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.
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.
Koutinas
Michalis
M
Centre for Process Systems Engineering, Department of Chemical Engineering and Chemical Technology, South Kensington Campus, Imperial College London, London SW7 2AZ, UK.
Lam
Ming-Chi
MC
Kiparissides
Alexandros
A
Silva-Rocha
Rafael
R
Godinho
Miguel
M
Livingston
Andrew G
AG
Pistikopoulos
Efstratios N
EN
de Lorenzo
Victor
V
Dos Santos
Vitor A P Martins
VA
Mantalaris
Athanasios
A
D001673:Biodegradation, Environmental; D015964:Gene Expression Regulation, Bacterial; D008954:Models, Biological; D008962:Models, Theoretical; D015394:Molecular Structure; D010957:Plasmids / Q000235:genetics / Q000378:metabolism; D016958:Pseudomonas putida / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic; D014992:Xylenes / Q000737:chemistry / Q000378:metabolism*
D014992:Xylenes; C031285:3-xylene