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Feng C, Chen J, Ye W, Wang Z. Nitrile hydratase as a promising biocatalyst: recent advances and future prospects. Biotechnol Lett 2024:10.1007/s10529-024-03530-y. [PMID: 39269672 DOI: 10.1007/s10529-024-03530-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 08/05/2024] [Accepted: 08/28/2024] [Indexed: 09/15/2024]
Abstract
Amides are an important type of synthetic intermediate used in the chemical, agrochemical, pharmaceutical, and nutraceutical industries. The traditional chemical process of converting nitriles into the corresponding amides is feasible but is restricted because of the harsh conditions required. In recent decades, nitrile hydratase (NHase, EC 4.2.1.84) has attracted considerable attention because of its application in nitrile transformation as a prominent biocatalyst. In this review, we provide a comprehensive survey of recent advances in NHase research in terms of natural distribution, enzyme screening, and molecular modification on the basis of its characteristics and catalytic mechanism. Additionally, industrial applications and recent significant biotechnology advances in NHase bioengineering and immobilization techniques are systematically summarized. Moreover, the current challenges and future perspectives for its further development in industrial applications for green chemistry were also discussed. This study contributes to the current state-of-the-art, providing important technical information for new NHase applications in manufacturing industries.
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Affiliation(s)
- Chao Feng
- Department of Urology, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Jing Chen
- Department of Urology, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Wenxin Ye
- Department of Urology, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Zhanshi Wang
- Department of Urology, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang Province, China.
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Zhang H, Rong Z, Li Y, Yin Z, Lu C, Zhao H, Kong L, Meng L, Ding X. NIT24 and NIT29-mediated IAA synthesis of Xanthomonas oryzae pv. oryzicola suppresses immunity and boosts growth in rice. MOLECULAR PLANT PATHOLOGY 2024; 25:e13409. [PMID: 38069667 PMCID: PMC10788589 DOI: 10.1111/mpp.13409] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/20/2023] [Indexed: 01/17/2024]
Abstract
Auxin plays a pivotal role in the co-evolution of plants and microorganisms. Xanthomonas oryzae pv. oryzicola (Xoc) stands as a significant factor that affects rice yield and quality. However, the current understanding of Xoc's capability for indole 3-acetic acid (IAA) synthesis and its mechanistic implications remains elusive. In this study, we performed a comprehensive genomic analysis of Xoc strain RS105, leading to the identification of two nitrilase enzyme family (NIT) genes, designated as AKO15524.1 and AKO15829.1, subsequently named NIT24 and NIT29, respectively. Our investigation unveiled that the deletion of NIT24 and NIT29 resulted in a notable reduction in IAA synthesis capacity within RS105, thereby impacting extracellular polysaccharide production. This deficiency was partially ameliorated through exogenous IAA supplementation. The study further substantiated that NIT24 and NIT29 have nitrilase activity and the ability to catalyse IAA production in vitro. The lesion length and bacterial population statistics experiments confirmed that NIT24 and NIT29 positively regulated the pathogenicity of RS105, suggesting that NIT24 and NIT29 may regulate Xoc invasion by affecting IAA synthesis. Furthermore, our analysis corroborated mutant strains, RS105_ΔNIT24 and RS105_ΔNIT29, which elicited the outbreak of reactive oxygen species, the deposition of callose and the upregulation of defence-related gene expression in rice. IAA exerted a significant dampening effect on the immune responses incited by these mutant strains in rice. In addition, the absence of NIT24 and NIT29 affected the growth-promoting effect of Xoc on rice. This implies that Xoc may promote rice growth by secreting IAA, thus providing a more suitable microenvironment for its own colonization. In summary, our study provides compelling evidence for the existence of a nitrilase-dependent IAA biosynthesis pathway in Xoc. IAA synthesis-related genes promote Xoc colonization by inhibiting rice immune defence response and affecting rice growth by increasing IAA content in Xoc.
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Affiliation(s)
- Haimiao Zhang
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
| | - Zixuan Rong
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
| | - Yang Li
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
| | - Ziyi Yin
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
| | - Chongchong Lu
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
| | - Haipeng Zhao
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
| | - Lingguang Kong
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
| | - Lun Meng
- Shike Modern Agriculture Investment Co., LtdHezeChina
| | - Xinhua Ding
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
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Soil Microbial Co-Occurrence Patterns under Controlled-Release Urea and Fulvic Acid Applications. Microorganisms 2022; 10:microorganisms10091823. [PMID: 36144425 PMCID: PMC9502011 DOI: 10.3390/microorganisms10091823] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/17/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022] Open
Abstract
The increasing amount of agricultural applications of controlled-release urea (CRU) and fulvic acids (FA) demands a better understanding of FA’s effects on microbially mediated nitrogen (N) nutrient cycling. Herein, a 0–60 day laboratory experiment and a consecutive pot experiment (2016–2018) were carried out to reveal the effects of using CRU on soil microbial N-cycling processes and soil fertility, with and without the application of FA. Compared to the CRU treatment, the CRU+FA treatment boosted wheat yield by 22.1%. To reveal the mechanism of CRU+FA affecting the soil fertility, soil nutrient supply and microbial community were assessed and contrasted in this research. From 0–60 days, compared with the CRU treatment, leaching NO3−-N content of CRU+FA was dramatically decreased by 12.7–84.2% in the 20 cm depth of soil column. Different fertilizers and the day of fertilization both have an impact on the soil microbiota. The most dominant bacterial phyla Actinobacteria and Proteobacteria were increased with CRU+FA treatment during 0–60 days. Network analysis revealed that microbial co-occurrence grew more intensive during the CRU+FA treatment, and the environmental change enhanced the microbial community. The CRU+FA treatment, in particular, significantly decreased the relative abundance of Sphingomonas, Lysobacter and Nitrospira associated with nitrification reactions, Nocardioides and Gaiella related to denitrification reactions. Meanwhile, the CRU+FA treatment grew the relative abundance of Ensifer, Blastococcus, and Pseudolabrys that function in N fixation, and then could reduce NH4+-N and NO3−-N leaching and improve the soil nutrient supply. In conclusion, the synergistic effects of slow nutrition release of CRU and growth promoting of FA could improve the soil microbial community of N cycle, reduce the loss of nutrients, and increase the wheat yield.
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Ahmad S, Cui D, Zhong G, Liu J. Microbial Technologies Employed for Biodegradation of Neonicotinoids in the Agroecosystem. Front Microbiol 2021; 12:759439. [PMID: 34925268 PMCID: PMC8675359 DOI: 10.3389/fmicb.2021.759439] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
Neonicotinoids are synthetic pesticides widely used for the control of various pests in agriculture throughout the world. They mainly attack the nicotinic acetylcholine receptors, generate nervous stimulation, receptor clot, paralysis and finally cause death. They are low volatile, highly soluble and have a long half-life in soil and water. Due to their extensive use, the environmental residues have immensely increased in the last two decades and caused many hazardous effects on non-target organisms, including humans. Hence, for the protection of the environment and diversity of living organism's the degradation of neonicotinoids has received widespread attention. Compared to the other methods, biological methods are considered cost-effective, eco-friendly and most efficient. In particular, the use of microbial species makes the degradation of xenobiotics more accessible fast and active due to their smaller size. Since this degradation also converts xenobiotics into less toxic substances, the various metabolic pathways for the microbial degradation of neonicotinoids have been systematically discussed. Additionally, different enzymes, genes, plasmids and proteins are also investigated here. At last, this review highlights the implementation of innovative tools, databases, multi-omics strategies and immobilization techniques of microbial cells to detect and degrade neonicotinoids in the environment.
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Affiliation(s)
- Sajjad Ahmad
- Key Laboratory of Integrated Pest Management of Crop in South China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, China
| | - Dongming Cui
- Key Laboratory of Integrated Pest Management of Crop in South China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, China
| | - Guohua Zhong
- Key Laboratory of Integrated Pest Management of Crop in South China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, China
| | - Jie Liu
- Key Laboratory of Integrated Pest Management of Crop in South China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, China
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Shen JD, Cai X, Wang M, Liu ZQ, Zheng YG. Proposed mechanism for post-translational self-modification of Co-NHase based on Co 2+ diffusion limitation. Biotechnol J 2021; 16:e2100103. [PMID: 34363653 DOI: 10.1002/biot.202100103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 07/14/2021] [Accepted: 07/27/2021] [Indexed: 11/05/2022]
Abstract
BACKGROUND Nitrile hydratase (NHase), was an excellent biocatalyst for the synthesis of amide compounds. NHase was typical heterodimeric metalloprotein, required of the assistance of activator for active expressions. In this work, we found a special Co-NHase HBA from Caldalkalibacillus thermarum, which had the ability of post-translational self-modification and could incorporate Co2+ into the catalytic center in the absence of activator. METHOD AND RESULTS We simulated the movement of Co2+ in silico and established a hypothetical model to predict the Co2+ incorporation efficiency (XCo ) of NHases. According to the simulation results, NHase mutants with different positive charge distribution were constructed. Compared with wild-type, the Co2+ incorporation efficiency of K1 (M10K) was increased by 2.1-fold from 0.36 to 0.76, and the specific activity was increased by 3.2-fold from 136.3 to 432.0 U/mg, while mutant K1H1 (M10K, D11H) and K2H2 (M10K, D11H, E20K, N21H) lost the ability of post-translation self-modification. CONCLUSIONS AND IMPLICATIONS The interactions of positively charged residues near the catalytic center, such as lysine with strong electrostatic repulsive interaction, arginine with weak electrostatic repulsive interaction and histidine with metal affinity, could limit the free diffusion of Co2+ in NHase and affect the efficiency of post-translational self-modification. This work also provided an effective strategy for protein engineering of NHases and other metalloenzymes. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ji-Dong Shen
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xue Cai
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Ming Wang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Zhi-Qiang Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yu-Guo Zheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
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Yang W, Fan Z, Jiang H, Zhao Y, Guo L, Dai Y. Biotransformation of flonicamid and sulfoxaflor by multifunctional bacterium Ensifer meliloti CGMCC 7333. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2020; 56:122-131. [PMID: 33283619 DOI: 10.1080/03601234.2020.1852854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Flonicamid is a novel, selective, systemic pyridinecarboxamide insecticide that effectively controls hemipterous pests. Sulfoxaflor, a sulfoximine insecticide, effectively controls many sap-feeding insect pests. Ensifer meliloti CGMCC 7333 transforms flonicamid into N-(4-trifluoromethylnicotinoyl) glycinamide (TFNG-AM). Resting cells of E. meliloti CGMCC 7333 (optical density at 600 nm [OD600] = 5) transformed 67.20% of the flonicamid in a 200-mg/L solution within 96 h. E. meliloti CGMCC 7333 transforms sulfoxaflor into N-(methyl(oxido){1-[6-(trifluoromethyl) pyridin-3-yl] ethyl}-k4-sulfanylidene) urea (X11719474). E. meliloti CGMCC 7333 resting cells (OD600 = 5) transformed 89.36% of the sulfoxaflor in a 200 mg/L solution within 96 h. On inoculating 2 mL of E. meliloti CGMCC 7333 (OD600 = 10) into soil containing 80 mg/kg flonicamid, 91.1% of the flonicamid was transformed within 9 d (half-life 2.6 d). On inoculating 2 mL of E. meliloti CGMCC 7333 (OD600 = 10) into soil containing 80 mg/kg sulfoxaflor, 83.9% of the sulfoxaflor was transformed within 9 d (half-life 3.4 d). Recombinant Escherichia coli harboring the E. meliloti CGMCC 7333 nitrile hydratase (NHase)-encoding gene and NHase both showed the ability to transform flonicamid or sulfoxaflor into their corresponding amides, TFNG-AM and X11719474, respectively. These findings may help develop a bioremediation agent for the elimination of flonicamid and sulfoxaflor contamination.
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Affiliation(s)
- Wenlong Yang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, People's Republic of China
| | - Zhixia Fan
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, People's Republic of China
| | - Huoyong Jiang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, People's Republic of China
| | - Yunxiu Zhao
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, People's Republic of China
| | - Ling Guo
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, People's Republic of China
| | - Yijun Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, People's Republic of China
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Cheng Z, Xia Y, Zhou Z. Recent Advances and Promises in Nitrile Hydratase: From Mechanism to Industrial Applications. Front Bioeng Biotechnol 2020; 8:352. [PMID: 32391348 PMCID: PMC7193024 DOI: 10.3389/fbioe.2020.00352] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 03/30/2020] [Indexed: 12/21/2022] Open
Abstract
Nitrile hydratase (NHase, EC 4.2.1.84) is one type of metalloenzyme participating in the biotransformation of nitriles into amides. Given its catalytic specificity in amide production and eco-friendliness, NHase has overwhelmed its chemical counterpart during the past few decades. However, unclear catalytic mechanism, low thermostablity, and narrow substrate specificity limit the further application of NHase. During the past few years, numerous studies on the theoretical and industrial aspects of NHase have advanced the development of this green catalyst. This review critically focuses on NHase research from recent years, including the natural distribution, gene types, posttranslational modifications, expression, proposed catalytic mechanism, biochemical properties, and potential applications of NHase. The developments of NHase described here are not only useful for further application of NHase, but also beneficial for the development of the fields of biocatalysis and biotransformation.
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Affiliation(s)
| | | | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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