赤红球菌MSA1基因组尺度代谢网络模型的构建及其用于芳香酚类污染物降解预测分析

卢孟虎; 侯雅男; 刘志华; 李海波; 韩懿; 张道虹; 黄聪

doi:10.13205/j.hjgc.202609007

赤红球菌MSA1基因组尺度代谢网络模型的构建及其用于芳香酚类污染物降解预测分析

doi: 10.13205/j.hjgc.202609007

1. 天津城建大学, 天津 300384;
2. 中国科学院天津工业生物技术研究中心, 天津 300308

基金项目:

国家自然科学基金项目“基于数字细胞模型的人工极简产氢微生物菌群构建与优化”（52470168）；天津城建大学低碳比市政污水节能低碳治理中波联合研究中心建设

详细信息

作者简介:
卢孟虎(1997—),男,硕士研究生,主要研究方向为污水处理与资源化。lumh@tib.cas.cn

通讯作者:
侯雅男(1989—),女,副教授,主要研究方向为污水处理与资源化。houyn2013@163.com

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出版历程
- 收稿日期: 2025-01-23
- 网络出版日期: 2026-11-05

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

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

摘要

摘要: 芳香酚类污染物因其高浓度与广域分布特性，已对生态系统稳定性和人类健康构成系统性威胁。研究以污染物降解菌Rhodococcus ruber-MSA14为对象，基于COBRA框架构建基因组尺度代谢模型（GEMs），并利用通量平衡分析（FBA）和通量变异性分析（FVA）等方法对模型进行修正和验证。通过37种碳源拓宽模型底物范围，并使用先进的酶预测工具（ECRECer），补充注释了m-cresol和4-chlorophenol降解关键基因，构建了高质量模型GEMs_3，模拟了间甲基苯酚（m-cresol）、对氯苯酚（4-chlorophenol）和苯酚（phenol）的代谢通量分析，对实际生长和降解与模型预测进行了拟合分析。研究表明：模型模拟的污染物降解趋势与实验数据之间表现出较高的相关性，具体体现在针对m-cresol的降解模拟，R²值为0.9497；对氯苯酚4-chlorophenol的降解模拟，R²值为0.9556；phenol的降解模拟，R²值为0.8281。进一步利用构建的模型分析了Rhodococcus ruber-MSA14在污染物降解中的潜在过表达靶点，为优化菌株的降解能力及其遗传改造提供了具体的靶向信息。研究成果可为Rhodococcus ruber-MSA14在芳香酚类污染物降解中的应用提供理论依据，并为基于代谢网络的基因改造与生物修复策略提供指导。
- 赤红球菌MSA14 /
- 基因组尺度代谢网络模型 /
- 芳香化合物 /
- 代谢途径 /
- 基因预测
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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