A fast, robust, and tunable synthetic gene oscillator

A fast, robust, and tunable synthetic gene oscillator

2008 November 27 | Jesse Stricker1,*, Scott Cookson1,*, Matthew R. Bennett1,2,*, William H. Mather1, Lev S. Tsimring2, Jeff Hasty1,2,3
A fast, robust, and tunable synthetic gene oscillator was developed in Escherichia coli. This oscillator, designed using a previously modeled network with linked positive and negative feedback loops, exhibits fast, robust, and persistent oscillations with tunable periods as short as 13 minutes. The oscillator was constructed using a hybrid promoter, P_lac/ara-1, which is activated by arabinose and repressed by IPTG. The system was tested using a microfluidic platform for single-cell microscopy, revealing robust and persistent oscillations in nearly all cells. The oscillatory period could be tuned by altering inducer levels, temperature, and media source. Computational modeling showed that a time delay in the negative feedback loop is crucial for robust oscillations, while the positive feedback loop enhances robustness and tunability. The oscillator was found to be extremely robust across a wide range of inducer conditions and temperatures. The period could be tuned by varying arabinose levels, and the oscillator functioned in minimal medium with glucose. The oscillator was constructed according to design principles from previous theoretical work, but a new computational model was developed to better describe experimental observations. This model incorporated details previously omitted, such as protein-DNA binding, multimerization, translation, DNA looping, enzymatic degradation, and protein folding, leading to a more accurate and robust model. The model showed that oscillations can occur without positive feedback, due to a delay in the negative feedback loop. The oscillator was constructed in E. coli using a promoter that is activated in the absence of LacI or in the presence of IPTG. The oscillator was found to be robust and tunable, with oscillations not as distinct as in the dual-feedback oscillator but still showing regularity. The findings highlight the importance of considering intermediate steps in gene circuit design for robustness and tunability. The oscillator's robustness and tunability make it suitable for applications such as expression schemes that can circumvent cellular adaptability, centralized clocks that coordinate intracellular behavior, and reverse-engineering platforms that measure the global response of the genome to an oscillatory perturbation. The oscillator was validated using both single-cell microscopy and flow cytometry, showing consistent oscillatory periods. The model was found to be robust to parameter variations and accurately described the dynamics of the oscillator for a wide range of inducer concentrations. The results demonstrate the potential of synthetic gene oscillators in synthetic biology for applications requiring precise control of cellular behavior.A fast, robust, and tunable synthetic gene oscillator was developed in Escherichia coli. This oscillator, designed using a previously modeled network with linked positive and negative feedback loops, exhibits fast, robust, and persistent oscillations with tunable periods as short as 13 minutes. The oscillator was constructed using a hybrid promoter, P_lac/ara-1, which is activated by arabinose and repressed by IPTG. The system was tested using a microfluidic platform for single-cell microscopy, revealing robust and persistent oscillations in nearly all cells. The oscillatory period could be tuned by altering inducer levels, temperature, and media source. Computational modeling showed that a time delay in the negative feedback loop is crucial for robust oscillations, while the positive feedback loop enhances robustness and tunability. The oscillator was found to be extremely robust across a wide range of inducer conditions and temperatures. The period could be tuned by varying arabinose levels, and the oscillator functioned in minimal medium with glucose. The oscillator was constructed according to design principles from previous theoretical work, but a new computational model was developed to better describe experimental observations. This model incorporated details previously omitted, such as protein-DNA binding, multimerization, translation, DNA looping, enzymatic degradation, and protein folding, leading to a more accurate and robust model. The model showed that oscillations can occur without positive feedback, due to a delay in the negative feedback loop. The oscillator was constructed in E. coli using a promoter that is activated in the absence of LacI or in the presence of IPTG. The oscillator was found to be robust and tunable, with oscillations not as distinct as in the dual-feedback oscillator but still showing regularity. The findings highlight the importance of considering intermediate steps in gene circuit design for robustness and tunability. The oscillator's robustness and tunability make it suitable for applications such as expression schemes that can circumvent cellular adaptability, centralized clocks that coordinate intracellular behavior, and reverse-engineering platforms that measure the global response of the genome to an oscillatory perturbation. The oscillator was validated using both single-cell microscopy and flow cytometry, showing consistent oscillatory periods. The model was found to be robust to parameter variations and accurately described the dynamics of the oscillator for a wide range of inducer concentrations. The results demonstrate the potential of synthetic gene oscillators in synthetic biology for applications requiring precise control of cellular behavior.
Reach us at info@study.space
[slides and audio] A fast%2C robust%2C and tunable synthetic gene oscillator