The regulatory logic of m-xylene biodegradation by Pseudomonas putida mt-2 exposed by dynamic modelling of the principal node Ps/Pr of the TOL plasmid

Authors

  • Michalis Koutinas,

    1. Centre for Process Systems Engineering, Department of Chemical Engineering and Chemical Technology, South Kensington Campus, Imperial College London, London SW7 2AZ, UK.
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    • These authors contributed equally to this work.

  • Ming-Chi Lam,

    1. Centre for Process Systems Engineering, Department of Chemical Engineering and Chemical Technology, South Kensington Campus, Imperial College London, London SW7 2AZ, UK.
    2. Systems and Synthetic Biology Group, Helmholtz Center for Infection Research (HZI), Inhoffenstrasse 7, D-38124 Braunschweig, Germany.
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    • These authors contributed equally to this work.

  • Alexandros Kiparissides,

    1. Centre for Process Systems Engineering, Department of Chemical Engineering and Chemical Technology, South Kensington Campus, Imperial College London, London SW7 2AZ, UK.
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  • Rafael Silva-Rocha,

    1. Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
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  • Miguel Godinho,

    1. Systems and Synthetic Biology Group, Helmholtz Center for Infection Research (HZI), Inhoffenstrasse 7, D-38124 Braunschweig, Germany.
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  • Andrew G. Livingston,

    1. Centre for Process Systems Engineering, Department of Chemical Engineering and Chemical Technology, South Kensington Campus, Imperial College London, London SW7 2AZ, UK.
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  • Efstratios N. Pistikopoulos,

    1. Centre for Process Systems Engineering, Department of Chemical Engineering and Chemical Technology, South Kensington Campus, Imperial College London, London SW7 2AZ, UK.
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  • Victor De Lorenzo,

    1. Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
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  • Vitor A. P. Martins Dos Santos,

    Corresponding author
    1. Systems and Synthetic Biology Group, Helmholtz Center for Infection Research (HZI), Inhoffenstrasse 7, D-38124 Braunschweig, Germany.
    2. Chair for Systems and Synthetic Biology, Wageningen University, Dreijenplein 310, 6703 HB Wageningen, the Netherlands.
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    • These authors contributed equally to this work.

  • Athanasios Mantalaris

    Corresponding author
    1. Centre for Process Systems Engineering, Department of Chemical Engineering and Chemical Technology, South Kensington Campus, Imperial College London, London SW7 2AZ, UK.
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    • These authors contributed equally to this work.


E-mail a.mantalaris@imperial.ac.uk; Tel. (+44) 20 7594 5601; Fax: (+44) 20 7594 5638;

E-mail: vds@helmholtz-hzi.de; Tel. (+49) 531 6181 4008; Fax: (+49) 531 6181 4049.

Summary

The structure of the extant transcriptional control network of the TOL plasmid pWW0 born by Pseudomonas putida mt-2 for biodegradation of m-xylene is far more complex than one would consider necessary from a mere engineering point of view. In order to penetrate the underlying logic of such a network, which controls a major environmental cleanup bioprocess, we have developed a dynamic model of the key regulatory node formed by the Ps/Pr promoters of pWW0, where the clustering of control elements is maximal. The model layout was validated with batch cultures estimating parameter values and its predictive capability was confirmed with independent sets of experimental data. The model revealed how regulatory outputs originated in the divergent and overlapping Ps/Pr segment, which expresses the transcription factors XylS and XylR respectively, are computed into distinct instructions to the upper and lower catabolic xyl operons for either simultaneous or stepwise consumption of m-xylene and/or succinate. In this respect, the model reveals that the architecture of the Ps/Pr is poised to discriminate the abundance of alternative and competing C sources, in particular m-xylene versus succinate. The proposed framework provides a first systemic understanding of the causality and connectivity of the regulatory elements that shape this exemplary regulatory network, facilitating the use of model analysis towards genetic circuit optimization.

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