Chapter 13 In Silico Control of Biomolecular Processes

By implementing an external feedback loop one can tightly control the expression of a gene over many cell generations with quantitative accuracy. Controlling precisely the level of a protein of interest will be useful to probe quantitatively the dynamical properties of cellular processes and to drive complex, syntheticallyengineered networks. In this chapter we describe 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 osmo-stress responsive promoter and playing with the osmolarity of the cells environment, we demonstrate that long-term control can indeed be achieved for both time-constant and time-varying target profiles, at the population level, and even at the single-cell level.

[1]  Hana El-Samad,et al.  Building robust functionality in synthetic circuits using engineered feedback regulation. , 2013, Current opinion in biotechnology.

[2]  F. Fages,et al.  Long-term model predictive control of gene expression at the population and single-cell levels , 2012, Proceedings of the National Academy of Sciences.

[3]  J. Lygeros,et al.  Moment-based inference predicts bimodality in transient gene expression , 2012, Proceedings of the National Academy of Sciences.

[4]  Jeff Hasty,et al.  Antagonistic gene transcripts regulate adaptation to new growth environments , 2011, Proceedings of the National Academy of Sciences.

[5]  D. Pincus,et al.  In silico feedback for in vivo regulation of a gene expression circuit , 2011, Nature Biotechnology.

[6]  Jared E. Toettcher,et al.  Light-based feedback for controlling intracellular signaling dynamics , 2011, Nature Methods.

[7]  Mario di Bernardo,et al.  Analysis, design and implementation of a novel scheme for in-vivo control of synthetic gene regulatory networks , 2011, Autom..

[8]  Megan N. McClean,et al.  The Dynamical Systems Properties of the HOG Signaling Cascade , 2011, Journal of signal transduction.

[9]  James J. Collins,et al.  Tunable Signal Processing in Synthetic MAP Kinase Cascades , 2011, Cell.

[10]  Massimo Vergassola,et al.  Bacterial strategies for chemotaxis response , 2010, Proceedings of the National Academy of Sciences.

[11]  A. Oudenaarden,et al.  A Systems-Level Analysis of Perfect Adaptation in Yeast Osmoregulation , 2009, Cell.

[12]  M. Elowitz,et al.  Frequency-modulated nuclear localization bursts coordinate gene regulation , 2008, Nature.

[13]  Christoph H. Borchers,et al.  A Systems-Biology Analysis of Feedback Inhibition in the Sho1 Osmotic-Stress-Response Pathway , 2007, Current Biology.

[14]  E. Klipp,et al.  Integrative model of the response of yeast to osmotic shock , 2005, Nature Biotechnology.

[15]  António Martins,et al.  A member of the sugar transporter family, Stl1p is the glycerol/H+ symporter in Saccharomyces cerevisiae. , 2005, Molecular biology of the cell.

[16]  R. Weiss,et al.  Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[17]  I. Herskowitz,et al.  Unique and redundant roles for HOG MAPK pathway components as revealed by whole-genome expression analysis. , 2003, Molecular biology of the cell.

[18]  Prahlad T. Ram,et al.  MAP Kinase Phosphatase As a Locus of Flexibility in a Mitogen-Activated Protein Kinase Signaling Network , 2002, Science.

[19]  Eulàlia de Nadal,et al.  Dealing with osmostress through MAP kinase activation , 2002, EMBO reports.

[20]  S. Hohmann Osmotic Stress Signaling and Osmoadaptation in Yeasts , 2002, Microbiology and Molecular Biology Reviews.

[21]  J. Doyle,et al.  Robust perfect adaptation in bacterial chemotaxis through integral feedback control. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[22]  François Fages,et al.  Towards Real-Time Control of Gene Expression: Controlling the Hog Signaling Cascade , 2011, Pacific Symposium on Biocomputing.