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Li Q, Ma Q, Zhou Y, Jiang X, Parales RE, Zhao S, Zhuang Y, Ruan Z. Isolation, identification, and degradation mechanism by multi-omics of mesotrione-degrading Amycolatopsis nivea La24. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:134951. [PMID: 38917628 DOI: 10.1016/j.jhazmat.2024.134951] [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: 03/20/2024] [Revised: 06/03/2024] [Accepted: 06/16/2024] [Indexed: 06/27/2024]
Abstract
Mesotrione is a herbicide used in agricultural production; however, its stability and long-term residues pose ecological risks to soil health and subsequent crops. In this research, the strain Amycolatopsis nivea La24 was identified as capable of completely degrading 50 mg∙L-1 mesotrione within 48 h. It exhibited a broad adaptability to various environment and could degrade three sulfonylurea herbicides (nicosulfuron, chlorimuron-methyl, and cinosulfuron). Non-target metabonomic and mass spectrometry demonstrated that La24 strain broke down the mesotrione parent molecule by targeting the β-diketone bond and nitro group, resulting in the production of five possible degradation products. The differentially expressed genes were significantly enriched in fatty acid degradation, amino acid metabolism, and other pathways, and the differentially metabolites in glutathione metabolism, arginine/proline metabolism, cysteine/methionine metabolism, and other pathways. Additionally, it was confirmed by heterologous expression that nitroreductase was directly involved in the mesotrione degradation, and NDMA-dependent methanol dehydrogenase would increase the resistance to mesotrione. Finally, the intracellular response of La24 during mesotrione degradation was proposed. This work provides insight for a comprehensive understanding of the mesotrione biodegradation mechanism, significantly expands the resources for pollutant degradation, and offers the potential for a more sustainable solution to address herbicide pollution in soil.
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Affiliation(s)
- Qingqing Li
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; National Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingyun Ma
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; National Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yiqing Zhou
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xu Jiang
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rebecca E Parales
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Shumiao Zhao
- National Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yan Zhuang
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhiyong Ruan
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Cho DH, Kim S, Lee Y, Shin Y, Choi S, Oh J, Kim HT, Park SH, Park K, Bhatia SK, Yang YH. Enhanced theanine production with reduced ATP supply by alginate entrapped Escherichia coli co-expressing γ-glutamylmethylamide synthetase and polyphosphate kinase. Enzyme Microb Technol 2024; 175:110394. [PMID: 38277867 DOI: 10.1016/j.enzmictec.2024.110394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 01/28/2024]
Abstract
L-theanine is an amino acid with a unique flavor and many therapeutic effects. Its enzymatic synthesis has been actively studied and γ-Glutamylmethylamide synthetase (GMAS) is one of the promising enzymes in the biological synthesis of theanine. However, the theanine biosynthetic pathway with GMAS is highly ATP-dependent and the supply of external ATP was needed to achieve high concentration of theanine production. As a result, this study aimed to investigate polyphosphate kinase 2 (PPK2) as ATP regeneration system with hexametaphosphate. Furthermore, the alginate entrapment method was employed to immobilize whole cells containing both gmas and ppk2 together resulting in enhanced reusability of the theanine production system with reduced supply of ATP. After immobilization, theanine production was increased to 239 mM (41.6 g/L) with a conversion rate of 79.7% using 15 mM ATP and the reusability was enhanced, maintaining a 100% conversion rate up to the fifth cycles and 60% of conversion up to eighth cycles. It could increase long-term storage property for future uses up to 35 days with 75% activity of initial activity. Overall, immobilization of both production and cofactor regeneration system could increase the stability and reusability of theanine production system.
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Affiliation(s)
- Do Hyun Cho
- Department of Biological Engineering, College of Engineering, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Suwon Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Yeda Lee
- Department of Biological Engineering, College of Engineering, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Yuni Shin
- Department of Biological Engineering, College of Engineering, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Suhye Choi
- Department of Biological Engineering, College of Engineering, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Jinok Oh
- Department of Biological Engineering, College of Engineering, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Hee Taek Kim
- Department of Food Science and Technology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - See-Hyoung Park
- Department of Biological and Chemical Engineering, Hongik University, Sejong 30016, Republic of Korea
| | - Kyungmoon Park
- Department of Biological and Chemical Engineering, Hongik University, Sejong 30016, Republic of Korea
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea; Institute for Ubiquitous Information Technology and Applications, Konkuk University, Seoul 05029, Republic of Korea
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea; Institute for Ubiquitous Information Technology and Applications, Konkuk University, Seoul 05029, Republic of Korea.
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Li ZL, Sun CQ, Qing ZL, Li ZM, Liu HL. Engineering the thermal stability of a polyphosphate kinase by ancestral sequence reconstruction to expand the temperature boundary for an industrially applicable ATP regeneration system. Appl Environ Microbiol 2024; 90:e0157423. [PMID: 38236018 PMCID: PMC10880597 DOI: 10.1128/aem.01574-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 12/06/2023] [Indexed: 01/19/2024] Open
Abstract
ATP-dependent energy-consuming enzymatic reactions are widely used in cell-free biocatalysis. However, the direct addition of large amounts of expensive ATP can greatly increase cost, and enzymatic production is often difficult to achieve as a result. Although a polyphosphate kinase (PPK)-polyphosphate-based ATP regeneration system has the potential to solve this challenge, the generally poor thermal stability of PPKs limits the widespread use of this method. In this paper, we evaluated the thermal stability of a PPK from Sulfurovum lithotrophicum (SlPPK2). After directed evolution and computation-supported design, we found that SlPPK2 is very recalcitrant and cannot acquire beneficial mutations. Inspired by the usually outstanding stability of ancestral enzymes, we reconstructed the ancestral sequence of the PPK family and used it as a guide to construct three heat-stable variants of SlPPK2, of which the L35F/T144S variant has a half-life of more than 14 h at 60°C. Molecular dynamics simulations were performed on all enzymes to analyze the reasons for the increased thermal stability. The results showed that mutations at these two positions act synergistically from the interior and surface of the protein, leading to a more compact structure. Finally, the robustness of the L35F/T144S variant was verified in the synthesis of nucleotides at high temperature. In practice, the use of this high-temperature ATP regeneration system can effectively avoid byproduct accumulation. Our work extends the temperature boundary of ATP regeneration and has great potential for industrial applications.IMPORTANCEATP regeneration is an important basic applied study in the field of cell-free biocatalysis. Polyphosphate kinase (PPK) is an enzyme tool widely used for energy regeneration during enzymatic reactions. However, the thermal stability of the PPKs reported to date that can efficiently regenerate ATP is usually poor, which greatly limits their application. In this study, the thermal stability of a difficult-to-engineer PPK from Sulfurovum lithotrophicum was improved, guided by an ancestral sequence reconstruction strategy. The optimal variant has a 4.5-fold longer half-life at 60°C than the wild-type enzyme, thus enabling the extension of the temperature boundary for ATP regeneration. The ability of this variant to regenerate ATP was well demonstrated during high-temperature enzymatic production of nucleotides.
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Affiliation(s)
- Zong-Lin Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Chuan-Qi Sun
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Zhou-Lei Qing
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Zhi-Min Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai, China
| | - Hong-Lai Liu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
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Zhou M, Wei L, Wu C, Chen W, Tang Z. Systematic Engineering of Escherichia coli for Efficient Production of Cytidine 5'-Monophosphate. ACS OMEGA 2024; 9:6663-6668. [PMID: 38371780 PMCID: PMC10870394 DOI: 10.1021/acsomega.3c07713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/05/2024] [Accepted: 01/19/2024] [Indexed: 02/20/2024]
Abstract
Cytidine 5'-monophosphate (CMP) was widely applied in the food and pharmaceutical industries. Currently, CMP is mainly produced by enzyme catalysis. However, the starting materials for enzyme catalysis were relatively expensive. Therefore, seeking a low-cost production process for CMP was attractive. In this study, Escherichia coli (E. coli) was systematically modified to produce CMP. First, a the cytidine-producing strain was constructed by deleting cdd, rihA, rihB, and rihC. Second, the genes involved in the pyrimidine precursor competing pathway and negative regulation were deleted to increase cyti dine biosynthesis. Third, the deletion of the genes that caused the loss of CMP phosphatase activity led to the accumulation of CMP, and the overexpression of the rate-limiting step genes and feedback inhibition resistance genes greatly increased the yield of CMP. The yield of CMP was further increased to 1013.6 mg/L by blocking CMP phosphorylation. Ultimately, the yield of CMP reached 15.3 g/L in a 50 L bioreactor. Overall, the engineered E. coli with a high yield of CMP was successfully constructed and showed the potential for industrial production.
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Affiliation(s)
- Min Zhou
- Institute
of Biopharmaceuticals, School of Pharmaceutical Sciences, Taizhou University, Taizhou 318000, China
| | - Liyuan Wei
- Institute
of Biopharmaceuticals, School of Pharmaceutical Sciences, Taizhou University, Taizhou 318000, China
| | - Chongzhi Wu
- Institute
of Biopharmaceuticals, School of Pharmaceutical Sciences, Taizhou University, Taizhou 318000, China
| | - Wei Chen
- Hangzhou
Hizyme Biotech Co., Ltd., Hangzhou 310011, China
| | - Zhengju Tang
- Taizhou
Central Hospital (Taizhou University Hospital), Taizhou 318000, China
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