A microfluidic device for inferring metabolic landscapes in yeast monolayer colonies

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Abstract

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 labelled 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, e.g., 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.

Data availability

All data presented in the figure article and supplementary information are available on a Zenodo repository with the following DOI 10.5281/zenodo.2557396

The following data sets were generated

1. Marinkovic Z
2. Vulin C
3. Acman M
4. Song X
5. Di Meglio JM
6. Lindner AB
7. Hersen P
(2019) Lab513/Landscape of Gene Expression Dataset
Zenodo, 10.5281/zenodo.2557396.

https://zenodo.org/record/2557396#.XRM5megzbZs

Article and author information

Author details

Zoran Marinkovic

Laboratoire Matière et Systèmes Complexes, CNRS, Universite Paris Diderot, Paris, France

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-7720-2802
Clément Vulin

Laboratoire Matière et Systèmes Complexes, CNRS, Universite Paris Diderot, Paris, France

Competing interests
The authors declare that no competing interests exist.
Mislav Acman

Laboratoire Matière et Systèmes Complexes, CNRS, Universite Paris Diderot, Paris, France

Competing interests
The authors declare that no competing interests exist.
Xiaohu Song

Center for Research and Interdisciplinarity, Paris Descartes University, Paris, France

Competing interests
The authors declare that no competing interests exist.
Jean-Marc Di Meglio

Laboratoire Matière et Systèmes Complexes, CNRS, Universite Paris Diderot, Paris, France

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-0446-4550
Ariel B Lindner

Center for Research and Interdisciplinarity, Paris Descartes University, Paris, France

For correspondence
ariel.lindner@inserm.fr

Competing interests
The authors declare that no competing interests exist.
Pascal Hersen

Laboratoire Matière et Systèmes Complexes, CNRS, Universite Paris Diderot, Paris, France

For correspondence
pascal.hersen@univ-paris-diderot.fr

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-2379-4280

Funding

European Commission (724813)

Pascal Hersen

Agence Nationale de la Recherche (ICEBERG-ANR-10-BINF-06-01)

Pascal Hersen

Agence Nationale de la Recherche (ANR-16-CE12-0025-01)

Pascal Hersen

Agence Nationale de la Recherche (ANR-11-LABX-0071)

Pascal Hersen

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.