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Phase Separation in Liposomes Determined by Ergosterol and Classified Using Machine Learning

Published online by Cambridge University Press:  19 September 2022

Tsuyoshi Yoda Open the ORCID record for Tsuyoshi Yoda [Opens in a new window]
Tsuyoshi Yoda*
Affiliation:
Aomori Prefectural Industrial Technology Research Center, Hachinohe Industrial Research Institute, Hachinohe City, Aomori 039-2245, Japan The United Graduate School of Agricultural Sciences, Iwate University, Morioka City, Iwate 020-8550, Japan
*
Email: [email protected]
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Abstract

Recent studies indicated that ergosterol (Erg) helps form strongly ordered lipid domains in membranes that depend on their chemical characters. However, direct evidence of concentration-dependent interaction of Erg with lipid membranes has not been reported. We studied the Erg concentration-dependent changes in the phase behaviors of membranes using cell-sized liposomes containing 1,2-Dioleoyl-sn-glycero-3-phosphocholine (DOPC)/1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC). We observed the concentration range of phase separation in ternary membranes was significantly wider when Erg rather than cholesterol (Chol) was used as the sterol component. We used machine learning for the first time to analyze microscopic images of cell-sized liposomes and identify phase-separated structures. The automated method was successful in identifying homogeneous membranes but performance remained data-limited for the identification of phase separation domains characterized by more complex features.

Keywords

ergosterolliposomemachine learningmicroscopic observationphase separation
Type
Biological Applications
Information
Microscopy and Microanalysis , Volume 28 , Issue 6 , December 2022 , pp. 2130 - 2137
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Copyright
Copyright © The Author(s), 2022. Published by Cambridge University Press on behalf of the Microscopy Society of America

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References

Akiyama, H, Hamada, T, Nagatsuka, Y, Kobayashi, S, Hira-bayashi, Y & Murakami-Murofushi, K (2011). A possible mechanism of cholesteryl glucoside formation involved in heat shock response in the animal cell membrane. Cytologia 76, 19–25.CrossRefGoogle Scholar
Alberts, B, Johnson, A, Lewis, J, Raff, M, Roberts, K, Walter, P, Bray, D & Watson, J (2012). Molecular Biology of the Cell, Classic Textbook, 5th ed. New York: Garland Science.Google Scholar
Angelova, MI, Bitbol, A, Seigneuret, M, Staneva, G, Kodama, A, Sakuma, Y, Kawakatsu, T, Imai, M & Puff, N (2018). pH sensing by lipids in membranes: The fundamentals of pH-driven migration, polarization and deformations of lipid bilayer assemblies. Biochim Biophys Acta Biomembr 1860, 2042–2063.CrossRefGoogle ScholarPubMed
Ayuyan, AG & Cohen, FS (2006). Lipid peroxides promote large rafts: Effects of excitation of probes in fluorescence microscopy and electrochemical reactions during vesicle formation. Biophys J 91, 2172–2183.CrossRefGoogle ScholarPubMed
Bacia, K, Schwille, P & Kurzchalia, T (2005). Sterol structure determines the separation of phases and the curvature of the liquid-ordered phase in model membranes. Proc Natl Acad Sci USA 102, 3272–3277.CrossRefGoogle ScholarPubMed
Bagatolli, L & Kumar, PBS (2009). Phase behavior of multicomponent membranes: Experimental and computational techniques. Soft Matter 5, 3234–3238.CrossRefGoogle Scholar
Baumgart, T, Hess, ST & Webb, WW (2003). Imaging coexisting fluid domains in biomembrane models coupling curvature and line tension. Nature 425, 821–824.CrossRefGoogle ScholarPubMed
Beattie, ME, Veatch, SL, Stottrup, BL & Keller, SL (2005). Sterol structure determines miscibility versus melting transitions in lipid vesicles. Biophys J 89, 1760–1768.CrossRefGoogle ScholarPubMed
Bieberich, E (2021). Lipid Rafts Methods and Protocols. New York, NY: Humana Press Inc.CrossRefGoogle Scholar
Bui, TT, Suga, K, Kuhl, TL & Umakoshi, H (2019 a). Melting-temperature-dependent interactions of ergosterol with unsaturated and saturated lipids in model membranes. Langmuir 35, 10640–10647.CrossRefGoogle ScholarPubMed
Bui, TT, Suga, K & Umakoshi, H (2016). Roles of sterol derivatives in regulating the properties of phospholipid bilayer systems. Langmuir 32, 6176–6184.CrossRefGoogle ScholarPubMed
Bui, TT, Suga, K & Umakoshi, H (2019 b). Ergosterol-induced ordered phase in ternary lipid mixture systems of unsaturated and saturated phospholipid membranes. J Phys Chem B 123, 6161–6168.CrossRefGoogle ScholarPubMed
Chadani, T, Ohnuki, S, Isogai, A, Goshima, T, Kashima, M, Ghanegolmohammadi, F, Nishi, T, Hirata, D, Watanabe, D, Kitamoto, K, Akao, T & Ohya, Y (2021). Genome editing to generate sake yeast strains with eight mutations that confer excellent brewing characteristics. Cells 10, 1299.CrossRefGoogle ScholarPubMed
Cicuta, P & Donald, AM (2007). Microrheology: A review of the method and applications. Soft Matter 3, 1449–1455.CrossRefGoogle ScholarPubMed
Cicuta, P, Keller, SL & Veatch, SL (2007). Diffusion of liquid domains in lipid bilayer membranes. J Phys Chem B 111, 3328–3331.CrossRefGoogle ScholarPubMed
Egorov, E, Pieters, C, Korach-Rechtman, H, Shklover, J & Schroeder, A (2021). Robotics, microfluidics, nanotechnology and AI in the synthesis and evaluation of liposomes and polymeric drug delivery systems. Drug Deliv Transl Res 11, 345–352.CrossRefGoogle ScholarPubMed
Hamada, T, Kishimoto, Y, Nagasaki, T & Takagi, M (2011 a). Lateral phase separation in tense membranes. Soft Matter 7, 9061–9068.CrossRefGoogle Scholar
Hamada, T, Miura, Y, Ishii, K, Araki, S, Yoshikawa, K, Vestergaard, M & Takagi, M (2007). Dynamic processes in endocytic transformation of a raft-exhibiting giant liposome. J Phys Chem B 111, 10853–10857.CrossRefGoogle ScholarPubMed
Hamada, T, Miura, Y, Komatsu, Y, Kishimoto, Y, Vestergaard, V & Takagi, M (2008). Construction of asymmetric cell-sized lipid vesicles from lipid-coated water-in-oil microdroplets. J Phys Chem B 112, 14678–14681.CrossRefGoogle ScholarPubMed
Hamada, T, Morita, M, Miyakawa, M, Sugimoto, R, Hatanaka, A, Vestergaard, MC & Takagi, M (2012). Size-dependent partitioning of nano/microparticles mediated by membrane lateral heterogeneity. J Am Chem Soc 134, 13990–13996.CrossRefGoogle ScholarPubMed
Hamada, T, Sugimoto, R, Nagasaki, T & Takagi, M (2011 b). Photochemical control of membrane raft organization. Soft Matter 7, 220–224. Available at https://teachablemachine.withgoogle.com/ (accessed 29 July 2021).CrossRefGoogle Scholar
Himeno, H, Shimokawa, N, Komura, S, Andelman, D, Hamada, T & Takagi, M (2014). Charge-induced phase separation in lipid membranes. Soft Matter 10, 7959–7967.CrossRefGoogle ScholarPubMed
Ishii, K, Hamada, T, Hatakeyama, M, Sugimoto, R, Nagasaki, T & Takagi, M (2009). Reversible control of exo- and endo-budding transitions in a photosensitive lipid membrane. Chem Bio Chem 10, 251–256.CrossRefGoogle Scholar
Löpez, CA, Vesselinov, VV, Gnanakaran, S & Alexandrov, BS (2019). Unsupervised machine learning for analysis of phase separation in ternary lipid mixture. J Chem Theory Comput 15, 6343–6357.CrossRefGoogle ScholarPubMed
McIntosh, TJ (2007). Lipid Rafts. Totowa, NJ: Humana Press Inc.CrossRefGoogle Scholar
Morales-Penningston, NF, Wu, J, Farkas, ER, Goh, SL, Kon-yakhina, TM, Zheng, JY, Webb, WW & Feigenson, GW (2010). GUV preparation and imaging: Minimizing artifacts. Biochim Biophys Acta Biomembr 1798, 1324–1332.CrossRefGoogle ScholarPubMed
Morita, M, Hamada, T, Tendo, Y, Hata, T, Vestergaard, MC & Takagi, M (2012). Selective localization of Alzheimer's amyloid beta in membrane lateral compartments. Soft Matter 8, 2816–2819.CrossRefGoogle Scholar
Morita, M, Hamada, T, Vestergaard, MC & Takagi, M (2014). Endo- and exocytic budding transformation of slow-diffusing membrane domains induced by Alzheimer's amyloid beta. Phys Chem Chem Phys 16, 8773–8777.CrossRefGoogle ScholarPubMed
Morita, M & Noda, N (2021). Membrane shape dynamics-based analysis of the physical properties of giant unilamellar vesicles prepared by inverted emulsion and hydration techniques. Langmuir 37, 2268–2275.CrossRefGoogle ScholarPubMed
Morita, M, Onoe, H, Yanagisawa, M, Ito, H, Ichikawa, M, Fuji-wara, K, Saito, H & Takinoue, M (2015). Droplet-shooting and size-filtration (DSSF) method for synthesis of cell-sized liposomes with controlled lipid compositions. Chem Bio Chem 16, 2029–2035.CrossRefGoogle ScholarPubMed
Morita, M, Vestergaard, M, Hamada, T & Takagi, M (2010). Real-time observation of model membrane dynamics induced by Alzheimer's amyloid beta. Biophys Chem 147, 81–86.CrossRefGoogle ScholarPubMed
Ohya, Y, Sese, J, Yukawa, M, Sano, F, Nakatani, Y, Saito, TL, Saka, A, Fukuda, T, Ishihara, S, Oka, S, Suzuki, G, Watanabe, M, Hirata, A, Ohtani, M, Sawai, H, Fraysse, N, Latgé, J, François, JM, Aebi, M, Tanaka, S, Muramatsu, S, Araki, H, Sonoike, K, Nogami, S & Morishita, S (2005). High-dimensional and large-scale phenotyping of yeast mutants. Proc Natl Acad Sci USA 102, 19015–19020.CrossRefGoogle ScholarPubMed
Phan, HTT, Yoda, T, Chahal, B, Morita, M & Takagi, M (2014). Structure-dependent interactions of polyphenols with a biomimetic membrane system. Biochim Biophys Acta 1838, 2670–2677.CrossRefGoogle ScholarPubMed
Saeki, D, Hamada, T & Yoshikawa, K (2006). Domain-growth kinetics in a cell-sized liposome. J Phys Soc Jpn 75, 013602.CrossRefGoogle Scholar
Sato, Y, Endo, M, Morita, M, Takinoue, M, Sugiyama, H, Murata, S, Nomura, SM & Suzuki, Y (2018). Environment-dependent self-assembly of DNA origami lattices on phase-separated lipid membranes. Adv Mater Interfaces 5, 1800437.CrossRefGoogle Scholar
Scherfeld, D, Kahya, N & Schwille, P (2003). Lipid dynamics and domain formation in model membranes composed of ternary mixtures of unsaturated and saturated phosphatidylcholines and cholesterol. Biophys J 85, 3758–3768.CrossRefGoogle ScholarPubMed
Sharma, N, Phan, HTT, Yoda, T, Shimokawa, N, Vestergaard, MC & Takagi, M (2019). Effects of capsaicin on biomimetic membranes. Biomimetics 4, 17.CrossRefGoogle ScholarPubMed
Simons, K & Ikonen, E (1997). Functional rafts in cell membranes. Nature 387, 569–572.CrossRefGoogle ScholarPubMed
Singer, SJ & Nicolson, GL (1972). The fluid mosaic model of the structure of cell membranes. Science 175, 720–731.CrossRefGoogle ScholarPubMed
Stevens, MM, Honerkamp-Smith, AR & Keller, SL (2010). Solubility limits of cholesterol, lanosterol, ergosterol, stigmasterol, and b-sitosterol in electroformed lipid vesicles. Soft Matter 6, 9061–9068.CrossRefGoogle Scholar
Sugahara, K, Shimokawa, N & Takagi, M (2015). Destabilization of phase-separated structures in local anesthetic-containing model biomembranes. Chem Lett 44, 1604–1606.CrossRefGoogle Scholar
Talbot, EL, Kotar, J, Michele, LD & Cicuta, P (2019). Directed tubule growth from giant unilamellar vesicles in a thermal gradient. Soft Matter 15, 1676–1683.CrossRefGoogle Scholar
Tanaka-Takiguchi, Y, Itoh, T, Tsujita, K, Yamada, S, Yanagisawa, M, Fujiwara, K, Yamamoto, A, Ichikawa, M & Takiguchi, K (2013). Physicochemical analysis from real-time imaging of liposome tubulation reveals the characteristics of individual f-bar domain proteins. Langmuir 29, 328–336.CrossRefGoogle ScholarPubMed
Usery, RD, Enoki, TA, Wickramasinghe, SP, Weiner, MD, Tsai, WC, Kim, MB, Wang, S, Torng, TL, Ackerman, DG, Heberle, FA, Katsaras, J & Feigenson, GW (2017). Line tension controls liquid-disordered + liquid-ordered domain size transition in lipid bilayers. Biophys J 112, 1431–1443.CrossRefGoogle ScholarPubMed
Veatch, SL, Cicuta, P, Sengupta, P, Honerkamp-Smith, A, Holowka, D & Baird, B (2008). Critical fluctuations in plasma membrane vesicles. ACS Chem Biol 35, 287–293.CrossRefGoogle Scholar
Veatch, SL & Keller, SL (2003). Separation of liquid phases in giant vesicles of ternary mixtures of phospholipids and cholesterol. Biophys J 85, 3074–3083.CrossRefGoogle ScholarPubMed
Vestergaard, M, Hamada, T, Morita, M & Takagi, M (2010). Cholesterol, lipids, amyloid beta, and Alzheimer's. Cur Alzh Res 7, 262–270.CrossRefGoogle ScholarPubMed
Vestergaard, M, Hamada, T & Takagi, M (2008). Using model membranes for the study of amyloid beta: Lipid interactions and neurotoxicity. Biotech Bioeng 99, 753–763.CrossRefGoogle Scholar
Vestergaard, MC, Yoda, T, Hamada, T, Akazawa, Y, Yoshida, Y & Takagi, M (2011). The effect of oxycholesterols on thermo-induced membrane dynamics. Biochim Biophys Acta Biomembr 1808, 2245–2251.CrossRefGoogle ScholarPubMed
Wachtler, V & Balasubramanian, MK (2006). Yeast lipid rafts? – An emerging view. Trends Cell Biol 16, 1–4.CrossRefGoogle ScholarPubMed
Walter, V, Ruscher, C, Benzerara, O, Marques, CM & Thalmann, F (2020). A machine learning study of the two states model for lipid bilayer phase transitions. Phys Chem Chem Phys 22, 19147–19154.CrossRefGoogle ScholarPubMed
Yabuuchi, S, Endo, S, Baek, K, Hoshino, K, Tsujino, Y, Vestergaard, MC & Takagi, M (2017). Raft-dependent endocytic movement and intracellular cluster formation during T cell activation triggered by concanavalin A. J Biosci Bioeng 124, 685–693.CrossRefGoogle Scholar
Yanagisawa, M, Imai, M, Masui, T, Komura, S & Ohta, T (2007). Growth dynamics of domains in ternary fluid vesicles. Biophys J 92, 115–125.CrossRefGoogle ScholarPubMed
Yanagisawa, M, Shimokawa, N, Ichikawa, M & Yoshikawa, K (2012). Micro-segregation induced by bulky-head lipids: Formation of characteristic patterns in a giant vesicle. Soft Matter 8, 488–495.CrossRefGoogle Scholar
Yoda, T, Ogura, A & Saito, T (2020). Influence of ethyl caproate on the size of lipid vesicles and yeast cells. Biomimetics 5, 16.CrossRefGoogle ScholarPubMed
Yoda, T & Saito, T (2020). Size of cells and physicochemical properties of membranes are related to flavor production during sake brewing in the yeast Saccharomyces cerevisiae. Membranes 10, 440.CrossRefGoogle ScholarPubMed
Yoda, T, Shibuya, K & Myoubudani, H (2018). Preparation of activated carbon fibers from mixtures of cotton and polyester fibers. Measurement 125, 572–576.CrossRefGoogle Scholar
Yoda, T, Shibuya, K & Myoubudani, H (2019). Preparation and adsorption performance evaluation of activated carbon fibers derived from rayon. SN Appl Sci 1, 1029.CrossRefGoogle Scholar
Yoda, T, Vestergaard, MC, Akazawa-Ogawa, Y, Yoshida, Y, Hamada, T & Takagi, M (2010). Dynamic response of a cholesterol-containing model membrane to oxidative stress. Chem Lett 39, 1273–1274.CrossRefGoogle Scholar
Yoda, T, Vestergaard, MC, Hamada, T, Le, PTM & Takagi, M (2012). Thermo-induced vesicular dynamics of membranes containing cholesterol derivatives. Lipids 47, 813–820.CrossRefGoogle ScholarPubMed
Yoda, T, Yamada, Y & Chounan, Y (2021). Effects of isovaleraldehyde on cell-sized lipid bilayer vesicles. Biophys Chem 279, 106698.CrossRefGoogle ScholarPubMed