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Title: 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: Koutinas, Michalis 
Lam, Ming Chi 
Kiparissides, Alexandros 
Silva-Rocha, Rafael 
Godinho, Miguel 
Livingston, Andrew G 
Pistikopoulos, Efstratios N. 
de Lorenzo, Victor 
Dos Santos, Vitor A P Martins 
Mantalaris, Athanasios 
Keywords: Biological model;Bioremediation;Gene expression regulation;Genetic transcription;Pseudomonas putida;3-xylene
Category: Biological Sciences
Field: Natural Sciences
Issue Date: Jun-2010
Source: Environmental Microbiology, 2010, Volume 12, Issue 6, Pages 1705-1718
Journal: Environmental Microbiology 
Abstract: 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.
ISSN: 1462-2920
DOI: 10.1111/j.1462-2920.2010.02245.x
Rights: © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd
Type: Article
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