High-frequency Noise Attenuation of a Two-component System Responding to Short-pulse Input

Abstract

Among the various biological devices developed and characterized in synthetic biology, light-sensing biological devices can serve as an input-output system owing to their light modulation property. The well-characterized devices in living systems are useful for modulating cellular sensing and transducing information. In this study, we examined short pulse responsiveness of a light-sensing two-component system (TCS), Cph8-OmpR, which was generated by replacing the sensor domain of the EnvZ-OmpR osmoregulatory system with the light sensor Cph1. We varied the input pulse width of the Cph8-OmpR system and found that an input width of <1 s was sufficient to alter the accumulation of a reporter gene upregulated by Cph8 phosphorylation of OmpR. Based on this result and the mathematical model showing that the timescale for the upstream Cph8-activity transition was much faster than that of downstream gene expression, we evaluated the merit of a TCS with such an unbalanced cascade. Our mathematical simulation of a cascade TCS suggests that high-frequency noise arising from fast transitions in kinase activity was attenuated throughout the cascade reaction. In terms of noise attenuation, these results can contribute to analyze biological cascade systems with the balance of reaction rates in each process.

OptoCRISPRi-HD: Engineering a Bacterial Green-Light-Activated CRISPRi System with a High Dynamic Range

“…In CcaS-CcaR v2.0, systematic investigations have shown that the pathway switching is relatively insensitive to CcaS abundance: the amount of CcaS should be above the lowest level and below the limiting of PCB; as for PCB production, the same study tested a series of promoters to control the transcription level of hoI and pcyA , among which the J 23108 promoter led to the best dynamic range without causing cell toxicity or spontaneous mutation in this part of the circuit. Meanwhile, mathematical models , and experiments suggested that the CcaR level is crucial for an enhanced dynamic range in CcaS–CcaR TCS. Based on such knowledge, we decided to retain the levels of CcaS and PCB in CcaS-CcaR v2.0 as they were already optimized in E.…”

“…promoters to control the transcription level of hoI and pcyA, among which the J23108 promoter led to the best dynamic range without causing cell toxicity or spontaneous mutation in this part of the circuit. Meanwhile, mathematical models 32,33 and experiments 12 suggested that the CcaR level is crucial for an enhanced dynamic range in CcaS−CcaR TCS. Based on such knowledge, we decided to retain the levels of CcaS and PCB in CcaS-CcaR v2.0 as they were already optimized in E. coli previously.…”

OptoCRISPRi-HD: engineering a green-light activated CRISPRi system with high dynamic range

“…A high dynamic range indicates strong effects when "switched on" and low leakage when "switched off". Mathematic models 31,32 and experiments 11 suggested that CcaR level is crucial for enhanced dynamic range in CcaS-CcaR TCS. In this study, we tested a series of CcaR expression levels to find the best dynamic range for optoCRISPRi-HD.…”