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Li X, Yu H, Liu S, Ma B, Wu X, Zheng X, Xu Y. Discovery, characterization and mechanism of a Microbacterium esterase for key d-biotin chiral intermediate synthesis. BIORESOUR BIOPROCESS 2024; 11:59. [PMID: 38879848 PMCID: PMC11180644 DOI: 10.1186/s40643-024-00776-2] [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: 02/27/2024] [Accepted: 06/07/2024] [Indexed: 06/19/2024] Open
Abstract
Esterases are crucial biocatalysts in chiral compound synthesis. Herein, a novel esterase EstSIT01 belonging to family V was identified from Microbacterium chocolatum SIT101 through genome mining and phylogenetic analysis. EstSIT01 demonstrated remarkable efficiency in asymmetrically hydrolyzing meso-dimethyl ester [Dimethyl cis-1,3-Dibenzyl-2-imidazolidine-4,5-dicarboxyate], producing over 99% yield and 99% enantiomeric excess (e.e.) for (4S, 5R)-monomethyl ester, a crucial chiral intermediate during the synthesis of d-biotin. Notably, the recombinant E. coli expressing EstSIT01 exhibited over 40-fold higher activity than that of the wild strain. EstSIT01 displays a preference for short-chain p-NP esters. The optimal temperature and pH were 45 °C and 10.0, with Km and kcat values of 0.147 mmol/L and 5.808 s- 1, respectively. Molecular docking and MD simulations suggest that the high stereoselectivity for meso-diester may attribute to the narrow entrance tunnel and unique binding pocket structure. Collectively, EstSIT01 holds great potential for preparing chiral carboxylic acids and esters.
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Affiliation(s)
- Xinjia Li
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 100 Haiquan Road, Shanghai, 201418, China
- Xianghu Laboratory, Hangzhou, 311231, China
| | - Haoran Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Shengli Liu
- Shandong Lonct Enzymes Co., Ltd, Linyi, 276400, China
| | - Baodi Ma
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 100 Haiquan Road, Shanghai, 201418, China
| | - Xiaomei Wu
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 100 Haiquan Road, Shanghai, 201418, China
| | - Xuesong Zheng
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, 100 Haiquan Road, Shanghai, 201418, China
| | - Yi Xu
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 100 Haiquan Road, Shanghai, 201418, China.
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Ninck S, Klaus T, Kochetkova TV, Esser SP, Sewald L, Kaschani F, Bräsen C, Probst AJ, Kublanov IV, Siebers B, Kaiser M. Environmental activity-based protein profiling for function-driven enzyme discovery from natural communities. ENVIRONMENTAL MICROBIOME 2024; 19:36. [PMID: 38831353 PMCID: PMC11145796 DOI: 10.1186/s40793-024-00577-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 05/06/2024] [Indexed: 06/05/2024]
Abstract
BACKGROUND Microbial communities are important drivers of global biogeochemical cycles, xenobiotic detoxification, as well as organic matter decomposition. Their major metabolic role in ecosystem functioning is ensured by a unique set of enzymes, providing a tremendous yet mostly hidden enzymatic potential. Exploring this enzymatic repertoire is therefore not only relevant for a better understanding of how microorganisms function in their natural environment, and thus for ecological research, but further turns microbial communities, in particular from extreme habitats, into a valuable resource for the discovery of novel enzymes with potential applications in biotechnology. Different strategies for their uncovering such as bioprospecting, which relies mainly on metagenomic approaches in combination with sequence-based bioinformatic analyses, have emerged; yet accurate function prediction of their proteomes and deciphering the in vivo activity of an enzyme remains challenging. RESULTS Here, we present environmental activity-based protein profiling (eABPP), a multi-omics approach that extends genome-resolved metagenomics with mass spectrometry-based ABPP. This combination allows direct profiling of environmental community samples in their native habitat and the identification of active enzymes based on their function, even without sequence or structural homologies to annotated enzyme families. eABPP thus bridges the gap between environmental genomics, correct function annotation, and in vivo enzyme activity. As a showcase, we report the successful identification of active thermostable serine hydrolases from eABPP of natural microbial communities from two independent hot springs in Kamchatka, Russia. CONCLUSIONS By reporting enzyme activities within an ecosystem in their native state, we anticipate that eABPP will not only advance current methodological approaches to sequence homology-guided enzyme discovery from environmental ecosystems for subsequent biocatalyst development but also contributes to the ecological investigation of microbial community interactions by dissecting their underlying molecular mechanisms.
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Affiliation(s)
- Sabrina Ninck
- Chemical Biology, Centre of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany.
| | - Thomas Klaus
- Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany
| | - Tatiana V Kochetkova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Prospekt 60-Let Oktyabrya 7-2, Moscow, 117312, Russia
| | - Sarah P Esser
- Environmental Metagenomics, Research Centre One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany
| | - Leonard Sewald
- Chemical Biology, Centre of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Farnusch Kaschani
- Chemical Biology, Centre of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Christopher Bräsen
- Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany
| | - Alexander J Probst
- Environmental Metagenomics, Research Centre One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany
- Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
- Centre of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Prospekt 60-Let Oktyabrya 7-2, Moscow, 117312, Russia
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany.
| | - Markus Kaiser
- Chemical Biology, Centre of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany.
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Tanveer S, Ilyas N, Akhtar N, Akhtar N, Bostan N, Hasnain Z, Niaz A, Zengin G, Gafur A, Fitriatin BN. Unlocking the interaction of organophosphorus pesticide residues with ecosystem: Toxicity and bioremediation. ENVIRONMENTAL RESEARCH 2024; 249:118291. [PMID: 38301757 DOI: 10.1016/j.envres.2024.118291] [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: 10/10/2023] [Revised: 12/28/2023] [Accepted: 01/20/2024] [Indexed: 02/03/2024]
Abstract
Organophosphorus adulteration in the environment creates terrestrial and aquatic pollution. It causes acute and subacute toxicity in plants, humans, insects, and animals. Due to the excessive use of organophosphorus pesticides, there is a need to develop environmentally friendly, economical, and bio-based strategies. The microbiomes, that exist in the soil, can reduce the devastating effects of organophosphates. The use of cell-free enzymes and yeast is also an advanced method for the degradation of organophosphates. Plant-friendly bacterial strains, that exist in the soil, can help to degrade these contaminants by oxidation-reduction reactions, enzymatic breakdown, and adsorption. The bacterial strains mostly from the genus Bacillus, Pseudomonas, Acinetobacter, Agrobacterium, and Rhizobium have the ability to hydrolyze the bonds of organophosphate compounds like profenofos, quinalphos, malathion, methyl-parathion, and chlorpyrifos. The native bacterial strains also promote the growth abilities of plants and help in detoxification of organophosphate residues. This bioremediation technique is easy to use, relatively cost-effective, very efficient, and ensures the safety of the environment. This review covers the literature gap by describing the major effects of organophosphates on the ecosystem and their bioremediation by using native bacterial strains.
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Affiliation(s)
- Sadaf Tanveer
- Department of Botany, PMAS Arid Agriculture University Rawalpindi, Pakistan.
| | - Noshin Ilyas
- Department of Botany, PMAS Arid Agriculture University Rawalpindi, Pakistan.
| | - Nosheen Akhtar
- Department of Botany, PMAS Arid Agriculture University Rawalpindi, Pakistan.
| | - Nazish Akhtar
- Department of Botany, PMAS Arid Agriculture University Rawalpindi, Pakistan.
| | - Nageen Bostan
- Department of Botany, PMAS Arid Agriculture University Rawalpindi, Pakistan.
| | - Zuhair Hasnain
- Department of Agronomy, PMAS Arid Agriculture University Rawalpindi, Pakistan.
| | - Abdullah Niaz
- Pesticide Residue Laboratory, Institute of Soil Chemistry & Environmental Sciences, Kala Shah Kaku, Punjab, Pakistan.
| | - Gokhan Zengin
- Department of Biology, Science Faculty, Selcuk University, 42130, Konya, Turkey.
| | - Abdul Gafur
- Sinarmas Forestry Corporate Research and Development, Perawang, 28772, Indonesia.
| | - Betty Natalie Fitriatin
- Department of Soil Science and Land Resouces Management, Agriculture Faculty, Universitas Padjadjaran, Indonesia.
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Ghosh D, Yadav S, Bag S, Mallick AI, De P. Antibacterial activity of hydrophobicity modulated cationic polymers with enzyme and pH-responsiveness. J Mater Chem B 2024; 12:2894-2904. [PMID: 38436419 DOI: 10.1039/d3tb02801a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
The membrane lipid compositions of prokaryotic and eukaryotic cells are inherently different in many aspects, although some similarities exist in their structure and composition. Therefore, selective targeting of membrane lipids with a compound of therapeutic value, such as an antibacterial copolymer, is often challenging. Hence, developing an ideal copolymer with antibacterial properties demands hydrophobicity/hydrophilicity balance with a high biosafety profile. To integrate hydrophobic/hydrophilic balance and cationic charge in an alternating antibacterial copolymer with enzyme and pH-responsiveness, a lysine appended styrenic monomer was copolymerized with a fatty acid (octanoic acid (OA) or myristic acid (MA)) tethered maleimide monomer via reversible addition-fragmentation chain transfer (RAFT) polymerization. A range of microscopic analyses, including dynamic light scattering (DLS), confirmed the formation of nanoaggregates (size ∼30-40 nm) by these polymers in aqueous solution with positive zeta potential (cationic surface charge). Hydrophobic Nile red (NR) dye was successfully encapsulated in the nanoaggregates, and the in vitro release kinetics of the NR dye were monitored at different pHs and in the presence or absence of esterase/lipase. The in vitro release kinetics of NR revealed ∼85% dye release in the presence of pH 5.5 and lipase, suggesting their suitability for pH/enzyme-triggered therapeutic payload delivery. The standard broth microdilution assay showed significant bactericidal activity against both Gram-positive (Bacillus subtilis) and Gram-negative (Escherichia coli) bacteria with an MIC50 value <30 μg mL-1. The effect of polymeric nanoaggregates on bacterial morphology and in vitro survival was further confirmed by field emission scanning electron microscopy (FESEM), agar gel disk diffusion assay, and bacterial live/dead cell count. The significantly low hemolytic activity against red blood cells (RBCs) (HC50 >103 μg mL-1) and nontoxic effect on human intestinal epithelial cells (INT 407) (EC50 >500 μg mL-1) ensure that the polymer nanoaggregates are safe for in vivo use and can serve as a potent antibacterial polymer.
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Affiliation(s)
- Desoshree Ghosh
- Polymer Research Centre and Centre for Advanced Functional Materials, Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal 741246, India.
| | - Sandeep Yadav
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal 741246, India.
| | - Sagar Bag
- Polymer Research Centre and Centre for Advanced Functional Materials, Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal 741246, India.
| | - Amirul Islam Mallick
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal 741246, India.
| | - Priyadarsi De
- Polymer Research Centre and Centre for Advanced Functional Materials, Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal 741246, India.
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Yang H, Yu H, Stolarzewicz IA, Tang W. Enantioselective Transformations in the Synthesis of Therapeutic Agents. Chem Rev 2023; 123:9397-9446. [PMID: 37417731 DOI: 10.1021/acs.chemrev.3c00010] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
The proportion of approved chiral drugs and drug candidates under medical studies has surged dramatically over the past two decades. As a consequence, the efficient synthesis of enantiopure pharmaceuticals or their synthetic intermediates poses a profound challenge to medicinal and process chemists. The significant advancement in asymmetric catalysis has provided an effective and reliable solution to this challenge. The successful application of transition metal catalysis, organocatalysis, and biocatalysis to the medicinal and pharmaceutical industries has promoted drug discovery by efficient and precise preparation of enantio-enriched therapeutic agents, and facilitated the industrial production of active pharmaceutical ingredient in an economic and environmentally friendly fashion. The present review summarizes the most recent applications (2008-2022) of asymmetric catalysis in the pharmaceutical industry ranging from process scales to pilot and industrial levels. It also showcases the latest achievements and trends in the asymmetric synthesis of therapeutic agents with state of the art technologies of asymmetric catalysis.
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Affiliation(s)
- He Yang
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Hanxiao Yu
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Izabela A Stolarzewicz
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Wenjun Tang
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
- School of Chemistry and Material Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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6
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Cheng J, Du H, Zhou MS, Ji Y, Xie YQ, Huang HB, Zhang SH, Li F, Xiang L, Cai QY, Li YW, Li H, Li M, Zhao HM, Mo CH. Substrate-enzyme interactions and catalytic mechanism in a novel family VI esterase with dibutyl phthalate-hydrolyzing activity. ENVIRONMENT INTERNATIONAL 2023; 178:108054. [PMID: 37354883 DOI: 10.1016/j.envint.2023.108054] [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: 03/11/2023] [Revised: 05/19/2023] [Accepted: 06/17/2023] [Indexed: 06/26/2023]
Abstract
Microbial degradation has been confirmed as effective and environmentally friendly approach to remediate phthalates from the environment, and hydrolase is an effective element for contaminant degradation. In the present study, a novel dibutyl phthalate (DBP)-hydrolyzing carboxylesterase (named PS06828) from Pseudomonas sp. PS1 was heterogeneously expressed in E. coli, which was identified as a new member of the lipolytic family VI. Purified PS06828 could efficiently degrade DBP with a wide range of temperature (25-37 °C) and pH (6.5-9.0). Multi-spectroscopy methods combined with molecular docking were employed to study the interaction of PS06828 with DBP. Fluorescence and UV-visible absorption spectra revealed the simultaneous presence of static and dynamic component in the fluorescence quenching of PS06828 by DBP. Synchronous fluorescence and circular dichroism spectra showed inconspicuous alteration in micro-environmental polarity around amino acid residues but obvious increasing of α-helix and reducing of β-sheet and random coil in protein conformation. Based on the information on exact binding sites of DBP on PS06828 provided by molecular docking, the catalytic mechanism mediated by key residues (Ser113, Asp166, and His197) was proposed and subsequently confirmed by site-directed mutagenesis. The results can strengthen our mechanistic understanding of family VI esterase involved in hydrolysis of phthalic acid esters, and provide a solid foundation for further enzymatic modification.
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Affiliation(s)
- Jiliang Cheng
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Huan Du
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China; Guangzhou Customs Technology Center, No. 66 Huacheng Avenue, Tianhe District, Guangzhou, China
| | - Meng-Sha Zhou
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yuan Ji
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - You-Qun Xie
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - He-Biao Huang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Shu-Hui Zhang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Fen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Lei Xiang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Quan-Ying Cai
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yan-Wen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Hui Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Meng Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Hai-Ming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| | - Ce-Hui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
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7
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Role of N-Terminal Extensional Long α-Helix in the Arylesterase from Lacticaseibacillus rhamnosus GG on Catalysis and Stability. Catalysts 2023. [DOI: 10.3390/catal13020441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023] Open
Abstract
In the α/β hydrolases superfamily, the extra module modulated enzymatic activity, substrate specificity, and stability. The functional role of N-terminal extensional long α-helix (Ala2-Glu29, designated as NEL-helix) acting as the extra module in the arylesterase LggEst from Lacticaseibacillus rhamnosus GG had been systemically investigated by deletion mutagenesis, biochemical characterization, and biophysical methods. The deletion of the NEL-helix did not change the overall structure of this arylesterase. The deletion of the NEL-helix led to the shifting of optimal pH into the acidity and the loss of thermophilic activity. The deletion of the NEL-helix produced a 10.6-fold drop in catalytic activity towards the best substrate pNPC10. NEL-Helix was crucial for the thermostability, chemical resistance, and organic solvents tolerance. The deletion of the NEL-helix did not change the overall rigidity of enzyme structure and only reduced the local rigidity of the active site. Sodium deoxycholate might partially replenish the loss of activity caused by the deletion of the NEL-helix. Our research further enriched the functional role of the extra module on catalysis and stability in the α/β hydrolase fold superfamily.
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Lai Y, Zhang T, Huang L, Li W, Lin W. Monitoring cell viability in N-nitrosodiethylamine induced acute hepatitis and detection of hydrazine in solution and gas phase with Dual-function fluorescent probes. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130207. [PMID: 36332275 DOI: 10.1016/j.jhazmat.2022.130207] [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: 08/11/2022] [Revised: 09/30/2022] [Accepted: 10/15/2022] [Indexed: 06/16/2023]
Abstract
The highly toxic N-nitrosodiethylamine (NDEA) and hydrazine (N2H4) caused severe environmental contamination and serious health risks. Herein, we designed the two-photon ratiometric fluorescent probe (Nap-2), emission maximum shifted from 466 nm to 571 nm, to monitor cell viability of NDEA induced acute hepatitis via esterase activity detection. Furthermore, the probe Nap-2 evaluate the hydrazine (N2H4) content in the solution and gas phase. It is worth mentioning that we used NDEA induced acute hepatitis in the mice and evaluated the negative correlation of esterase activity in the tissue cells and serum with Nap-2. The probe Nap-2 exhibited that acute hepatitis induced by NDEA decreased cell viability. Furthermore, we made convenient test papers using Nap-2 to detect N2H4 in solution and gas phase. After adding N2H4, the fluorescence color changed from blue to yellow and was visible to the naked eye. This work provides a convenient tool and method for evaluating the toxicity of NDEA induced acute hepatitis and detecting N2H4 in the environment.
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Affiliation(s)
- Youbo Lai
- Guangxi Key Laboratory of Electrochemical Energy Materials, Institute of Optical Materials and Chemical Biology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, PR China
| | - Tengteng Zhang
- Guangxi Key Laboratory of Electrochemical Energy Materials, Institute of Optical Materials and Chemical Biology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, PR China
| | - Ling Huang
- Guangxi Key Laboratory of Electrochemical Energy Materials, Institute of Optical Materials and Chemical Biology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, PR China
| | - Wenxiu Li
- Guangxi Key Laboratory of Electrochemical Energy Materials, Institute of Optical Materials and Chemical Biology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, PR China
| | - Weiying Lin
- Guangxi Key Laboratory of Electrochemical Energy Materials, Institute of Optical Materials and Chemical Biology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, PR China.
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9
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Paz A, Zerva A, Topakas E. Evaluation of olive mill wastewater as culture medium to produce lipolytic enzymes by Bacillus aryabhattai BA03. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2023. [DOI: 10.1016/j.bcab.2023.102643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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10
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Application of Milk Permeate as an Inducer for the Production of Microbial Recombinant Lipolytic Enzymes. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation9010027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Recombinantly produced enzymes are applied in many fields, ranging from medicine to food and nutrition, production of detergents, textile, leather, paper, pulp, and plastics. Thus, the cost-effectiveness of recombinant enzyme synthesis is an important issue in biotechnological industry. Isopropyl-β-D-thiogalactoside (IPTG), an analog of lactose, is currently the most widely used chemical agent for the induction of recombinant enzyme synthesis. However, the use of IPTG can lead to production of toxic elements and can introduce physiological stress to cells. Thus, this study aims to find a simpler, cheaper, and safer way to produce recombinant enzymes. In this study, production of several previously designed recombinant lipolytic enzymes (GDEst-95 esterase, GD-95RM lipase, fused GDEst-lip lipolytic enzyme, and putative cutinase Cut+SP from Streptomyces scabiei 87.22) is induced in E. coli BL21 (DE3) using 4 mM milk permeate, a type of waste of the milk manufacturing process possessing >82% lactose. The SDS-PAGE analysis clearly indicates synthesis of all target enzymes during a 2–12 h post-induction timeframe. Further investigation of GDEst-95, GD-95RM, GDEst-lip, and Cut+SP biocatalysts was carried out spectrophotometrically and using zymography method, confirming production of fully active enzymes.
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11
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Nazarian Z, Arab SS. Discovery of carboxylesterases via metagenomics: Putative enzymes that contribute to chemical kinetic resolution. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.07.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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12
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Nagaroor V, Gummadi SN. An overview of mammalian and microbial hormone-sensitive lipases (lipolytic family IV): biochemical properties and industrial applications. Biotechnol Genet Eng Rev 2022:1-30. [PMID: 36154870 DOI: 10.1080/02648725.2022.2127071] [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: 06/20/2022] [Accepted: 09/13/2022] [Indexed: 11/02/2022]
Abstract
In mammals, hormone-sensitive lipase (EC 3.1.1.79) is an intracellular lipase that significantly regulates lipid metabolism. Mammalian HSL is more active towards diacylglycerol but lacks a lid covering the active site. Dyslipidemia, hepatic steatosis, cancer, and cancer-associated cachexia are symptoms of HSL pathophysiology. Certain microbial proteins show a sequence homologous to the catalytic domain of mammalian HSL, hence called microbial HSL. They possess a funnel-shaped substrate-binding pocket and restricted length of acyl chain esters, thus known as esterases. These enzymes have broad substrate specificities and are capable of stereo, regio, and enantioselective, making them attractive biocatalysts in a wide range of industrial applications in the production of flavors, pharmaceuticals, biosensors, and fine chemicals. This review will provide insight into mammalian and microbial HSLs, their sources, structural features related to substrate specificity, thermal stability, and their applications.
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Affiliation(s)
- Vijayalakshmi Nagaroor
- Applied and Industrial Microbiology laboratory (AIM lab), Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Sathyanarayana N Gummadi
- Applied and Industrial Microbiology laboratory (AIM lab), Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
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Matrawy AA, Khalil AI, Embaby AM. Molecular study on recombinant cold-adapted, detergent- and alkali stable esterase (EstRag) from Lysinibacillus sp.: a member of family VI. World J Microbiol Biotechnol 2022; 38:217. [PMID: 36070019 PMCID: PMC9452428 DOI: 10.1007/s11274-022-03402-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/26/2022] [Indexed: 11/30/2022]
Abstract
Cold-adapted esterases have potential industrial applications. To fulfil the global continuous demand for these enzymes, a cold-adapted esterase member of family VI from Lysinibacillus sp. YS11 was cloned on pET-28b (+) vector and expressed in E. coli BL21(DE3) Rosetta cells for the first time. The open reading frame (654 bp: GenBank MT120818.1) encodes a polypeptide (designated EstRag: 217 amino acid residues). EstRag amino acid sequence has conserved esterase signature motifs: pentapeptide (GFSQG) and catalytic triad Ser110-Asp163-His194. EstRag 3D predicted model, built with LOMETS3 program, showed closest structural similarity to PDB 1AUO_A (esterase: Pseudomonas fluorescens); TM-align score program inferences. Purified EstRag to 9.28-fold, using Ni2+affinity agarose matrix, showed a single protein band (25 kDa) on SDS-PAGE, Km (0.031 mM) and Kcat/Km (657.7 s−1 mM−1) on p-NP-C2. Temperature and pH optima of EstRag were 35 °C and 8.0, respectively. EstRag was fully stable at 5–30 °C for 120 min and at pH(s) 8.0–10.0 after 24 h. EstRag activity (391.46 ± 0.009%) was impressively enhanced after 30 min preincubation with 5 mM Cu2+. EstRag retained full stability after 30 min pre-incubation with 0.1%(v/v) SDS, Triton X-100, and Tween-80. EstRag promising characteristics motivate performing guided evolution and industrial applications prospective studies.
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Affiliation(s)
- Amira A Matrawy
- Environmental Studies Department, Institute of Graduate Studies and Research, Alexandria University, 163 Horreya Avenue, P.O. Box 832, Chatby, 21526, Alexandria, Egypt
| | - Ahmed I Khalil
- Environmental Studies Department, Institute of Graduate Studies and Research, Alexandria University, 163 Horreya Avenue, P.O. Box 832, Chatby, 21526, Alexandria, Egypt
| | - Amira M Embaby
- Biotechnology Department, Institute of Graduate Studies and Research, Alexandria University, 163 Horreya Avenue, P.O. Box 832, Chatby, 21526, Alexandria, Egypt.
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14
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Soumya P, Kochupurackal J. An Esterase with Increased Acetone Tolerance from Bacillus subtilis E9 over Expressed in E. coli BL21 Using pTac Bs-est Vector. Mol Biotechnol 2022; 64:814-824. [PMID: 35137334 DOI: 10.1007/s12033-022-00458-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 01/30/2022] [Indexed: 02/06/2023]
Abstract
Bacillus subtilis E9 was identified as a potential strain producing esterase. The gene coding esterase from B. subtilis E9 was amplified using esterase-specific primers and the sequence was translated in silico. The presence of conserved catalytic triad amino acid residues (His-Ser-Asp/Glu) confirmed the functional nature of the esterase enzyme. Docking studies conducted with modeled protein and the ligand p-nitrophenyl acetate showed that the amino acid residues interacting with the ligand were Ser77, His76, and Gly103. The gene coding for esterase from B. subtilis E9 was cloned into an assembled vector having Tac promoter (pTac), pUC origin of replication, Ni-Histidine residues, ampicillin cassette, and T7 terminator using Golden gate DNA assembly method. The generated pTac Bs-est (4598 bp) recombinant plasmid was transformed and heterologously expressed in Escherichia coli BL21 (DE3) strain. The tagged recombinant protein was purified to yield 43.4% pure protein with specific activity of 772 U/mg. The purified recombinant protein was subjected to peptide sequencing and the identity was confirmed as esterase by peptide tandem mass fragmentation method using the LC-MS/MS analysis. The purified recombinant esterase was found to be organic solvent stable and tolerant up to 5 days retaining around 95% residual activity in 30-90% v/v Acetone. The recombinant esterase expressed in our study was found to exhibit better organic solvent stability and tolerance than compared to the original bacterial esterase from B. subtilis E9, a property which could be explored in the biocatalytic and synthetic transformation reactions for industrial applications.
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Affiliation(s)
- P Soumya
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala, 686560, India
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15
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Zhang H, Cheng Z, Wei L, Yu X, Wang Z, Zhang Y. Semi-rational protein engineering of a novel esterase from Bacillus aryabhattai (BaCE) for resolution of (R,S)-ethyl indoline-2-carboxylate to prepare (S)-indoline-2-carboxylic acid. Bioorg Chem 2022; 120:105602. [DOI: 10.1016/j.bioorg.2022.105602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/12/2021] [Accepted: 01/04/2022] [Indexed: 11/25/2022]
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16
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Jones K, Snodgrass HM, Belsare K, Dickinson BC, Lewis JC. Phage-Assisted Continuous Evolution and Selection of Enzymes for Chemical Synthesis. ACS CENTRAL SCIENCE 2021; 7:1581-1590. [PMID: 34584960 PMCID: PMC8461764 DOI: 10.1021/acscentsci.1c00811] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Indexed: 05/04/2023]
Abstract
Ligand-dependent biosensors are valuable tools for coupling the intracellular concentrations of small molecules to easily detectable readouts such as absorbance, fluorescence, or cell growth. While ligand-dependent biosensors are widely used for monitoring the production of small molecules in engineered cells and for controlling or optimizing biosynthetic pathways, their application to directed evolution for biocatalysts remains underexplored. As a consequence, emerging continuous evolution technologies are rarely applied to biocatalyst evolution. Here, we develop a panel of ligand-dependent biosensors that can detect a range of small molecules. We demonstrate that these biosensors can link enzymatic activity to the production of an essential phage protein to enable biocatalyst-dependent phage-assisted continuous evolution (PACE) and phage-assisted continuous selection (PACS). By combining these phage-based evolution and library selection technologies, we demonstrate that we can evolve enzyme variants with improved and expanded catalytic properties. Finally, we show that the genetic diversity resulting from a highly mutated PACS library is enriched for active enzyme variants with altered substrate scope. These results lay the foundation for using phage-based continuous evolution and selection technologies to engineer biocatalysts with novel substrate scope and reactivity.
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Affiliation(s)
- Krysten
A. Jones
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Harrison M. Snodgrass
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Ketaki Belsare
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Bryan C. Dickinson
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- E-mail:
| | - Jared C. Lewis
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
- E-mail:
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17
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Liu X, Zhao M, Fan X, Fu Y. Enhanced Production of (S)-2-arylpropionic Acids by Protein Engineering and Whole-Cell Catalysis. Front Bioeng Biotechnol 2021; 9:697677. [PMID: 34307324 PMCID: PMC8293918 DOI: 10.3389/fbioe.2021.697677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/16/2021] [Indexed: 11/29/2022] Open
Abstract
Esterases are important biocatalysts for chemical synthesis. Several bHSL family esterases have been used to prepare (S)-2-arylpropionic acids with stronger anti-inflammatory effects via kinetic resolution. Here, we presented the discovery of key residues that controlled the enantioselectivity of bHSL family esterases to ethyl 2-arylpropionates, through careful analysis of the structural information and molecular docking. A new bHSL family esterase, Est924, was identified as a promising catalyst for kinetic resolution of racemic ethyl 2-arylpropionates with slight (R)-stereopreference. Using Est924 as the starting enzyme, protein engineering was conducted at hotspots, and the substitution of A203 was proved to enhance the enantioselectivity. The stereopreference of the mutant M1 (A203W) was inverted to ethyl (S)-2-arylpropionates, and this stereopreference was further improved in variant M3 (I202F/A203W/G208F). In addition, the optimal variant, M3, was also suitable for the resolution of ibuprofen ethyl ester and ketoprofen ethyl ester, and their efficient (S)-isomers were synthesized. Next, the whole-cell catalyst harboring M3 was used to prepare (S)-ketoprofen. (S)-ketoprofen with 86%ee was produced by whole-cell catalyst with a single freeze-thaw cycle, and the cells could be reused for at least five cycles. Our results suggested that Est924 variants could kinetically resolve economically important racemates for industrial production and further offer the opportunity for the rational design of enzyme enantioselectivity. Moreover, it is an economical process to prepare optically pure (S)-ketoprofen and (S)-naproxen by using an engineered strain harboring M3 as the catalyst.
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Affiliation(s)
- Xiaolong Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Urban Pollutant Conversion, Anhui Province Key Laboratory of Biomass Clean Energy, iChEM, University of Science and Technology of China, Hefei, China
| | - Meng Zhao
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Xinjiong Fan
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Yao Fu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Urban Pollutant Conversion, Anhui Province Key Laboratory of Biomass Clean Energy, iChEM, University of Science and Technology of China, Hefei, China
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18
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Bhatt P, Zhou X, Huang Y, Zhang W, Chen S. Characterization of the role of esterases in the biodegradation of organophosphate, carbamate, and pyrethroid pesticides. JOURNAL OF HAZARDOUS MATERIALS 2021; 411:125026. [PMID: 33461010 DOI: 10.1016/j.jhazmat.2020.125026] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/08/2020] [Accepted: 12/30/2020] [Indexed: 06/12/2023]
Abstract
Ester-containing organophosphate, carbamate, and pyrethroid (OCP) pesticides are used worldwide to minimize the impact of pests and increase agricultural production. The toxicity of these chemicals to humans and other organisms has been widely reported. Chemically, these pesticides share an ester bond in their parent structures. A particular group of hydrolases, known as esterases, can catalyze the first step in ester-bond hydrolysis, and this initial regulatory metabolic reaction accelerates the degradation of OCP pesticides. Esterases can be naturally found in plants, animals, and microorganisms. Previous research on the esterase enzyme mechanisms revealed that the active sites of esterases contain serine residues that catalyze reactions via a nucleophilic attack on the substrates. In this review, we have compiled the previous research on esterases from different sources to determine and summarize the current knowledge of their properties, classifications, structures, mechanisms, and their applications in the removal of pesticides from the environment. This review will enhance the understanding of the scientific community when studying esterases and their applications for the degradation of broad-spectrum ester-containing pesticides.
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Affiliation(s)
- Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Xiaofan Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yaohua Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Wenping Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
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19
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Cai Y, Rao L, Zou Y. Genome Mining Discovery of a C 4-Alkylated Dihydroisocoumarin Pathway in Fungi. Org Lett 2021; 23:2337-2341. [PMID: 33688736 DOI: 10.1021/acs.orglett.1c00458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A fungal C4-alkylated dihydroisocoumarin pathway was discovered and elucidated. This pathway includes the following (1) a nonreducing polyketide synthase and a P450 collaboratively synthesize hydroxylated C3-methylated isocoumarin 3; (2) a methyltransferase methylates 3 to 8; and (3) importantly, an esterase specifically catalyzes a ring reconstruction process of 8 to C4-alkylated dihydroisocoumarin 10. Our discovery fills the gap in the enzymatic transformation process of natural C4-alkylated isocoumarin derivates.
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Affiliation(s)
- Yun Cai
- College of Pharmaceutical Sciences, Medical Research Institute, Southwest University, Chongqing 400715, China
| | - Li Rao
- College of Pharmaceutical Sciences, Medical Research Institute, Southwest University, Chongqing 400715, China
| | - Yi Zou
- College of Pharmaceutical Sciences, Medical Research Institute, Southwest University, Chongqing 400715, China
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20
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Ou J, Yuan X, Liu Y, Zhang P, Xu W, Tang K. Lipase from pseudomonas cepacia immobilized into ZIF-8 as bio-catalyst for enantioselective hydrolysis and transesterification. Process Biochem 2021. [DOI: 10.1016/j.procbio.2020.12.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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21
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Boyko KM, Kryukova MV, Petrovskaya LE, Kryukova EA, Nikolaeva AY, Korzhenevsky DA, Lomakina GY, Novototskaya-Vlasova KA, Rivkina EM, Dolgikh DA, Kirpichnikov MP, Popov VO. Structural and Biochemical Characterization of a Cold-Active PMGL3 Esterase with Unusual Oligomeric Structure. Biomolecules 2021; 11:biom11010057. [PMID: 33466452 PMCID: PMC7824956 DOI: 10.3390/biom11010057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/30/2020] [Accepted: 01/03/2021] [Indexed: 11/23/2022] Open
Abstract
The gene coding for a novel cold-active esterase PMGL3 was previously obtained from a Siberian permafrost metagenomic DNA library and expressed in Escherichia coli. We elucidated the 3D structure of the enzyme which belongs to the hormone-sensitive lipase (HSL) family. Similar to other bacterial HSLs, PMGL3 shares a canonical α/β hydrolase fold and is presumably a dimer in solution but, in addition to the dimer, it forms a tetrameric structure in a crystal and upon prolonged incubation at 4 °C. Detailed analysis demonstrated that the crystal tetramer of PMGL3 has a unique architecture compared to other known tetramers of the bacterial HSLs. To study the role of the specific residues comprising the tetramerization interface of PMGL3, several mutant variants were constructed. Size exclusion chromatography (SEC) analysis of D7N, E47Q, and K67A mutants demonstrated that they still contained a portion of tetrameric form after heat treatment, although its amount was significantly lower in D7N and K67A compared to the wild type. Moreover, the D7N and K67A mutants demonstrated a 40 and 60% increase in the half-life at 40 °C in comparison with the wild type protein. Km values of these mutants were similar to that of the wt PMGL3. However, the catalytic constants of the E47Q and K67A mutants were reduced by ~40%.
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Affiliation(s)
- Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia;
- Correspondence: (K.M.B.); (L.E.P.)
| | - Mariya V. Kryukova
- Kurchatov Complex of NBICS-Technologies, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (M.V.K.); (A.Y.N.); (D.A.K.)
| | - Lada E. Petrovskaya
- Department of Bioengineering, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.A.K.); (D.A.D.); (M.P.K.)
- Correspondence: (K.M.B.); (L.E.P.)
| | - Elena A. Kryukova
- Department of Bioengineering, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.A.K.); (D.A.D.); (M.P.K.)
| | - Alena Y. Nikolaeva
- Kurchatov Complex of NBICS-Technologies, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (M.V.K.); (A.Y.N.); (D.A.K.)
| | - Dmitry A. Korzhenevsky
- Kurchatov Complex of NBICS-Technologies, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (M.V.K.); (A.Y.N.); (D.A.K.)
| | - Galina Yu. Lomakina
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
- Department of Fundamental Sciences, Bauman Moscow State Technical University, 105005 Moscow, Russia
| | - Ksenia A. Novototskaya-Vlasova
- Laboratory of Soil Cryology, Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, 142290 Pushchino, Russia; (K.A.N.-V.); (E.M.R.)
| | - Elizaveta M. Rivkina
- Laboratory of Soil Cryology, Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, 142290 Pushchino, Russia; (K.A.N.-V.); (E.M.R.)
| | - Dmitry A. Dolgikh
- Department of Bioengineering, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.A.K.); (D.A.D.); (M.P.K.)
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Mikhail P. Kirpichnikov
- Department of Bioengineering, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.A.K.); (D.A.D.); (M.P.K.)
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Vladimir O. Popov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia;
- Kurchatov Complex of NBICS-Technologies, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (M.V.K.); (A.Y.N.); (D.A.K.)
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22
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Kryukova MV, Petrovskaya LE, Novototskaya-Vlasova KA, Kryukova EA, Yakimov SA, Nikolaeva AY, Boyko KM, Dolgikh DA, Kirpichnikov MP. Effect of Cysteine Residue Substitution in the GCSAG Motif of the PMGL2 Esterase Active Site on the Enzyme Properties. BIOCHEMISTRY (MOSCOW) 2021; 85:709-716. [PMID: 32586234 DOI: 10.1134/s0006297920060085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The gene coding for PMGL2 esterase, which belongs to the family of mammalian hormone-sensitive lipases (HSLs), was discovered by screening a metagenomic DNA library from a permafrost soil. The active site of PMGL2 contains conserved GXSXG motif which includes Cys173 residue next to the catalytic Ser174. In order to clarify the functional role of the cysteine residue in the GCSAG motif, we constructed a number of PMGL2 mutants with Cys173 substitutions and studied their properties. The specific activity of the C173D mutant exceeded the specific activity of the wild-type enzyme (wtPMGL2) by 60%, while the C173T/C202S mutant displayed reduced catalytic activity. The activity of the C173D mutant with p-nitrophenyl octanoate was 15% higher, while the activity of the C173T/C202S mutant was 17% lower compared to wtPMGL2. The C173D mutant was also characterized by a high activity at low temperatures (20-35°C) and significant loss of thermal stability. The kcat value for this protein was 56% higher than for the wild-type enzyme. The catalytic constants of the C173S mutant were close to those of wtPMGL2; this enzyme also demonstrated the highest thermal stability among the studied mutants. The obtained results demonstrate that substitutions of amino acid residues adjacent to the catalytic serine residue in the GXSXG motif can have a significant effect on the properties of PMGL2 esterase.
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Affiliation(s)
- M V Kryukova
- Kurchatov NBICS-Technologies Complex, Kurchatov Institute National Research Centre, Moscow, 123182, Russia
| | - L E Petrovskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - K A Novototskaya-Vlasova
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - E A Kryukova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - S A Yakimov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - A Y Nikolaeva
- Kurchatov NBICS-Technologies Complex, Kurchatov Institute National Research Centre, Moscow, 123182, Russia
| | - K M Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - D A Dolgikh
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.,Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - M P Kirpichnikov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.,Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
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23
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Wu S, Snajdrova R, Moore JC, Baldenius K, Bornscheuer UT. Biocatalysis: Enzymatic Synthesis for Industrial Applications. Angew Chem Int Ed Engl 2021; 60:88-119. [PMID: 32558088 PMCID: PMC7818486 DOI: 10.1002/anie.202006648] [Citation(s) in RCA: 540] [Impact Index Per Article: 180.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Indexed: 12/12/2022]
Abstract
Biocatalysis has found numerous applications in various fields as an alternative to chemical catalysis. The use of enzymes in organic synthesis, especially to make chiral compounds for pharmaceuticals as well for the flavors and fragrance industry, are the most prominent examples. In addition, biocatalysts are used on a large scale to make specialty and even bulk chemicals. This review intends to give illustrative examples in this field with a special focus on scalable chemical production using enzymes. It also discusses the opportunities and limitations of enzymatic syntheses using distinct examples and provides an outlook on emerging enzyme classes.
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Affiliation(s)
- Shuke Wu
- Institute of BiochemistryDept. of Biotechnology & Enzyme CatalysisGreifswald UniversityFelix-Hausdorff-Strasse 417487GreifswaldGermany
| | - Radka Snajdrova
- Novartis Institutes for BioMedical ResearchGlobal Discovery Chemistry4056BaselSwitzerland
| | - Jeffrey C. Moore
- Process Research and DevelopmentMerck & Co., Inc.126 E. Lincoln AveRahwayNJ07065USA
| | - Kai Baldenius
- Baldenius Biotech ConsultingHafenstr. 3168159MannheimGermany
| | - Uwe T. Bornscheuer
- Institute of BiochemistryDept. of Biotechnology & Enzyme CatalysisGreifswald UniversityFelix-Hausdorff-Strasse 417487GreifswaldGermany
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24
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Benítez-Mateos AI, Contente ML, Roura Padrosa D, Paradisi F. Flow biocatalysis 101: design, development and applications. REACT CHEM ENG 2021. [DOI: 10.1039/d0re00483a] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Flow biocatalysis: where to start? This tutorial review aims to guide and inspire new-comers to the field to boost the potential of flow biocatalysis.
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Affiliation(s)
| | | | | | - Francesca Paradisi
- Department of Chemistry and Biochemistry
- University of Bern
- Bern
- Switzerland
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25
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Immobilization of lipase AYS on UiO-66-NH2 metal-organic framework nanoparticles as a recyclable biocatalyst for ester hydrolysis and kinetic resolution. Sep Purif Technol 2020. [DOI: 10.1016/j.seppur.2020.117398] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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26
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Wu S, Snajdrova R, Moore JC, Baldenius K, Bornscheuer UT. Biokatalyse: Enzymatische Synthese für industrielle Anwendungen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006648] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Shuke Wu
- Institut für Biochemie Abt. Biotechnologie & Enzymkatalyse Universität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Deutschland
| | - Radka Snajdrova
- Novartis Institutes for BioMedical Research Global Discovery Chemistry 4056 Basel Schweiz
| | - Jeffrey C. Moore
- Process Research and Development Merck & Co., Inc. 126 E. Lincoln Ave Rahway NJ 07065 USA
| | - Kai Baldenius
- Baldenius Biotech Consulting Hafenstraße 31 68159 Mannheim Deutschland
| | - Uwe T. Bornscheuer
- Institut für Biochemie Abt. Biotechnologie & Enzymkatalyse Universität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Deutschland
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27
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Dou Z, Xu G, Ni Y. Efficient microbial resolution of racemic methyl 3-cyclohexene-1-carboxylate as chiral precursor of Edoxaban by newly identified Acinetobacter sp. JNU9335. Enzyme Microb Technol 2020; 139:109580. [PMID: 32732031 DOI: 10.1016/j.enzmictec.2020.109580] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/21/2020] [Accepted: 04/17/2020] [Indexed: 10/24/2022]
Abstract
Optically active 3-cyclohexene-1-carboxylic acid (CHCA) derivatives are important pharmaceutical intermediates. Due to the special rotatable structure, enantioselective preparation of chiral CHCA is hard to achieve. To identify efficient and enantioselective hydrolases for the biosynthesis of CHCA from methyl 3-cyclohexene-1-carboxylate (CHCM), target-oriented screening from soil samples and gene mining from genome database were explored. All putative hydrolases attempted displayed low enantioselectivity. A hydrolase-producing strain JNU9335 was successfully identified with relatively high enantioselectivity, and was designated as a strain of Acinetobacter sp. according to 16S rDNA sequence and phylogenetic analysis. After optimization, strain JNU9335 could produce 233 U·L‒1 hydrolase with E value of 21. Isooctane/aqueous biphasic system is favorable for the enzymatic resolution of CHCM, the E value of JNU9335 could further be increased to 36. The newly identified JNU9335 could tolerate as high as 1.0 M CHCM, producing (S)-CHCM with ees of 99.6% and isolation yield of 34.7%. This study provides an efficient biocatalyst for the preparation of chiral 3-cyclohexene-1-carboxylic acid derivatives.
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Affiliation(s)
- Zhe Dou
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
| | - Guochao Xu
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
| | - Ye Ni
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
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28
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Sales JCS, de Castro AM, Ribeiro BD, Z. Coelho MA. Supplementation of watermelon peels as an enhancer of lipase and esterase production byYarrowia lipolyticain solid-state fermentation and their potential use as biocatalysts in poly(ethylene terephthalate) (PET) depolymerization reactions. BIOCATAL BIOTRANSFOR 2020. [DOI: 10.1080/10242422.2020.1782387] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Julio Cesar S. Sales
- Department of Biochemistry, Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Aline M. de Castro
- Biotechnology Division, Research and Development Center, PETROBRAS, Rio de Janeiro, Brazil
| | - Bernardo D. Ribeiro
- Department of Biochemical Engineering, School of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maria Alice Z. Coelho
- Department of Biochemical Engineering, School of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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29
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Wu Z, Liu C, Zhang Z, Zheng R, Zheng Y. Amidase as a versatile tool in amide-bond cleavage: From molecular features to biotechnological applications. Biotechnol Adv 2020; 43:107574. [PMID: 32512219 DOI: 10.1016/j.biotechadv.2020.107574] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 12/27/2022]
Abstract
Amidases (EC 3. 5. 1. X) are versatile biocatalysts for synthesis of chiral carboxylic acids, α-amino acids and amides due to their hydrolytic and acyl transfer activity towards the C-N linkages. They have been extensively exploited and studied during the past years for their high specific activity and excellent enantioselectivity involved in various biotechnological applications in pharmaceutical and agrochemical industries. Additionally, they have attracted considerable attentions in biodegradation and bioremediation owing to environmental pressures. Motivated by industrial demands, crystallographic investigations and catalytic mechanisms of amidases based on structural biology have witnessed a dramatic promotion in the last two decades. The protein structures showed that different types of amidases have their typical stuctural elements, such as the conserved AS domains in signature amidases and the typical architecture of metal-associated active sites in acetamidase/formamidase family amidases. This review provides an overview of recent research advances in various amidases, with a focus on their structural basis of phylogenetics, substrate specificities and catalytic mechanisms as well as their biotechnological applications. As more crystal structures of amidases are determined, the structure/function relationships of these enzymes will also be further elucidated, which will facilitate molecular engineering and design of amidases to meet industrial requirements.
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Affiliation(s)
- Zheming Wu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Changfeng Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Zhaoyu Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Renchao Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China.
| | - Yuguo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
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30
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Mei RF, Shi YX, Duan WH, Ding H, Zhang XR, Cai L, Ding ZT. Biotransformation of α-terpineol by Alternaria alternata. RSC Adv 2020; 10:6491-6496. [PMID: 35496018 PMCID: PMC9049759 DOI: 10.1039/c9ra08042b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/15/2020] [Indexed: 11/29/2022] Open
Abstract
α-Terpineol (1), the main volatile constituent in some traditional Chinese medicines, has been reported to be metabolized to 4R-oleuropeic acid by the larvae of common cutworms. The present study verified that α-terpineol could be converted to 4R-oleuropeic acid (2) and (1S,2R,4R)-p-menthane-1,2,8-triol (3) by Alternaria alternata fermentation. Using shortened fermentation times, 7-hydroxy-α-terpineol (2a) was identified as an oxidative intermediate, which was consistent with the hypothesis put forward by previous studies. Cytochrome P450 enzymes were also confirmed to catalyze this biotransformation. This is the first study on the biotransformation of α-terpineol by microbial fermentation.
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Affiliation(s)
- Rui-Feng Mei
- Functional Molecules Analysis and Biotransformation Key Laboratory of Universities in Yunnan Province, Key Laboratory of Medicinal Chemistry for Natural Resource Ministry of Education, School of Chemical Science and Technology, Yunnan University Kunming 650091 P. R. China
| | - Ya-Xian Shi
- Functional Molecules Analysis and Biotransformation Key Laboratory of Universities in Yunnan Province, Key Laboratory of Medicinal Chemistry for Natural Resource Ministry of Education, School of Chemical Science and Technology, Yunnan University Kunming 650091 P. R. China
| | - Wei-He Duan
- Functional Molecules Analysis and Biotransformation Key Laboratory of Universities in Yunnan Province, Key Laboratory of Medicinal Chemistry for Natural Resource Ministry of Education, School of Chemical Science and Technology, Yunnan University Kunming 650091 P. R. China
| | - Hao Ding
- Functional Molecules Analysis and Biotransformation Key Laboratory of Universities in Yunnan Province, Key Laboratory of Medicinal Chemistry for Natural Resource Ministry of Education, School of Chemical Science and Technology, Yunnan University Kunming 650091 P. R. China
| | - Xiao-Ran Zhang
- Functional Molecules Analysis and Biotransformation Key Laboratory of Universities in Yunnan Province, Key Laboratory of Medicinal Chemistry for Natural Resource Ministry of Education, School of Chemical Science and Technology, Yunnan University Kunming 650091 P. R. China
| | - Le Cai
- Functional Molecules Analysis and Biotransformation Key Laboratory of Universities in Yunnan Province, Key Laboratory of Medicinal Chemistry for Natural Resource Ministry of Education, School of Chemical Science and Technology, Yunnan University Kunming 650091 P. R. China
| | - Zhong-Tao Ding
- Functional Molecules Analysis and Biotransformation Key Laboratory of Universities in Yunnan Province, Key Laboratory of Medicinal Chemistry for Natural Resource Ministry of Education, School of Chemical Science and Technology, Yunnan University Kunming 650091 P. R. China
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Boyko KM, Kryukova MV, Petrovskaya LE, Nikolaeva AY, Korzhenevsky DA, Novototskaya-Vlasova KA, Rivkina EM, Dolgikh DA, Kirpichnikov MP, Popov VO. Crystal structure of PMGL2 esterase from the hormone-sensitive lipase family with GCSAG motif around the catalytic serine. PLoS One 2020; 15:e0226838. [PMID: 31990908 PMCID: PMC6986724 DOI: 10.1371/journal.pone.0226838] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/05/2019] [Indexed: 12/26/2022] Open
Abstract
Lipases comprise a large class of hydrolytic enzymes which catalyze the cleavage of the ester bonds in triacylglycerols and find numerous biotechnological applications. Previously, we have cloned the gene coding for a novel esterase PMGL2 from a Siberian permafrost metagenomic DNA library. We have determined the 3D structure of PMGL2 which belongs to the hormone-sensitive lipase (HSL) family and contains a new variant of the active site motif, GCSAG. Similar to many other HSLs, PMGL2 forms dimers in solution and in the crystal. Our results demonstrated that PMGL2 and structurally characterized members of the GTSAG motif subfamily possess a common dimerization interface that significantly differs from that of members of the GDSAG subfamily of known structure. Moreover, PMGL2 had a unique organization of the active site cavity with significantly different topology compared to the other lipolytic enzymes from the HSL family with known structure including the distinct orientation of the active site entrances within the dimer and about four times larger size of the active site cavity. To study the role of the cysteine residue in GCSAG motif of PMGL2, the catalytic properties and structure of its double C173T/C202S mutant were examined and found to be very similar to the wild type protein. The presence of the bound PEG molecule in the active site of the mutant form allowed for precise mapping of the amino acid residues forming the substrate cavity.
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Affiliation(s)
- Konstantin M. Boyko
- Department of Enzyme Engineering, Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Marya V. Kryukova
- Kurchatov Complex of NBICS-technologies, National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Lada E. Petrovskaya
- Department of Bioengineering, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alena Y. Nikolaeva
- Kurchatov Complex of NBICS-technologies, National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Dmitry A. Korzhenevsky
- Kurchatov Complex of NBICS-technologies, National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Ksenia A. Novototskaya-Vlasova
- Laboratory of Soil Cryology, Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Elizaveta M. Rivkina
- Laboratory of Soil Cryology, Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Dmitry A. Dolgikh
- Department of Bioengineering, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Department of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail P. Kirpichnikov
- Department of Bioengineering, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Department of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Vladimir O. Popov
- Department of Enzyme Engineering, Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- Kurchatov Complex of NBICS-technologies, National Research Centre "Kurchatov Institute", Moscow, Russia
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32
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Xue D, Yao D, You X, Gong C. Green Synthesis of the Flavor Esters with a Marine Candida parapsilosis Esterase Expressed in Saccharomyces cerevisiae. Indian J Microbiol 2020; 60:175-181. [PMID: 32255850 DOI: 10.1007/s12088-020-00856-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 01/04/2020] [Indexed: 01/04/2023] Open
Abstract
The green synthesis of the flavor esters, n-propyl acetate, isobutyl acetate and isoamyl acetate had the advantages over the chemical synthesis. The esterase from Candida parapsilosis could transform n-propanol, isobutanol and isoamyl alcohol into n-propyl acetate, isobutyl acetate and isoamyl acetate, respectively. The esterase was expressed in Saccharomyces cerevisiae. At 30 °C for 1 d, the concentration of n-propyl acetate, isobutyl acetate and isoamyl acetate synthesized by the esterase expressed in Saccharomyces cerevisiae was 24.6 mg/100 mL, 8.3 mg/100 mL, 5.6 mg/100 mL, respectively. Expression of the esterase has a practical significance for flavor ester synthesis by green biochemical process.
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Affiliation(s)
- Dongsheng Xue
- 1Key Laboratory of Fermentation Engineering (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, 430068 People's Republic of China
| | - Donghai Yao
- 1Key Laboratory of Fermentation Engineering (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, 430068 People's Republic of China
| | - Xihuo You
- China Agricultural Huawei Biopharmaceuticals Ltd Company, Wuxue, 435300 People's Republic of China
| | - Chunjie Gong
- 1Key Laboratory of Fermentation Engineering (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, 430068 People's Republic of China
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33
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Kryukova M, Petrovskaya L, Kryukova E, Lomakina G, Yakimov S, Maksimov E, Boyko K, Popov V, Dolgikh D, Kirpichnikov M. Thermal Inactivation of a Cold-Active Esterase PMGL3 Isolated from the Permafrost Metagenomic Library. Biomolecules 2019; 9:E880. [PMID: 31888238 PMCID: PMC6995580 DOI: 10.3390/biom9120880] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/10/2019] [Accepted: 12/14/2019] [Indexed: 12/17/2022] Open
Abstract
PMGL3 is a cold-adapted esterase which was recently isolated from the permafrost metagenomic library. It exhibits maximum activity at 30 °C and low stability at elevated temperatures (40 °C and higher). Sequence alignment has revealed that PMGL3 is a member of the hormone-sensitive lipase (HSL) family. In this work, we demonstrated that incubation at 40 °C led to the inactivation of the enzyme (t1/2 = 36 min), which was accompanied by the formation of tetramers and higher molecular weight aggregates. In order to increase the thermal stability of PMGL3, its two cysteines Cys49 and Cys207 were substituted by the hydrophobic residues, which are found at the corresponding positions of thermostable esterases from the HSL family. One of the obtained mutants, C207F, possessed improved stability at 40 °C (t1/2 = 169 min) and increased surface hydrophobicity, whereas C49V was less stable in comparison with the wild type PMGL3. Both mutants exhibited reduced values of Vmax and kcat, while C207F demonstrated increased affinity to the substrate, and improved catalytic efficiency.
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Affiliation(s)
- M.V. Kryukova
- Kurchatov Complex of NBICS-technologies, National Research Centre “Kurchatov Institute”, Akad. Kurchatova sqr 1, 123182 Moscow, Russia
| | - L.E. Petrovskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - E.A. Kryukova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - G.Yu. Lomakina
- Department of Chemistry, Lomonosov Moscow State University, Leninskiye Gory, 1/3, 119991 Moscow, Russia;
| | - S.A. Yakimov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - E.G. Maksimov
- Department of Biology, Lomonosov Moscow State University, Leninskie gory, 1, bld 12, 119234 Moscow, Russia;
| | - K.M. Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia;
| | - V.O. Popov
- Kurchatov Complex of NBICS-technologies, National Research Centre “Kurchatov Institute”, Akad. Kurchatova sqr 1, 123182 Moscow, Russia
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia;
| | - D.A. Dolgikh
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Leninskie gory, 1, bld 12, 119234 Moscow, Russia;
| | - M.P. Kirpichnikov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Leninskie gory, 1, bld 12, 119234 Moscow, Russia;
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Zhang P, Cheng Q, Xu W, Tang K. Modeling and optimization of lipase-catalyzed hydrolysis for production of (S)-2-phenylbutyric acid enhanced by hydroxyethyl-β-cyclodextrin. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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35
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Carpen A, Bonomi F, Iametti S, Marengo M. Effects of starch addition on the activity and specificity of food-grade lipases. Biotechnol Appl Biochem 2019; 66:607-616. [PMID: 31056790 DOI: 10.1002/bab.1761] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 04/24/2019] [Indexed: 11/07/2022]
Abstract
Lipases are surface-active enzymes, acting on their substrates at the polar/nonpolar interface in emulsions. This study was aimed to test whether their activity, specificity, and the rates of formation/degradation of the various hydrolysis intermediates (i.e., mono- and diglycerides of interest as surface-active agents) could be modulated by adhesion of the triglyceride substrates as a thin layer on the surface of solids. These hypotheses were tested by using an array of food-grade lipases used in bakery, testing various types of starch as the "solid" phase. Starch-dependent increase in the hydrolysis rate was tested by pH-stat techniques on pure triglycerides and on food-grade oils in diluted emulsions. Starch-related improvements in the rate of fatty acids release were most evident at temperatures above 40 °C, and when using maize starch instead of wheat starch. Starch-dependent changes in the nature of the hydrolysis products were tested by chromatographic profiling of ethyl ether extracts from aqueous slurries containing up to 33% fat and 33% starch. Accumulation of mono- and diglycerides as hydrolysis intermediates was found to be modulated by the type of oil being used, by the reaction conditions, as well as by the enzyme nature and amount.
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Affiliation(s)
- Aristodemo Carpen
- Section of Chemical and Biomolecular Sciences, Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Francesco Bonomi
- Section of Chemical and Biomolecular Sciences, Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Stefania Iametti
- Section of Chemical and Biomolecular Sciences, Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Mauro Marengo
- Section of Chemical and Biomolecular Sciences, Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Milan, Italy
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36
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Wu X, Yang S, Yu H, Ye L, Su B, Shao Z. Improved enantioselectivity of E. coli BioH in kinetic resolution of methyl ( S)-3-cyclohexene-1-carboxylate by combinatorial modulation of steric and aromatic interactions. Biosci Biotechnol Biochem 2019; 83:1263-1269. [PMID: 30938230 DOI: 10.1080/09168451.2019.1597620] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
As a chiral precursor for the important anticoagulant Edoxaban, enantioselective synthesis of (S)-3-cyclohexene-1-carboxylic acid is of great significance. The complicated procedures and generation of massive solid waste discourage its chemical synthesis, and the alternative biocatalysis route calls for an enzyme capable of asymmetric hydrolysis of racemic methyl-3-cyclohexene-1-carboxylate. To this end, we engineered the E. coli esterase BioH for improved S-enantioselectivity via rational design. By combinatorial modulation of steric and aromatic interactions, a positive mutant Mu3 (L24A/W81A/L209A) with relatively high S-selectivity in hydrolyzing racemic methyl-3-cyclohexene-1-carboxylate was obtained, improving the enantiomeric excess from 32.3% (the wild type) to 70.9%. Molecular dynamics simulation was conducted for both (R)- or (S)- complexes of the wild type and Mu3 to provide hints for the mechanism behind the increased S-selectivity. Moreover, the reaction conditions of Mu3 in methyl-3-cyclohexene-1-carboxylate hydrolysis was optimized to improve the conversion rate to 2 folds.
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Affiliation(s)
- Xiafen Wu
- a College of Pharmaceutical Science , Zhejiang University of Technology , Hangzhou , PR China
| | - Shengli Yang
- a College of Pharmaceutical Science , Zhejiang University of Technology , Hangzhou , PR China
| | - Hongwei Yu
- b Institute of Bioengineering, College of Chemical and Biological Engineering , Zhejiang University , Hangzhou , PR China
| | - Lidan Ye
- b Institute of Bioengineering, College of Chemical and Biological Engineering , Zhejiang University , Hangzhou , PR China
| | - Bingmei Su
- c Fujian Key Laboratory of Marine Enzyme Engineering, College of Biological Science and Engineering , Fuzhou University , Fuzhou , PR China
| | - Zehui Shao
- a College of Pharmaceutical Science , Zhejiang University of Technology , Hangzhou , PR China
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37
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Oliveira DM, Mota TR, Oliva B, Segato F, Marchiosi R, Ferrarese-Filho O, Faulds CB, Dos Santos WD. Feruloyl esterases: Biocatalysts to overcome biomass recalcitrance and for the production of bioactive compounds. BIORESOURCE TECHNOLOGY 2019; 278:408-423. [PMID: 30704902 DOI: 10.1016/j.biortech.2019.01.064] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/14/2019] [Accepted: 01/16/2019] [Indexed: 05/25/2023]
Abstract
Ferulic acid and its hydroxycinnamate derivatives represent one of the most abundant forms of low molecular weight phenolic compounds in plant biomass. Feruloyl esterases are part of a microorganism's plant cell wall-degrading enzymatic arsenal responsible for cleaving insoluble wall-bound hydroxycinnamates and soluble cytosolic conjugates. Stimulated by industrial requirements, accelerating scientific discoveries and knowledge transfer, continuous improvement efforts have been made to identify, create and repurposed biocatalysts dedicated to plant biomass conversion and biosynthesis of high-added value molecules. Here we review the basic knowledge and recent advances in biotechnological characteristics and the gene content encoding for feruloyl esterases. Information about several enzymes is systematically organized according to their function, biochemical properties, substrate specificity, and biotechnological applications. This review contributes to further structural, functional, and biotechnological R&D both for obtaining hydroxycinnamates from agricultural by-products as well as for lignocellulose biomass treatments aiming for production of bioethanol and other derivatives of industrial interest.
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Affiliation(s)
- Dyoni M Oliveira
- Department of Biochemistry, State University of Maringá, Maringá, Paraná, Brazil.
| | - Thatiane R Mota
- Department of Biochemistry, State University of Maringá, Maringá, Paraná, Brazil
| | - Bianca Oliva
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, São Paulo, Brazil
| | - Fernando Segato
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, São Paulo, Brazil
| | - Rogério Marchiosi
- Department of Biochemistry, State University of Maringá, Maringá, Paraná, Brazil
| | | | - Craig B Faulds
- Aix-Marseille Université, INRA UMR 1163 Biodiversité et Biotechnologie Fongiques (BBF), 13009 Marseille, France
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38
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Gavin DP, Murphy EJ, Foley AM, Castilla IA, Reen FJ, Woods DF, Collins SG, O'Gara F, Maguire AR. Identification of an Esterase Isolated Using Metagenomic Technology which Displays an Unusual Substrate Scope and its Characterisation as an Enantioselective Biocatalyst. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201801691] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Declan P. Gavin
- School of Chemistry; Analytical and Biological Chemistry Research Facility; Synthesis and Solid State Pharmaceutical Centre; University College Cork; T12 K8AF Cork Ireland
| | - Edel J. Murphy
- School of Chemistry; Analytical and Biological Chemistry Research Facility; University College Cork; T12 K8AF Cork Ireland
| | - Aoife M. Foley
- School of Chemistry; Analytical and Biological Chemistry Research Facility; Synthesis and Solid State Pharmaceutical Centre; University College Cork; T12 K8AF Cork Ireland
| | - Ignacio Abreu Castilla
- BIOMERIT Research Centre; School of Microbiology; University College Cork; T12 K8AF Cork Ireland
| | - F. Jerry Reen
- School of Microbiology; University College Cork; T12 K8AF Cork Ireland
| | - David F. Woods
- BIOMERIT Research Centre; School of Microbiology; University College Cork; T12 K8AF Cork Ireland
| | - Stuart G. Collins
- School of Chemistry; Analytical and Biological Chemistry Research Facility; Synthesis and Solid State Pharmaceutical Centre; University College Cork; T12 K8AF Cork Ireland
| | - Fergal O'Gara
- BIOMERIT Research Centre; School of Microbiology; University College Cork; T12 K8AF Cork Ireland
- Human Microbiome Programme, School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute; Curtin University; Perth WA 6102 Australia
- Telethon Kids Institute; Perth WA 6008 Australia
| | - Anita R. Maguire
- School of Chemistry; School of Pharmacy; Analytical and Biological Chemistry Research Facility; Synthesis and Solid State Pharmaceutical Centre; University College Cork; T12 K8AF Cork Ireland
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39
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Preparation of Sterically Demanding 2,2-Disubstituted-2-Hydroxy Acids by Enzymatic Hydrolysis. Catalysts 2019. [DOI: 10.3390/catal9020113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Preparation of optically-pure derivatives of 2-hydroxy-2-(3-hydroxyphenyl)-2-phenylacetic acid of general structure 2 was accomplished by enzymatic hydrolysis of the correspondent esters. A screening with commercial hydrolases using the methyl ester of 2-hydroxy-2-(3-hydroxyphenyl)-2-phenylacetic acid (1a) showed that crude pig liver esterase (PLE) was the only preparation with catalytic activity. Low enantioselectivity was observed with substrates 1a–d, whereas PLE-catalysed hydrolysis of 1e proceeded with good enantioselectivity (E = 28), after optimization. Enhancement of the enantioselectivity was obtained by chemical re-esterification of enantiomerically enriched 2e, followed by sequential enzymatic hydrolysis with PLE. The preparation of optically-pure (S)-2e was validated on multi-milligram scale.
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40
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Zhang PL, Cheng Q, Xu W, Tang KW. Enzymatic Enantioselective Hydrolysis of 2-(3-Chlorophenyl) Propionic Acid Ester Enhanced by PEG: Experiment and Optimization. Ind Eng Chem Res 2018. [DOI: 10.1021/acs.iecr.8b02377] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pan-Liang Zhang
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, Hunan, China
| | - Qing Cheng
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, Hunan, China
| | - Weifeng Xu
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, Hunan, China
| | - Ke-Wen Tang
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, Hunan, China
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41
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White A, Koelper A, Russell A, Larsen EM, Kim C, Lavis LD, Hoops GC, Johnson RJ. Fluorogenic structure activity library pinpoints molecular variations in substrate specificity of structurally homologous esterases. J Biol Chem 2018; 293:13851-13862. [PMID: 30006352 DOI: 10.1074/jbc.ra118.003972] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/11/2018] [Indexed: 01/08/2023] Open
Abstract
Cellular esterases catalyze many essential biological functions by performing hydrolysis reactions on diverse substrates. The promiscuity of esterases complicates assignment of their substrate preferences and biological functions. To identify universal factors controlling esterase substrate recognition, we designed a 32-member structure-activity relationship (SAR) library of fluorogenic ester substrates and used this library to systematically interrogate esterase preference for chain length, branching patterns, and polarity to differentiate common classes of esterase substrates. Two structurally homologous bacterial esterases were screened against this library, refining their previously broad overlapping substrate specificity. Vibrio cholerae esterase ybfF displayed a preference for γ-position thioethers and ethers, whereas Rv0045c from Mycobacterium tuberculosis displayed a preference for branched substrates with and without thioethers. We determined that this substrate differentiation was partially controlled by individual substrate selectivity residues Tyr-119 in ybfF and His-187 in Rv0045c; reciprocal substitution of these residues shifted each esterase's substrate preference. This work demonstrates that the selectivity of esterases is tuned based on transition state stabilization, identifies thioethers as an underutilized functional group for esterase substrates, and provides a rapid method for differentiating structural isozymes. This SAR library could have multifaceted future applications, including in vivo imaging, biocatalyst screening, molecular fingerprinting, and inhibitor design.
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Affiliation(s)
- Alex White
- From the Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208-3443 and
| | - Andrew Koelper
- From the Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208-3443 and
| | - Arielle Russell
- From the Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208-3443 and
| | - Erik M Larsen
- From the Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208-3443 and
| | - Charles Kim
- the Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia 20147-2439
| | - Luke D Lavis
- the Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia 20147-2439
| | - Geoffrey C Hoops
- From the Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208-3443 and
| | - R Jeremy Johnson
- From the Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208-3443 and
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42
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De Vitis V, Nakhnoukh C, Pinto A, Contente ML, Barbiroli A, Milani M, Bolognesi M, Molinari F, Gourlay LJ, Romano D. A stereospecific carboxyl esterase from Bacillus coagulans hosting nonlipase activity within a lipase-like fold. FEBS J 2018; 285:903-914. [PMID: 29278448 DOI: 10.1111/febs.14368] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 11/30/2017] [Accepted: 12/20/2017] [Indexed: 11/30/2022]
Abstract
Microbial carboxylesterases are important biocatalysts that selectively hydrolyze an extensive range of esters. Here, we report the biochemical and structural characterization of an atypical carboxylesterase from Bacillus coagulans (BCE), endowed with high enantioselectivity toward different 1,2-O-isopropylideneglycerol (IPG or solketal) esters. BCE efficiently catalyzes the production of enantiopure (S)-IPG, a chiral building block for the synthesis of β-blockers, glycerophospholipids, and prostaglandins; efficient hydrolysis was observed up to 65 °C. To gain insight into the mechanistic bases of such enantioselectivity, we solved the crystal structures of BCE in apo- and glycerol-bound forms at resolutions of 1.9 and 1.8 Å, respectively. In silico docking studies on the BCE structure confirmed that IPG esters with small acyl chains (≤ C6) were easily accommodated in the active site pocket, indicating that small conformational changes are necessary to accept longer substrates. Furthermore, docking studies suggested that enantioselectivity may be due to an improved stabilization of the tetrahedral reaction intermediate for the S-enantiomer. Contrary to the above functional data implying nonlipolytic functions, BCE displays a lipase-like 3D structure that hosts a "lid" domain capping the main entrance to the active site. In lipases the lid mediates catalysis through interfacial activation, a process that we did not observe for BCE. Overall, we present the functional-structural properties of an atypical carboxyl esterase that has nonlipase-like functions, yet possesses a lipase-like 3D fold. Our data provide original enzymatic information in view of BCE applications as an inexpensive, efficient biocatalyst for the production of enantiopure (S)-IPG. DATABASE Coordinates and structure factors have been deposited in the Protein Data Bank (www.rcsb.org) under accession numbers 5O7G (apo-BCE) and 5OLU (glycerol-bound BCE).
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Affiliation(s)
- Valerio De Vitis
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Italy
| | | | - Andrea Pinto
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Italy
| | - Martina L Contente
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Italy.,School of Chemistry, University of Nottingham, UK
| | - Alberto Barbiroli
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Italy
| | - Mario Milani
- Biophysics Institute, National Research Council c/o, Department of Biosciences, Università degli Studi di Milano, Italy
| | - Martino Bolognesi
- Department of Biosciences, Università degli Studi di Milano, Italy.,Biophysics Institute, National Research Council c/o, Department of Biosciences, Università degli Studi di Milano, Italy.,Pediatric Research Center "Romeo e Enrica Invernizzi", Cryo Electron Microscopy Laboratory, University of Milano, Italy
| | - Francesco Molinari
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Italy
| | - Louise J Gourlay
- Department of Biosciences, Università degli Studi di Milano, Italy
| | - Diego Romano
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Italy
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43
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Relationships between Substrate Promiscuity and Chiral Selectivity of Esterases from Phylogenetically and Environmentally Diverse Microorganisms. Catalysts 2018. [DOI: 10.3390/catal8010010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Substrate specificity and selectivity of a biocatalyst are determined by the protein sequence and structure of its active site. Finding versatile biocatalysts acting against multiple substrates while at the same time being chiral selective is of interest for the pharmaceutical and chemical industry. However, the relationships between these two properties in natural microbial enzymes remain underexplored. Here, we performed an experimental analysis of substrate promiscuity and chiral selectivity in a set of 145 purified esterases from phylogenetically and environmentally diverse microorganisms, which were assayed against 96 diverse esters, 20 of which were enantiomers. Our results revealed a negative correlation between substrate promiscuity and chiral selectivity in the evaluated enzymes. Esterases displaying prominent substrate promiscuity and large catalytic environments are characterized by low chiral selectivity, a feature that has limited commercial value. Although a low level of substrate promiscuity does not guarantee high chiral selectivity, the probability that esterases with smaller active sites possess chiral selectivity factors of interest for industry (>25) is significantly higher than for promiscuous enzymes. Together, the present study unambiguously demonstrates that promiscuous and selective esterases appear to be rare in nature and that substrate promiscuity can be used as an indicator of the chiral selectivity level of esterases, and vice versa.
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44
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Charoenpanich J, Soongrung T, Chinnasri S, Suebchuea N, Suppoontong M, Thiemsawait S. A novel broad-temperature active and solvent stable esterase from a newly isolated Bacillus aerophilus. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2018. [DOI: 10.1016/j.bcab.2017.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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45
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Kotapati HK, Robinson JD, Lawrence DR, Fortner KR, Stanford CW, Powell DR, Wardenga R, Bornscheuer UT, Masterson DS. Diastereoselective Hydrolysis of Branched Malonate Diesters by Porcine Liver Esterase: Synthesis of 5‐Benzyl‐Substituted C
α
‐Methyl‐β‐proline and Catalytic Evaluation. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Hari Kiran Kotapati
- Department of Chemistry & Biochemistry The University of Southern Mississippi 118 College Drive, Box # 5043 39406 Hattiesburg Mississippi USA
| | - Jamarii D. Robinson
- Department of Chemistry & Biochemistry The University of Southern Mississippi 118 College Drive, Box # 5043 39406 Hattiesburg Mississippi USA
| | - Daniel R. Lawrence
- Department of Chemistry & Biochemistry The University of Southern Mississippi 118 College Drive, Box # 5043 39406 Hattiesburg Mississippi USA
| | - Kimberly R. Fortner
- Department of Chemistry & Biochemistry The University of Southern Mississippi 118 College Drive, Box # 5043 39406 Hattiesburg Mississippi USA
| | - Caleb W. Stanford
- Department of Chemistry & Biochemistry The University of Southern Mississippi 118 College Drive, Box # 5043 39406 Hattiesburg Mississippi USA
| | - Douglas R. Powell
- Department of Chemistry and Biochemistry University of Oklahoma 101 Stephenson Parkway 73019‐5251 Norman Oklahoma USA
| | - Rainer Wardenga
- Enzymicals AG Walther‐Rathenau‐Str. 49a 17489 Greifswald Germany
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis University of Greifswald Institute of Biochemistry Felix‐Hausdorff‐Str. 4 17487 Greifswald Germany
| | - Douglas S. Masterson
- Department of Chemistry & Biochemistry The University of Southern Mississippi 118 College Drive, Box # 5043 39406 Hattiesburg Mississippi USA
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46
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Meinert C, Schrobback K, Levett PA, Lutton C, Sah RL, Klein TJ. Tailoring hydrogel surface properties to modulate cellular response to shear loading. Acta Biomater 2017; 52:105-117. [PMID: 27729233 PMCID: PMC5385162 DOI: 10.1016/j.actbio.2016.10.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/20/2016] [Accepted: 10/07/2016] [Indexed: 12/17/2022]
Abstract
Biological tissues at articulating surfaces, such as articular cartilage, typically have remarkable low-friction properties that limit tissue shear during movement. However, these frictional properties change with trauma, aging, and disease, resulting in an altered mechanical state within the tissues. Yet, it remains unclear how these surface changes affect the behaviour of embedded cells when the tissue is mechanically loaded. Here, we developed a cytocompatible, bilayered hydrogel system that permits control of surface frictional properties without affecting other bulk physicochemical characteristics such as compressive modulus, mass swelling ratio, and water content. This hydrogel system was applied to investigate the effect of variations in surface friction on the biological response of human articular chondrocytes to shear loading. Shear strain in these hydrogels during dynamic shear loading was significantly higher in high-friction hydrogels than in low-friction hydrogels. Chondrogenesis was promoted following dynamic shear stimulation in chondrocyte-encapsulated low-friction hydrogel constructs, whereas matrix synthesis was impaired in high-friction constructs, which instead exhibited increased catabolism. Our findings demonstrate that the surface friction of tissue-engineered cartilage may act as a potent regulator of cellular homeostasis by governing the magnitude of shear deformation during mechanical loading, suggesting a similar relationship may also exist for native articular cartilage. STATEMENT OF SIGNIFICANCE Excessive mechanical loading is believed to be a major risk factor inducing pathogenesis of articular cartilage and other load-bearing tissues. Yet, the mechanisms leading to increased transmission of mechanical stimuli to cells embedded in the tissue remain largely unexplored. Here, we demonstrate that the tribological properties of loadbearing tissues regulate cellular behaviour by governing the magnitude of mechanical deformation arising from physiological tissue function. Based on these findings, we propose that changes to articular surface friction as they occur with trauma, aging, or disease, may initiate tissue pathology by increasing the magnitude of mechanical stress on embedded cells beyond a physiological level.
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Affiliation(s)
- Christoph Meinert
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland 4059, Australia.
| | - Karsten Schrobback
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland 4059, Australia.
| | - Peter A Levett
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland 4059, Australia.
| | - Cameron Lutton
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland 4059, Australia.
| | - Robert L Sah
- Department of Bioengineering, University of California-San Diego, La Jolla, CA 92093, United States.
| | - Travis J Klein
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland 4059, Australia.
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47
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Solid-state fermentative production of aroma esters by Myroides sp. ZB35 and its complete genome sequence. J Biotechnol 2017; 245:28-33. [PMID: 28174040 DOI: 10.1016/j.jbiotec.2017.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 01/31/2017] [Accepted: 02/04/2017] [Indexed: 11/20/2022]
Abstract
Consumers prefer biotechnological food products with high nutritional values and good flavors. Solid-state fermentation is a commonly used technique with a long history. In the present study, Myroides sp. ZB35 was used in solid-state fermentative production of aroma volatiles on a rice medium. Using the headspace solid phase microextraction coupled with gas chromatography-mass spectrometry technique and authentic standards, 22 esters with molecular weight ranging from 102 to 172 were identified. At 192h, the esters reached a total concentration of 1774μg/kg. Subsequently, the complete genome of ZB35 was sequenced using the PacBio RS II platform. ZB35 has a single circular chromosome of 4,065,010bp with a GC content of 34.1% and six putative novel esterase genes were found. ZB35 is the first bacterium here discovered being capable of producing so many kinds of aroma esters. The data revealed here would provide helpful information for further developing this strain as a promising source of aroma esters relevant in food and fragrance industries and the source of novel enzymes with potential usages.
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48
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Böttcher D, Zägel P, Schmidt M, Bornscheuer UT. A Microtiter Plate-Based Assay to Screen for Active and Stereoselective Hydrolytic Enzymes in Enzyme Libraries. Methods Mol Biol 2017; 1539:197-204. [PMID: 27900690 DOI: 10.1007/978-1-4939-6691-2_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A procedure for the high-throughput screening (HTS) of esterases is described. This includes a pretest for discrimination of active and inactive clones using an agar plate overlay assay, the enzyme expression in microtiter plates and the measurement of activity and enantioselectivity (E) of the esterase variants using acetates of secondary alcohols as model substrates. Acetic acid released is converted in an enzyme cascade leading to the stoichiometric formation of NADH, which is quantified in a spectrophotometer. The method allows screening of several thousand mutants per day and has already been successfully applied to identify an esterase mutant with an E > 100 towards an important building block for organic synthesis. This protocol can also be used for lipases and possibly other hydrolases that are expressed in soluble form in conventional E. coli strains.
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Affiliation(s)
- Dominique Böttcher
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Patrick Zägel
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Marlen Schmidt
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Uwe T Bornscheuer
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany.
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49
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Hinze J, Süss P, Strohmaier S, Bornscheuer UT, Wardenga R, von Langermann J. Recombinant Pig Liver Esterase-Catalyzed Synthesis of (1S,4R)-4-Hydroxy-2-cyclopentenyl Acetate Combined with Subsequent Enantioselective Crystallization. Org Process Res Dev 2016. [DOI: 10.1021/acs.oprd.6b00093] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Janine Hinze
- University of Rostock, Institute of Chemistry, Albert-Einstein-Str. 3a, 18059 Rostock, Germany
| | - Philipp Süss
- Enzymicals AG, Walther-Rathenau-Str.
49a, 17489 Greifswald, Germany
- University of Greifswald, Institute of Biochemistry, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Silja Strohmaier
- University of Rostock, Institute of Chemistry, Albert-Einstein-Str. 3a, 18059 Rostock, Germany
- School
of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Uwe T. Bornscheuer
- University of Greifswald, Institute of Biochemistry, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Rainer Wardenga
- Enzymicals AG, Walther-Rathenau-Str.
49a, 17489 Greifswald, Germany
| | - Jan von Langermann
- University of Rostock, Institute of Chemistry, Albert-Einstein-Str. 3a, 18059 Rostock, Germany
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50
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Structural and biochemical characterisation of Archaeoglobus fulgidus esterase reveals a bound CoA molecule in the vicinity of the active site. Sci Rep 2016; 6:25542. [PMID: 27160974 PMCID: PMC4861933 DOI: 10.1038/srep25542] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 04/18/2016] [Indexed: 11/28/2022] Open
Abstract
A new carboxyl esterase, AF-Est2, from the hyperthermophilic archaeon Archaeoglobus fulgidus has been cloned, over-expressed in Escherichia coli and biochemically and structurally characterized. The enzyme has high activity towards short- to medium-chain p-nitrophenyl carboxylic esters with optimal activity towards the valerate ester. The AF-Est2 has good solvent and pH stability and is very thermostable, showing no loss of activity after incubation for 30 min at 80 °C. The 1.4 Å resolution crystal structure of AF-Est2 reveals Coenzyme A (CoA) bound in the vicinity of the active site. Despite the presence of CoA bound to the AF-Est2 this enzyme has no CoA thioesterase activity. The pantetheine group of CoA partially obstructs the active site alcohol pocket suggesting that this ligand has a role in regulation of the enzyme activity. A comparison with closely related α/β hydrolase fold enzyme structures shows that the AF-Est2 has unique structural features that allow CoA binding. A comparison of the structure of AF-Est2 with the human carboxyl esterase 1, which has CoA thioesterase activity, reveals that CoA is bound to different parts of the core domain in these two enzymes and approaches the active site from opposite directions.
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