1
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Yang Y, Li X, Li X, Wang J, Song D. Quantitative assessment, molecular docking and novel metabolic pathways reveal the interaction mechanisms between norfloxacin biodegradation and environmental implications. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134521. [PMID: 38718513 DOI: 10.1016/j.jhazmat.2024.134521] [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: 01/12/2024] [Revised: 03/26/2024] [Accepted: 04/30/2024] [Indexed: 05/30/2024]
Abstract
Norfloxacin (NOR) is widely used in medicine and animal husbandry, but its accumulation in the environment poses a substantial threat to ecological and human health. Traditional physical, chemical, and rudimentary biological methods often fall short in mitigating NOR contamination, necessitating innovative biological approaches. This study proposes an engineered bacterial consortium found in marine sediment as a strategy to enhance NOR degradation through inter-strain co-metabolism of diverse substrates. Strategically supplementing the engineered bacterial consortium with exogenous carbon sources and metal ions boosted the activity of key degradation enzymes like laccase, manganese peroxidase, and dehydrogenase. Iron and amino acids demonstrated synergistic effects, resulting in a remarkable 70.8% reduction in NOR levels. The innovative application of molecular docking elucidated enzyme interactions with NOR, uncovering potential biodegradation mechanisms. Quantitative assessment reinforced the efficiency of NOR degradation within the engineered bacterial consortium. Four metabolic routes are herein proposed: acetylation, defluorination, ring scission, and hydroxylation. Notably, this study discloses distinctive, co-operative metabolic pathways for NOR degradation within the specific microbial community. These findings provide new ways of understanding and investigating the bioremediation potential of NOR contaminants, which may lead to the development of more sustainable and effective environmental management strategies.
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Affiliation(s)
- Yuru Yang
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xiong'e Li
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xinyi Li
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Jiaxin Wang
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Donghui Song
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin 300457, China; Key Laboratory of Marine Resource Chemistry and Food Technology (TUST), Ministry of Education, Tianjin 300457, China.
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2
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Łomża P, Krucoń T, Tabernacka A. Potential of Microbial Communities to Perform Dehalogenation Processes in Natural and Anthropogenically Modified Environments-A Metagenomic Study. Microorganisms 2023; 11:1702. [PMID: 37512875 PMCID: PMC10385969 DOI: 10.3390/microorganisms11071702] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/15/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Halogenated organic compounds (HOCs) pose a serious problem for the environment. Many are highly toxic and accumulate both in soil and in organisms. Their biological transformation takes place by dehalogenation, in which the halogen substituents are detached from the carbon in the organic compound by enzymes produced by microorganisms. This increases the compounds' water solubility and bioavailability, reduces toxicity, and allows the resulting compound to become more susceptible to biodegradation. The microbial halogen cycle in soil is an important part of global dehalogenation processes. The aim of the study was to examine the potential of microbial communities inhabiting natural and anthropogenically modified environments to carry out the dehalogenation process. The potential of microorganisms was assessed by analyzing the metagenomes from a natural environment (forest soils) and from environments subjected to anthropopression (agricultural soil and sludge from wastewater treatment plants). Thirteen genes encoding enzymes with dehalogenase activity were identified in the metagenomes of both environments, among which, 2-haloacid dehalogenase and catechol 2,3-dioxygenase were the most abundant genes. Comparative analysis, based on comparing taxonomy, identified genes, total halogens content and content of DDT derivatives, demonstrated the ability of microorganisms to transform HOCs in both environments, indicating the presence of these compounds in the environment for a long period of time and the adaptive need to develop mechanisms for their detoxification. Metagenome analyses and comparative analyses indicate the genetic potential of microorganisms of both environments to carry out dehalogenation processes, including dehalogenation of anthropogenic HOCs.
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Affiliation(s)
- Pola Łomża
- Department of Biology, Faculty of Building Services, Hydro and Environmental Engineering, Warsaw University of Technology, 20 Nowowiejska Street, 00-653 Warsaw, Poland
| | - Tomasz Krucoń
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology, University of Warsaw, 1 Miecznikowa Street, 02-089 Warsaw, Poland
| | - Agnieszka Tabernacka
- Department of Biology, Faculty of Building Services, Hydro and Environmental Engineering, Warsaw University of Technology, 20 Nowowiejska Street, 00-653 Warsaw, Poland
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3
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Oyewusi HA, Akinyede KA, Abdul Wahab R, Huyop F. In silico analysis of a putative dehalogenase from the genome of halophilic bacterium Halomonas smyrnensis AAD6T. J Biomol Struct Dyn 2023; 41:319-335. [PMID: 34854349 DOI: 10.1080/07391102.2021.2006085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Microbial-assisted removal of natural or synthetic pollutants is the prevailing green, low-cost technology to treat polluted environments. However, the challenge with enzyme-assisted bioremediation is the laborious nature of dehalogenase-producing microorganisms' bioprospecting. This bottleneck could be circumvented by in-silico analysis of certain microorganisms' whole-genome sequences to predict their protein functions and enzyme versatility for improved biotechnological applications. Herein, this study performed structural analysis on a dehalogenase (DehHsAAD6) from the genome of Halomonas smyrnensis AAD6 by molecular docking and molecular dynamic (MD) simulations. Other bioinformatics tools were also employed to identify substrate preference (haloacids and haloacetates) of the DehHsAAD6. The DehHsAAD6 preferentially degraded haloacids and haloacetates (-3.2-4.8 kcal/mol) and which formed three hydrogen bonds with Tyr12, Lys46, and Asp182. MD simulations data revealed the higher stability of DehHsAAD6-haloacid- (RMSD 0.22-0.3 nm) and DehHsAAD6-haloacetates (RMSF 0.05-0.14 nm) complexes, with the DehHsAAD6-L-2CP complex being the most stable. The detail of molecular docking calculations ranked complexes with the lowest binding free energies as: DehHsAAD6-L-2CP complex (-4.8 kcal/mol) = DehHsAAD6-MCA (-4.8 kcal/mol) < DehHsAAD6-TCA (-4.5 kcal/mol) < DehHsAAD6-2,3-DCP (-4.1 kcal/mol) < DehHsAAD6-D-2CP (-3.9 kcal/mol) < DehHsAAD6-2,2-DCP (-3.5 kcal/mol) < DehHsAAD6-3CP (-3.2 kcal/mol). In a nutshell, the study findings offer valuable perceptions into the elucidation of possible reaction mechanisms of dehalogenases for extended substrate specificity and higher catalytic activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Department of Science Technology, Biochemistry unit, The Federal Polytechnic P.M.B, Ado Ekiti, Ekiti State, Nigeria
| | - Kolajo Adedamola Akinyede
- Department of Science Technology, Biochemistry unit, The Federal Polytechnic P.M.B, Ado Ekiti, Ekiti State, Nigeria.,Department of Medical Bioscience, University of the Western Cape, Bellville, Cape Town, South Africa
| | - Roswanira Abdul Wahab
- Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
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4
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Li Y, Wang T, Wang Y, Deng Z, Zhang L, Zhu A, Huang Y, Zhang C, Yuan M, Xie W. Tunable Photocatalytic Two-Electron Shuttle between Paired Redox Sites on Halide Perovskite Nanocrystals. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yonglong Li
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Haihe Laboratory of Sustainable Chemical Transformations, Renewable Energy Conversion and Storage Center, College of Chemistry, Nankai University, Weijin Rd. 94, Tianjin 300071, China
| | - Teng Wang
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Haihe Laboratory of Sustainable Chemical Transformations, Renewable Energy Conversion and Storage Center, College of Chemistry, Nankai University, Weijin Rd. 94, Tianjin 300071, China
| | - Ying Wang
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Haihe Laboratory of Sustainable Chemical Transformations, Renewable Energy Conversion and Storage Center, College of Chemistry, Nankai University, Weijin Rd. 94, Tianjin 300071, China
| | - Zhijie Deng
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Li Zhang
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Haihe Laboratory of Sustainable Chemical Transformations, Renewable Energy Conversion and Storage Center, College of Chemistry, Nankai University, Weijin Rd. 94, Tianjin 300071, China
| | - Aonan Zhu
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Haihe Laboratory of Sustainable Chemical Transformations, Renewable Energy Conversion and Storage Center, College of Chemistry, Nankai University, Weijin Rd. 94, Tianjin 300071, China
| | - Yanmin Huang
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Haihe Laboratory of Sustainable Chemical Transformations, Renewable Energy Conversion and Storage Center, College of Chemistry, Nankai University, Weijin Rd. 94, Tianjin 300071, China
| | - Cancan Zhang
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Haihe Laboratory of Sustainable Chemical Transformations, Renewable Energy Conversion and Storage Center, College of Chemistry, Nankai University, Weijin Rd. 94, Tianjin 300071, China
| | - Mingjian Yuan
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Haihe Laboratory of Sustainable Chemical Transformations, Renewable Energy Conversion and Storage Center, College of Chemistry, Nankai University, Weijin Rd. 94, Tianjin 300071, China
| | - Wei Xie
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Haihe Laboratory of Sustainable Chemical Transformations, Renewable Energy Conversion and Storage Center, College of Chemistry, Nankai University, Weijin Rd. 94, Tianjin 300071, China
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5
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Lameh F, Baseer AQ, Ashiru AG. Comparative molecular docking and molecular-dynamic simulation of wild-type- and mutant carboxylesterase with BTA-hydrolase for enhanced binding to plastic. Eng Life Sci 2022; 22:13-29. [PMID: 35024024 PMCID: PMC8727734 DOI: 10.1002/elsc.202100083] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 09/25/2021] [Accepted: 10/10/2021] [Indexed: 01/09/2023] Open
Abstract
According to the literature review, microbial degradation of polyethylene terephthalate by PETases has been detected effective and eco-friendly. However, the number of microorganisms capable of such feats is limited with some undesirable bioprospecting results. BTA-hydrolase has been already reported capable of degrading polyethylene terephthalate. Therefore, mutation by in silico site-directed mutagenesis means to introduce current isomer of PETase for polyethylene terephthalate degradative capability as a better approach to resolve this issue. This study aimed to use in silico site-directed mutagenesis to convert a carboxylesterase from Archaeoglobus fulgidus to BTA-hydrolase from Thermobifida fusca by replacing six amino acids in specific locations. This work was followed by molecular docking analysis with polyethylene terephthalate and polypropylene to compare their interactions. The best-docked enzyme-substrate complex was further subjected to molecular dynamics simulation to gauge the binding quality of the BTA-hydrolase, wild-type and mutant-carboxylesterase with only polyethylene terephthalate as a substrate. Results of molecular docking revealed lowest binding energy for the wild-type carboxylesterase-polypropylene complex (-7.5 kcal/mol). The root-mean-square deviation value was observed stable for BTA-hydrolase. Meanwhile, root-mean-square fluctuation was assessed with higher fluctuation for the mutated residue Lys178. Consequently, the Rg value for BTA-hydrolase-ligand complex (∼1.68 nm) was the lowest compared to the mutant and wild-type carboxylesterase. The collective data conveyed that mutations imparted a minimal change in the ability of the mutant carboxylesterase to bind to polyethylene terephthalate.
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Affiliation(s)
- Fatana Lameh
- Department of BotanyFaculty of BiologyKabul UniversityKabulAfghanistan
- Department of BiosciencesFaculty of ScienceUniversiti Teknologi MalaysiaJohor BahruMalaysia
| | - Abdul Qadeer Baseer
- Department of BiosciencesFaculty of ScienceUniversiti Teknologi MalaysiaJohor BahruMalaysia
- Department of BiologyFaculty of EducationKandahar UniversityKandaharAfghanistan
| | - Abubakar Garba Ashiru
- Department of ChemistryZamfara State College of EducationMaruNigeria
- Green Chemistry Research GroupDepartment of Chemistry, Faculty of ScienceUniversiti Teknologi MalaysiaJohor BahruMalaysia
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6
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Jin LQ, Jin YT, Zhang JW, Liu ZQ, Zheng YG. Enhanced catalytic efficiency and thermostability of glucose isomerase from Thermoanaerobacter ethanolicus via site-directed mutagenesis. Enzyme Microb Technol 2021; 152:109931. [PMID: 34688091 DOI: 10.1016/j.enzmictec.2021.109931] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 09/26/2021] [Accepted: 10/02/2021] [Indexed: 10/20/2022]
Abstract
Glucose isomerase (GI) is a key enzyme in the preparation of high fructose corn syrup (HFCS). In this study, a mutant TEGI-M-L38 M/V137 L (TEGI-M2) of glucose isomerase (TEGI-M) originated from Thermoanaerobacter ethanalicus CCSD1 was obtained by site-directed mutagenesis. The TEGI-M2 showed an optimal activity at 85 ℃ and pH 6.5 with the divalent cations Co2+ and Mg2+. The structural differences between TEGI-M and TEGI-M2 were investigated based on the homology modeling and molecular docking, to elucidate the mechanism of improvement in the enzymatic properties. Compared with the original enzyme, the TEGI-M2 showed a 2.0-fold increased enzyme activity and a decreased Km from 234.2 mM to 85.9 mM. Finally, the application of mutant TEGI-M2 in HFCS one-step biosynthesis was attempted, resulting in a d-fructose yield of 67.3 %, which was 14.3 % higher than that of TEGI-M. This improved catalytic performance of TEGI-M2 was of great importance for the industrial preparation of d-fructose in one-step process.
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Affiliation(s)
- Li-Qun Jin
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, PR China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Yi-Ting Jin
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, PR China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Jing-Wei Zhang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, PR China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Zhi-Qiang Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, PR China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China.
| | - Yu-Guo Zheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, PR China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China
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7
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Hu J, Zhang Y, Wu Y, Zheng J, Yu Z, Qian H, Yu J, Cheng Z, Chen J. Heterologous expression of bacterial cytochrome P450 from Microbacterium keratanolyticum ZY and its application in dichloromethane dechlorination. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 287:117597. [PMID: 34167002 DOI: 10.1016/j.envpol.2021.117597] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/20/2021] [Accepted: 06/12/2021] [Indexed: 06/13/2023]
Abstract
Dichloromethane (DCM) is a volatile halogenated hydrocarbon with teratogenic, mutagenic and carcinogenic effects. Biodegradation is generally regarded as an effective and economical approach of pollutant disposal. In this study, a novel strain was isolated and its cytochrome P450 was heterologously expressed for DCM degradation. The isolate, Microbacterium keratanolyticum ZY, was characterized as a Gram-positive, rod-shaped and flagella-existed bacterium without spores (GenBank No. SUB8814364; CCTCC M 2019953). After successive whole-genome sequencing, assembly and annotation, eight identified functional genes (encoding cytochrome P450, monooxygenase, dehalogenase and hydrolase) were successfully cloned and expressed in Escherichia coli BL21 (DE3). The recombinant strain expressing cytochrome P450 presented the highest degradation efficiency (90.6%). Moreover, the specific activity of the recombinant cytochrome P450 was more than 1.2 times that of the recombinant dehalogenase (from Methylobacterium rhodesianum H13) under their optimum conditions. The kinetics of DCM degradation by recombinant cytochrome P450 was well fitted with the Haldane model and the value of maximum specific degradation rate was determined to be 0.7 s-1. The DCM degradation might occur through successive hydroxylation, dehydrohalogenation, dechlorination and oxidation to generate gem-halohydrin, formyl chloride, formaldehyde and formic acid. The study helps to comprehensively understand the DCM dechlorination process under the actions of bacterial functional enzymes (cytochrome P450 and dehalogenase).
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Affiliation(s)
- Jun Hu
- College of Environment, Zhejiang University of Technology, 18 Chao-wang Road, Hangzhou, 310014, China
| | - Yan Zhang
- College of Environment, Zhejiang University of Technology, 18 Chao-wang Road, Hangzhou, 310014, China
| | - Yuexin Wu
- Zhejiang Haihe Environmental Technology Co., Ltd., 1389 Danxi Road, Jinhua, 321000, China
| | - Jiajun Zheng
- College of Environment, Zhejiang University of Technology, 18 Chao-wang Road, Hangzhou, 310014, China
| | - Zhiliang Yu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chao-wang Road, Hangzhou, 310014, China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, 18 Chao-wang Road, Hangzhou, 310014, China
| | - Jianming Yu
- College of Environment, Zhejiang University of Technology, 18 Chao-wang Road, Hangzhou, 310014, China.
| | - Zhuowei Cheng
- College of Environment, Zhejiang University of Technology, 18 Chao-wang Road, Hangzhou, 310014, China
| | - Jianmeng Chen
- College of Environment, Zhejiang University of Technology, 18 Chao-wang Road, Hangzhou, 310014, China
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8
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Zhao T, Yong X, Zhao Z, Dolce V, Li Y, Curcio R. Research status of Bacillus phytase. 3 Biotech 2021; 11:415. [PMID: 34485008 DOI: 10.1007/s13205-021-02964-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/27/2021] [Indexed: 10/20/2022] Open
Abstract
Phytic acid is abundant in seeds, roots and stems of plants, it acts as an anti-nutrient in food and feed industry, since it affects the absorption of nutrients by humans and monogastric animals. Furthermore, phosphorus produced through its decomposition by microorganisms can cause environmental pollution. Phytase degrades phytic acid generating precursors of inositol that can be used in clinical practice; in addition, phytase treatment can minimize the anti-nutritional effect of phytic acid. The use of phytase synthesized from Bacillus is more advantageous due to its high activity. Additionally, its good heat resistance under neutral conditions greatly fills the gap of commercial utilization of acid phytase. In this review, we summarize the latest research results on Bacillus phytase, including its physiological and biochemical characteristics, molecular structure information, calcium effects on its catalytic activity and stability, its catalytic mechanism and molecular modification.
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Affiliation(s)
- Ting Zhao
- College of Life Science and Technology, Xinjiang University, Urumqi, China
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, China
| | - Xihao Yong
- College of Life Science and Technology, Xinjiang University, Urumqi, China
- Faculty of Bioengineering, Sichuan University of Science and Engineering, Zigong, People's Republic of China
| | - Ziming Zhao
- Faculty of Bioengineering, Sichuan University of Science and Engineering, Zigong, People's Republic of China
| | - Vincenza Dolce
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Yuan Li
- College of Life Science and Technology, Xinjiang University, Urumqi, China
- Department of Bioscience, Biotechnology and Biopharmaceutics, University of Bari, Bari, Italy
| | - Rosita Curcio
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
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Oyewusi HA, Huyop F, Wahab RA. Molecular docking and molecular dynamics simulation of Bacillus thuringiensis dehalogenase against haloacids, haloacetates and chlorpyrifos. J Biomol Struct Dyn 2020; 40:1979-1994. [PMID: 33094694 DOI: 10.1080/07391102.2020.1835727] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The high dependency and surplus use of agrochemical products have liberated enormous quantities of toxic halogenated pollutants into the environment and threaten the well-being of humankind. Herein, this study performed molecular docking, molecular dynamic (MD) simulations, molecular mechanics-Poisson Boltzmann Surface Area (MM-PBSA) calculations on the DehH2 from Bacillus thuringiensis, to identify the order of which the enzyme degrades different substrates, haloacids, haloacetate and chlorpyrifos. The study discovered that the DehH2 favored the degradation of haloacids and haloacetates (-3.3 - 4.6 kcal/mol) and formed three hydrogen bonds with Asp125, Arg201 and Lys202. Despite the inconclusive molecular docking result, chlorpyrifos was consistently shown to be the least favored substrate of the DehH2 in MD simulations and MM-PBSA calculations. Results of MD simulations revealed the DehH2-haloacid- (RMSD 0.15 - 0.25 nm) and DehH2-haloacetates (RMSF 0.05 - 0.25 nm) were more stable, with the DehH2-L-2CP complex being the most stable while the least was the DehH2-chlorpyrifos (RMSD 0.295 nm; RMSF 0.05 - 0.59 nm). The Molecular Mechanics Poisson-Boltzmann Surface Area calculations showed the DehH2-L-2CP complex (-24.27 kcal/mol) having the lowest binding energy followed by DehH2-MCA (-22.78 kcal/mol), DehH2-D-2CP (-21.82 kcal/mol), DehH2-3CP (-21.11 kcal/mol), DehH2-2,2-DCP (-18.34 kcal/mol), DehH2-2,3-DCP (-8.34 kcal/mol), DehH2-TCA (-7.62 kcal/mol), while chlorpyrifos was unable to spontaneously bind to DehH2 (+127.16 kcal/mol). In a nutshell, the findings of this study offer valuable insights into the rational tailoring of the DehH2 for expanding its substrate specificity and catalytic activity in the near future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, Ado Ekiti PMB, Ekiti State, Nigeria
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Roswanira Abdul Wahab
- Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
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10
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Ni J, Liu Y, Shen C, Chen D, Xin Y, Liu Q. Bioinformatics, bacterial expression and enzyme activity analyses of dichloromethane dehalogenase from Methylobacterium rhodesianum H13. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1818622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Jianguo Ni
- Department of Environmental Engineering, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, Zhejiang, PR China
- Department of Linpu Environmental Protection, Hangzhou Ecological Environment Bureau of Xiaoshan Branch, Hangzhou, Zhejiang, PR China
| | - Ying Liu
- Department of Environmental Engineering, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, Zhejiang, PR China
| | - Chenjia Shen
- Department of Environmental Engineering, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, Zhejiang, PR China
| | - Dongzhi Chen
- Department of Environmental Engineering, College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang, PR China
| | - Yueyong Xin
- Department of Environmental Engineering, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, Zhejiang, PR China
| | - Qi Liu
- Department of Environmental Engineering, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, Zhejiang, PR China
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