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Molecules 2017, 22(8), 1242; doi:10.3390/molecules22081242

Systems Biology Approach to Bioremediation of Nitroaromatics: Constraint-Based Analysis of 2,4,6-Trinitrotoluene Biotransformation by Escherichia coli

1
Chemical Injuries Research Center, Baqiyatallah University of Medical Sciences, 1477893855 Tehran, Iran
2
Department of Pharmaceutics, School of Pharmacy, Baqiyatallah University of Medical Sciences, 1477893855 Tehran, Iran
3
Young Researchers and Elite Club, Islamic Azad University, 46115655 Tehran, Iran
4
Department of Biotechnology, Faculty of Advanced Sciences & Technology, Pharmaceutical Sciences Branch, Islamic Azad University (IAUPS), 194193311 Tehran, Iran
*
Author to whom correspondence should be addressed.
Received: 6 June 2017 / Revised: 22 June 2017 / Accepted: 23 June 2017 / Published: 14 August 2017
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Abstract

Microbial remediation of nitroaromatic compounds (NACs) is a promising environmentally friendly and cost-effective approach to the removal of these life-threating agents. Escherichia coli (E. coli) has shown remarkable capability for the biotransformation of 2,4,6-trinitro-toluene (TNT). Efforts to develop E. coli as an efficient TNT degrading biocatalyst will benefit from holistic flux-level description of interactions between multiple TNT transforming pathways operating in the strain. To gain such an insight, we extended the genome-scale constraint-based model of E. coli to account for a curated version of major TNT transformation pathways known or evidently hypothesized to be active in E. coli in present of TNT. Using constraint-based analysis (CBA) methods, we then performed several series of in silico experiments to elucidate the contribution of these pathways individually or in combination to the E. coli TNT transformation capacity. Results of our analyses were validated by replicating several experimentally observed TNT degradation phenotypes in E. coli cultures. We further used the extended model to explore the influence of process parameters, including aeration regime, TNT concentration, cell density, and carbon source on TNT degradation efficiency. We also conducted an in silico metabolic engineering study to design a series of E. coli mutants capable of degrading TNT at higher yield compared with the wild-type strain. Our study, therefore, extends the application of CBA to bioremediation of nitroaromatics and demonstrates the usefulness of this approach to inform bioremediation research. View Full-Text
Keywords: nitroaromatics; 2,4,6-trinitrotoluene; environment; bioremediation; biotransformation; bio-degradation; constraint-based analysis; systems biology; metabolic engineering nitroaromatics; 2,4,6-trinitrotoluene; environment; bioremediation; biotransformation; bio-degradation; constraint-based analysis; systems biology; metabolic engineering
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Iman, M.; Sobati, T.; Panahi, Y.; Mobasheri, M. Systems Biology Approach to Bioremediation of Nitroaromatics: Constraint-Based Analysis of 2,4,6-Trinitrotoluene Biotransformation by Escherichia coli. Molecules 2017, 22, 1242.

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