A microfluidic device for inferring metabolic landscapes in yeast monolayer colonies

• Published in: eLife Vol. 8
• Main Authors: Marinkovic, Zoran S, Vulin, Clément, Acman, Mislav, Song, Xiaohu, Di Meglio, Jean-Marc, Lindner, Ariel B, Hersen, Pascal
• Format: Journal Article
• Language: English
• Published: England eLife Science Publications, Ltd 01.07.2019; eLife Sciences Publications Ltd; eLife Sciences Publication; eLife Sciences Publications, Ltd
• Subjects: Amino acids; Bacteria; Biochemistry, Molecular Biology; Biofilms; Biophysics; Colonies; Equipment Design; Flow cytometry; Fluorescence; Gene expression; Gene Expression Regulation, Fungal - drug effects; Glucose; Glucose - metabolism; Glucose - pharmacology; Glucose Transport Proteins, Facilitative - genetics; Glucose Transport Proteins, Facilitative - metabolism; Growth rate; Hexose; Labels; Life Sciences; Metabolism; Metabolites; Microfluidics; Microfluidics - instrumentation; Monosaccharides; Morphogenesis; Nutrients; Physics of Living Systems; Physiological aspects; Physiology; Saccharomyces cerevisiae - drug effects; Saccharomyces cerevisiae - growth & development; Saccharomyces cerevisiae - metabolism; spatial organization; Tools and Resources; Transcription Factors - metabolism; yeast colony; Yeasts (Fungi); United States; Switzerland; Paris France; spatial organization; yeast colony; metabolism; microfluidics; physics of living systems; gene expression; S. cerevisiae
• ISSN: 2050-084X; 2050-084X
• DOI: 10.7554/elife.47951

Microbial colonies are fascinating structures in which growth and internal organization reflect complex morphogenetic processes. Here, we generated a microfluidics device with arrays of long monolayer yeast colonies to further global understanding of how intercellular metabolic interactions affect the internal structure of colonies within defined boundary conditions. We observed the emergence of stable glucose gradients using fluorescently labeled hexose transporters and quantified the spatial correlations with intra-colony growth rates and expression of other genes regulated by glucose availability. These landscapes depended on the external glucose concentration as well as secondary gradients, for example amino acid availability. This work demonstrates the regulatory genetic networks governing cellular physiological adaptation are the key to internal structuration of cellular assemblies. This approach could be used in the future to decipher the interplay between long-range metabolic interactions, cellular development and morphogenesis in more complex systems.