Construction of a genome-scale metabolic network model of <i>Rhodococcus ruber</i>-MSA1 and its application in prediction and analysis of aromatic phenol pollutant degradation

LU Menghu; HOU Ya'nan; LIU Zhihua; LI Haibo; HAN Yi; ZHANG Daohong; HUANG Cong

doi:10.13205/j.hjgc.202609007

Volume 44 Issue 9

Sep. 2026

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Article Navigation > ENVIRONMENTAL ENGINEERING > 2026 > 44(9): 59-68

LU Menghu, HOU Ya'nan, LIU Zhihua, LI Haibo, HAN Yi, ZHANG Daohong, HUANG Cong. Construction of a genome-scale metabolic network model of Rhodococcus ruber-MSA1 and its application in prediction and analysis of aromatic phenol pollutant degradation[J]. ENVIRONMENTAL ENGINEERING , 2026, 44(9): 59-68. doi: 10.13205/j.hjgc.202609007

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LU Menghu, HOU Ya'nan, LIU Zhihua, LI Haibo, HAN Yi, ZHANG Daohong, HUANG Cong. Construction of a genome-scale metabolic network model of Rhodococcus ruber-MSA1 and its application in prediction and analysis of aromatic phenol pollutant degradation[J]. ENVIRONMENTAL ENGINEERING , 2026, 44(9): 59-68. doi: 10.13205/j.hjgc.202609007

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Construction of a genome-scale metabolic network model of Rhodococcus ruber-MSA1 and its application in prediction and analysis of aromatic phenol pollutant degradation

doi: 10.13205/j.hjgc.202609007

1. Tianjin Chengjian University, Tianjin 300384, China;
2. Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China

Received Date: 2025-01-23
Available Online: 2026-11-05

Abstract

Abstract

Aromatic phenolic pollutants， due to their high concentration and widespread distribution characteristics， have posed a systematic threat to the stability of the ecosystem and human health. In this study， the pollutant-degrading bacterium Rhodococcus ruber-MSA14 was taken as the research object. A genome-scale metabolic model （GEMs） was constructed based on the COBRA framework. Methods such as flux balance analysis （FBA） and flux variability analysis （FVA） were employed to correct and validate the model. The substrate range of the model was broadened by using 37 carbon sources， and the advanced enzyme prediction tool （ECRECer） was utilized to supplement the annotation of key genes for m-cresol and 4-chlorophenol degradation. A high-quality model， GEMs_3， was constructed to simulate the metabolic flux analysis of m-cresol， 4-chlorophenol， and phenol. Fitting analysis were carried out between the actual growth and degradation and the model predictions. The research shows that there was a high correlation between the pollutant degradation trends simulated by the model and the experimental data. Specifically， for the degradation simulation of m-cresol， the R² value was 0.9497； for the degradation simulation of 4-chlorophenol， the R² value was 0.9556； and for the degradation simulation of phenol， the R² value was 0.8281. Furthermore， the constructed model was used to analyze the potential over-expression targets of Rhodococcus ruber-MSA14 in pollutant degradation，and it provided specific targeting information for optimizing the degradation ability of the strain and its genetic modification. This study provides a theoretical basis for the application of Rhodococcus ruber-MSA14 in the degradation of aromatic phenolic pollutants and offers guidance for gene modification and bioremediation strategies based on metabolic networks.
- Rhodococcus ruber-MSA14,
- genome-scale metabolic network model,
- aromatic compounds,
- metabolic pathways,
- gene prediction

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References(38)

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