The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene

Rafael Silva-Rocha,Víctor De Lorenzo,Javier Tamames,Hidde De Jong

doi:10.1186/1752-0509-5-191

Abstract

BackgroundThe genetic network of the TOL plasmid pWW0 of the soil bacterium Pseudomonas putida mt-2 for catabolism of m-xylene is an archetypal model for environmental biodegradation of aromatic pollutants. Although nearly every metabolic and transcriptional component of this regulatory system is known to an extraordinary molecular detail, the complexity of its architecture is still perplexing. To gain an insight into the inner layout of this network a logic model of the TOL system was implemented, simulated and experimentally validated. This analysis made sense of the specific regulatory topology out on the basis of an unprecedented network motif around which the entire genetic circuit for m-xylene catabolism gravitates.ResultsThe most salient feature of the whole TOL regulatory network is the control exerted by two distinct but still intertwined regulators (XylR and XylS) on expression of two separated catabolic operons (upper and lower) for catabolism of m-xylene. Following model reduction, a minimal modular circuit composed by five basic variables appeared to suffice for fully describing the operation of the entire system. In silico simulation of the effect of various perturbations were compared with experimental data in which specific portions of the network were activated with selected inducers: m-xylene, o-xylene, 3-methylbenzylalcohol and 3-methylbenzoate. The results accredited the ability of the model to faithfully describe network dynamics. This analysis revealed that the entire regulatory structure of the TOL system enables the action an unprecedented metabolic amplifier motif (MAM). This motif synchronizes expression of the upper and lower portions of a very long metabolic system when cells face the head pathway substrate, m-xylene.ConclusionLogic modeling of the TOL circuit accounted for the intricate regulatory topology of this otherwise simple metabolic device. The found MAM appears to ensure a simultaneous expression of the upper and lower segments of the m-xylene catabolic route that would be difficult to bring about with a standard substrate-responsive single promoter. Furthermore, it is plausible that the MAM helps to avoid biochemical conflicts between competing plasmid-encoded and chromosomally-encoded pathways in this bacterium.

Highlights

The genetic network of the TOL plasmid pWW0 of the soil bacterium Pseudomonas putida mt-2 for catabolism of m-xylene is an archetypal model for environmental biodegradation of aromatic pollutants
The dual activation mode of Pm by XylS is intriguing as it resembles, but does not entirely match, the feed forward loop (FFL) motif frequently found in regulatory networks [2,42]
Depending on the sign of the interaction between these components as well as the logic of signal integration at the target Z (e.g. AND or OR), the resulting FFL endows the circuit with different properties e.g. filtering transient changes in the input signal or delay in the ON/OFF responses [43]

Summary

Introduction

The genetic network of the TOL plasmid pWW0 of the soil bacterium Pseudomonas putida mt-2 for catabolism of m-xylene is an archetypal model for environmental biodegradation of aromatic pollutants. Prokaryotic regulatory networks are organized in a hierarchical way, on top of which a few transcriptional factors (TF) may coordinate the expression of hundreds of genes of different functional categories (including other new functions through horizontal gene transfer (HGT), typically by conjugative plasmids [4] This is because the new encoded traits must find a suitable functional and physical site in the recipient cells to secure their establishment in the new host [5], a process that is not devoid of regulatory, metabolic and structural problems [6]. Many conjugative plasmids of bacteria thriving in sites polluted by recalcitrant chemicals (e.g. compounds released by urban and industrial activity) determine autonomous catabolic systems for biodegradation of such unusual carbon sources [7] These mobile elements quickly spread through the microbial population of the site upon occurrence of a suitable environmental pressure [8,9,10]. The structure of such successful regulatory circuits is likely to bear both the problem and the solution somehow encrypted in their topology and their dynamics

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Conclusion