Confocal imaging of biomarkers at a single-cell resolution: quantifying 'living' in 3D-printable engineered living material based on Pluronic F-127 and yeast Saccharomyces cerevisiae

Biomaterials Research - Tập 26 - Trang 1-15 - 2022
Bojan Žunar1,2, Taiga Ito3, Christine Mosrin1, Yoshiyuki Sugahara3, Hélène Bénédetti1, Régis Guégan4,5, Béatrice Vallée1
1Centre de Biophysique Moléculaire (CBM), CNRS, UPR 4301, University of Orléans and INSERM, Orléans, France
2Department of Chemistry and Biochemistry, Laboratory for Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
3Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Tokyo, Japan
4Global Center for Advanced Science and Engineering, Faculty of Science and Engineering, Waseda University, Tokyo, Japan
5Institut des Sciences de la Terre d’Orléans (ISTO), UMR 7327, CNRS-Université d’Orléans, Orléans, France

Tóm tắt

Engineered living materials (ELMs) combine living cells with non-living scaffolds to obtain life-like characteristics, such as biosensing, growth, and self-repair. Some ELMs can be 3D-printed and are called bioinks, and their scaffolds are mostly hydrogel-based. One such scaffold is polymer Pluronic F127, a liquid at 4 °C but a biocompatible hydrogel at room temperature. In such thermally-reversible hydrogel, the microorganism-hydrogel interactions remain uncharacterized, making truly durable 3D-bioprinted ELMs elusive. We demonstrate the methodology to assess cell-scaffold interactions by characterizing intact alive yeast cells in cross-linked F127-based hydrogels, using genetically encoded ratiometric biosensors to measure intracellular ATP and cytosolic pH at a single-cell level through confocal imaging. When embedded in hydrogel, cells were ATP-rich, in exponential or stationary phase, and assembled into microcolonies, which sometimes merged into larger superstructures. The hydrogels supported (micro)aerobic conditions and induced a nutrient gradient that limited microcolony size. External compounds could diffuse at least 2.7 mm into the hydrogels, although for optimal yeast growth bioprinted structures should be thinner than 0.6 mm. Moreover, the hydrogels could carry whole-cell copper biosensors, shielding them from contaminations and providing them with nutrients. F127-based hydrogels are promising scaffolds for 3D-bioprinted ELMs, supporting a heterogeneous cell population primarily shaped by nutrient availability.

Tài liệu tham khảo

Rodrigo-Navarro A, Sankaran S, Dalby MJ, del Campo A, Salmeron-Sanchez M. Engineered living biomaterials. Nat Rev Mater. 2021;6(12):1175–90. Wangpraseurt D, You S, Sun Y, Chen S. Biomimetic 3D living materials powered by microorganisms. Trends Biotechnol. 2022;40(7):843–57. Chen H, Cheng Y, Tian J, Yang P, Zhang X, Chen Y, Hu Y, Wu J. Dissolved oxygen from microalgae-gel patch promotes chronic wound healing in diabetes. Sci Adv. 2020;6(20):eaba4311. Sawa M, Fantuzzi A, Bombelli P, Howe CJ, Hellgardt K, Nixon PJ. Electricity generation from digitally printed cyanobacteria. Nat Commun. 2017;8(1):1327. Liu X, Yuk H, Lin S, Parada GA, Tang T-C, Tham E, de la Fuente-Nunez C, Lu TK, Zhao X. 3D printing of living responsive materials and devices. Adv Mater. 2018;30(4):1704821. Wang J, Mignon A, Trenson G, Van Vlierberghe S, Boon N, De Belie N. A chitosan based pH-responsive hydrogel for encapsulation of bacteria for self-sealing concrete. Cem Concr Compos. 2018;93:309–22. Perez JJ, Francois NJ, Maroniche GA, Borrajo MP, Pereyra MA, Creus CM. A novel, green, low-cost chitosan-starch hydrogel as potential delivery system for plant growth-promoting bacteria. Carbohydr Polym. 2018;202:409–17. Wangpraseurt D, You S, Azam F, Jacucci G, Gaidarenko O, Hildebrand M, Kühl M, Smith AG, Davey MP, Smith A, et al. Bionic 3D printed corals. Nat Commun. 2020;11(1):1748. Merceron TK, Murphy SV. Chapter 14 - Hydrogels for 3D Bioprinting Applications. In: Atala A, Yoo JJ, editors. Essentials of 3D Biofabrication and Translation. Boston: Academic Press; 2015. p. 249–70. Saygili E, Dogan-Gurbuz AA, Yesil-Celiktas O, Draz MS. 3D bioprinting: A powerful tool to leverage tissue engineering and microbial systems. Bioprinting. 2020;18: e00071. Newman MJ, Balusubramanian M, Todd CW. Development of adjuvant-active nonionic block copolymers. Adv Drug Delivery Rev. 1998;32(3):199–223. Alexandridis P. Poly(ethylene oxide)/poly(propylene oxide) block copolymer surfactants. Curr Opin Colloid Interface Sci. 1997;2(5):478–89. Chaibundit C, Ricardo NMPS. Costa FdMLL, Yeates SG, Booth C: Micellization and Gelation of Mixed Copolymers P123 and F127 in Aqueous Solution. Langmuir. 2007;23(18):9229–36. Rill RL, Liu Y, Van Winkle DH, Locke BR. Pluronic copolymer liquid crystals: unique, replaceable media for capillary gel electrophoresis. J Chromatogr A. 1998;817(1):287–95. Shriky B, Kelly A, Isreb M, Babenko M, Mahmoudi N, Rogers S, Shebanova O, Snow T, Gough T. Pluronic F127 thermosensitive injectable smart hydrogels for controlled drug delivery system development. J Colloid Interface Sci. 2020;565:119–30. Ito T, Endo S, Sugahara Y, Tamate R, Guégan R. Preparation of biocompatible hydrogels reinforced by different nanosheets. RSC Adv. 2022;12(2):753–61. Millik SC, Dostie AM, Karis DG, Smith PT, McKenna M, Chan N, Curtis CD, Nance E, Theberge AB, Nelson A. 3D printed coaxial nozzles for the extrusion of hydrogel tubes toward modeling vascular endothelium. Biofabrication. 2019;11(4): 045009. Müller M, Becher J, Schnabelrauch M, Zenobi-Wong M. Nanostructured Pluronic hydrogels as bioinks for 3D bioprinting. Biofabrication. 2015;7(3): 035006. Butelmann T, Priks H, Parent Z, Johnston TG, Tamm T, Nelson A, Lahtvee PJ, Kumar R. Metabolism Control in 3D-Printed Living Materials Improves Fermentation. ACS Appl Bio Mater. 2021;4(9):7195–203. Sicard D, Legras J-L. Bread, beer and wine: Yeast domestication in the Saccharomyces sensu stricto complex. C R Biol. 2011;334(3):229–36. Pais P, Almeida V, Yılmaz M, Teixeira MC. Saccharomyces boulardii: What Makes It Tick as Successful Probiotic? J Fungi. 2020;6(2):78. Nielsen J. Yeast Systems Biology: Model Organism and Cell Factory. Biotechnol J. 2019;14(9):1800421. Lozančić M, Žunar B, Hrestak D, Lopandić K, Teparić R, Mrša V. Systematic comparison of cell wall-related proteins of different yeasts. J Fungi. 2021;7(2):128. Novačić A, Šupljika N, Bekavac N, Žunar B, Stuparević I, Hom Erik FY. Interplay of the RNA Exosome Complex and RNA-Binding Protein Ssd1 in Maintaining Cell Wall Stability in Yeast. Microbiol Spectrum. 2021;9(1):e00295-e221. Nandy SK, Srivastava RK. A review on sustainable yeast biotechnological processes and applications. Microbiol Res. 2018;207:83–90. Rahmat E, Kang Y. Yeast metabolic engineering for the production of pharmaceutically important secondary metabolites. Appl Microbiol Biotechnol. 2020;104(11):4659–74. Martin-Yken H. Yeast-Based Biosensors: Current Applications and New Developments. Biosensors. 2020;10(5):51. Johnston TG, Yuan S-F, Wagner JM, Yi X, Saha A, Smith P, Nelson A, Alper HS. Compartmentalized microbes and co-cultures in hydrogels for on-demand bioproduction and preservation. Nat Commun. 2020;11(1):563. Saha A, Johnston TG, Shafranek RT, Goodman CJ, Zalatan JG, Storti DW, Ganter MA, Nelson A. Additive manufacturing of catalytically active living materials. ACS Appl Mater Interfaces. 2018;10(16):13373–80. Priks H, Butelmann T, Illarionov A, Johnston TG, Fellin C, Tamm T, Nelson A, Kumar R, Lahtvee PJ. Physical Confinement Impacts Cellular Phenotypes within Living Materials. ACS Appl Bio Mater. 2020;3(7):4273–81. Liu W, Deng M, Yang C, Liu F, Guan X, Du Y, Wang L, Chu J. Genetically encoded single circularly permuted fluorescent protein-based intensity indicators. J Phys D: Appl Phys. 2020;53(11): 113001. Miesenböck G, De Angelis DA, Rothman JE. Visualizing secretion and synaptic transmission with pH-sensitive green fluorescent proteins. Nature. 1998;394(6689):192–5. Nasu Y, Shen Y, Kramer L, Campbell RE. Structure- and mechanism-guided design of single fluorescent protein-based biosensors. Nat Chem Biol. 2021;17(5):509–18. Molina RS, Qian Y, Wu J, Shen Y, Campbell RE, Drobizhev M, Hughes TE. Understanding the Fluorescence Change in Red Genetically Encoded Calcium Ion Indicators. Biophys J. 2019;116(10):1873–86. Kaczmarski JA, Mitchell JA, Spence MA, Vongsouthi V, Jackson CJ. Structural and evolutionary approaches to the design and optimization of fluorescence-based small molecule biosensors. Curr Opin Struct Biol. 2019;57:31–8. Žunar B, Mosrin C, Bénédetti H, Vallée B. Re-engineering of CUP1 promoter and Cup2/Ace1 transactivator to convert Saccharomyces cerevisiae into a whole-cell eukaryotic biosensor capable of detecting 10 nM of bioavailable copper. Biosens Bioelectron. 2022;214: 114502. World Health Organization. Guidelines for Drinking-water Quality. Malta: Gutenberg; 2011. Botman D, de Groot DH, Schmidt P, Goedhart J, Teusink B. In vivo characterisation of fluorescent proteins in budding yeast. Sci Rep. 2019;9(1):2234. Takaine M, Ueno M, Kitamura K, Imamura H, Yoshida S. Reliable imaging of ATP in living budding and fission yeast. J Cell Sci. 2019;132(8):jcs230649. Reifenrath M, Boles E. A superfolder variant of pH-sensitive pHluorin for in vivo pH measurements in the endoplasmic reticulum. Sci Rep. 2018;8(1):11985. Baker Brachmann C, Davies A, Cost GJ, Caputo E, Li J, Hieter P, Boeke JD. Designer deletion strains derived from Saccharomyces cerevisiae S288C: A useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast. 1998;14(2):115–32. Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, et al. Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012;9(7):676–82. Takaine M. QUEEN-based Spatiotemporal ATP Imaging in Budding and Fission Yeast. Bio-Protoc. 2019;9(15): e3320. Orij R, Postmus J, Ter Beek A, Brul S, Smits GJ. In vivo measurement of cytosolic and mitochondrial pH using a pH-sensitive GFP derivative in Saccharomyces cerevisiae reveals a relation between intracellular pH and growth. Microbiology. 2009;155(1):268–78. Botman D, van Heerden JH, Teusink B. An Improved ATP FRET Sensor For Yeast Shows Heterogeneity During Nutrient Transitions. ACS Sens. 2020;5(3):814–22. R Core Team. R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2021. Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S, Steinegger M. ColabFold: making protein folding accessible to all. Nat Methods. 2022;19(6):679–82. Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, Tunyasuvunakool K, Bates R, Žídek A, Potapenko A, et al. Highly accurate protein structure prediction with AlphaFold. Nature. 2021;596(7873):583–9. Balleza E, Kim JM, Cluzel P. Systematic characterization of maturation time of fluorescent proteins in living cells. Nat Methods. 2018;15(1):47–51. Serrano R. Energy Requirements for Maltose Transport in Yeast. Eur J Biochem. 1977;80(1):97–102. Özalp VC, Pedersen TR, Nielsen LJ, Olsen LF. Time-resolved Measurements of Intracellular ATP in the Yeast Saccharomyces cerevisiae using a New Type of Nanobiosensor. J Biol Chem. 2010;285(48):37579–88. Xu L, Bretscher A. Rapid Glucose Depletion Immobilizes Active Myosin V on Stabilized Actin Cables. Curr Biol. 2014;24(20):2471–9. Imai T, Ohno T. Measurement of yeast intracellular pH by image processing and the change it undergoes during growth phase. J Biotechnol. 1995;38(2):165–72. Valli M, Sauer M, Branduardi P, Borth N, Porro D, Mattanovich D. Intracellular pH Distribution in Saccharomyces cerevisiae Cell Populations, Analyzed by Flow Cytometry. Appl Environ Microbiol. 2005;71(3):1515–21. Valkonen M, Mojzita D, Penttilä M, Benčina M. Noninvasive High-Throughput Single-Cell Analysis of the Intracellular pH of Saccharomyces cerevisiae by Ratiometric Flow Cytometry. Appl Environ Microbiol. 2013;79(23):7179–87. Marsafari M, Ma J, Koffas M, Xu P. Genetically-encoded biosensors for analyzing and controlling cellular process in yeast. Curr Opin Biotechnol. 2020;64:175–82. Torello Pianale L, Rugbjerg P, Olsson L. Real-Time Monitoring of the Yeast Intracellular State During Bioprocesses With a Toolbox of Biosensors. Front Microbiol. 2022;12:802169. Váchová L, Palková Z. How structured yeast multicellular communities live, age and die? FEMS Yeast Res. 2018;18(4):foy033. Pothoulakis G, Ellis T. Synthetic gene regulation for independent external induction of the Saccharomyces cerevisiae pseudohyphal growth phenotype. Commun Biol. 2018;1(1):7. Palková Z, Váchová L. Life within a community: benefit to yeast long-term survival. FEMS Microbiol Rev. 2006;30(5):806–24. Nagarajan S, Kruckeberg AL, Schmidt KH, Kroll E, Hamilton M, McInnerney K, Summers R, Taylor T, Rosenzweig F. Uncoupling reproduction from metabolism extends chronological lifespan in yeast. Proc Natl Acad Sci USA. 2014;111(15):E1538. Sharma PK, Reilly MJ, Jones DN, Robinson PM, Bhatia SR. The effect of pharmaceuticals on the nanoscale structure of PEO–PPO–PEO micelles. Colloids Surf, B. 2008;61(1):53–60. Singla P, Singh O, Sharma S, Betlem K, Aswal VK, Peeters M, Mahajan RK. Temperature-Dependent Solubilization of the Hydrophobic Antiepileptic Drug Lamotrigine in Different Pluronic Micelles—A Spectroscopic, Heat Transfer Method, Small-Angle Neutron Scattering, Dynamic Light Scattering, and in Vitro Release Study. ACS Omega. 2019;4(6):11251–62. Li X, Uppala VVS, Cooksey TJ, Robertson ML, Madsen LA. Quantifying Drug Cargo Partitioning in Block Copolymer Micelle Solutions. ACS Appl Polym Mater. 2020;2(9):3749–55. Johnston TG, Fillman JP, Priks H, Butelmann T, Tamm T, Kumar R, Lahtvee P-J, Nelson A. Cell-Laden Hydrogels for Multikingdom 3D Printing. Macromol Biosci. 2020;20(8):2000121.