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A Chemostat Array Enables the Spatio-Temporal Analysis of the Yeast Proteome

N. Dénervaud, J. Becker, R. Delgado-Gonzalo, P. Damay, A.S. Rajkumar, M. Unser, D. Shore, F. Naef, S.J. Maerki

Proceedings of the National Academy of Sciences of the United States of America, vol. 110, no. 39, pp. 15842-15847, September 24, 2013.



Observing cellular responses to perturbations is central to generating and testing hypotheses in biology. We developed a massively parallel microchemostat array capable of growing and observing 1,152 yeast-GFP strains on the single-cell level with 20 min time resolution. We measured protein abundance and localization changes in 4,085 GFP-tagged strains in response to methyl methanesulfonate and analyzed 576 GFP strains in five additional conditions for a total of more than 10,000 unique experiments, providing a systematic view of the yeast proteome in flux. We observed that processing bodies formed rapidly and synchronously in response to UV irradiation, and in conjunction with 506 deletion-GFP strains, identified four gene disruptions leading to abnormal ribonucleotide-diphosphate reductase (Rnr4) localization. Our microchemostat platform enables the large-scale interrogation of proteomes in flux and permits the concurrent observation of protein abundance, localization, cell size, and growth parameters on the single-cell level for thousands of microbial cultures in one experiment.


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