High-frequency noise attenuation of a two-component system responding to short-pulse input

Akifumi Nishida, Ryoji Sekine, Daisuke Kiga, Masayuki Yamamura

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    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.

    Original languageEnglish
    Title of host publicationProceedings of the 2016 7th International Conference on Computational Systems-Biology and Bioinformatics, CSBio 2016
    PublisherAssociation for Computing Machinery
    Pages28-35
    Number of pages8
    VolumePart F126331
    ISBN (Electronic)9781450347945
    DOIs
    Publication statusPublished - 2016 Dec 19
    Event7th International Conference on Computational Systems-Biology and Bioinformatics, CSBio 2016 - Macau, Macao
    Duration: 2016 Dec 192016 Dec 22

    Other

    Other7th International Conference on Computational Systems-Biology and Bioinformatics, CSBio 2016
    CountryMacao
    CityMacau
    Period16/12/1916/12/22

    Fingerprint

    Phosphorylation
    Light modulation
    Sensors
    Gene expression
    Reaction rates
    Genes
    Mathematical models
    Synthetic Biology

    Keywords

    • Cascade system
    • High frequency noise attenuation
    • Light-sensing biological device
    • Short pulse responsiveness
    • Two-component

    ASJC Scopus subject areas

    • Human-Computer Interaction
    • Computer Networks and Communications
    • Computer Vision and Pattern Recognition
    • Software

    Cite this

    Nishida, A., Sekine, R., Kiga, D., & Yamamura, M. (2016). High-frequency noise attenuation of a two-component system responding to short-pulse input. In Proceedings of the 2016 7th International Conference on Computational Systems-Biology and Bioinformatics, CSBio 2016 (Vol. Part F126331, pp. 28-35). Association for Computing Machinery. https://doi.org/10.1145/3029375.3029377

    High-frequency noise attenuation of a two-component system responding to short-pulse input. / Nishida, Akifumi; Sekine, Ryoji; Kiga, Daisuke; Yamamura, Masayuki.

    Proceedings of the 2016 7th International Conference on Computational Systems-Biology and Bioinformatics, CSBio 2016. Vol. Part F126331 Association for Computing Machinery, 2016. p. 28-35.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    Nishida, A, Sekine, R, Kiga, D & Yamamura, M 2016, High-frequency noise attenuation of a two-component system responding to short-pulse input. in Proceedings of the 2016 7th International Conference on Computational Systems-Biology and Bioinformatics, CSBio 2016. vol. Part F126331, Association for Computing Machinery, pp. 28-35, 7th International Conference on Computational Systems-Biology and Bioinformatics, CSBio 2016, Macau, Macao, 16/12/19. https://doi.org/10.1145/3029375.3029377
    Nishida A, Sekine R, Kiga D, Yamamura M. High-frequency noise attenuation of a two-component system responding to short-pulse input. In Proceedings of the 2016 7th International Conference on Computational Systems-Biology and Bioinformatics, CSBio 2016. Vol. Part F126331. Association for Computing Machinery. 2016. p. 28-35 https://doi.org/10.1145/3029375.3029377
    Nishida, Akifumi ; Sekine, Ryoji ; Kiga, Daisuke ; Yamamura, Masayuki. / High-frequency noise attenuation of a two-component system responding to short-pulse input. Proceedings of the 2016 7th International Conference on Computational Systems-Biology and Bioinformatics, CSBio 2016. Vol. Part F126331 Association for Computing Machinery, 2016. pp. 28-35
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