Efficient and low-energy degradation of chlorobenzene via catA-mediated cleavage and bedC1 docking in a novel Burkholderia stabilis TF-2

• Published in: Chemosphere (Oxford) Vol. 364; p. 143065
• Main Authors: Xing, Zhilin, Gou, Fang, Zhang, Xiaoping, Gao, Yanhui, Ke, Xihong, Ran, Dongni, Wang, Peng, Guo, Jiangfeng, Wu, Heng, Peng, Chao, Zhao, Tiantao
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 01-09-2024
• Subjects: Burkholderia stabilis; Chlorobenzenes; Molecular docking; Multi-omic; Super-resistant strain; Burkholderia stabilis; Super-resistant strain; Chlorobenzenes; Multi-omic; Molecular docking; molecular docking; chlorobenzenes; multi-omic; super-resistant strain
• ISSN: 0045-6535; 1879-1298; 1879-1298
• DOI: 10.1016/j.chemosphere.2024.143065

In this study, a novel strain Burkholderia stabilis TF-2 capable of assimilatory and co-metabolic degradation of chlorobenzenes was obtained. The interaction between chlorobenzene (CB) and target enzymes, as well as the metabolic pathways in TF-2, were elucidated using multi-omics and molecular docking techniques. Results of degradation experiments indicated that TF-2 assimilated CB at a rate of 0.22–0.66 mg·gcell−1·h−1 in concentrations of 20–200 mg L−1. Additionally, TF-2 also used sodium succinate and sodium citrate as substrates to co-metabolize CB, with degradation rates of 0.26–2.00 and 0.31–1.72 mol·gcell−1·h−1, respectively. Whole-genome sequencing revealed over 18 novel genes associated with aromatic hydrocarbon degradation in TF-2. Transcriptomic analysis showed that CB induced the high expression of 119 genes involved in CB metabolism and late mineralization. The significant up-regulation of the bedC1 (encoding a ring-hydroxylated dioxygenase), CatA (chlorocatechol 1,2-dioxygenase), pcaJ (3-oxoadipate CoA-transferase alpha subunit) and fadA (acetyl-CoA acyltransferase) genes facilitated CB metabolism. Based on these findings, a metabolic pathway for CB was constructed, with the key step involving ortho cleavage of the aromatic ring under the action of the catA gene. Furthermore, molecular docking revealed that CB bound to bedC1 with −4.5 kcal mol−1 through hydrophobic bonds, π-stacking, and a halogen bond. These results provide strong support for development of efficient strains to enhance the removal of chlorinated organic compounds.
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•Novel CBs-degrading Burkholderia with capability of assimilation was isolated.•Genome, transcription, and metabolism involved in CB degradation was examined.•Novel metabolic pathway for biodegradation of CB was established in Burkholderia.•Molecular docking was applied for the first time in the study of CB degradation.•The connection between CB and target enzymes in Burkholderia was clearly revealed.