1
|
Tam NW, Becker A, Mangiarotti A, Cipitria A, Dimova R. Extracellular Vesicle Mobility in Collagen I Hydrogels Is Influenced by Matrix-Binding Integrins. ACS NANO 2024. [PMID: 39400273 DOI: 10.1021/acsnano.4c07186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2024]
Abstract
Extracellular vesicles (EVs) are a diverse population of membrane structures produced and released by cells into the extracellular space for the intercellular trafficking of cargo molecules. They are implicated in various biological processes, including angiogenesis, immunomodulation, and cancer cell signaling. While much research has focused on their biogenesis or their effects on recipient cells, less is understood about how EVs are capable of traversing diverse tissue environments and crossing biological barriers. Their interactions with extracellular matrix components are of particular interest, as such interactions govern diffusivity and mobility, providing a potential basis for organotropism. To start to untangle how EV-matrix interactions affect diffusivity, we use high speed epifluorescence microscopy, single particle tracking, and confocal reflectance microscopy to analyze particle mobility and localization in extracellular matrix-mimicking hydrogels composed of collagen I. EVs are compared with synthetic liposomes and extruded plasma membrane vesicles to better understand the importance of membrane composition on these interactions. By treating EVs with trypsin to digest surface proteins, we determine that proteins are primarily responsible for EV immobilization in collagen I hydrogels. We next use a synthetic peptide competitive inhibitor to narrow down the identity of the proteins involved to argynylglycylaspartic acid (RGD) motif-binding integrins, which interact with unincorporated or denatured nonfibrillar collagen. Moreover, the effect of integrin inhibition with RGD peptides has strong implications for the use of RGD-peptide-based drugs to treat certain cancers, as integrin inhibition appears to increase EV mobility, improving their ability to infiltrate tissue-like environments.
Collapse
Affiliation(s)
- Nicky W Tam
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, Potsdam 14476, Germany
| | | | - Agustín Mangiarotti
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, Potsdam 14476, Germany
| | - Amaia Cipitria
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, Potsdam 14476, Germany
- Group of Bioengineering in Regeneration and Cancer, Biogipuzkoa Health Research Institute, San Sebastián 20014, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao 48009, Spain
| | - Rumiana Dimova
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, Potsdam 14476, Germany
| |
Collapse
|
2
|
Shrestha D, Bahasoan Y, Eggeling C. Cellular Output and Physicochemical Properties of the Membrane-Derived Vesicles Depend on Chemical Stimulants. ACS APPLIED MATERIALS & INTERFACES 2024; 16:48982-48992. [PMID: 39250321 PMCID: PMC11420866 DOI: 10.1021/acsami.4c07234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 08/13/2024] [Accepted: 08/21/2024] [Indexed: 09/11/2024]
Abstract
Synthetic liposomes are widely used as drug delivery vehicles in biomedical treatments, such as for mRNA-based antiviral vaccines like those recently developed against SARS-CoV-2. Extracellular vesicles (EVs), which are naturally produced by cells, have emerged as a next-generation delivery system. However, key questions regarding their origin within cells remain unresolved. In this regard, plasma membrane vesicles (PMVs), which are essentially produced from the cellular plasma membrane (PM), present a promising alternative. Unfortunately, their properties relevant to biomedical applications have not be extensively studied. Therefore, we conducted a thorough investigation of the methods used in the production of PMVs. By leveraging advanced fluorescence techniques in microscopy and flow cytometry, we demonstrated a strong dependence of the physicochemical attributes of PMVs on the chemicals used during their production. Following established protocols employing chemicals such as paraformaldehyde (PFA), N-ethylmaleimide (NEM) or dl-dithiothreitol (DTT) and by developing a modified NEM-based method that involved a hypotonic shock step, we generated PMVs from THP-1 CD1d cells. We systematically compared key parameters such as vesicle output, their size distribution, vesicular content analysis, vesicular membrane lipid organization and the mobility of a transmembrane protein. Our results revealed distinct trends: PMVs isolated using NEM-based protocols closely resembled natural vesicles, whereas PFA induced significant molecular cross-linking, leading to notable changes in the biophysical properties of the vesicles. Furthermore, our novel NEM protocol enhanced the efficiency of PMV production. In conclusion, our study highlights the unique characteristics of chemically produced PMVs and offers insights into their potentially diverse yet valuable biological functions.
Collapse
Affiliation(s)
- Dilip Shrestha
- MRC
Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, U.K.
- Department
of Life Sciences, Imperial College London, London SW7 2AZ, U.K.
| | - Yusuf Bahasoan
- MRC
Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, U.K.
| | - Christian Eggeling
- MRC
Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, U.K.
- Department
of Biophysical Imaging, Leibniz Institute
of Photonic Technologies e.V., member of the Leibniz Centre for Photonics
in Infection Research (LPI), Albert- Einstein Strasse 9, 07745 Jena, Germany
- Institute
of Applied Optics and Biophysics, Friedrich Schiller University Jena, Max-Wien Platz 1, 07743 Jena, Germany
- Jena
Center for Soft Matter (JCSM), Philosophenweg 7, 07743 Jena, Germany
| |
Collapse
|
3
|
Zulueta Diaz YDLM, Arnspang EC. Super-resolution microscopy to study membrane nanodomains and transport mechanisms in the plasma membrane. Front Mol Biosci 2024; 11:1455153. [PMID: 39290992 PMCID: PMC11405310 DOI: 10.3389/fmolb.2024.1455153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 08/19/2024] [Indexed: 09/19/2024] Open
Abstract
Biological membranes are complex, heterogeneous, and dynamic systems that play roles in the compartmentalization and protection of cells from the environment. It is still a challenge to elucidate kinetics and real-time transport routes for molecules through biological membranes in live cells. Currently, by developing and employing super-resolution microscopy; increasing evidence indicates channels and transporter nano-organization and dynamics within membranes play an important role in these regulatory mechanisms. Here we review recent advances and discuss the major advantages and disadvantages of using super-resolution microscopy to investigate protein organization and transport within plasma membranes.
Collapse
Affiliation(s)
| | - Eva C Arnspang
- Department of Green Technology, SDU Biotechnology, University of Southern Denmark, Odense, Denmark
| |
Collapse
|
4
|
Chakraborty S, Mishra J, Roy A, Niharika, Manna S, Baral T, Nandi P, Patra S, Patra SK. Liquid-liquid phase separation in subcellular assemblages and signaling pathways: Chromatin modifications induced gene regulation for cellular physiology and functions including carcinogenesis. Biochimie 2024; 223:74-97. [PMID: 38723938 DOI: 10.1016/j.biochi.2024.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/08/2024] [Accepted: 05/04/2024] [Indexed: 05/24/2024]
Abstract
Liquid-liquid phase separation (LLPS) describes many biochemical processes, including hydrogel formation, in the integrity of macromolecular assemblages and existence of membraneless organelles, including ribosome, nucleolus, nuclear speckles, paraspeckles, promyelocytic leukemia (PML) bodies, Cajal bodies (all exert crucial roles in cellular physiology), and evidence are emerging day by day. Also, phase separation is well documented in generation of plasma membrane subdomains and interplay between membranous and membraneless organelles. Intrinsically disordered regions (IDRs) of biopolymers/proteins are the most critical sticking regions that aggravate the formation of such condensates. Remarkably, phase separated condensates are also involved in epigenetic regulation of gene expression, chromatin remodeling, and heterochromatinization. Epigenetic marks on DNA and histones cooperate with RNA-binding proteins through their IDRs to trigger LLPS for facilitating transcription. How phase separation coalesces mutant oncoproteins, orchestrate tumor suppressor genes expression, and facilitated cancer-associated signaling pathways are unravelling. That autophagosome formation and DYRK3-mediated cancer stem cell modification also depend on phase separation is deciphered in part. In view of this, and to linchpin insight into the subcellular membraneless organelle assembly, gene activation and biological reactions catalyzed by enzymes, and the downstream physiological functions, and how all these events are precisely facilitated by LLPS inducing organelle function, epigenetic modulation of gene expression in this scenario, and how it goes awry in cancer progression are summarized and presented in this article.
Collapse
Affiliation(s)
- Subhajit Chakraborty
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Jagdish Mishra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Ankan Roy
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Niharika
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Soumen Manna
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Tirthankar Baral
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Piyasa Nandi
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Subhajit Patra
- Department of Chemical Engineering, Maulana Azad National Institute of Technology, Bhopal, India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India.
| |
Collapse
|
5
|
Han J, Meade J, Devine D, Sadeghpour A, Rappolt M, Goycoolea FM. Chitosan-coated liposomal systems for delivery of antibacterial peptide LL17-32 to Porphyromonas gingivalis. Heliyon 2024; 10:e34554. [PMID: 39149035 PMCID: PMC11325287 DOI: 10.1016/j.heliyon.2024.e34554] [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: 02/18/2024] [Revised: 05/29/2024] [Accepted: 07/11/2024] [Indexed: 08/17/2024] Open
Abstract
Periodontal disease is triggered by surface bacterial biofilms where bacteria are less susceptible to antibiotic treatment. The development of liposome-based delivery mechanisms for the therapeutic use of antimicrobial peptides is an attractive alternative in this regard. The cationic antimicrobial peptide LL-37 (human cathelicidin) is well-known to exert antibacterial activity against P orphyromonas gingivalis, a keystone oral pathogen. However, the antibacterial activity of the 16-amino acid fragment (LL17-32) of LL-37, is unknown. In addition, there are still gaps in studies using liposomal formulations as delivery vehicles of antibacterial peptides against this pathogen. This study was designed to examine the influence of the different types of liposomal formulations to associate and deliver LL17-32 to act against P. gingivalis. Chitosans of varying Mw and degree of acetylation (DA) were adsorbed at the surface of soya lecithin (SL) liposomes. Their bulk (average hydrodynamic size, ζ-potential and membrane fluidity) and ultrastructural (d-spacing, half-bilayer thickness and the water layer thickness) biophysical properties were investigated by a panel of techniques (DLS, SAXS, M3-PALS, fluorescence spectroscopy and TEM imaging). Their association efficiency, in vitro release, stability, and efficacy in killing the periodontal pathogen P. gingivalis were also investigated. All liposomal systems possessed spherical morphologies and good shelf-life stabilities. Under physiological conditions, chitosan formulations with a high DA demonstrated enhanced stability in comparison to low DA-chitosan formulations. Chitosans and LL17-32 both decreased SL-liposomal membrane fluidity. LL17-32 exhibited a high degree of association with SL-liposomes without in vitro release. In biological studies, free LL17-32 or chitosans alone, demonstrated microbicidal activity against P. gingivalis, however this was attenuated when LL17-32 was loaded onto the SL-liposome delivery system, presumably due to the restrained release of the peptide. A property that could be harnessed in future studies (e.g., oral mucoadhesive slow-release formulations).
Collapse
Affiliation(s)
- Jinyang Han
- School of Food Science and Nutrition, University of Leeds, Woodhouse Ln, Leeds, LS2 9JT, United Kingdom
| | - Josephine Meade
- School of Dentistry, University of Leeds, Woodhouse Ln, Leeds, LS2 9JT, United Kingdom
| | - Deirdre Devine
- School of Dentistry, University of Leeds, Woodhouse Ln, Leeds, LS2 9JT, United Kingdom
| | - Amin Sadeghpour
- School of Food Science and Nutrition, University of Leeds, Woodhouse Ln, Leeds, LS2 9JT, United Kingdom
| | - Michael Rappolt
- School of Food Science and Nutrition, University of Leeds, Woodhouse Ln, Leeds, LS2 9JT, United Kingdom
| | - Francisco M Goycoolea
- School of Food Science and Nutrition, University of Leeds, Woodhouse Ln, Leeds, LS2 9JT, United Kingdom
- Department of Cell Biology and Histology, University of Murcia, Campus de Espinardo, Murcia, 30100, Spain
| |
Collapse
|
6
|
Zhukov A, Vereshchagin M. Polar Glycerolipids and Membrane Lipid Rafts. Int J Mol Sci 2024; 25:8325. [PMID: 39125896 PMCID: PMC11312961 DOI: 10.3390/ijms25158325] [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: 07/03/2024] [Revised: 07/24/2024] [Accepted: 07/27/2024] [Indexed: 08/12/2024] Open
Abstract
Current understanding of the structure and functioning of biomembranes is impossible without determining the mechanism of formation of membrane lipid rafts. The formation of liquid-ordered and disordered phases (Lo and Ld) and lipid rafts in membranes and their simplified models is discussed. A new consideration of the processes of formation of lipid phases Lo and Ld and lipid rafts is proposed, taking into account the division of each of the glycerophospholipids into several groups. Generally accepted three-component schemes for modeling the membrane structure are critically considered. A four-component scheme is proposed, which is designed to more accurately assume the composition of lipids in the resulting Lo and Ld phases. The role of the polar head groups of phospholipids and, in particular, phosphatidylethanolamine is considered. The structure of membrane rafts and the possible absence of a clear boundary between the Lo and Ld phases are discussed.
Collapse
Affiliation(s)
| | - Mikhail Vereshchagin
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow 127276, Russia;
| |
Collapse
|
7
|
Zhang C, Singla RK, Tang M, Shen B. Natural products act as game-changer potentially in treatment and management of sepsis-mediated inflammation: A clinical perspective. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 130:155710. [PMID: 38759311 DOI: 10.1016/j.phymed.2024.155710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 04/19/2024] [Accepted: 05/02/2024] [Indexed: 05/19/2024]
Abstract
BACKGROUND Sepsis, a life-threatening condition resulting from uncontrolled host responses to infection, poses a global health challenge with limited therapeutic options. Due to high heterogeneity, sepsis lacks specific therapeutic drugs. Additionally, there remains a significant gap in the clinical management of sepsis regarding personalized and precise medicine. PURPOSE This review critically examines the scientific landscape surrounding natural products in sepsis and sepsis-mediated inflammation, highlighting their clinical potential. METHODS Following the PRISMA guidelines, we retrieved articles from PubMed to explore potential natural products with therapeutic effects in sepsis-mediated inflammation. RESULTS 434 relevant in vitro and in vivo studies were identified and screened. Ultimately, 55 studies were obtained as the supporting resources for the present review. We divided the 55 natural products into three categories: those influencing the synthesis of inflammatory factors, those affecting surface receptors and modulatory factors, and those influencing signaling pathways and the inflammatory cascade. CONCLUSION Natural products' potential as game-changers in sepsis-mediated inflammation management lies in their ability to modulate hallmarks in sepsis, including inflammation, immunity, and coagulopathy, which provides new therapeutic avenues that are readily accessible and capable of undergoing rapid clinical validation and deployment, offering a gift from nature to humanity. Innovative techniques like bioinformatics, metabolomics, and systems biology offer promising solutions to overcome these obstacles and facilitate the development of natural product-based therapeutics, holding promise for personalized and precise sepsis management and improving patient outcomes. However, standardization, bioavailability, and safety challenges arise during experimental validation and clinical trials of natural products.
Collapse
Affiliation(s)
- Chi Zhang
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, 610212, PR China
| | - Rajeev K Singla
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, 610212, PR China; School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab-144411, India
| | - Min Tang
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, 610212, PR China; West China School of Nursing, Sichuan University, Chengdu, PR China
| | - Bairong Shen
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, 610212, PR China.
| |
Collapse
|
8
|
Wang J, Taki M, Ohba Y, Arita M, Yamaguchi S. Fluorescence Lifetime Imaging of Lipid Heterogeneity in the Inner Mitochondrial Membrane with a Super-photostable Environment-Sensitive Probe. Angew Chem Int Ed Engl 2024; 63:e202404328. [PMID: 38804831 DOI: 10.1002/anie.202404328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Indexed: 05/29/2024]
Abstract
The inner mitochondrial membrane (IMM) undergoes dynamic morphological changes, which are crucial for the maintenance of mitochondrial functions as well as cell survival. As the dynamics of the membrane are governed by its lipid components, a fluorescent probe that can sense spatiotemporal alterations in the lipid properties of the IMM over long periods of time is required to understand mitochondrial physiological functions in detail. Herein, we report a red-emissive IMM-labeling reagent with excellent photostability and sensitivity to its environment, which enables the visualization of the IMM ultrastructure using super-resolution microscopy as well as of the lipid heterogeneity based on the fluorescence lifetime at the single mitochondrion level. Combining the probe and fluorescence lifetime imaging microscopy (FLIM) showed that peroxidation of unsaturated lipids in the IMM by reactive oxygen species caused an increase in the membrane order, which took place prior to mitochondrial swelling.
Collapse
Affiliation(s)
- Junwei Wang
- Institute of Transformative Bio-Molecules, Nagoya University, Furo, Chikusa, Nagoya 464-8601, Japan
| | - Masayasu Taki
- Institute of Transformative Bio-Molecules, Nagoya University, Furo, Chikusa, Nagoya 464-8601, Japan
| | - Yohsuke Ohba
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Minato-ku, Tokyo 105-8512, Japan
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences (IMS), Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Makoto Arita
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Minato-ku, Tokyo 105-8512, Japan
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences (IMS), Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama-City University, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Human Biology-Microbiome-Quantum Research Center (WPI-Bio2Q), Keio University, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Shigehiro Yamaguchi
- Institute of Transformative Bio-Molecules, Nagoya University, Furo, Chikusa, Nagoya 464-8601, Japan
- Department of Chemistry, Graduate School of Science, Integrated Research Consortium on Chemical Sciences (IRCCS), Nagoya University, Furo, Chikusa, Nagoya 464-8602, Japan
| |
Collapse
|
9
|
Kettel P, Karagöz GE. Endoplasmic reticulum: Monitoring and maintaining protein and membrane homeostasis in the endoplasmic reticulum by the unfolded protein response. Int J Biochem Cell Biol 2024; 172:106598. [PMID: 38768891 DOI: 10.1016/j.biocel.2024.106598] [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: 03/18/2024] [Revised: 05/01/2024] [Accepted: 05/14/2024] [Indexed: 05/22/2024]
Abstract
The endoplasmic reticulum (ER) regulates essential cellular processes, including protein folding, lipid synthesis, and calcium homeostasis. The ER homeostasis is maintained by a conserved set of signaling cascades called the Unfolded Protein Response (UPR). How the UPR senses perturbations in ER homeostasis has been the subject of active research for decades. In metazoans, the UPR consists of three ER-membrane embedded sensors: IRE1, PERK and ATF6. These sensors detect the accumulation of misfolded proteins in the ER lumen and adjust protein folding capacity according to cellular needs. Early work revealed that the ER-resident chaperone BiP binds to all three UPR sensors in higher eukaryotes and BiP binding was suggested to regulate their activity. More recent data have shown that in higher eukaryotes the interaction of the UPR sensors with a complex network of chaperones and misfolded proteins modulates their activation and deactivation dynamics. Furthermore, emerging evidence suggests that the UPR monitors ER membrane integrity beyond protein folding defects. However, the mechanistic and structural basis of UPR activation by proteotoxic and lipid bilayer stress in higher eukaryotes remains only partially understood. Here, we review the current understanding of novel protein interaction networks and the contribution of the lipid membrane environment to UPR activation.
Collapse
Affiliation(s)
- Paulina Kettel
- Max Perutz Laboratories Vienna, Vienna BioCenter, Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - G Elif Karagöz
- Max Perutz Laboratories Vienna, Vienna BioCenter, Vienna, Austria; Medical University of Vienna, Vienna, Austria.
| |
Collapse
|
10
|
Pan X, Mastrella S, Khamzaaliyeva M, Ashley DD. Exploring the connections between ER-based lipid metabolism and plasma membrane nanodomain signaling. THE NEW PHYTOLOGIST 2024; 243:48-57. [PMID: 38757654 DOI: 10.1111/nph.19815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/26/2024] [Indexed: 05/18/2024]
Abstract
Recent advancements in our understanding of cell membrane dynamics have shed light on the importance of plasma membrane (PM) nanodomains in plant cell signaling. Nevertheless, many aspects of membrane nanodomains, including their regulatory mechanisms and biological functions, remain enigmatic. To address this knowledge gap, our review article proposes a novel perspective wherein signaling pathways target endoplasmic reticulum (ER)-based lipid metabolism to exert control over the formation and function of membrane nanodomains. Subsequently, these nanodomains reciprocate by influencing the localization and activity of signaling molecules at the PM. We place a specific emphasis on ER-based enzymatic reactions, given the ER's central role in membrane lipid biosynthesis and its capacity to directly impact PM lipid composition, particularly with regard to saturation levels - an essential determinant of nanodomain properties. The interplay among cell signaling, glycerolipid metabolism, and PM nanodomain may create feedforward/feedback loops that fine-tune cellular responses to developmental and environmental cues.
Collapse
Affiliation(s)
- Xue Pan
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, M1C 1A4, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Sophia Mastrella
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, M1C 1A4, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Mohinur Khamzaaliyeva
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, M1C 1A4, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Didier-Deschamps Ashley
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, M1C 1A4, Canada
| |
Collapse
|
11
|
Schaefer KG, Russell CM, Pyron RJ, Conley EA, Barrera FN, King GM. Polymerization mechanism of the Candida albicans virulence factor candidalysin. J Biol Chem 2024; 300:107370. [PMID: 38750794 PMCID: PMC11193009 DOI: 10.1016/j.jbc.2024.107370] [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: 03/05/2024] [Revised: 04/16/2024] [Accepted: 05/06/2024] [Indexed: 06/11/2024] Open
Abstract
Candida albicans is a commensal fungus that can cause epithelial infections and life-threatening invasive candidiasis. The fungus secretes candidalysin (CL), a peptide that causes cell damage and immune activation by permeation of epithelial membranes. The mechanism of CL action involves strong peptide assembly into polymers in solution. The free ends of linear CL polymers can join, forming loops that become pores upon binding to membranes. CL polymers constitute a therapeutic target for candidiasis, but little is known about CL self-assembly in solution. Here, we examine the assembly mechanism of CL in the absence of membranes using complementary biophysical tools, including a new fluorescence polymerization assay, mass photometry, and atomic force microscopy. We observed that CL assembly is slow, as tracked with the fluorescent marker C-laurdan. Single-molecule methods showed that CL polymerization involves a convolution of four processes. Self-assembly begins with the formation of a basic subunit, thought to be a CL octamer that is the polymer seed. Polymerization proceeds via the addition of octamers, and as polymers grow they can curve and form loops. Alternatively, secondary polymerization can occur and cause branching. Interplay between the different rates determines the distribution of CL particle types, indicating a kinetic control mechanism. This work elucidates key physical attributes underlying CL self-assembly which may eventually evoke pharmaceutical development.
Collapse
Affiliation(s)
| | - Charles M Russell
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Robert J Pyron
- Genome Science and Technology, University of Tennessee, Knoxville, Tennessee
| | - Elizabeth A Conley
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee.
| | - Gavin M King
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri; Department of Biochemistry, University of Missouri, Columbia, Missouri.
| |
Collapse
|
12
|
Ren Z, Wang K, Zhang Y, Chen H, Zhu Y, Li H, Lou J, Wang H, Xu C. Transient hydroxycholesterol treatment restrains TCR signaling to promote long-term immunity. Cell Chem Biol 2024; 31:920-931.e6. [PMID: 38759618 DOI: 10.1016/j.chembiol.2024.04.005] [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: 11/17/2023] [Revised: 03/20/2024] [Accepted: 04/16/2024] [Indexed: 05/19/2024]
Abstract
T cell receptor (TCR) plays a fundamental role in adaptive immunity, and TCR-T cell therapy holds great promise for treating solid tumors and other diseases. However, there is a noticeable absence of chemical tools tuning TCR activity. In our study, we screened natural sterols for their regulatory effects on T cell function and identified 7-alpha-hydroxycholesterol (7a-HC) as a potent inhibitor of TCR signaling. Mechanistically, 7a-HC promoted membrane binding of CD3ε cytoplasmic domain, a crucial signaling component of the TCR-CD3 complex, through alterations in membrane physicochemical properties. Enhanced CD3ε membrane binding impeded the condensation between CD3ε and the key kinase Lck, thereby inhibiting Lck-mediated TCR phosphorylation. Transient treatments of TCR-T cells with 7a-HC resulted in reduced signaling strength, increased memory cell populations, and superior long-term antitumor functions. This study unveils a chemical regulation of TCR signaling, which can be exploited to enhance the long-term efficacy of TCR-T cell therapy.
Collapse
Affiliation(s)
- Zhengxu Ren
- Key Laboratory of Multi-Cell Systems, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Kun Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yong Zhang
- Key Laboratory of Epigenetic Regulation and Intervention, Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hui Chen
- Key Laboratory of Epigenetic Regulation and Intervention, Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yiming Zhu
- Key Laboratory of Multi-Cell Systems, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hua Li
- Key Laboratory of Multi-Cell Systems, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jizhong Lou
- Key Laboratory of Epigenetic Regulation and Intervention, Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Haopeng Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
| | - Chenqi Xu
- Key Laboratory of Multi-Cell Systems, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
| |
Collapse
|
13
|
von Lersner A, Fernandes F, Ozawa PM, Jackson M, Masureel M, Ho H, Lima SM, Vagner T, Sung BH, Wehbe M, Franze K, Pua H, Wilson JT, Irish JM, Weaver AM, Di Vizio D, Zijlstra A. Multiparametric Single-Vesicle Flow Cytometry Resolves Extracellular Vesicle Heterogeneity and Reveals Selective Regulation of Biogenesis and Cargo Distribution. ACS NANO 2024; 18:10464-10484. [PMID: 38578701 PMCID: PMC11025123 DOI: 10.1021/acsnano.3c11561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/07/2024]
Abstract
Mammalian cells release a heterogeneous array of extracellular vesicles (EVs) that contribute to intercellular communication by means of the cargo that they carry. To resolve EV heterogeneity and determine if cargo is partitioned into select EV populations, we developed a method named "EV Fingerprinting" that discerns distinct vesicle populations using dimensional reduction of multiparametric data collected by quantitative single-EV flow cytometry. EV populations were found to be discernible by a combination of membrane order and EV size, both of which were obtained through multiparametric analysis of fluorescent features from the lipophilic dye Di-8-ANEPPS incorporated into the lipid bilayer. Molecular perturbation of EV secretion and biogenesis through respective ablation of the small GTPase Rab27a and overexpression of the EV-associated tetraspanin CD63 revealed distinct and selective alterations in EV populations, as well as cargo distribution. While Rab27a disproportionately affects all small EV populations with high membrane order, the overexpression of CD63 selectively increased the production of one small EV population of intermediate membrane order. Multiplexing experiments subsequently revealed that EV cargos have a distinct, nonrandom distribution with CD63 and CD81 selectively partitioning into smaller vs larger EVs, respectively. These studies not only present a method to probe EV biogenesis but also reveal how the selective partitioning of cargo contributes to EV heterogeneity.
Collapse
Affiliation(s)
- Ariana
K. von Lersner
- Program in
Cancer Biology, Vanderbilt University, Nashville, Tennessee 37232, United
States
| | - Fabiane Fernandes
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Institute
of Applied Biosciences and Chemistry, Hogeschool
Arnhem en Nijmegen University of Applied Sciences, Nijmegen 6525 EM, Gelderland, Netherlands
| | - Patricia Midori
Murobushi Ozawa
- The
Center
for EV Research, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department
of Cell and Developmental Biology, Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
| | - Marques Jackson
- Department
of Research Pathology, Genentech, San Francisco, California 94080, United States
| | - Matthieu Masureel
- Department
of Structural Biology, Genentech, San Francisco, California 94080, United States
| | - Hoangdung Ho
- Department
of Structural Biology, Genentech, San Francisco, California 94080, United States
| | - Sierra M. Lima
- Department
of Cell and Developmental Biology, Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
| | - Tatyana Vagner
- Department
of Surgery, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Bong Hwan Sung
- The
Center
for EV Research, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department
of Cell and Developmental Biology, Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
| | - Mohamed Wehbe
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Kai Franze
- Department
of Research Pathology, Genentech, San Francisco, California 94080, United States
- KNIME
GmbH, Konstanz 78467, Germany
| | - Heather Pua
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- The
Center
for EV Research, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - John T. Wilson
- Program in
Cancer Biology, Vanderbilt University, Nashville, Tennessee 37232, United
States
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- The
Center
for EV Research, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jonathan M. Irish
- Program in
Cancer Biology, Vanderbilt University, Nashville, Tennessee 37232, United
States
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Department
of Cell and Developmental Biology, Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
| | - Alissa M. Weaver
- Program in
Cancer Biology, Vanderbilt University, Nashville, Tennessee 37232, United
States
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- The
Center
for EV Research, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department
of Cell and Developmental Biology, Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
| | - Dolores Di Vizio
- Department
of Surgery, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Andries Zijlstra
- Program in
Cancer Biology, Vanderbilt University, Nashville, Tennessee 37232, United
States
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- The
Center
for EV Research, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department
of Research Pathology, Genentech, San Francisco, California 94080, United States
| |
Collapse
|
14
|
Park S, Pastor RW, Im W. Binary bilayer simulations for partitioning within membranes. Methods Enzymol 2024; 701:123-156. [PMID: 39025570 DOI: 10.1016/bs.mie.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Membrane proteins (MPs) often show preference for one phase over the other, which is characterized by the partition coefficient, Kp. The physical mechanisms underlying Kp have been only inferred indirectly from experiments due to the unavailability of detailed structures and compositions of ordered phases. Molecular dynamics (MD) simulations can complement these details and thus, in principle, provide further insights into the partitioning of MPs between two phases. However, the application of MD has remained difficult due to long time scales required for equilibration and large system size for the phase stability, which have not been fully resolved even in free energy simulations. This chapter describes the recently developed binary bilayer simulation method, where the membrane is composed of two laterally attached membrane patches. The binary bilayer system (BBS) is designed to preserve the lateral packing of both phases in a significantly smaller size compared to that required for macroscopic phase separation. These characteristics are advantageous in partitioning simulations, as the length scale for diffusion across the system can be significantly smaller. Hence the BBS can be efficiently employed in both conventional MD and free energy simulations, though sampling in ordered phases remains difficult due to slow diffusion. Development of efficient lipid swapping methods and its combination with the BBS would be a useful approach for partitioning in coexisting phases.
Collapse
Affiliation(s)
- Soohyung Park
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, PA, United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Wonpil Im
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, PA, United States.
| |
Collapse
|
15
|
Erazo-Oliveras A, Muñoz-Vega M, Salinas ML, Wang X, Chapkin RS. Dysregulation of cellular membrane homeostasis as a crucial modulator of cancer risk. FEBS J 2024; 291:1299-1352. [PMID: 36282100 PMCID: PMC10126207 DOI: 10.1111/febs.16665] [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: 06/18/2022] [Revised: 09/09/2022] [Accepted: 10/24/2022] [Indexed: 11/07/2022]
Abstract
Cellular membranes serve as an epicentre combining extracellular and cytosolic components with membranous effectors, which together support numerous fundamental cellular signalling pathways that mediate biological responses. To execute their functions, membrane proteins, lipids and carbohydrates arrange, in a highly coordinated manner, into well-defined assemblies displaying diverse biological and biophysical characteristics that modulate several signalling events. The loss of membrane homeostasis can trigger oncogenic signalling. More recently, it has been documented that select membrane active dietaries (MADs) can reshape biological membranes and subsequently decrease cancer risk. In this review, we emphasize the significance of membrane domain structure, organization and their signalling functionalities as well as how loss of membrane homeostasis can steer aberrant signalling. Moreover, we describe in detail the complexities associated with the examination of these membrane domains and their association with cancer. Finally, we summarize the current literature on MADs and their effects on cellular membranes, including various mechanisms of dietary chemoprevention/interception and the functional links between nutritional bioactives, membrane homeostasis and cancer biology.
Collapse
Affiliation(s)
- Alfredo Erazo-Oliveras
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Mónica Muñoz-Vega
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Michael L. Salinas
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Xiaoli Wang
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Robert S. Chapkin
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
- Center for Environmental Health Research; Texas A&M University; College Station, Texas, 77843; USA
| |
Collapse
|
16
|
Neukam M, Sala P, Brunner AD, Ganß K, Palladini A, Grzybek M, Topcheva O, Vasiljević J, Broichhagen J, Johnsson K, Kurth T, Mann M, Coskun Ü, Solimena M. Purification of time-resolved insulin granules reveals proteomic and lipidomic changes during granule aging. Cell Rep 2024; 43:113836. [PMID: 38421874 DOI: 10.1016/j.celrep.2024.113836] [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: 06/05/2023] [Revised: 12/29/2023] [Accepted: 02/05/2024] [Indexed: 03/02/2024] Open
Abstract
Endocrine cells employ regulated exocytosis of secretory granules to secrete hormones and neurotransmitters. Secretory granule exocytosis depends on spatiotemporal variables such as proximity to the plasma membrane and age, with newly generated granules being preferentially released. Despite recent advances, we lack a comprehensive view of the molecular composition of insulin granules and associated changes over their lifetime. Here, we report a strategy for the purification of insulin secretory granules of distinct age from insulinoma INS-1 cells. Tagging the granule-resident protein phogrin with a cleavable CLIP tag, we obtain intact fractions of age-distinct granules for proteomic and lipidomic analyses. We find that the lipid composition changes over time, along with the physical properties of the membrane, and that kinesin-1 heavy chain (KIF5b) as well as Ras-related protein 3a (RAB3a) associate preferentially with younger granules. Further, we identify the Rho GTPase-activating protein (ARHGAP1) as a cytosolic factor associated with insulin granules.
Collapse
Affiliation(s)
- Martin Neukam
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany.
| | - Pia Sala
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Center of Membrane Biochemistry and Lipid Research, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | | | - Katharina Ganß
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Alessandra Palladini
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Center of Membrane Biochemistry and Lipid Research, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | - Michal Grzybek
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Center of Membrane Biochemistry and Lipid Research, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | - Oleksandra Topcheva
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Jovana Vasiljević
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Johannes Broichhagen
- Department of Chemical Biology, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Thomas Kurth
- TU Dresden, Center for Molecular and Cellular Bioengineering (CMCB), Technology Platform, Electron Microscopy and Histology Facility, 01307 Dresden, Saxony, Germany
| | - Matthias Mann
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Ünal Coskun
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Center of Membrane Biochemistry and Lipid Research, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | - Michele Solimena
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany.
| |
Collapse
|
17
|
Kang C, Fujioka K, Sun R. Atomistic Insight into the Lipid Nanodomains of Synaptic Vesicles. J Phys Chem B 2024; 128:2707-2716. [PMID: 38325816 DOI: 10.1021/acs.jpcb.3c07982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Membrane curvature, once regarded as a passive consequence of membrane composition and cellular architecture, has been shown to actively modulate various properties of the cellular membrane. These changes could also lead to segregation of the constituents of the membrane, generating nanodomains with precise biological properties. Proteins often linked with neurodegeneration (e.g., tau, alpha-synuclein) exhibit an unintuitive affinity for synaptic vesicles in neurons, which are reported to lack distinct, ordered nanodomains based on their composition. In this study, all-atom molecular dynamics simulations are used to study a full-scale synaptic vesicle of realistic Gaussian curvature and its effect on the membrane dynamics and lipid nanodomain organization. Compelling indicators of nanodomain formation, from the perspective of composition, surface areas per lipid, order parameter, and domain lifetime, are identified in the vesicle membrane, which are absent in a flat bilayer of the same lipid composition. Therefore, our study supports the idea that curvature may induce phase separation in an otherwise fluid, disordered membrane.
Collapse
Affiliation(s)
- Christopher Kang
- Department of Chemistry, The University of Hawai'i, Ma̅noa, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Kazuumi Fujioka
- Department of Chemistry, The University of Hawai'i, Ma̅noa, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Rui Sun
- Department of Chemistry, The University of Hawai'i, Ma̅noa, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| |
Collapse
|
18
|
Doherty W, Benson S, Pepdjonovic L, Koppes AN, Koppes RA. Cell Line and Media Composition Influence the Production of Giant Plasma Membrane Vesicles. ACS Biomater Sci Eng 2024; 10:1880-1891. [PMID: 38374716 PMCID: PMC10934252 DOI: 10.1021/acsbiomaterials.3c01596] [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: 10/27/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/21/2024]
Abstract
Giant plasma membrane vesicles (GPMVs) have been utilized as a model to study phase separation in the plasma membrane. Additionally, GPMVs have been employed as vehicle for delivering molecular cargo, including small molecule drugs and nanoparticles. Nearly all examples of GPMV production use a defined salt buffer that is a stark contrast to typical cell culture medium. In this study, we demonstrate that the addition of formaldehyde and dithiothreitol to a standard culture medium was capable of generating GPMVs at a concentration equal to or higher than the traditional production buffer. These methods were evaluated for two human cell lines: kidney endothelial and Schwann cells (SCs). Morphological properties of the resultant GPMVs exhibited no significant differences between the two formulations. Factors such as pH and seeding density significantly influenced the production of GPMVs in both mediums. The cell type and seeding density was shown to influence the number of GPMVs to the greatest extent. SCs yield more GPMVs at higher seeding densities compared to endothelial cells. Stability of the membrane of the GPMVs produced in both mediums was evaluated by monitoring passive diffusion of two fluorescently tagged dextrans (3 and 10 kDa). Regardless of the production formulation or cell type, approximately 85% GPMVs are impermeable to either dextran. Cold storage for on-demand use and shipping are essential for broader use of GPMVs. Toward this aim, we have evaluated the GMPV number and morphologies following storage at -80 °C and in liquid nitrogen. A significant loss of the GPMV number, ∼30%, was observed following storage across production formulations as well as cell types. Our results indicate that smaller GMPVs, <5 μm are more stable for preservation. In conclusion, GPMVs can be produced in a broad range of formulations, exhibit a high degree of stability, and can undergo cold storage for further adoption.
Collapse
Affiliation(s)
- William Doherty
- Department
of Chemical Engineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Sarah Benson
- Department
of Chemical Engineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Lisa Pepdjonovic
- Department
of Chemical Engineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Abigail N. Koppes
- Department
of Chemical Engineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
- Department
of Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
- Department
of Bioengineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Ryan A. Koppes
- Department
of Chemical Engineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| |
Collapse
|
19
|
Dong PT, Tian J, Kobayashi-Kirschvink KJ, Cen L, McLean JS, Bor B, Shi W, He X. Episymbiotic Saccharibacteria induce intracellular lipid droplet production in their host bacteria. THE ISME JOURNAL 2024; 18:wrad034. [PMID: 38366018 PMCID: PMC10939385 DOI: 10.1093/ismejo/wrad034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/07/2023] [Accepted: 12/20/2023] [Indexed: 02/18/2024]
Abstract
Saccharibacteria (formerly TM7) are a group of widespread and genetically diverse ultrasmall bacteria with highly reduced genomes that belong to Candidate Phyla Radiation, a large monophyletic lineage with poorly understood biology. Nanosynbacter lyticus type strain TM7x is the first Saccharibacteria member isolated from the human oral microbiome. With restrained metabolic capacities, TM7x lives on the surface of, and forms an obligate episymbiotic relationship with its bacterial host, Schaalia odontolytica strain XH001. The symbiosis allows TM7x to propagate but presents a burden to host bacteria by inducing stress response. Here, we employed super-resolution fluorescence imaging to investigate the physical association between TM7x and XH001. We showed that the binding with TM7x led to a substantial alteration in the membrane fluidity of XH001. We also revealed the formation of intracellular lipid droplets in XH001 when forming episymbiosis with TM7x, a feature that has not been reported in oral bacteria. The TM7x-induced lipid droplets accumulation in XH001 was confirmed by label-free Raman spectroscopy, which also unveiled additional phenotypical features when XH001 cells are physically associated with TM7x. Further exploration through culturing XH001 under various stress conditions showed that lipid droplets accumulation was a general response to stress. A survival assay demonstrated that the presence of lipid droplets plays a protective role in XH001, enhancing its survival under adverse conditions. In conclusion, our study sheds new light on the intricate interaction between Saccharibacteria and their host bacteria, highlighting the potential benefit conferred by TM7x to its host and further emphasizing the context-dependent nature of symbiotic relationships.
Collapse
Affiliation(s)
- Pu-Ting Dong
- Department of Microbiology, The ADA Forsyth Institute, Boston, MA 02142, United States
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, MA 02115, United States
| | - Jing Tian
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, Beijing 100081, China
| | - Koseki J Kobayashi-Kirschvink
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Laser Biomedical Research Center, G. R. Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Lujia Cen
- Department of Microbiology, The ADA Forsyth Institute, Boston, MA 02142, United States
| | - Jeffrey S McLean
- Department of Periodontics, University of Washington, Seattle, WA 98195, United States
| | - Batbileg Bor
- Department of Microbiology, The ADA Forsyth Institute, Boston, MA 02142, United States
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, MA 02115, United States
| | - Wenyuan Shi
- Department of Microbiology, The ADA Forsyth Institute, Boston, MA 02142, United States
| | - Xuesong He
- Department of Microbiology, The ADA Forsyth Institute, Boston, MA 02142, United States
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, MA 02115, United States
| |
Collapse
|
20
|
Chaudhury A, Swarnakar S, Pattnaik GP, Varshney GK, Chakraborty H, Basu JK. Peptide-Induced Fusion of Dynamic Membrane Nanodomains: Implications in a Viral Entry. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:17713-17722. [PMID: 38031897 DOI: 10.1021/acs.langmuir.3c02230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Enveloped viruses infect host cells via protein-mediated membrane fusion. However, insights into the microscopic rearrangement induced by the viral proteins and peptides have not yet emerged. Here, we report a new methodology to extract viral fusion peptide (FP)-mediated biomembrane dynamical nanodomain fusion parameter, λ, based on stimulated emission depletion microscopy coupled with fluorescence correlation spectroscopy. We also define another dynamical parameter membrane gradient, defined in terms of the ratio of average lipid diffusion coefficients across dynamic crossover length scales, ξ. Significantly, we observe that λ as well as these mobility gradients are larger in the stiffer liquid-ordered (Lo) phase compared to the liquid-disordered phase and are more effective at the smaller nanodomain interfaces, which are only present in the Lo phase. The results could possibly help to resolve a long-standing puzzle about the enhanced fusogenicity of FP in the Lo phase. Results obtained from the diffusion results have been correlated with the human immunodeficiency virus gp41 FP-induced membrane fusion.
Collapse
Affiliation(s)
- Anurag Chaudhury
- Department of Physics, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Shovon Swarnakar
- Department of Physics, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | | | - Gopal K Varshney
- Department of Physics, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Hirak Chakraborty
- School of Chemistry, Sambalpur University, Jyoti Vihar, Burla, Odisha 768019, India
| | - Jaydeep Kumar Basu
- Department of Physics, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| |
Collapse
|
21
|
Xie M, Koch EHW, van Walree CA, Sobota A, Sonnen AFP, Breukink E, Killian JA, Lorent JH. Two separate mechanisms are involved in membrane permeabilization during lipid oxidation. Biophys J 2023; 122:4503-4517. [PMID: 37905401 PMCID: PMC10719051 DOI: 10.1016/j.bpj.2023.10.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/18/2023] [Accepted: 10/25/2023] [Indexed: 11/02/2023] Open
Abstract
Lipid oxidation is a universal degradative process of cell membrane lipids that is induced by oxidative stress and reactive oxygen and nitrogen species (RONS) in multiple pathophysiological situations. It has been shown that certain oxidized lipids alter membrane properties, leading to a loss of membrane function. Alteration of membrane properties is thought to depend on the initial membrane lipid composition, such as the number of acyl chain unsaturations. However, it is unclear how oxidative damage is related to biophysical properties of membranes. We therefore set out to quantify lipid oxidation through various analytical methods and determine key biophysical membrane parameters using model membranes containing lipids with different degrees of lipid unsaturation. As source for RONS, we used cold plasma, which is currently developed as treatment for infections and cancer. Our data revealed complex lipid oxidation that can lead to two main permeabilization mechanisms. The first one appears upon direct contact of membranes with RONS and depends on the formation of truncated oxidized phospholipids. These lipids seem to be partly released from the bilayer, implying that they are likely to interact with other membranes and potentially act as signaling molecules. This mechanism is independent of lipid unsaturation, does not rely on large variations in lipid packing, and is most probably mediated via short-living RONS. The second mechanism takes over after longer incubation periods and probably depends on the continued formation of lipid oxygen adducts such as lipid hydroperoxides or ketones. This mechanism depends on lipid unsaturation and involves large variations in lipid packing. This study indicates that polyunsaturated lipids, which are present in mammalian membranes rather than in bacteria, do not sensitize membranes to instant permeabilization by RONS but could promote long-term damage.
Collapse
Affiliation(s)
- Min Xie
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Utrecht, the Netherlands
| | - Eveline H W Koch
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Utrecht, the Netherlands
| | - Cornelis A van Walree
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Utrecht, the Netherlands; University College Utrecht, Campusplein 1, Utrecht, the Netherlands
| | - Ana Sobota
- Atmospheric Pressure Non-Thermal Plasmas and Their Interaction with Targets, Applied Physics Department, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Andreas F P Sonnen
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Utrecht, the Netherlands; Pathology Department, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Eefjan Breukink
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Utrecht, the Netherlands
| | - J Antoinette Killian
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Utrecht, the Netherlands
| | - Joseph H Lorent
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Utrecht, the Netherlands; Cellular and Molecular Pharmacology, Translational Research from Experimental and Clinical Pharmacology to Treatment Optimization, Louvain Drug Research Institute, UCLouvain, Brussels, Belgium.
| |
Collapse
|
22
|
Clarke RJ. Electrostatic switch mechanisms of membrane protein trafficking and regulation. Biophys Rev 2023; 15:1967-1985. [PMID: 38192346 PMCID: PMC10771482 DOI: 10.1007/s12551-023-01166-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 11/17/2023] [Indexed: 01/10/2024] Open
Abstract
Lipid-protein interactions are normally classified as either specific or general. Specific interactions refer to lipid binding to specific binding sites within a membrane protein, thereby modulating the protein's thermal stability or kinetics. General interactions refer to indirect effects whereby lipids affect membrane proteins by modulating the membrane's physical properties, e.g., its fluidity, thickness, or dipole potential. It is not widely recognized that there is a third distinct type of lipid-protein interaction. Intrinsically disordered N- or C-termini of membrane proteins can interact directly but nonspecifically with the surrounding membrane. Many peripheral membrane proteins are held to the cytoplasmic surface of the plasma membrane via a cooperative combination of two forces: hydrophobic anchoring and electrostatic attraction. An acyl chain, e.g., myristoyl, added post-translationally to one of the protein's termini inserts itself into the lipid matrix and helps hold peripheral membrane proteins onto the membrane. Electrostatic attraction occurs between positively charged basic amino acid residues (lysine and arginine) on one of the protein's terminal tails and negatively charged phospholipid head groups, such as phosphatidylserine. Phosphorylation of either serine or tyrosine residues on the terminal tails via regulatory protein kinases allows for an electrostatic switch mechanism to control trafficking of the protein. Kinase action reduces the positive charge on the protein's tail, weakening the electrostatic attraction and releasing the protein from the membrane. A similar mechanism regulates many integral membrane proteins, but here only electrostatic interactions are involved, and the electrostatic switch modulates protein activity by altering the stabilities of different protein conformational states.
Collapse
Affiliation(s)
- Ronald J. Clarke
- School of Chemistry, University of Sydney, Sydney, NSW 2006 Australia
- The University of Sydney Nano Institute, Sydney, NSW 2006 Australia
| |
Collapse
|
23
|
Chen X, Yang Q, Kong W, Ge Y, He J, Yan A, Li D. High spatial-resolved heat manipulating membrane heterogeneity alters cellular migration and signaling. Proc Natl Acad Sci U S A 2023; 120:e2312603120. [PMID: 37983503 PMCID: PMC10691225 DOI: 10.1073/pnas.2312603120] [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: 07/26/2023] [Accepted: 10/23/2023] [Indexed: 11/22/2023] Open
Abstract
Plasma membrane heterogeneity is a key biophysical regulatory principle of membrane protein dynamics, which further influences downstream signal transduction. Although extensive biophysical and cell biology studies have proven membrane heterogeneity is essential to cell fate, the direct link between membrane heterogeneity regulation to cellular function remains unclear. Heterogeneous structures on plasma membranes, such as lipid rafts, are transiently assembled, thus hard to study via regular techniques. Indeed, it is nearly impossible to perturb membrane heterogeneity without changing plasma membrane compositions. In this study, we developed a high-spatial resolved DNA-origami-based nanoheater system with specific lipid heterogeneity targeting to manipulate the local lipid environmental temperature under near-infrared (NIR) laser illumination. Our results showed that the targeted heating of the local lipid environment influences the membrane thermodynamic properties, which further triggers an integrin-associated cell migration change. Therefore, the nanoheater system was further applied as an optimized therapeutic agent for wound healing. Our strategy provides a powerful tool to dynamically manipulate membrane heterogeneity and has the potential to explore cellular function through changes in plasma membrane biophysical properties.
Collapse
Affiliation(s)
- Xiaoqing Chen
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai200241, China
| | - Qianyun Yang
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai200241, China
| | - Wenyan Kong
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai201210, China
| | - Yifan Ge
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai201210, China
| | - Jie He
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai200241, China
| | - An Yan
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai200241, China
| | - Di Li
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai200241, China
| |
Collapse
|
24
|
Kumar A, Daschakraborty S. Anomalous lateral diffusion of lipids during the fluid/gel phase transition of a lipid membrane. Phys Chem Chem Phys 2023; 25:31431-31443. [PMID: 37962400 DOI: 10.1039/d3cp04081j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
A lipid membrane undergoes a phase transition from fluid to gel phase upon changing external thermodynamic conditions, such as decreasing temperature and increasing pressure. Extremophilic organisms face the challenge of preventing this deleterious phase transition. The main focus of their adaptive strategy is to facilitate effective temperature sensing through sensor proteins, relying on the drastic changes in packing density and membrane fluidity during the phase transition. Although the changes in packing density parameters due to the fluid/gel phase transition are studied in detail, the impact on membrane fluidity is less explored in the literature. Understanding the lateral diffusive dynamics of lipids in response to temperature, particularly during the fluid/gel phase transition, is albeit crucial. Here we have simulated the phase transition of a single component lipid membrane composed of dipalmitoylphosphatidylcholine (DPPC) lipids using a coarse-grained (CG) model and studied the changes of the structural and dynamical properties. It is observed that near the phase transition point, both fluid and gel phase domains coexist together. The dynamics remains highly non-Gaussian for a long time even when the mean square displacement reaches the Fickian regime at a much earlier time. This Fickian yet non-Gaussian diffusion (FnGD) is a characteristic of a highly heterogeneous system, previously observed for the lateral diffusion of lipids in raft mimetic membranes having liquid-ordered and liquid-disordered phases co-existing together. We have analyzed the molecular trajectories and calculated the jump-diffusion of the lipids, stemming from sudden jump translations, using a translational jump-diffusion (TJD) approach. An overwhelming contribution of the jump-diffusion of the lipids is observed suggesting anomalous diffusion of lipids during fluid/gel phase transition of the membrane. These results are important in unravelling the intricate nature of lipid diffusion during the phase transition of the membrane and open up a new possibility of investigating the most significant change of membrane properties during phase transition, which can be effectively sensed by proteins.
Collapse
Affiliation(s)
- Abhay Kumar
- Department of Chemistry, Indian Institute of Technology Patna, Bihar 801106, India.
| | | |
Collapse
|
25
|
Enoki TA, Heberle FA. Experimentally determined leaflet-leaflet phase diagram of an asymmetric lipid bilayer. Proc Natl Acad Sci U S A 2023; 120:e2308723120. [PMID: 37939082 PMCID: PMC10655556 DOI: 10.1073/pnas.2308723120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/11/2023] [Indexed: 11/10/2023] Open
Abstract
We have determined the partial leaflet-leaflet phase diagram of an asymmetric lipid bilayer at ambient temperature using asymmetric giant unilamellar vesicles (aGUVs). Symmetric GUVs with varying amounts of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine and DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) were hemifused to a supported lipid bilayer (SLB) composed of DOPC, resulting in lipid exchange between their outer leaflets. The GUVs and SLB contained a red and green lipid fluorophore, respectively, thus enabling the use of confocal fluorescence imaging to determine both the extent of lipid exchange (quantified for individual vesicles by the loss of red intensity and gain of green intensity) and the presence or absence of phase separation in aGUVs. Consistent with previous reports, we found that hemifusion results in large variation in outer leaflet exchange for individual GUVs, which allowed us to interrogate the phase behavior at multiple points within the asymmetric composition space of the binary mixture. When initially symmetric GUVs showed coexisting gel and fluid domains, aGUVs with less than ~50% outer leaflet exchange were also phase-separated. In contrast, aGUVs with greater than 50% outer leaflet exchange were uniform and fluid. In some cases, we also observed three coexisting bilayer-spanning phases: two registered phases and an anti-registered phase. These results suggest that a relatively large unfavorable midplane interaction between ordered and disordered phases in opposing leaflets (i.e., a midplane surface tension) can overwhelm the driving force for lateral phase separation within one of the leaflets, resulting in an asymmetric bilayer with two uniformly mixed leaflets that is poised to phase-separate upon leaflet scrambling.
Collapse
Affiliation(s)
- Thais A. Enoki
- Department of Chemistry, University of Tennessee, Knoxville, TN37996
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY14853
| | | |
Collapse
|
26
|
Shelby SA, Veatch SL. The Membrane Phase Transition Gives Rise to Responsive Plasma Membrane Structure and Function. Cold Spring Harb Perspect Biol 2023; 15:a041395. [PMID: 37553204 PMCID: PMC10626261 DOI: 10.1101/cshperspect.a041395] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Several groups have recently reported evidence for the emergence of domains in cell plasma membranes when membrane proteins are organized by ligand binding or assembly of membrane proximal scaffolds. These domains recruit and retain components that favor the liquid-ordered phase, adding to a decades-old literature interrogating the contribution of membrane phase separation in plasma membrane organization and function. Here we propose that both past and present observations are consistent with a model in which membranes have a high compositional susceptibility, arising from their thermodynamic state in a single phase that is close to a miscibility phase transition. This rigorous framework naturally allows for both transient structure in the form of composition fluctuations and long-lived structure in the form of induced domains. In this way, the biological tuning of plasma membrane composition enables a responsive compositional landscape that facilitates and augments cellular biochemistry vital to plasma membrane functions.
Collapse
Affiliation(s)
- Sarah A Shelby
- Biochemistry & Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, Tennessee 37996, USA
| | - Sarah L Veatch
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA
| |
Collapse
|
27
|
Sarkar T, Farago O. Characterizing the heterogeneity of membrane liquid-ordered domains. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:99. [PMID: 37847322 DOI: 10.1140/epje/s10189-023-00359-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 09/27/2023] [Indexed: 10/18/2023]
Abstract
We use a lattice model of a ternary mixture containing saturated and unsaturated lipids with cholesterol (Chol), to study the structural properties characterizing the coexistence between the liquid-disordered and liquid-ordered phases. Depending on the affinity of the saturated and unsaturated lipids, the system may exhibit macroscopic (thermodynamic) liquid-liquid phase separation or be divided into small-size liquid-ordered domains surrounded by a liquid-disordered matrix. In both cases, it is found that the nanoscale structure of the liquid-ordered regions is heterogeneous, and that they are partitioned into Chol-rich sub-domains and Chol-free, gel-like, nano-clusters. This emerges as a characteristic feature of the liquid-ordered state, which helps distinguishing between liquid-ordered domains in a two-phase mixture, and similar-looking domains in a one-phase mixture that are rich in saturated lipids and Chol, but are merely thermal density fluctuations. The nano-structure heterogeneity of the liquid-ordered phase can be detected by suitable experimental spectroscopic methods and is observed also in atomistic computer simulations.
Collapse
Affiliation(s)
- Tanmoy Sarkar
- Department of Theoretical Physics, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
| | - Oded Farago
- Biomedical Engineering Department, Ben Gurion University of the Negev, 84105, Beer Sheva, Israel.
| |
Collapse
|
28
|
Dong PT, Tian J, Kobayashi-Kirschvink KJ, Cen L, McLean JS, Bor B, Shi W, He X. Episymbiotic bacterium induces intracellular lipid droplet production in its host bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.06.556576. [PMID: 37732248 PMCID: PMC10508740 DOI: 10.1101/2023.09.06.556576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Saccharibacteria (formerly TM7) Nanosynbacter lyticus type strain TM7x exhibits a remarkably compact genome and an extraordinarily small cell size. This obligate epibiotic parasite forms a symbiotic relationship with its bacterial host, Schaalia odontolytica, strain XH001 (formerly Actinomyces odontolyticus strain XH001). Due to its limited genome size, TM7x possesses restrained metabolic capacities, predominantly living on the surface of its bacterial host to sustain this symbiotic lifestyle. To comprehend this intriguing, yet understudied interspecies interaction, a thorough understanding of the physical interaction between TM7x and XH001 is imperative. In this study, we employed super-resolution fluorescence imaging to investigate the physical association between TM7x and XH001. We found that the binding with TM7x led to a substantial alteration in the membrane fluidity of the host bacterium XH001. Unexpectedly, we revealed the formation of intracellular lipid droplets in XH001 when forming episymbiosis with TM7x, a feature not commonly observed in oral bacteria cells. The TM7x-induced LD accumulation in XH001 was further confirmed by label-free non-invasive Raman spectroscopy, which also unveiled additional phenotypical features when XH001 cells are physically associated with TM7x. Further exploration through culturing host bacterium XH001 alone under various stress conditions showed that LD accumulation was a general response to stress. Intriguingly, a survival assay demonstrated that the presence of LDs likely plays a protective role in XH001, enhancing its overall survival under adverse conditions. In conclusion, our study sheds new light on the intricate interaction between Saccharibacteria and its host bacterium, highlighting the potential benefit conferred by TM7x to its host, and further emphasizing the context-dependent nature of symbiotic relationships.
Collapse
Affiliation(s)
- Pu-Ting Dong
- Department of Microbiology, the Forsyth Institute, Boston, MA 02142, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Jing Tian
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, Beijing 100081, China
| | - Koseki J. Kobayashi-Kirschvink
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Laser Biomedical Research Center, G. R. Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lujia Cen
- Department of Microbiology, the Forsyth Institute, Boston, MA 02142, USA
| | - Jeffrey S. McLean
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA
| | - Batbileg Bor
- Department of Microbiology, the Forsyth Institute, Boston, MA 02142, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Wenyuan Shi
- Department of Microbiology, the Forsyth Institute, Boston, MA 02142, USA
| | - Xuesong He
- Department of Microbiology, the Forsyth Institute, Boston, MA 02142, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, MA 02115, USA
| |
Collapse
|
29
|
Xu Y, Song D, Wang W, Li S, Yue T, Xia T, Shi Y. Clec12a inhibits MSU-induced immune activation through lipid raft expulsion. Life Sci Alliance 2023; 6:e202301938. [PMID: 37339805 PMCID: PMC10282328 DOI: 10.26508/lsa.202301938] [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: 01/20/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/22/2023] Open
Abstract
Monosodium uric acid (MSU) crystal, the etiological agent of gout, has been shown to trigger innate immune responses via multiple pathways. It is known that MSU-induced lipid sorting on plasma membrane promotes the phosphorylation of Syk and eventually leads to the activation of phagocytes. However, whether this membrane lipid-centric mechanism is regulated by other processes is unclear. Previous studies showed that Clec12a, a member of the C-type lectin receptor family, is reported to recognize MSU and suppresses this crystalline structure-induced immune activation. How this scenario is integrated into the lipid sorting-mediated inflammatory responses by MSU, and particularly, how Clec12a intercepts lipid raft-originated signaling cascade remains to be elucidated. Here, we found that the ITIM motif of Clec12a is dispensable for its inhibition of MSU-mediated signaling; instead, the transmembrane domain of Clec12a disrupts MSU-induced lipid raft recruitment and thus attenuates downstream signals. Single amino acid mutagenesis study showed the critical role of phenylalanine in the transmembrane region for the interactions between C-type lectin receptors and lipid rafts, which is critical for the regulation of MSU-mediated lipid sorting and phagocyte activation. Overall, our study provides new insights for the molecular mechanisms of solid particle-induced immune activation and may lead to new strategies in inflammation control.
Collapse
Affiliation(s)
- Ying Xu
- Institute for Immunology, School of Medicine, Tsinghua University, Beijing, China
| | - Dingka Song
- Institute for Immunology, School of Medicine, Tsinghua University, Beijing, China
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Wang
- Institute of Coastal Environmental Pollution Control, Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Shixin Li
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Tongtao Yue
- Institute of Coastal Environmental Pollution Control, Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Tie Xia
- Institute for Immunology, School of Medicine, Tsinghua University, Beijing, China
| | - Yan Shi
- Institute for Immunology, School of Medicine, Tsinghua University, Beijing, China
- Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute, University of Calgary, Calgary, Canada
| |
Collapse
|
30
|
Park S, Levental I, Pastor RW, Im W. Unsaturated Lipids Facilitate Partitioning of Transmembrane Peptides into the Liquid Ordered Phase. J Chem Theory Comput 2023; 19:5303-5314. [PMID: 37417947 PMCID: PMC10413867 DOI: 10.1021/acs.jctc.3c00398] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Indexed: 07/08/2023]
Abstract
The affinity of single-pass transmembrane (TM) proteins for ordered membrane phases has been reported to depend on their lipidation, TM length, and lipid accessible surface area. In this work, the raft affinities of the TM domain of the linker for activation of T cells and its depalmitoylated variant are assessed using free energy simulations in a binary bilayer system composed of two laterally patched bilayers of ternary liquid ordered (Lo) and liquid disordered (Ld) phases. These phases are modeled by distinct compositions of distearoylphosphatidylcholine, palmitoyloleoylphosphatidylcholine (POPC), and cholesterol, and the simulations were carried out for 4.5 μs/window. Both peptides are shown to preferentially partition into the Ld phase in agreement with model membrane experiments and previous simulations on ternary lipid mixtures but not with measurements on giant plasma membrane vesicles where the Lo is slightly preferred. However, the 500 ns average relaxation time of lipid rearrangement around the peptide precluded a quantitative analysis of free energy differences arising from peptide palmitoylation and two different lipid compositions. When in the Lo phase, peptides reside in regions rich in POPC and interact preferentially with its unsaturated tail. Hence, the detailed substructure of the Lo phase is an important modulator of peptide partitioning, in addition to the inherent properties of the peptide.
Collapse
Affiliation(s)
- Soohyung Park
- Departments
of Biological Sciences and Chemistry, Lehigh
University, Bethlehem, Pennsylvania 18015, United States
| | - Ilya Levental
- Department
of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22903-1738, United States
| | - Richard W. Pastor
- Laboratory
of Computational Biology, National Heart,
Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Wonpil Im
- Departments
of Biological Sciences and Chemistry, Lehigh
University, Bethlehem, Pennsylvania 18015, United States
| |
Collapse
|
31
|
Sakamoto K, Akimoto T, Muramatsu M, Sansom MSP, Metzler R, Yamamoto E. Heterogeneous biological membranes regulate protein partitioning via fluctuating diffusivity. PNAS NEXUS 2023; 2:pgad258. [PMID: 37593200 PMCID: PMC10427746 DOI: 10.1093/pnasnexus/pgad258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/22/2023] [Accepted: 07/27/2023] [Indexed: 08/19/2023]
Abstract
Cell membranes phase separate into ordered L o and disordered L d domains depending on their compositions. This membrane compartmentalization is heterogeneous and regulates the localization of specific proteins related to cell signaling and trafficking. However, it is unclear how the heterogeneity of the membranes affects the diffusion and localization of proteins in L o and L d domains. Here, using Langevin dynamics simulations coupled with the phase-field (LDPF) method, we investigate several tens of milliseconds-scale diffusion and localization of proteins in heterogeneous biological membrane models showing phase separation into L o and L d domains. The diffusivity of proteins exhibits temporal fluctuations depending on the field composition. Increases in molecular concentrations and domain preference of the molecule induce subdiffusive behavior due to molecular collisions by crowding and confinement effects, respectively. Moreover, we quantitatively demonstrate that the protein partitioning into the L o domain is determined by the difference in molecular diffusivity between domains, molecular preference of domain, and molecular concentration. These results pave the way for understanding how biological reactions caused by molecular partitioning may be controlled in heterogeneous media. Moreover, the methodology proposed here is applicable not only to biological membrane systems but also to the study of diffusion and localization phenomena of molecules in various heterogeneous systems.
Collapse
Affiliation(s)
- Ken Sakamoto
- Department of System Design Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Takuma Akimoto
- Department of Physics, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Mayu Muramatsu
- Department of Mechanical Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Ralf Metzler
- Institute of Physics & Astronomy, University of Potsdam, Potsdam-Golm 14476, Germany
- Asia Pacific Centre for Theoretical Physics, Pohang 37673, Republic of Korea
| | - Eiji Yamamoto
- Department of System Design Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan
| |
Collapse
|
32
|
Puff N. Critical Role of Molecular Packing in Lo Phase Membrane Solubilization. MEMBRANES 2023; 13:652. [PMID: 37505018 PMCID: PMC10385406 DOI: 10.3390/membranes13070652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/29/2023]
Abstract
Membrane solubilization induced by Triton X-100 (TX-100) was investigated. Different membrane compositions and phase states were studied along the detergent titration. Expected solubilization profiles were obtained but new information is provided. The fluorescence of nitrobenzoxadiazole (NBD)-labeled lipids indicates that the liquid-ordered (Lo)/liquid-disordered (Ld) phase coexistence is barely unaffected at sub-solubilizing detergent concentrations and highlights the vesicle-to-micelle transition. Moreover, the location of the NBD group in the bilayer emphasizes a detergent-membrane interaction in the case of the insoluble Lo phase membrane. It has also been shown that the molecular packing of the membrane loosens in the presence of TX-100, regardless of the solubilization profile. Motivated by studies on GPMVs, the solubilization of less ordered Lo phase membranes was considered in order to improve the effect of molecular packing on the extent of solubilization. Membranes composed of SM and Chol in an equimolar ratio doped with different amounts of PC were studied. The more ordered the Lo phase membrane is in the absence of detergent, the less likely it is to be solubilized. Furthermore, and in contrast to what is observed for membranes exhibiting an Lo/Ld phase coexistence, a very small decrease in the molecular packing of the Lo phase membrane radically modifies the extent of solubilization. These results have implications for the reliability of TX-100 insolubility as a method to detect ordered domains.
Collapse
Affiliation(s)
- Nicolas Puff
- Faculté des Sciences et Ingénierie, Sorbonne Université, UFR 925 Physics, F-75005 Paris, France
- Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS, Université Paris Cité, F-75013 Paris, France
| |
Collapse
|
33
|
Yordanova V, Hazarosova R, Vitkova V, Momchilova A, Robev B, Nikolova B, Krastev P, Nuss P, Angelova MI, Staneva G. Impact of Truncated Oxidized Phosphatidylcholines on Phospholipase A 2 Activity in Mono- and Polyunsaturated Biomimetic Vesicles. Int J Mol Sci 2023; 24:11166. [PMID: 37446342 DOI: 10.3390/ijms241311166] [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: 05/23/2023] [Revised: 06/26/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
The interplay between inflammatory and redox processes is a ubiquitous and critical phenomenon in cell biology that involves numerous biological factors. Among them, secretory phospholipases A2 (sPLA2) that catalyze the hydrolysis of the sn-2 ester bond of phospholipids are key players. They can interact or be modulated by the presence of truncated oxidized phosphatidylcholines (OxPCs) produced under oxidative stress from phosphatidylcholine (PC) species. The present study examined this important, but rarely considered, sPLA2 modulation induced by the changes in biophysical properties of PC vesicles comprising various OxPC ratios in mono- or poly-unsaturated PCs. Being the most physiologically active OxPCs, 1-palmitoyl-2-(5'-oxo-valeroyl)-sn-glycero-3-phosphocholine (POVPC) and 1-palmitoyl-2-glutaryl-sn-glycero-3-phosphocholine (PGPC) have been selected for our study. Using fluorescence spectroscopy methods, we compared the effect of OxPCs on the lipid order as well as sPLA2 activity in large unilamellar vesicles (LUVs) made of the heteroacid PC, either monounsaturated [1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)], or polyunsaturated [1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (PDPC)] at a physiological temperature. The effect of OxPCs on vesicle size was also assessed in both the mono- and polyunsaturated PC matrices. Results: OxPCs decrease the membrane lipid order of POPC and PDPC mixtures with PGPC inducing a much larger decrease in comparison with POVPC, indicative that the difference takes place at the glycerol level. Compared with POPC, PDPC was able to inhibit sPLA2 activity showing a protective effect of PDPC against enzyme hydrolysis. Furthermore, sPLA2 activity on its PC substrates was modulated by the OxPC membrane content. POVPC down-regulated sPLA2 activity, suggesting anti-inflammatory properties of this truncated oxidized lipid. Interestingly, PGPC had a dual and opposite effect, either inhibitory or enhancing on sPLA2 activity, depending on the protocol of lipid mixing. This difference may result from the chemical properties of the shortened sn-2-acyl chain residues (aldehyde group for POVPC, and carboxyl for PGPC), being, respectively, zwitterionic or anionic under hydration at physiological conditions.
Collapse
Affiliation(s)
- Vesela Yordanova
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria
| | - Rusina Hazarosova
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria
| | - Victoria Vitkova
- Institute of Solid State Physics, Bulgarian Academy of Sciences, 72 Tzarigradsko Chaussee Blvd., 1784 Sofia, Bulgaria
| | - Albena Momchilova
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria
| | - Bozhil Robev
- Department of Medical Oncology, University Hospital "Sv. Ivan Rilski", 15 Acad. Ivan Geshov Blvd., 1431 Sofia, Bulgaria
| | - Biliana Nikolova
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria
| | - Plamen Krastev
- Cardiology Clinic, University Hospital "St. Ekaterina", 52 Pencho Slaveikov Blvd., 1431 Sofia, Bulgaria
| | - Philippe Nuss
- Centre de Recherche Saint-Antoine, INSERM UMRS 938, Sorbonne Université, 75012 Paris, France
- Department of Psychiatry, Saint-Antoine Hospital, DMU Neuroscience, Sorbonne University, Assistance Publique-Hôpitaux de Paris (AP-HP), 75012 Paris, France
| | - Miglena I Angelova
- Department of Physics, Faculty of Sciences and Engineering, Sorbonne University, 75005 Paris, France
- Matière et Systèmes Complexes (MSC), CNRS UMR 7057, University Paris Cite-Diderot, 75013 Paris, France
| | - Galya Staneva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria
| |
Collapse
|
34
|
Whiting R, Stanton S, Kucheriava M, Smith AR, Pitts M, Robertson D, Kammer J, Li Z, Fologea D. Hypo-Osmotic Stress and Pore-Forming Toxins Adjust the Lipid Order in Sheep Red Blood Cell Membranes. MEMBRANES 2023; 13:620. [PMID: 37504986 PMCID: PMC10385129 DOI: 10.3390/membranes13070620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/07/2023] [Accepted: 06/22/2023] [Indexed: 07/29/2023]
Abstract
Lipid ordering in cell membranes has been increasingly recognized as an important factor in establishing and regulating a large variety of biological functions. Multiple investigations into lipid organization focused on assessing ordering from temperature-induced phase transitions, which are often well outside the physiological range. However, particular stresses elicited by environmental factors, such as hypo-osmotic stress or protein insertion into membranes, with respect to changes in lipid status and ordering at constant temperature are insufficiently described. To fill these gaps in our knowledge, we exploited the well-established ability of environmentally sensitive membrane probes to detect intramembrane changes at the molecular level. Our steady state fluorescence spectroscopy experiments focused on assessing changes in optical responses of Laurdan and diphenylhexatriene upon exposure of red blood cells to hypo-osmotic stress and pore-forming toxins at room temperature. We verified our utilized experimental systems by a direct comparison of the results with prior reports on artificial membranes and cholesterol-depleted membranes undergoing temperature changes. The significant changes observed in the lipid order after exposure to hypo-osmotic stress or pore-forming toxins resembled phase transitions of lipids in membranes, which we explained by considering the short-range interactions between membrane components and the hydrophobic mismatch between membrane thickness and inserted proteins. Our results suggest that measurements of optical responses from the membrane probes constitute an appropriate method for assessing the status of lipids and phase transitions in target membranes exposed to mechanical stresses or upon the insertion of transmembrane proteins.
Collapse
Affiliation(s)
- Rose Whiting
- Department of Physics, Boise State University, Boise, ID 83725, USA
- Biomolecular Sciences Graduate Program, Boise State University, Boise, ID 83725, USA
| | - Sevio Stanton
- Department of Physics, Boise State University, Boise, ID 83725, USA
| | | | - Aviana R Smith
- Department of Physics, Boise State University, Boise, ID 83725, USA
| | - Matt Pitts
- Department of Physics, Boise State University, Boise, ID 83725, USA
- Biomolecular Sciences Graduate Program, Boise State University, Boise, ID 83725, USA
| | - Daniel Robertson
- Department of Physics, Boise State University, Boise, ID 83725, USA
| | - Jacob Kammer
- Department of Physics, Boise State University, Boise, ID 83725, USA
- Department of Family Medicine, Idaho College of Osteopathic Medicine, Meridian, ID 83642, USA
| | - Zhiyu Li
- Department of Physics, Boise State University, Boise, ID 83725, USA
| | - Daniel Fologea
- Department of Physics, Boise State University, Boise, ID 83725, USA
- Biomolecular Sciences Graduate Program, Boise State University, Boise, ID 83725, USA
| |
Collapse
|
35
|
Polita A, Stancikaitė M, Žvirblis R, Maleckaitė K, Dodonova-Vaitkūnienė J, Tumkevičius S, Shivabalan AP, Valinčius G. Designing a green-emitting viscosity-sensitive 4,4-difluoro-4-bora-3a,4a-diaza- s-indacene (BODIPY) probe for plasma membrane viscosity imaging. RSC Adv 2023; 13:19257-19264. [PMID: 37377877 PMCID: PMC10291278 DOI: 10.1039/d3ra04126c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 06/29/2023] Open
Abstract
Viscosity is a key characteristic of lipid membranes - it governs the passive diffusion of solutes and affects the lipid raft formation and membrane fluidity. Precise determination of viscosity values in biological systems is of great interest and viscosity-sensitive fluorescent probes offer a convenient solution for this task. In this work we present a novel membrane-targeting and water-soluble viscosity probe BODIPY-PM, which is based on one of the most frequently used probes BODIPY-C10. Despite its regular use, BODIPY-C10 suffers from poor integration into liquid-ordered lipid phases and lack of water solubility. Here, we investigate the photophysical characteristics of BODIPY-PM and demonstrate that solvent polarity only slightly affects the viscosity-sensing qualities of BODIPY-PM. In addition, with fluorescence lifetime imaging microscopy (FLIM), we imaged microviscosity in complex biological systems - large unilamellar vesicles (LUVs), tethered bilayer membranes (tBLMs) and live lung cancer cells. Our study showcases that BODIPY-PM preferentially stains the plasma membranes of live cells, equally well partitions into both liquid-ordered and liquid-disordered phases and reliably distinguishes lipid phase separation in tBLMs and LUVs.
Collapse
Affiliation(s)
- Artūras Polita
- Institute of Biochemistry, Life Sciences Center, Vilnius University Saulėtekio Av. 7 Vilnius LT-10257 Lithuania
| | - Milda Stancikaitė
- Center of Physical Sciences and Technology Saulėtekio Av. 3 Vilnius LT-10257 Lithuania
| | - Rokas Žvirblis
- Life Sciences Center, Institute of Biotechnology, Vilnius University Saulėtekio Av. 7 Vilnius LT-10257 Lithuania
| | - Karolina Maleckaitė
- Center of Physical Sciences and Technology Saulėtekio Av. 3 Vilnius LT-10257 Lithuania
| | - Jelena Dodonova-Vaitkūnienė
- Institute of Chemistry, Faculty of Chemistry and Geosciences, Vilnius University Naugarduko St. 24 Vilnius LT-03225 Lithuania
| | - Sigitas Tumkevičius
- Institute of Chemistry, Faculty of Chemistry and Geosciences, Vilnius University Naugarduko St. 24 Vilnius LT-03225 Lithuania
| | - Arun Prabha Shivabalan
- Institute of Biochemistry, Life Sciences Center, Vilnius University Saulėtekio Av. 7 Vilnius LT-10257 Lithuania
| | - Gintaras Valinčius
- Institute of Biochemistry, Life Sciences Center, Vilnius University Saulėtekio Av. 7 Vilnius LT-10257 Lithuania
| |
Collapse
|
36
|
Moreno-Pescador G, Arastoo MR, Ruhoff VT, Chiantia S, Daniels R, Bendix PM. Thermoplasmonic Vesicle Fusion Reveals Membrane Phase Segregation of Influenza Spike Proteins. NANO LETTERS 2023; 23:3377-3384. [PMID: 37040311 PMCID: PMC10141563 DOI: 10.1021/acs.nanolett.3c00371] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Many cellular processes involve the lateral organization of integral and peripheral membrane proteins into nanoscale domains. Despite the biological significance, the mechanisms that facilitate membrane protein clustering into nanoscale lipid domains remain enigmatic. In cells, the analysis of membrane protein phase affinity is complicated by the size and temporal nature of ordered and disordered lipid domains. To overcome these limitations, we developed a method for delivering membrane proteins from transfected cells into phase-separated model membranes that combines optical trapping with thermoplasmonic-mediated membrane fusion and confocal imaging. Using this approach, we observed clear phase partitioning into the liquid disordered phase following the transfer of GFP-tagged influenza hemagglutinin and neuraminidase from transfected cell membranes to giant unilamellar vesicles. The generic platform presented here allows investigation of the phase affinity of any plasma membrane protein which can be labeled or tagged with a fluorescent marker.
Collapse
Affiliation(s)
| | - Mohammad Reza Arastoo
- Niels
Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 København Ø, Denmark
| | | | - Salvatore Chiantia
- Institute
of Biochemistry and Biology, University
of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Robert Daniels
- Division
of Viral Products, Center for Biologics
Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Poul Martin Bendix
- Niels
Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 København Ø, Denmark
- Email
| |
Collapse
|
37
|
Sarkar T, Farago O. A lattice model of ternary mixtures of lipids and cholesterol with tunable domain sizes. SOFT MATTER 2023; 19:2417-2429. [PMID: 36930060 DOI: 10.1039/d2sm01025a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Much of our understanding of the physical properties of raft domains in biological membranes, and some insight into the mechanisms underlying their formation stem from atomistic simulations of simple model systems, especially ternary mixtures consisting of saturated and unsaturated lipids, and cholesterol (Chol). To explore the properties of such systems at large spatial scales, we here present a simple ternary mixture lattice model, involving a small number of nearest neighbor interaction terms. Monte Carlo simulations of mixtures with different compositions show excellent agreement with experimental and atomistic simulation observations across multiple scales, ranging from the local distributions of lipids to the phase diagram of the system. The simplicity of the model allows us to identify the roles played by the different interactions between components, and the interplay between them. Importantly, by changing the value of one of the model parameters, we can tune the size of the liquid-ordered domains, thereby simulating both Type II mixtures exhibiting macroscopic phase separation and Type I mixtures with nanoscopic domains. The Type II mixture simulation results fit well to the experimentally determined phase diagram of mixtures containing saturated DPPC/unsaturated DOPC/Chol. When the tunable parameter is changed, we obtain the Type I version of DPPC/DOPC/Chol, i.e., a mixture not showing thermodynamic phase transitions but one that may be fitted to the same phase diagram if local measures are used to distinguish between the different states. Our model results suggest that short range packing is likely to be a key regulator of the stability and size distribution of biological rafts.
Collapse
Affiliation(s)
- Tanmoy Sarkar
- Department of Biomedical Engineering, Ben Gurion University of the Negev, Be'er Sheva 84105, Israel.
| | - Oded Farago
- Department of Biomedical Engineering, Ben Gurion University of the Negev, Be'er Sheva 84105, Israel.
| |
Collapse
|
38
|
Gupta A, Kallianpur M, Roy DS, Engberg O, Chakrabarty H, Huster D, Maiti S. Different membrane order measurement techniques are not mutually consistent. Biophys J 2023; 122:964-972. [PMID: 36004780 PMCID: PMC10111216 DOI: 10.1016/j.bpj.2022.08.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/10/2022] [Accepted: 08/19/2022] [Indexed: 11/25/2022] Open
Abstract
"Membrane order" is a term commonly used to describe the elastic and mechanical properties of the lipid bilayer, though its exact meaning is somewhat context- and method dependent. These mechanical properties of the membrane control many cellular functions and are measured using various biophysical techniques. Here, we ask if the results obtained from various techniques are mutually consistent. Such consistency cannot be assumed a priori because these techniques probe different spatial locations and different spatial and temporal scales. We evaluate the change of membrane order induced by serotonin using nine different techniques in lipid bilayers of three different compositions. Serotonin is an important neurotransmitter present at 100s of mM concentrations in neurotransmitter vesicles, and therefore its interaction with the lipid bilayer is biologically relevant. Our measurement tools include fluorescence of lipophilic dyes (Nile Red, Laurdan, TMA-DPH, DPH), whose properties are a function of membrane order; atomic force spectroscopy, which provides a measure of the force required to indent the lipid bilayer; 2H solid-state NMR spectroscopy, which measures the molecular order of the lipid acyl chain segments; fluorescence correlation spectroscopy, which provides a measure of the diffusivity of the probe in the membrane; and Raman spectroscopy, where spectral intensity ratios are affected by acyl chain order. We find that different measures often do not correlate with each other and sometimes even yield conflicting results. We conclude that no probe provides a general measure of membrane order and that any inference based on the change of membrane order measured by a particular probe may be unreliable.
Collapse
Affiliation(s)
- Ankur Gupta
- Tata Institute of Fundamental Research, Colaba, Mumbai, India
| | | | | | - Oskar Engberg
- Institute of Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | | | - Daniel Huster
- Tata Institute of Fundamental Research, Colaba, Mumbai, India; Institute of Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany.
| | - Sudipta Maiti
- Tata Institute of Fundamental Research, Colaba, Mumbai, India.
| |
Collapse
|
39
|
Refinement of Singer-Nicolson fluid-mosaic model by microscopy imaging: Lipid rafts and actin-induced membrane compartmentalization. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184093. [PMID: 36423676 DOI: 10.1016/j.bbamem.2022.184093] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/22/2022]
Abstract
This year celebrates the 50th anniversary of the Singer-Nicolson fluid mosaic model for biological membranes. The next level of sophistication we have achieved for understanding plasma membrane (PM) structures, dynamics, and functions during these 50 years includes the PM interactions with cortical actin filaments and the partial demixing of membrane constituent molecules in the PM, particularly raft domains. Here, first, we summarize our current knowledge of these two structures and emphasize that they are interrelated. Second, we review the structure, molecular dynamics, and function of raft domains, with main focuses on raftophilic glycosylphosphatidylinositol-anchored proteins (GPI-APs) and their signal transduction mechanisms. We pay special attention to the results obtained by single-molecule imaging techniques and other advanced microscopy methods. We also clarify the limitations of present optical microscopy methods for visualizing raft domains, but emphasize that single-molecule imaging techniques can "detect" raft domains associated with molecules of interest in the PM.
Collapse
|
40
|
Huang A, Adler J, Parmryd I. Optimised generalized polarisation analysis of C-laurdan reveals clear order differences between T cell membrane compartments. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184094. [PMID: 36379264 DOI: 10.1016/j.bbamem.2022.184094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/15/2022]
Abstract
Heterogenous packing of plasma membrane lipids is important for cellular processes like signalling, adhesion and sorting of membrane components. Solvatochromic membrane fluorophores that respond to changes from liquid-ordered (lo) phase to liquid-disordered (ld) by red shifts in their emission spectra are often used to assess lipid packing. Their response can be quantified using generalized polarisation (GP) using fluorescence microscopy images from two emission ranges, preferably from a region of interest (ROI) limited to a specific membrane compartment. However, image quality is limited by Poisson noise and convolution by the point spread function of the imaging system. Examining GP-analysis of C-laurdan labelled T cells using the image restoration procedure deconvolution, we demonstrate that deconvolution substantially improves the image resolution by making the plasma membrane clearly discernible and facilitating plasma membrane ROI selection. We conclude that automatic ROI selection has advantages over manual ROI selection when it comes to reproducibility and speed, but reliable GP-measurements can also be obtained by manually demarcated ROIs. We find that deconvolution enhances the difference in GP-values between the plasma and intracellular membranes and demonstrate that moving an intensity defined plasma membrane ROI outwards from the cell further improves this differentiation. By systematically changing the key deconvolution regularization parameter signal to noise, we establish a protocol for deconvolution optimisation applicable to any solvatochromic dye and imaging system. The image processing and ROI selection protocol presented improves both the resolution and precision of GP-measurement and will enable detection of smaller changes in membrane order than is currently achievable.
Collapse
Affiliation(s)
- Ainsley Huang
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jeremy Adler
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ingela Parmryd
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
| |
Collapse
|
41
|
Levental I, Lyman E. Regulation of membrane protein structure and function by their lipid nano-environment. Nat Rev Mol Cell Biol 2023; 24:107-122. [PMID: 36056103 PMCID: PMC9892264 DOI: 10.1038/s41580-022-00524-4] [Citation(s) in RCA: 151] [Impact Index Per Article: 151.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2022] [Indexed: 02/04/2023]
Abstract
Transmembrane proteins comprise ~30% of the mammalian proteome, mediating metabolism, signalling, transport and many other functions required for cellular life. The microenvironment of integral membrane proteins (IMPs) is intrinsically different from that of cytoplasmic proteins, with IMPs solvated by a compositionally and biophysically complex lipid matrix. These solvating lipids affect protein structure and function in a variety of ways, from stereospecific, high-affinity protein-lipid interactions to modulation by bulk membrane properties. Specific examples of functional modulation of IMPs by their solvating membranes have been reported for various transporters, channels and signal receptors; however, generalizable mechanistic principles governing IMP regulation by lipid environments are neither widely appreciated nor completely understood. Here, we review recent insights into the inter-relationships between complex lipidomes of mammalian membranes, the membrane physicochemical properties resulting from such lipid collectives, and the regulation of IMPs by either or both. The recent proliferation of high-resolution methods to study such lipid-protein interactions has led to generalizable insights, which we synthesize into a general framework termed the 'functional paralipidome' to understand the mutual regulation between membrane proteins and their surrounding lipid microenvironments.
Collapse
Affiliation(s)
- Ilya Levental
- Department of Molecular Physiology and Biological Physics, Center for Molecular and Cell Physiology, University of Virginia, Charlottesville, VA, USA.
| | - Ed Lyman
- Department of Physics and Astronomy, Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA.
| |
Collapse
|
42
|
Tohumeken S, Deme P, Yoo SW, Gupta S, Rais R, Slusher BS, Haughey NJ. Neuronal deletion of nSMase2 reduces the production of Aβ and directly protects neurons. Neurobiol Dis 2023; 177:105987. [PMID: 36603748 DOI: 10.1016/j.nbd.2023.105987] [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: 07/22/2022] [Revised: 12/28/2022] [Accepted: 01/01/2023] [Indexed: 01/03/2023] Open
Abstract
Extracellular vesicles (EVs) have been proposed to regulate the deposition of Aβ. Multiple publications have shown that APP, amyloid processing enzymes and Aβ peptides are associated with EVs. However, very little Aβ is associated with EVs compared with the total amount Aβ present in human plasma, CSF, or supernatants from cultured neurons. The involvement of EVs has largely been inferred by pharmacological inhibition or whole body deletion of the sphingomyelin hydrolase neutral sphingomyelinase-2 (nSMase2) that is a key regulator for the biogenesis of at-least one population of EVs. Here we used a Cre-Lox system to selectively delete nSMase2 from pyramidal neurons in APP/PS1 mice (APP/PS1-SMPD3-Nex1) and found a ∼ 70% reduction in Aβ deposition at 6 months of age and ∼ 35% reduction at 12 months of age in both cortex and hippocampus. Brain ceramides were increased in APP/PS1 compared with Wt mice, but were similar to Wt in APP/PS1-SMPD3-Nex1 mice suggesting that elevated brain ceramides in this model involves neuronally expressed nSMase2. Reduced levels of PSD95 and deficits of long-term potentiation in APP/PS1 mice were normalized in APP/PS1-SMPD3-Nex1 mice. In contrast, elevated levels of IL-1β, IL-8 and TNFα in APP/PS1 mice were not normalized in APP/PS1-SMPD3-Nex1 mice compared with APP/PS1 mice. Mechanistic studies showed that the size of liquid ordered membrane microdomains was increased in APP/PS1 mice, as were the amounts of APP and BACE1 localized to these microdomains. Pharmacological inhibition of nSMase2 activity with PDDC reduced the size of the liquid ordered membrane microdomains, reduced the localization of APP with BACE1 and reduced the production of Aβ1-40 and Aβ1-42. Although inhibition of nSMase2 reduced the release and increased the size of EVs, very little Aβ was associated with EVs in all conditions tested. We also found that nSMase2 directly protected neurons from the toxic effects of oligomerized Aβ and preserved neural network connectivity despite considerable Aβ deposition. These data demonstrate that nSMase2 plays a role in the production of Aβ by stabilizing the interaction of APP with BACE1 in liquid ordered membrane microdomains, and directly protects neurons from the toxic effects of Aβ. The effects of inhibiting nSMase2 on EV biogenesis may be independent from effects on Aβ production and neuronal protection.
Collapse
Affiliation(s)
- Sehmus Tohumeken
- The Johns Hopkins University School of Medicine, Departments of Neurology, United States of America
| | - Pragney Deme
- The Johns Hopkins University School of Medicine, Departments of Neurology, United States of America
| | - Seung Wan Yoo
- The Johns Hopkins University School of Medicine, Departments of Neurology, United States of America
| | - Sujasha Gupta
- The Johns Hopkins University School of Medicine, Departments of Neurology, United States of America
| | - Rana Rais
- The Johns Hopkins University School of Medicine, Departments of Psychiatry, United States of America
| | - Barbara S Slusher
- The Johns Hopkins University School of Medicine, Departments of Neurology, United States of America; The Johns Hopkins University School of Medicine, Departments of Johns Hopkins Drug Discovery, United States of America; The Johns Hopkins University School of Medicine, Departments of Psychiatry, United States of America; The Johns Hopkins University School of Medicine, Departments of Pharmacology and Molecular Sciences, United States of America; The Johns Hopkins University School of Medicine, Departments of Department of Oncology, United States of America; The Johns Hopkins University School of Medicine, Departments of Department of Neuroscience, United States of America; The Johns Hopkins University School of Medicine, Departments of Department of Medicine, Baltimore, MD, United States of America
| | - Norman J Haughey
- The Johns Hopkins University School of Medicine, Departments of Neurology, United States of America; The Johns Hopkins University School of Medicine, Departments of Johns Hopkins Drug Discovery, United States of America.
| |
Collapse
|
43
|
van Buren L, Koenderink GH, Martinez-Torres C. DisGUVery: A Versatile Open-Source Software for High-Throughput Image Analysis of Giant Unilamellar Vesicles. ACS Synth Biol 2023; 12:120-135. [PMID: 36508359 PMCID: PMC9872171 DOI: 10.1021/acssynbio.2c00407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Indexed: 12/14/2022]
Abstract
Giant unilamellar vesicles (GUVs) are cell-sized aqueous compartments enclosed by a phospholipid bilayer. Due to their cell-mimicking properties, GUVs have become a widespread experimental tool in synthetic biology to study membrane properties and cellular processes. In stark contrast to the experimental progress, quantitative analysis of GUV microscopy images has received much less attention. Currently, most analysis is performed either manually or with custom-made scripts, which makes analysis time-consuming and results difficult to compare across studies. To make quantitative GUV analysis accessible and fast, we present DisGUVery, an open-source, versatile software that encapsulates multiple algorithms for automated detection and analysis of GUVs in microscopy images. With a performance analysis, we demonstrate that DisGUVery's three vesicle detection modules successfully identify GUVs in images obtained with a wide range of imaging sources, in various typical GUV experiments. Multiple predefined analysis modules allow the user to extract properties such as membrane fluorescence, vesicle shape, and internal fluorescence from large populations. A new membrane segmentation algorithm facilitates spatial fluorescence analysis of nonspherical vesicles. Altogether, DisGUVery provides an accessible tool to enable high-throughput automated analysis of GUVs, and thereby to promote quantitative data analysis in synthetic cell research.
Collapse
Affiliation(s)
- Lennard van Buren
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZDelft, The Netherlands
| | - Gijsje Hendrika Koenderink
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZDelft, The Netherlands
| | - Cristina Martinez-Torres
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZDelft, The Netherlands
| |
Collapse
|
44
|
Caveolin-1 dolines form a distinct and rapid caveolae-independent mechanoadaptation system. Nat Cell Biol 2023; 25:120-133. [PMID: 36543981 PMCID: PMC9859760 DOI: 10.1038/s41556-022-01034-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/21/2022] [Indexed: 12/24/2022]
Abstract
In response to different types and intensities of mechanical force, cells modulate their physical properties and adapt their plasma membrane (PM). Caveolae are PM nano-invaginations that contribute to mechanoadaptation, buffering tension changes. However, whether core caveolar proteins contribute to PM tension accommodation independently from the caveolar assembly is unknown. Here we provide experimental and computational evidence supporting that caveolin-1 confers deformability and mechanoprotection independently from caveolae, through modulation of PM curvature. Freeze-fracture electron microscopy reveals that caveolin-1 stabilizes non-caveolar invaginations-dolines-capable of responding to low-medium mechanical forces, impacting downstream mechanotransduction and conferring mechanoprotection to cells devoid of caveolae. Upon cavin-1/PTRF binding, doline size is restricted and membrane buffering is limited to relatively high forces, capable of flattening caveolae. Thus, caveolae and dolines constitute two distinct albeit complementary components of a buffering system that allows cells to adapt efficiently to a broad range of mechanical stimuli.
Collapse
|
45
|
Isik OA, Cizmecioglu O. Rafting on the Plasma Membrane: Lipid Rafts in Signaling and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1436:87-108. [PMID: 36648750 DOI: 10.1007/5584_2022_759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The plasma membrane is not a uniform phospholipid bilayer; it has specialized membrane nano- or microdomains called lipid rafts. Lipid rafts are small cholesterol and sphingolipid-rich plasma membrane islands. Although their existence was long debated, their presence in the plasma membrane of living cells is now well accepted with the advent of super-resolution imaging techniques. It is interesting to note that lipid rafts function to compartmentalize receptors and their regulators and substantially modulate cellular signaling. In this review, we will examine the role of lipid rafts and caveolae-lipid raft-like microdomains with a distinct 3D morphology-in cellular signaling. Moreover, we will investigate how raft compartmentalized signaling regulates diverse physiological processes such as proliferation, apoptosis, immune signaling, and development. Also, the deregulation of lipid raft-mediated signaling during tumorigenesis and metastasis will be explored.
Collapse
Affiliation(s)
- Ozlem Aybuke Isik
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Onur Cizmecioglu
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey.
| |
Collapse
|
46
|
Yasuda T, Watanabe H, Hirosawa KM, Suzuki KGN, Suga K, Hanashima S. Fluorescence Spectroscopic Analysis of Lateral and Transbilayer Fluidity of Exosome Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:14695-14703. [PMID: 36421004 PMCID: PMC9731264 DOI: 10.1021/acs.langmuir.2c02258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 11/10/2022] [Indexed: 06/16/2023]
Abstract
Exosomes are small extracellular vesicles (sEVs) involved in distal cell-cell communication and cancer migration by transferring functional cargo molecules. Membrane domains similar to lipid rafts are assumed to occur in exosome membranes and are involved in interactions with target cells. However, the bilayer membrane properties of these small vesicles have not been fully investigated. Therefore, we examined the fluidity, lateral domain separation, and transbilayer asymmetry of exosome membranes using fluorescence spectroscopy. Although there were some differences between the exosomes, TMA-DPH anisotropy showing moderate lipid chain order indicated that ordered phases comprised a significant proportion of exosome membranes. Selective TEMPO quenching of the TMA-DPH fluorescence in the liquid-disordered phase indicated that 40-50% of the exosome membrane area belonged to the ordered phase based on a phase-separated model. Furthermore, NBD-PC in the outer leaflet showed longer fluorescence lifetimes than those in the inner leaflets. Therefore, the exosome membranes maintained transbilayer asymmetry with a topology similar to that of the plasma membranes. In addition, the lateral and transbilayer orders of exosome membranes obtained from different cell lines varied, probably depending on the different membrane lipid components and compositions partially derived from donor cells. As these higher membrane orders and asymmetric topologies are similar to those of cell membranes with lipid rafts, raft-like functional domains are possibly enriched on exosome membranes. These domains likely play key roles in the biological functions and cellular uptake of exosomes by facilitating selective membrane interactions with target organs.
Collapse
Affiliation(s)
- Tomokazu Yasuda
- Graduate
School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka560-0043, Japan
| | - Hirofumi Watanabe
- Graduate
School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka560-0043, Japan
| | - Koichiro M. Hirosawa
- Institute
for Glyco-core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu501-1193, Japan
| | - Kenichi G. N. Suzuki
- Institute
for Glyco-core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu501-1193, Japan
| | - Keishi Suga
- Department
of Chemical Engineering, Tohoku University, 6-6-07, Aoba, Aramaki-aza, Aoba-ku, Sendai, Miyagi980-8579, Japan
| | - Shinya Hanashima
- Graduate
School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka560-0043, Japan
| |
Collapse
|
47
|
Abstract
Micromechanics techniques are playing an increasing role in characterization of biomembranes. The mechanical properties of membranes play an important role for a whole range of cellular processes. Lipid-protein biomembranes display lateral heterogeneity, domain formation, and morphological changes at mesoscopic and nanoscopic length scales. An attempt is made to introduce how membrane's material properties can be measured. Both fluctuation analysis and micro-pipette aspiration experiments have been used to quantify the micromechanics of membranes. The relationship between the structure and function of biomembranes is a critical concern in modern biology. This overview calls for a deeper understanding of how the cell complexity might be related to the mechanical properties of the lipid-protein membrane. Mechanical properties can influence cellular response to processes like adhesion, transport, differentiation, proliferation and migration.
Collapse
|
48
|
Lee HW, Pati TK, Lee IJ, Lee JM, Kim BR, Kwak SY, Kim HM. In Vivo Simultaneous Imaging of Plasma Membrane and Lipid Droplets in Hepatic Steatosis using Red-Emissive Two-Photon Probes. Anal Chem 2022; 94:15100-15107. [PMID: 36265084 DOI: 10.1021/acs.analchem.2c03285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The plasma membrane, which is a phosphoglyceride bilayer at the outer edge of the cell, plays diverse and important roles in biological systems. Visualization of the plasma membrane in live samples is important for various applications in biological functions. We developed an amphiphilic two-photon (TP) fluorescent probe (THQ-Mem) to selectively monitor the plasma membrane in live samples. This probe exhibited red emission (620-700 nm), large TP absorption cross sections (δmax > 790 GM), and high selectivity to the plasma membrane. In cultured cells and in vivo hepatic tissue imaging, THQ-Mem showed bright TP-excited fluorescence (TPEF) and remarkable selectivity for the plasma membrane. Furthermore, simultaneous in vivo imaging with THQ-Mem and a TP lipid droplet probe could serve as an efficient tool to monitor morphological and physiological changes in the plasma membrane and lipid droplets.
Collapse
Affiliation(s)
- Hyo Won Lee
- Department of Energy Systems Research and Department of Chemistry, Ajou University, Suwon 16499, Korea
| | - Tanmay Kumar Pati
- Department of Energy Systems Research and Department of Chemistry, Ajou University, Suwon 16499, Korea
| | - In-Jeong Lee
- Three-Dimensional Immune System Imaging Core Facility, Ajou University, Suwon 16499, Korea
| | - Jeong-Mi Lee
- Three-Dimensional Immune System Imaging Core Facility, Ajou University, Suwon 16499, Korea
| | - Bo Ra Kim
- Department of Energy Systems Research and Department of Chemistry, Ajou University, Suwon 16499, Korea
| | - Sun Young Kwak
- Department of Energy Systems Research and Department of Chemistry, Ajou University, Suwon 16499, Korea
| | - Hwan Myung Kim
- Department of Energy Systems Research and Department of Chemistry, Ajou University, Suwon 16499, Korea
| |
Collapse
|
49
|
Matsuzaki T, Terutsuki D, Sato S, Ikarashi K, Sato K, Mitsuno H, Okumura R, Yoshimura Y, Usami S, Mori Y, Fujii M, Takemi S, Nakabayashi S, Yoshikawa HY, Kanzaki R. Low Surface Potential with Glycoconjugates Determines Insect Cell Adhesion at Room Temperature. J Phys Chem Lett 2022; 13:9494-9500. [PMID: 36201238 PMCID: PMC9575668 DOI: 10.1021/acs.jpclett.2c01673] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Cell-coupled field-effect transistor (FET) biosensors have attracted considerable attention because of their high sensitivity to biomolecules. The use of insect cells (Sf21) as a core sensor element is advantageous due to their stable adhesion to sensors at room temperature. Although visualization of the insect cell-substrate interface leads to logical amplification of signals, the spatiotemporal processes at the interfaces have not yet been elucidated. We quantitatively monitored the adhesion dynamics of Sf21 using interference reflection microscopy (IRM). Specific adhesion signatures with ring-like patches along the cellular periphery were detected. A combination of zeta potential measurements and lectin staining identified specific glycoconjugates with low electrostatic potentials. The ring-like structures were disrupted after cholesterol depletion, suggesting a raft domain along the cell periphery. Our results indicate dynamic and asymmetric cell adhesion is due to low electrostatic repulsion with fluidic sugar rafts. We envision the logical design of cell-sensor interfaces with an electrical model that accounts for actual adhesion interfaces.
Collapse
Affiliation(s)
- Takahisa Matsuzaki
- Center
for Future Innovation, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 565-0871, Japan
- Department
of Applied Physics, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- Division
of Strategic Research and Development, Saitama
University, Shimo-Okubo 255, Sakura-Ku, Saitama 338-8570, Japan
| | - Daigo Terutsuki
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-Ku, Tokyo 153-8904, Japan
- Department
of Finemechanics, Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-aza Aoba, Aoba-Ku, Sendai, 980-8579 Japan
| | - Shoma Sato
- Department
of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-Ku, Saitama 338-8570, Japan
| | - Kohei Ikarashi
- Department
of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-Ku, Saitama 338-8570, Japan
| | - Kohei Sato
- Graduate
School of Science and Technology, Shizuoka
University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan
- Course
of Applied Chemistry and Biochemical Engineering, Department of Engineering,
Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan
- Department
of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, Shizuoka 432-8561, Japan
- Research
Institute of Green Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan
| | - Hidefumi Mitsuno
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-Ku, Tokyo 153-8904, Japan
| | - Ryu Okumura
- Department
of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
- WPI
Immunology Frontier Research Center, Osaka
University, Osaka 565-0871, Japan
- Integrated
Frontier Research for Medical Science Division, Institute for Open
and Transdisciplinary Research Initiatives, Osaka University, Osaka 565-0871, Japan
| | - Yudai Yoshimura
- Department
of Applied Physics, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shigeyoshi Usami
- Division
of Electrical, Electronic and Info communications Engineering, Graduate
School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yusuke Mori
- Division
of Electrical, Electronic and Info communications Engineering, Graduate
School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Mai Fujii
- Department
of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-Ku, Saitama 338-8570, Japan
| | - Shota Takemi
- Area
of Regulatory Biology, Division of Life Science, Graduate School of
Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-Ku, Saitama 338-8570, Japan
| | - Seiichiro Nakabayashi
- Division
of Strategic Research and Development, Saitama
University, Shimo-Okubo 255, Sakura-Ku, Saitama 338-8570, Japan
- Department
of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-Ku, Saitama 338-8570, Japan
| | - Hiroshi Y. Yoshikawa
- Department
of Applied Physics, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Ryohei Kanzaki
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-Ku, Tokyo 153-8904, Japan
| |
Collapse
|
50
|
Effect of Coffee on the Bioavailability of Sterols. Foods 2022; 11:foods11192935. [PMID: 36230011 PMCID: PMC9563500 DOI: 10.3390/foods11192935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/12/2022] [Accepted: 09/16/2022] [Indexed: 11/24/2022] Open
Abstract
Absorption at the intestinal epithelium is a major determinant of cholesterol levels in the organism, influencing the entry of dietary cholesterol and the excretion of endogenous cholesterol. Several strategies are currently being followed to reduce cholesterol absorption, using both pharmacological agents or food ingredients with hypocholesterolemic properties. Coffee has recently been shown to affect cholesterol bioaccessibility, although it has not been shown if this translates into a decrease on cholesterol bioavailability. In this work, coffee obtained with different commercial roasting (light and dark) and grinding (finer and coarser) was evaluated regarding their effect on cholesterol absorption through Caco-2 monolayers, mimicking the intestinal epithelium. The fluorescent dehydroergosterol was used as a sterol model, which was shown to permeate Caco-2 monolayers with a low-to-moderate permeability coefficient depending on its concentration. In the presence of coffee extracts, a 50% decrease of the sterol permeability coefficient was observed, showing their potential to affect sterol bioavailability. This was attributed to an increased sterol precipitation and its deposition on the apical epithelial surface. A higher hypocholesterolemic effect was observed for the dark roasting and finer grinding, showing that the modulation of these technological processing parameters may produce coffees with optimized hypocholesterolemic activity.
Collapse
|