Format

Send to

Choose Destination
Nat Methods. 2014 Apr;11(4):449-55. doi: 10.1038/nmeth.2884. Epub 2014 Mar 9.

Characterizing bacterial gene circuit dynamics with optically programmed gene expression signals.

Author information

1
Graduate Program in Applied Physics, Rice University, Houston, Texas, USA.
2
Department of Bioengineering, Rice University, Houston, Texas, USA.
3
1] Department of Bioengineering, Rice University, Houston, Texas, USA. [2] Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, USA.

Abstract

Gene circuits are dynamical systems that regulate cellular behaviors, often using protein signals as inputs and outputs. Here we have developed an optogenetic 'function generator' method for programming tailor-made gene expression signals in live bacterial cells. We designed precomputed light sequences based on experimentally calibrated mathematical models of light-switchable two-component systems and used them to drive intracellular protein levels to match user-defined reference time courses. We used this approach to generate accelerated and linearized dynamics, sinusoidal oscillations with desired amplitudes and periods, and a complex waveform, all with unprecedented accuracy and precision. We also combined the function generator with a dual fluorescent protein reporter system, analogous to a dual-channel oscilloscope, to reveal that a synthetic repressible promoter linearly transforms repressor signals with an approximate 7-min delay. Our approach will enable a new generation of dynamical analyses of synthetic and natural gene circuits, providing an essential step toward the predictive design and rigorous understanding of biological systems.

PMID:
24608181
DOI:
10.1038/nmeth.2884
[Indexed for MEDLINE]

Supplemental Content

Full text links

Icon for Nature Publishing Group
Loading ...
Support Center