In silico feasibility of novel biodegradation pathways for 1,2,4-trichlorobenzene.

BMC Systems Biology
Stacey D FinleyVassily Hatzimanikatis

Abstract

Bioremediation offers a promising pollution treatment method in the reduction and elimination of man-made compounds in the environment. Computational tools to predict novel biodegradation pathways for pollutants allow one to explore the capabilities of microorganisms in cleaning up the environment. However, given the wealth of novel pathways obtained using these prediction methods, it is necessary to evaluate their relative feasibility, particularly within the context of the cellular environment. We have utilized a computational framework called BNICE to generate novel biodegradation routes for 1,2,4-trichlorobenzene (1,2,4-TCB) and incorporated the pathways into a metabolic model for Pseudomonas putida. We studied the cellular feasibility of the pathways by applying metabolic flux analysis (MFA) and thermodynamic constraints. We found that the novel pathways generated by BNICE enabled the cell to produce more biomass than the known pathway. Evaluation of the flux distribution profiles revealed that several properties influenced biomass production: 1) reducing power required, 2) reactions required to generate biomass precursors, 3) oxygen utilization, and 4) thermodynamic topology of the pathway. Based on pathway analysis, MFA,...Continue Reading

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Software Mentioned

META
TMFA
Biochemical Network Integrated Computational Explorer ( BNICE )
FVA
Pathway Prediction System ( PPS )
BNICE
Flux variability analysis ( FVA )
Excel

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