Long-term model predictive control of gene expression at the population and single-cell levels.
Gene expression plays a central role in the orchestration of cellular processes. The use of inducible promoters to change the expression level of a gene from its physiological level has significantly contributed to the understanding of the functioning of regulatory networks. However, from a quantitative point of view, their use is limited to short-term, population-scale studies to average out cell-to-cell variability and gene expression noise and limit the nonpredictable effects of internal feedback loops that may antagonize the inducer action. Here, we show that, by implementing an external feedback loop, one can tightly control the expression of a gene over many cell generations with quantitative accuracy. To reach this goal, we developed a platform for real-time, closed-loop control of gene expression in yeast that integrates microscopy for monitoring gene expression at the cell level, microfluidics to manipulate the cells' environment, and original software for automated imaging, quantification, and model predictive control. By using an endogenous osmostress responsive promoter and playing with the osmolarity of the cells environment, we show that long-term control can, indeed, be achieved for both time-constant and time-varying target profiles at the population and even the single-cell levels. Importantly, we provide evidence that real-time control can dynamically limit the effects of gene expression stochasticity. We anticipate that our method will be useful to quantitatively probe the dynamic properties of cellular processes and drive complex, synthetically engineered networks.
Contraintes Research Group, Institut National de Recherche en Informatique et en Automatique, INRIA Paris-Rocquencourt, 78150 Rocquencourt, France.
Jannis
J
Uhlendorf
Agnès
A
Miermont
Thierry
T
Delaveau
Gilles
G
Charvin
François
F
Fages
Samuel
S
Bottani
Gregory
G
Batt
Pascal
P
Hersen
D003491:Cybernetics / Q000379:methods*; D025461:Feedback, Physiological / Q000502:physiology; D015966:Gene Expression Regulation, Fungal / Q000502:physiology*; D005990:Glycerol / Q000378:metabolism; D044085:Microfluidics; D020928:Mitogen-Activated Protein Kinases / Q000235:genetics / Q000378:metabolism; D008954:Models, Biological; D009994:Osmolar Concentration; D009997:Osmotic Pressure / Q000502:physiology; D011237:Predictive Value of Tests; D012441:Saccharomyces cerevisiae / Q000166:cytology / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D012985:Software Design; D013269:Stochastic Processes; D049490:Systems Biology / Q000379:methods*
D029701:Saccharomyces cerevisiae Proteins; C088589:HOG1 protein, S cerevisiae; D020928:Mitogen-Activated Protein Kinases; D005990:Glycerol