute, Fondazione del Piemonte per l'Oncologia (FPO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Candiolo, 10060 Torino, Italy
- Collegio Carlo Alberto, Piazza Arbarello 8, 10122 Torino, Italy
- Istituto Nazionale di Fisica Nucleare (INFN), Italy
| | - Andrea Gamba
- Institute of Condensed Matter Physics and Complex Systems, Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
- Italian Institute for Genomic Medicine c/o Candiolo Cancer Institute, Fondazione del Piemonte per l'Oncologia (FPO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Candiolo, 10060 Torino, Italy
- Istituto Nazionale di Fisica Nucleare (INFN), Italy
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46
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Siggel M, Bhaskara RM, Moesser MK, D̵ikić I, Hummer G. FAM134B-RHD Protein Clustering Drives Spontaneous Budding of Asymmetric Membranes. J Phys Chem Lett 2021; 12:1926-1931. [PMID: 33591770 PMCID: PMC8028312 DOI: 10.1021/acs.jpclett.1c00031] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/10/2021] [Indexed: 05/28/2023]
Abstract
Living cells constantly remodel the shape of their lipid membranes. In the endoplasmic reticulum (ER), the reticulon homology domain (RHD) of the reticulophagy regulator 1 (RETR1/FAM134B) forms dense autophagic puncta that are associated with membrane removal by ER-phagy. In molecular dynamics (MD) simulations, we find that FAM134B-RHD spontaneously forms clusters, driven in part by curvature-mediated attractions. At a critical size, as in a nucleation process, the FAM134B-RHD clusters induce the formation of membrane buds. The kinetics of budding depends sensitively on protein concentration and bilayer asymmetry. Our MD simulations shed light on the role of FAM134B-RHD in ER-phagy and show that membrane asymmetry can be used to modulate the kinetic barrier for membrane remodeling.
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Affiliation(s)
- Marc Siggel
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
| | - Ramachandra M. Bhaskara
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
- Institute
of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Buchmann
Institute of Molecular Life Sciences, Goethe
University Frankfurt, Max-von-Laue Straße 15, 60438 Frankfurt am Main, Germany
| | - Melanie K. Moesser
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
| | - Ivan D̵ikić
- Institute
of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Max
Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
- Buchmann
Institute of Molecular Life Sciences, Goethe
University Frankfurt, Max-von-Laue Straße 15, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
- Institute
of Biophysics, Goethe University Frankfurt, 60438 Frankfurt
am Main, Germany
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47
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Clathrin senses membrane curvature. Biophys J 2021; 120:818-828. [PMID: 33524373 DOI: 10.1016/j.bpj.2020.12.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/23/2020] [Accepted: 12/07/2020] [Indexed: 11/21/2022] Open
Abstract
The ability of proteins to assemble at sites of high membrane curvature is essential to diverse membrane remodeling processes, including clathrin-mediated endocytosis. Multiple adaptor proteins within the clathrin pathway have been shown to sense regions of high membrane curvature, leading to local recruitment of the clathrin coat. Because clathrin triskelia do not bind to the membrane directly, it has remained unclear whether the clathrin coat plays an active role in sensing membrane curvature or is passively recruited by adaptor proteins. Using a synthetic tag to assemble clathrin directly on membrane surfaces, here we show that clathrin is a strong sensor of membrane curvature, comparable with previously studied adaptor proteins. Interestingly, this sensitivity arises from clathrin assembly rather than from the properties of unassembled triskelia, suggesting that triskelia have preferred angles of interaction, as predicted by earlier structural data. Furthermore, when clathrin is recruited by adaptors, its curvature sensitivity is amplified by 2- to 10-fold, such that the resulting protein complex is up to 100 times more likely to assemble on a highly curved surface compared with a flatter one. This exquisite sensitivity points to a synergistic relationship between the coat and its adaptor proteins, which enables clathrin to pinpoint sites of high membrane curvature, an essential step in ensuring robust membrane traffic. More broadly, these findings suggest that protein networks, rather than individual protein domains, are likely the most potent drivers of membrane curvature sensing.
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Jan Z, Drab M, Drobne D, Bedina Zavec A, Benčina M, Drasler B, Hočevar M, Krek JL, Pađen L, Pajnič M, Repar N, Šimunič B, Štukelj R, Kralj-Iglič V. Decrease in Cellular Nanovesicles Concentration in Blood of Athletes More Than 15 Hours After Marathon. Int J Nanomedicine 2021; 16:443-456. [PMID: 33505159 PMCID: PMC7829122 DOI: 10.2147/ijn.s282200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/12/2020] [Indexed: 12/30/2022] Open
Abstract
Introduction Cellular nanovesicles (CNVs), that are shed from cells, have been recognized as promising indicators of health status. We analyzed the effect of long-distance running on concentration of CNVs, along with some standard blood parameters, in 27 athletes two days before and >15 hours after physical effort. Methods CNVs were isolated by repetitive centrifugation and washing of samples, and assessed by flow cytometry. Cholinesterase (ChE) and glutathione S-transferase (GST) activity were measured spectrophotometrically. Interleukin 6 (IL-6) and tumor necrosis factor-α (TNF-α) concentrations were measured using enzyme-linked immunosorbent assay (ELISA). C-reactive protein (CRP) was measured with immunoturbidimetric determination and lipidogram parameters were measured by enzymatic colorimetric assay. Flow cytometry was used for blood cell count and mean platelet volume (MPV) measurement. Results More than 15 hours after physical effort a decrease was found in CNVs' concentration in isolates from blood (46%; p<0.05), in ChE activity in whole blood (47%; p<0.001), in plasma (34%; p<0.01), and in erythrocyte suspension (54%; p<0.001), as well as in GST activity in erythrocyte suspension (16%; p<0.01) and in IL-6 concentration in plasma (63%; p<0.05). We found no change in GST activity in plasma and in TNF-α concentration in plasma. Correlations (>0.8; p<0.001) between CNVs' concentration and ChE activity, and GST activity, respectively, in erythrocyte suspension were found. Conclusion We found that >15 hours post-physical effort, CNVs' concentration was below the initial value, concomitant with other measured parameters: ChE and GST activity as well as IL-6 concentration, indicating a favorable effect of physical effort on health status. CNVs' concentration and ChE activity in isolates from peripheral blood proved to have potential as indicators of the response of the human body to inflammation after physical effort. Physical activity should be considered as an important factor in preparation of subjects for blood sampling in procedures focusing on CNV-containing diagnostic and therapeutic compounds.
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Affiliation(s)
- Zala Jan
- Laboratory of Clinical Biophysics, Faculty of Health Sciences, University of Ljubljana, Ljubljana, Slovenia
| | - Mitja Drab
- Laboratory of Physics, Faculty of Electrical Engineering, University of Ljubljana, Ljubljana, Slovenia
| | - Damjana Drobne
- Nanobiology and Nanotoxicology Group, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Apolonija Bedina Zavec
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Barbara Drasler
- Nanobiology and Nanotoxicology Group, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Matej Hočevar
- Physics and Chemistry of Materials, Laboratory of Surface Engineering and Applied Surface Science, The Institute of Metals and Technology, Ljubljana, Slovenia
| | - Judita Lea Krek
- Laboratory of Clinical Biophysics, Faculty of Health Sciences, University of Ljubljana, Ljubljana, Slovenia
| | - Ljubiša Pađen
- Laboratory of Clinical Biophysics, Faculty of Health Sciences, University of Ljubljana, Ljubljana, Slovenia
| | - Manca Pajnič
- Laboratory of Clinical Biophysics, Faculty of Health Sciences, University of Ljubljana, Ljubljana, Slovenia
| | - Neža Repar
- Nanobiology and Nanotoxicology Group, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Boštjan Šimunič
- Institute for Kinesiology Research, Science and Research Centre Koper, Koper, Slovenia
| | - Roman Štukelj
- Laboratory of Clinical Biophysics, Faculty of Health Sciences, University of Ljubljana, Ljubljana, Slovenia
| | - Veronika Kralj-Iglič
- Laboratory of Clinical Biophysics, Faculty of Health Sciences, University of Ljubljana, Ljubljana, Slovenia
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Bibissidis N, Betlem K, Cordoyiannis G, Bonhorst FPV, Goole J, Raval J, Daniel M, Góźdź W, Iglič A, Losada-Pérez P. Correlation between adhesion strength and phase behaviour in solid-supported lipid membranes. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.114492] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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50
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Woodward X, Kelly CV. Single-lipid dynamics in phase-separated supported lipid bilayers. Chem Phys Lipids 2020; 233:104991. [PMID: 33121937 DOI: 10.1016/j.chemphyslip.2020.104991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 11/26/2022]
Abstract
Phase separation is a fundamental organizing mechanism on cellular membranes. Lipid phases have complex dependencies on the membrane composition, curvature, tension, and temperature. Lipid diffusion rates vary by up to ten-fold between liquid-disordered (Ld) and liquid-ordered (Lo) phases depending on the membrane composition, measurement technique, and the surrounding environment. This manuscript reports the lipid diffusion on phase-separated supported lipid bilayers (SLBs) with varying temperature, composition, and lipid phase. Lipid diffusion is measured by single-particle tracking (SPT) and fluorescence correlation spectroscopy (FCS) via custom data acquisition and analysis protocols that apply to diverse membranes systems. Traditionally, SPT is sensitive to diffuser aggregation, whereas the diffusion rates reported by FCS are unaffected by the presence of immobile aggregates. Within this manuscript, we report (1) improved single-particle tracking analysis of lipid diffusion, (2) comparison and consistency between diffusion measurement methods for non-Brownian diffusers, and (3) the application of these methods to measure the phase, temperature, and composition dependencies in lipid diffusion. We demonstrate improved SPT analysis methods that yield consistent FCS and SPT diffusion results even when most fluorescent lipids are frequently confined within aggregates within the membrane. With varying membrane composition and temperature, we demonstrate differences in diffusion between the Ld and Lo phases of SLBs.
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Affiliation(s)
- Xinxin Woodward
- Department of Physics and Astronomy, Wayne State University, Detroit, MI, United States
| | - Christopher V Kelly
- Department of Physics and Astronomy, Wayne State University, Detroit, MI, United States.
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