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Erguven H, Wang L, Gutierrez B, Beaven AH, Sodt AJ, Izgu EC. Biomimetic Vesicles with Designer Phospholipids Can Sense Environmental Redox Cues. JACS AU 2024; 4:1841-1853. [PMID: 38818047 PMCID: PMC11134385 DOI: 10.1021/jacsau.4c00041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/06/2024] [Accepted: 03/26/2024] [Indexed: 06/01/2024]
Abstract
Cell-like materials that sense environmental cues can serve as next-generation biosensors and help advance the understanding of intercellular communication. Currently, bottom-up engineering of protocell models from molecular building blocks remains a grand challenge chemists face. Herein, we describe giant unilamellar vesicles (GUVs) with biomimetic lipid membranes capable of sensing environmental redox cues. The GUVs employ activity-based sensing through designer phospholipids that are fluorescently activated in response to specific reductive (hydrogen sulfide) or oxidative (hydrogen peroxide) conditions. These synthetic phospholipids are derived from 1,2-dipalmitoyl-rac-glycero-3-phosphocholine and they possess a headgroup with heterocyclic aromatic motifs. Despite their structural deviation from the phosphocholine headgroup, the designer phospholipids (0.5-1.0 mol %) mixed with natural lipids can vesiculate, and the resulting GUVs (7-20 μm in diameter) remain intact over the course of redox sensing. All-atom molecular dynamics simulations gave insight into how these lipids are positioned within the hydrophobic core of the membrane bilayer and at the membrane-water interface. This work provides a purely chemical method to investigate potential redox signaling and opens up new design opportunities for soft materials that mimic protocells.
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Affiliation(s)
- Huseyin Erguven
- Department
of Chemistry and Chemical Biology, Rutgers
University, New Brunswick, New Jersey 08854, United States
| | - Liming Wang
- Department
of Chemistry and Chemical Biology, Rutgers
University, New Brunswick, New Jersey 08854, United States
| | - Bryan Gutierrez
- Department
of Chemistry and Chemical Biology, Rutgers
University, New Brunswick, New Jersey 08854, United States
| | - Andrew H. Beaven
- Unit
on Membrane Chemical Physics, Eunice Kennedy Shriver National Institute
of Child Health and Human Development, National
Institutes of Health, Bethesda, Maryland 20892, United States
- Postdoctoral
Research Associate Program, National Institute
of General Medical Sciences, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Alexander J. Sodt
- Unit
on Membrane Chemical Physics, Eunice Kennedy Shriver National Institute
of Child Health and Human Development, National
Institutes of Health, Bethesda, Maryland 20892, United States
| | - Enver Cagri Izgu
- Department
of Chemistry and Chemical Biology, Rutgers
University, New Brunswick, New Jersey 08854, United States
- Cancer
Institute of New Jersey, Rutgers University, New Brunswick, New Jersey 08901, United States
- Rutgers
Center for Lipid Research, New Jersey Institute
for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey 08901, United States
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2
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Wu T, Zeng Z, Yu Y. Role of Probiotics in Gut Microbiome and Metabolome in Non-Alcoholic Fatty Liver Disease Mouse Model: A Comparative Study. Microorganisms 2024; 12:1020. [PMID: 38792849 PMCID: PMC11124503 DOI: 10.3390/microorganisms12051020] [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: 04/11/2024] [Revised: 05/10/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is the most prevalent chronic liver condition worldwide. Numerous studies conducted recently have demonstrated a connection between the dysbiosis of the development of NAFLD and gut microbiota. Rebuilding a healthy gut ecology has been proposed as a strategy involving the use of probiotics. The purpose of this work is to investigate and compare the function of probiotics Akkermansia muciniphila (A. muciniphila) and VSL#3 in NAFLD mice. Rodent NAFLD was modeled using a methionine choline-deficient diet (MCD) with/without oral probiotic delivery. Subsequently, qPCR, histological staining, and liver function tests were conducted. Mass spectrometry-based analysis and 16S rDNA gene sequencing were used to investigate the liver metabolome and gut microbiota. We found that while both A. muciniphila and VSL#3 reduced hepatic fat content, A. muciniphila outperformed VSL#3. Furthermore, probiotic treatment restored the β diversity of the gut flora and A. muciniphila decreased the abundance of pathogenic bacteria such as Ileibacterium valens. These probiotics altered the metabolism in MCD mice, especially the glycerophospholipid metabolism. In conclusion, our findings distinguished the role of A. muciniphila and VSL#3 in NAFLD and indicated that oral-gavage probiotics remodel gut microbiota and improve metabolism, raising the possibility of using probiotics in the cure of NAFLD.
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Affiliation(s)
| | - Zheng Zeng
- Department of Infectious Diseases, Peking University First Hospital, Beijing 100034, China;
| | - Yanyan Yu
- Department of Infectious Diseases, Peking University First Hospital, Beijing 100034, China;
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3
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John Peter AT, Kornmann B. Uncovering mechanisms of interorganelle lipid transport by enzymatic mass tagging. FEBS Lett 2024; 598:1292-1298. [PMID: 38268324 DOI: 10.1002/1873-3468.14810] [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: 10/18/2023] [Revised: 12/11/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024]
Abstract
Lipid trafficking is critical for the biogenesis and expansion of organelle membranes. Lipid transport proteins (LTPs) have been proposed to facilitate lipid transport at contact sites between organelles. Despite the fundamental importance of LTPs in cell physiology, our knowledge on the mechanisms of interorganelle lipid distribution remains poor due to the scarcity of assays to monitor lipid flux in vivo. In this review, we highlight the recent development of a versatile method named METALIC (Mass tagging-Enabled Tracking of Lipids in Cells), which uses a combination of enzymatic mass tagging and mass spectrometry to track lipid flux between organelles inside living cells. We discuss the methodology, its distinct advantages, limitations as well as its potential to unearth the pipelines of lipid transport and LTP function in vivo.
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White-Mathieu BM, Baskin JM. Super-Resolution Imaging of Clickable Lipids With Lipid Expansion Microscopy (LExM). Curr Protoc 2024; 4:e1051. [PMID: 38779885 PMCID: PMC11125533 DOI: 10.1002/cpz1.1051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Fluorescent imaging of cellular membranes is challenged by the size of lipid bilayers, which are smaller than the diffraction limit of light. Recently, expansion microscopy (ExM) has emerged as an approachable super-resolution method that requires only widely accessible confocal microscopes. In this method, biomolecules of interest are anchored to hydrogel-based, polymeric networks that are expanded through osmosis to physically separate and resolve features smaller than the diffraction limit of light. Whereas ExM has been employed for super-resolution imaging of proteins, DNA, RNA, and glycans, the application of this method to the study of lipids is challenged by the requirement of permeabilization procedures that remove lipids and compromise the integrity of the membrane. Here, we describe our recently developed protocols for lipid expansion microscopy (LExM), a method that enables ExM of membranes without permeabilization. These detailed protocols and accompanying commentary sections aim to make LExM accessible to any experimentalist interested in imaging membranes with super-resolution. © 2024 Wiley Periodicals LLC. Basic Protocol 1: LExM of alkyne-choline lipids Basic Protocol 2: LExM of IMPACT-labeled lipids Basic Protocol 3: LExM of clickable cholesterol Basic Protocol 4: Determining the expansion factor.
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Affiliation(s)
- Brittany M. White-Mathieu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jeremy M. Baskin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
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5
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Lesiak L, Dadina N, Zheng S, Schelvis M, Schepartz A. A Bright, Photostable, and Far-Red Dye That Enables Multicolor, Time-Lapse, and Super-Resolution Imaging of Acidic Organelles. ACS CENTRAL SCIENCE 2024; 10:19-27. [PMID: 38292604 PMCID: PMC10823512 DOI: 10.1021/acscentsci.3c01173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/15/2023] [Accepted: 11/21/2023] [Indexed: 02/01/2024]
Abstract
Lysosomes have long been known for their acidic lumens and efficient degradation of cellular byproducts. In recent years, it has become clear that their function is far more sophisticated, involving multiple cell signaling pathways and interactions with other organelles. Unfortunately, their acidic interior, fast dynamics, and small size make lysosomes difficult to image with fluorescence microscopy. Here we report a far-red small molecule, HMSiR680-Me, that fluoresces only under acidic conditions, causing selective labeling of acidic organelles in live cells. HMSiR680-Me can be used alongside other far-red dyes in multicolor imaging experiments and is superior to existing lysosome probes in terms of photostability and maintaining cell health and lysosome motility. We demonstrate that HMSiR680-Me is compatible with overnight time-lapse experiments as well as time-lapse super-resolution microscopy with a frame rate of 1.5 fps for at least 1000 frames. HMSiR680-Me can also be used alongside silicon rhodamine dyes in a multiplexed super-resolution microscopy experiment to visualize interactions between mitochondria and lysosomes with only a single excitation laser and simultaneous depletion. We envision this dye permitting a more detailed study of the role of lysosomes in dynamic cellular processes and disease.
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Affiliation(s)
- Lauren Lesiak
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Neville Dadina
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Shuai Zheng
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Marianne Schelvis
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Alanna Schepartz
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Department
of Molecular and Cell Biology, University
of California, Berkeley, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California 94720, United States
- Chan
Zuckerberg Biohub, San Francisco, San Francisco, California 94158, United States
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Kotlova ER, Senik SV, Pozhvanov GA, Prokopiev IA, Boldyrev IA, Manzhieva BS, Amigud EY, Puzanskiy RK, Khakulova AA, Serebryakov EB. Uptake and Metabolic Conversion of Exogenous Phosphatidylcholines Depending on Their Acyl Chain Structure in Arabidopsis thaliana. Int J Mol Sci 2023; 25:89. [PMID: 38203257 PMCID: PMC10778594 DOI: 10.3390/ijms25010089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/11/2023] [Accepted: 12/16/2023] [Indexed: 01/12/2024] Open
Abstract
Fungi and plants are not only capable of synthesizing the entire spectrum of lipids de novo but also possess a well-developed system that allows them to assimilate exogenous lipids. However, the role of structure in the ability of lipids to be absorbed and metabolized has not yet been characterized in detail. In the present work, targeted lipidomics of phosphatidylcholines (PCs) and phosphatidylethanolamines (PEs), in parallel with morphological phenotyping, allowed for the identification of differences in the effects of PC molecular species introduced into the growth medium, in particular, typical bacterial saturated (14:0/14:0, 16:0/16:0), monounsaturated (16:0/18:1), and typical for fungi and plants polyunsaturated (16:0/18:2, 18:2/18:2) species, on Arabidopsis thaliana. For comparison, the influence of an artificially synthesized (1,2-di-(3-(3-hexylcyclopentyl)-propanoate)-sn-glycero-3-phosphatidylcholine, which is close in structure to archaeal lipids, was studied. The phenotype deviations stimulated by exogenous lipids included changes in the length and morphology of both the roots and leaves of seedlings. According to lipidomics data, the main trends in response to exogenous lipid exposure were an increase in the proportion of endogenic 18:1/18:1 PC and 18:1_18:2 PC molecular species and a decrease in the relative content of species with C18:3, such as 18:3/18:3 PC and/or 16:0_18:3 PC, 16:1_18:3 PE. The obtained data indicate that exogenous lipid molecules affect plant morphology not only due to their physical properties, which are manifested during incorporation into the membrane, but also due to the participation of exogenous lipid molecules in the metabolism of plant cells. The results obtained open the way to the use of PCs of different structures as cellular regulators.
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Affiliation(s)
- Ekaterina R. Kotlova
- Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint-Petersburg, Russia; (S.V.S.); (G.A.P.); (I.A.P.); (B.S.M.); (E.Y.A.); (R.K.P.)
| | - Svetlana V. Senik
- Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint-Petersburg, Russia; (S.V.S.); (G.A.P.); (I.A.P.); (B.S.M.); (E.Y.A.); (R.K.P.)
| | - Gregory A. Pozhvanov
- Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint-Petersburg, Russia; (S.V.S.); (G.A.P.); (I.A.P.); (B.S.M.); (E.Y.A.); (R.K.P.)
- Department of Botany and Ecology, Faculty of Biology, Herzen State Pedagogical University, 191186 Saint-Petersburg, Russia
| | - Ilya A. Prokopiev
- Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint-Petersburg, Russia; (S.V.S.); (G.A.P.); (I.A.P.); (B.S.M.); (E.Y.A.); (R.K.P.)
| | - Ivan A. Boldyrev
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Bairta S. Manzhieva
- Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint-Petersburg, Russia; (S.V.S.); (G.A.P.); (I.A.P.); (B.S.M.); (E.Y.A.); (R.K.P.)
| | - Ekaterina Ya. Amigud
- Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint-Petersburg, Russia; (S.V.S.); (G.A.P.); (I.A.P.); (B.S.M.); (E.Y.A.); (R.K.P.)
- Department of Botany and Ecology, Faculty of Biology, Herzen State Pedagogical University, 191186 Saint-Petersburg, Russia
| | - Roman K. Puzanskiy
- Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint-Petersburg, Russia; (S.V.S.); (G.A.P.); (I.A.P.); (B.S.M.); (E.Y.A.); (R.K.P.)
| | - Anna A. Khakulova
- Chemical Analysis and Materials Research Core Facility Center, Reseach Park, Saint-Petersburg State University, 199034 Saint-Petersburg, Russia; (A.A.K.); (E.B.S.)
| | - Evgeny B. Serebryakov
- Chemical Analysis and Materials Research Core Facility Center, Reseach Park, Saint-Petersburg State University, 199034 Saint-Petersburg, Russia; (A.A.K.); (E.B.S.)
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7
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Lesiak L, Dadina N, Zheng S, Schelvis M, Schepartz A. A Bright, Photostable Dye that Enables Multicolor, Time Lapse, and Super-Resolution Imaging of Acidic Organelles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.552058. [PMID: 37577591 PMCID: PMC10418513 DOI: 10.1101/2023.08.04.552058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Lysosomes have long been known for their acidic lumen and efficient degradation of cellular byproducts. In recent years it has become clear that their function is far more sophisticated, involving multiple cell signaling pathways and interactions with other organelles. Unfortunately, their acidic interior, fast dynamics, and small size makes lysosomes difficult to image with fluorescence microscopy. Here we report a far-red small molecule, HMSiR680-Me, that fluoresces only under acidic conditions, causing selective labeling of acidic organelles in live cells. HMSiR680-Me can be used alongside other far-red dyes in multicolor imaging experiments and is superior to existing lysosome probes in terms of photostability and maintaining cell health and lysosome motility. We demonstrate that HMSiR680-Me is compatible with overnight time lapse experiments, as well as time lapse super-resolution microscopy with a fast frame rate for at least 1000 frames. HMSiR680-Me can also be used alongside silicon rhodamine dyes in a multiplexed super-resolution microscopy experiment to visualize interactions between the inner mitochondrial membrane and lysosomes with only a single excitation laser and simultaneous depletion. We envision this dye permitting more detailed study of the role of lysosomes in dynamic cellular processes and disease.
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Affiliation(s)
- Lauren Lesiak
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Neville Dadina
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Shuai Zheng
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Marianne Schelvis
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Alanna Schepartz
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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Abstract
Lipids are key components of all organisms. We are well educated in their use as fuel and their essential role to form membranes. We also know much about their biosynthesis and metabolism. We are also aware that most lipids have signaling character meaning that a change in their concentration or location constitutes a signal that helps a living cell to respond to changes in the environment or to fulfill its specific function ranging from secretion to cell division. What is much less understood is how lipids change location in cells over time and what other biomolecules they interact with at each stage of their lifetime. Due to the large number of often quite similar lipid species and the sometimes very short lifetime of signaling lipids, we need highly specific tools to manipulate and visualize lipids and lipid-protein interactions. If successfully applied, these tools provide fabulous opportunities for discovery.In this Account, I summarize the development of synthetic tools from our lab that were designed to address crucial properties that allow them to function as tools in live cell experiments. Techniques to change the concentration of lipids by adding a small molecule or by light are described and complemented by examples of biological findings made when applying the tools. This ranges from chemical dimerizer-based systems to synthetic "caged" lipid derivatives. Furthermore, I discuss the problem of locating a lipid in an intact cell. Synthetic molecular probes are described that help to unravel the lipid location and to determine their binding proteins. These location studies require in-cell lipid tagging by click chemistry, photo-cross-linking to prevent further movement and the "caging" groups to avoid premature metabolism. The combination of these many technical features in a single tool allows for the analysis of not only lipid fluxes through metabolism but also lipid transport from one membrane to another as well as revealing the lipid interactome in a cell-dependent manner. This latter point is crucial because with these multifunctional tools in combination with lipidomics we can now address differences in healthy versus diseased cells and ultimately find the changes that are essential for disease development and new therapeutics that prevent these changes.
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Affiliation(s)
- Carsten Schultz
- Department of Chemical Physiology and
Biochemistry, Oregon Health & Science
University, Portland, Oregon 97239, United States
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