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Wei J, Luo J, Peng T, Zhou P, Zhang J, Yang F. Comparative genomic analysis and functional investigations for MCs catabolism mechanisms and evolutionary dynamics of MCs-degrading bacteria in ecology. ENVIRONMENTAL RESEARCH 2024; 248:118336. [PMID: 38295970 DOI: 10.1016/j.envres.2024.118336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 01/06/2024] [Accepted: 01/27/2024] [Indexed: 02/07/2024]
Abstract
Microcystins (MCs) significantly threaten the ecosystem and public health. Biodegradation has emerged as a promising technology for removing MCs. Many MCs-degrading bacteria have been identified, including an indigenous bacterium Sphingopyxis sp. YF1 that could degrade MC-LR and Adda completely. Herein, we gained insight into the MCs biodegradation mechanisms and evolutionary dynamics of MCs-degrading bacteria, and revealed the toxic risks of the MCs degradation products. The biochemical characteristics and genetic repertoires of strain YF1 were explored. A comparative genomic analysis was performed on strain YF1 and six other MCs-degrading bacteria to investigate their functions. The degradation products were investigated, and the toxicity of the intermediates was analyzed through rigorous theoretical calculation. Strain YF1 might be a novel species that exhibited versatile substrate utilization capabilities. Many common genes and metabolic pathways were identified, shedding light on shared functions and catabolism in the MCs-degrading bacteria. The crucial genes involved in MCs catabolism mechanisms, including mlr and paa gene clusters, were identified successfully. These functional genes might experience horizontal gene transfer events, suggesting the evolutionary dynamics of these MCs-degrading bacteria in ecology. Moreover, the degradation products for MCs and Adda were summarized, and we found most of the intermediates exhibited lower toxicity to different organisms than the parent compound. These findings systematically revealed the MCs catabolism mechanisms and evolutionary dynamics of MCs-degrading bacteria. Consequently, this research contributed to the advancement of green biodegradation technology in aquatic ecology, which might protect human health from MCs.
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Affiliation(s)
- Jia Wei
- Xiangya School of Public Health, Central South University, Changsha, Hunan, 410078, China
| | - Jiayou Luo
- Xiangya School of Public Health, Central South University, Changsha, Hunan, 410078, China.
| | - Tangjian Peng
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, University of South China, Hengyang, Hunan, 421001, China
| | - Pengji Zhou
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, University of South China, Hengyang, Hunan, 421001, China
| | - Jiajia Zhang
- Xiangya School of Public Health, Central South University, Changsha, Hunan, 410078, China
| | - Fei Yang
- Xiangya School of Public Health, Central South University, Changsha, Hunan, 410078, China; Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, University of South China, Hengyang, Hunan, 421001, China.
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Teng J, Xu Q, Zhang H, Yu R, Liu C, Song M, Cao X, Du X, Tao S, Yan H. Enzymatic mechanism of MlrB for catalyzing linearized microcystins by Sphingopyxis sp. USTB-05. Front Microbiol 2024; 15:1389235. [PMID: 38711965 PMCID: PMC11070527 DOI: 10.3389/fmicb.2024.1389235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 04/08/2024] [Indexed: 05/08/2024] Open
Abstract
Microcystins (MCs) are the most widespread cyanobacterial toxins in eutrophic water body. As high toxic intermediate metabolites, linearized MCs are further catalyzed by linearized microcystinase (MlrB) of Sphingopyxis sp. USTB-05. Here MlrB structure was studied by comprizing with a model representative of the penicillin-recognizing enzyme family via homology modeling. The key active sites of MlrB were predicted by molecular docking, and further verified by site-directed mutagenesis. A comprehensive enzymatic mechanism for linearized MCs biodegradation by MlrB was proposed: S77 transferred a proton to H307 to promote a nucleophilic attack on the peptide bond (Ala-Leu in MC-LR or Ala-Arg in MC-RR) of linearized MCs to form the amide intermediate. Then water was involved to break the peptide bond and produced the tetrapeptide as product. Meanwhile, four amino acid residues (K80, Y171, N173 and D245) acted synergistically to stabilize the substrate and intermediate transition states. This study firstly revealed the enzymatic mechanism of MlrB for biodegrading linearized MCs with both computer simulation and experimental verification.
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Affiliation(s)
- Junhui Teng
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China
| | - Qianqian Xu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China
| | - Haiyang Zhang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China
| | - Ruipeng Yu
- Beijing Institute for Drug Control, Beijing, China
| | - Chao Liu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China
| | - Meijie Song
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China
| | - Xiaoyu Cao
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China
| | - Xinyue Du
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China
| | - Suxuan Tao
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China
| | - Hai Yan
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China
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Cheng L, Wang L, Wang X, Ou Y, Liu H, Hou X, Yan L, Li X. The various effect of cow manure compost on the degradation of imazethapyr in different soil types. CHEMOSPHERE 2023:139325. [PMID: 37356585 DOI: 10.1016/j.chemosphere.2023.139325] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/15/2023] [Accepted: 06/23/2023] [Indexed: 06/27/2023]
Abstract
Adding compost to soil is an effective strategy to promote the degradation of organic pollutants and reduce ecological risks. However, the effect of compost on the degradation of imazethapyr (IMET) in different soil types is not clear. To address this issue, a pot experiment was conducted, and high-throughput sequencing and mass spectrometry technology were used to identify the influence of cow manure compost on the degradation efficiency of IMET in black soil and saline-alkali soil and the role of key microorganisms. The results showed that adding compost to black soil increased the degradation rate of IMET by 12.58% and shortened the half-life by 53.37%, while in saline-alkali soil, the degradation rate of IMET decreased by 6.99% with no significant change in the half-life. High-throughput sequencing results showed that adding cow manure compost (mass ratio of 4%) significantly increased the abundance of bacterial families capable of degrading organic pollutants in black soil, but had an inhibitory effect on this bacterial community in saline-alkali soil. Redundancy analysis (RDA) results showed that total organic carbon (TOC), alkali-hydrolyzable nitrogen (AN), ammonia nitrogen (NH4+-N) and nitrate nitrogen (NO3--N) were the main factors driving microbial community variation. Mass spectrometry analysis indicated that IMET generated three metabolites during the degradation process. Sphingomonadaceae and Vicinamibacteraceae could accelerate the breaking of side-chain alkyl groups, while Chitinophagaceae could cause the rearrangement of the imidazole ring structure, gradually metabolizing IMET into small organic molecules. The application of appropriate cow manure compost can promote the development of IMET-degrading bacteria by adjusting the organic carbon and dissolved nitrogen content in black soil. In the future, the quantitative effects of organic fertilizer application on the IMET degradation process in different soil types should be further analyzed, and microbial isolation and purification should be used to enhance the ability of microorganisms to degrade herbicides.
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Affiliation(s)
- Lei Cheng
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China; State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China; Jilin Provincial Engineering Center of CWs Design in Cold Region & Beautiful Country Construction, Changchun, 130102, China
| | - Lixia Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China; Jilin Provincial Engineering Center of CWs Design in Cold Region & Beautiful Country Construction, Changchun, 130102, China
| | - Xinhong Wang
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China.
| | - Yang Ou
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China; Jilin Provincial Engineering Center of CWs Design in Cold Region & Beautiful Country Construction, Changchun, 130102, China.
| | - Huiping Liu
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China; State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China; Jilin Provincial Engineering Center of CWs Design in Cold Region & Beautiful Country Construction, Changchun, 130102, China
| | - Xia Hou
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China; State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Liming Yan
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China; State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Xinyi Li
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China; State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
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