Abstract
Atrazine is an herbicide and a pollutant of great environmental concern that is naturally biodegraded by microbial communities. Paenarthrobacter aurescens TC1 is one of the most studied degraders of this herbicide. Here, we developed a genome scale metabolic model for P. aurescens TC1, iRZ1179, to study the atrazine degradation process at organism level. Constraint based flux balance analysis and time dependent simulations were used to explore the organism’s phenotypic landscape. Simulations aimed at designing media optimized for supporting growth and enhancing degradation, by passing the need in strain design via genetic modifications. Growth and degradation simulations were carried with more than 100 compounds consumed by P. aurescens TC1. In vitro validation confirmed the predicted classification of different compounds as efficient, moderate or poor stimulators of growth. Simulations successfully captured previous reports on the use of glucose and phosphate as bio-stimulators of atrazine degradation, supported by in vitro validation. Model predictions can go beyond supplementing the medium with a single compound and can predict the growth outcomes for higher complexity combinations. Hence, the analysis demonstrates that the exhaustive power of the genome scale metabolic reconstruction allows capturing complexities that are beyond common biochemical expertise and knowledge and further support the importance of computational platforms for the educated design of complex media. The model presented here can potentially serve as a predictive tool towards achieving optimal biodegradation efficiencies and for the development of ecologically friendly solutions for pollutant degradation.
Highlights
Atrazine is an herbicide and a pollutant of great environmental concern that is naturally biodegraded by microbial communities
P. aurescens TC1 is an ideal candidate for the study of atrazine bioremediation using a genome scale metabolic model reconstruction
The genome of P. aurescens TC1 is composed of a circular chromosome of 4.6 Mb coding for 4,222 open reading frames (ORFs) as well as two plasmids, 0.3 Mb each, coding for additional ~ 600 ORFs51
Summary
Atrazine is an herbicide and a pollutant of great environmental concern that is naturally biodegraded by microbial communities. We developed a genome scale metabolic model for P. aurescens TC1, iRZ1179, to study the atrazine degradation process at organism level. Constraint based metabolic modelling approaches have become widely used as an in silico tool for organism-level phenotyping and the subsequent development of metabolic engineering s trategies[28,29] Such approaches follow four key steps: (1) data acquisition—mainly genome sequencing information, basic cell-physiological and biochemical knowledge and some experimental data on cell growth; (2) model reconstruction—translating data into structured mathematical representation; (3) constraint-based optimization simulations—the prediction of growth rate, substrate uptake rates, and byproduct rates under different growth conditions or following knockout mutations, in the absence of kinetic information[30,31,32,33,34,35,36]; and (4) experimental validation. We describe the process of reconstruction of a genome-scale metabolic model of P. aurescens TC1 and its evaluation as a predictive tool for the fast and low-cost screening of potential nutritional supplements that can serve as bio-stimulators of degradation
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