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Fluorescent Reporter Genes and the Analysis of Bacterial Regulatory Networks

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Hybrid Systems Biology (HSB 2014)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 7699))

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Abstract

The understanding of the regulatory networks controlling the adaptation of bacteria to changes in their environment is critically dependent on the ability to monitor the dynamics of gene expression. Here, we review the use of fluorescent reporter genes for dynamically quantifying promoter activity and other quantities characterizing gene expression. We discuss critical physical and biological parameters in the design, development, and use of fluorescent reporter strains. Moreover, we review measurement models that have been proposed to interpret primary fluorescence data and inference methods for estimating gene expression profiles from these data. As an illustration of the use of fluorescent reporter strains for analyzing bacterial regulatory networks, we consider two applications in the model bacterium Escherichia coli in some detail: the joint control of gene expression by global physiological effects and specific regulatory interactions, and the importance of protein stability for the inference and analysis of transcriptional regulatory networks. We conclude by discussing some current trends in the use of fluorescent reporter genes.

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Acknowledgements

This work was supported by the Investissements d’avenir Bio-informatique programme under project Reset (ANR-11-BINF-0005).

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Authors and Affiliations

  1. INRIA, Grenoble - Rhône-Alpes Research Centre, 655 avenue de l’Europe, Montbonnot, 38334, Saint-Ismier Cedex, France

    Hidde de Jong & Johannes Geiselmann

  2. Laboratoire Interdisciplinaire de Physique (LIPhy, CNRS UMR 5588), Université Grenoble Alpes, 140 Avenue de la Physique - BP 87, 38402, Saint Martin d’Hères, France

    Johannes Geiselmann

Authors
  1. Hidde de Jong
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Correspondence to Hidde de Jong .

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Editors and Affiliations

  1. "CNRS-VERIMAG, University of Grenoble-Alpes (UGA), Grenoble, France

    Oded Maler

  2. West Virginia University, Morgantown, West Virginia, USA

    Ádám Halász

  3. VERIMAG, Gieres, France

    Thao Dang

  4. University of Udine, Udine, Italy

    Carla Piazza

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de Jong, H., Geiselmann, J. (2015). Fluorescent Reporter Genes and the Analysis of Bacterial Regulatory Networks. In: Maler, O., Halász, Á., Dang, T., Piazza, C. (eds) Hybrid Systems Biology. HSB 2014. Lecture Notes in Computer Science(), vol 7699. Springer, Cham. https://doi.org/10.1007/978-3-319-27656-4_2

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  • DOI: https://doi.org/10.1007/978-3-319-27656-4_2

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