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Zhao J, Ma M, Zeng Z, Wan D, Yan X, Xia J, Yu P, Gong D. Production, purification, properties and current perspectives for modification and application of microbial lipases. Prep Biochem Biotechnol 2024; 54:1001-1016. [PMID: 38445829 DOI: 10.1080/10826068.2024.2323196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
With the industrialization and development of modern science, the application of enzymes as green and environmentally friendly biocatalysts in industry has been increased widely. Among them, lipase (EC. 3.1.1.3) is a very prominent biocatalyst, which has the ability to catalyze the hydrolysis and synthesis of ester compounds. Many lipases have been isolated from various sources, such as animals, plants and microorganisms, among which microbial lipase is the enzyme with the most diverse enzymatic properties and great industrial application potential. It therefore has promising applications in many industries, such as food and beverages, waste treatment, biofuels, leather, textiles, detergent formulations, ester synthesis, pharmaceuticals and medicine. Although many microbial lipases have been isolated and characterized, only some of them have been commercially exploited. In order to cope with the growing industrial demands and overcome these shortcomings to replace traditional chemical catalysts, the preparation of new lipases with thermal/acid-base stability, regioselectivity, organic solvent tolerance, high activity and yield, and reusability through excavation and modification has become a hot research topic.
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Affiliation(s)
- Junxin Zhao
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- Jiangxi Province Key Laboratory of Edible and Medicinal Resources Exploitation, Nanchang University, Nanchang, China
- School of Food Science and Technology, Nanchang University, Nanchang, China
| | - Maomao Ma
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- Jiangxi Province Key Laboratory of Edible and Medicinal Resources Exploitation, Nanchang University, Nanchang, China
- School of Food Science and Technology, Nanchang University, Nanchang, China
| | - Zheling Zeng
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- Jiangxi Province Key Laboratory of Edible and Medicinal Resources Exploitation, Nanchang University, Nanchang, China
- School of Resource and Environmental and Chemical Engineering, Nanchang University, Nanchang, China
| | - Dongman Wan
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- Jiangxi Province Key Laboratory of Edible and Medicinal Resources Exploitation, Nanchang University, Nanchang, China
- School of Food Science and Technology, Nanchang University, Nanchang, China
| | - Xianghui Yan
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- Jiangxi Province Key Laboratory of Edible and Medicinal Resources Exploitation, Nanchang University, Nanchang, China
- School of Resource and Environmental and Chemical Engineering, Nanchang University, Nanchang, China
| | - Jiaheng Xia
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- Jiangxi Province Key Laboratory of Edible and Medicinal Resources Exploitation, Nanchang University, Nanchang, China
- School of Resource and Environmental and Chemical Engineering, Nanchang University, Nanchang, China
| | - Ping Yu
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- Jiangxi Province Key Laboratory of Edible and Medicinal Resources Exploitation, Nanchang University, Nanchang, China
- School of Resource and Environmental and Chemical Engineering, Nanchang University, Nanchang, China
| | - Deming Gong
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- Jiangxi Province Key Laboratory of Edible and Medicinal Resources Exploitation, Nanchang University, Nanchang, China
- New Zealand Institute of Natural Medicine Research, Auckland, New Zealand
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Khodakarami Fard Z, Shirazinejad A, Mohammadi M, Hashemi SMB. Molecular Cloning of the Extracellular Lipases of Bacillus Amyloliquefaciens Isolated from Agrifood Wastes. IRANIAN JOURNAL OF BIOTECHNOLOGY 2024; 22:e3797. [PMID: 39220339 PMCID: PMC11364930 DOI: 10.30498/ijb.2024.417315.3797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 03/09/2024] [Indexed: 09/04/2024]
Abstract
Background The lipase enzyme (EC: 3.1.1.3) is one of the most important catalysts in food, dairy, detergent, and textile industries. Objective This study was performed to identify, isolate and characterize of lipase producing bacterial strain from agrifood wastes and to identify and characterize of their lipase genes. Materials and Methods In the present study, two lipase-producing isolates were identified from the effluent of Golbahar meat products and Soveyda vegetable oil factories using in silico and in vitro approaches. Results The results of morphological, biochemical, and molecular characterizations showed that both lipase-producing isolates belong to the Bacillus amyloliquefaciens species. Phylogenetic analysis confirmed the results of phenotypic, biochemical, and molecular characterizations. The results showed differences between LipA and LipB in the Golbahar and Soveyda isolates. Three different amino acids (residues 14, 100, and 165) were observed in LipA and one different amino acid (residue 102) was detected in LipB extracellular lipases. The protein molecular weight of the two extracted lipases ranged from 20 to 25 kDa. The identified extracellular lipases also had different physicochemical features. The maximum lipase activity of the Golbahar and Soveyda isolates was observed at 45 °C and at the pH of 8, but the Golbahar isolates exhibited higher lipase activity compared to the Soveyda isolates. The Golbahar and Soveyda isolates exhibited different activities in the presence of some ions, inhibitors, denaturing agents, and organic solvents and the Golbahar isolates showed better lipase activity than the Soveyda isolates. Conclusions In this study, two extracellular lipase-producing isolates of B. amyloliquefaciens were identified from different food industries, and their characteristics were investigated. The results of various investigations showed that the lipases produced by the Golbahar isolate have better characteristics than the lipases of the Soveyda isolate. The Golbahar lipases have a suitable temperature and pH activity range and maintain their activity in the presence of some ions, inhibitors, denaturing agents, and organic solvents. After further investigation, the Golbahar isolate lipase can be used in various industries. In addition, this lipase can be used enzyme engineering processes and its activity can be arbitrarily changed by targeted mutations. The results of this study can increase our knowledge of extracellular lipases and may turn out to have industrial applications.
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Affiliation(s)
- Zahra Khodakarami Fard
- Department of Food Science and Technology, Sarvestan Branch, Islamic Azad University, Sarvestan, Iran
| | - Alireza Shirazinejad
- Department of Food Science and Technology, Sarvestan Branch, Islamic Azad University, Sarvestan, Iran
| | - Mohsen Mohammadi
- Department of Pharmacognosy and Pharmaceutical Biotechnology, Faculty of Pharmacy, Lorestan University of Medical Sciences, Khorramabad, Iran
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Pourhassan ZN, Cui H, Muckhoff N, Davari MD, Smits SHJ, Schwaneberg U, Schmitt L. A step forward to the optimized HlyA type 1 secretion system through directed evolution. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12653-7. [PMID: 37405436 PMCID: PMC10386944 DOI: 10.1007/s00253-023-12653-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/08/2023] [Accepted: 06/19/2023] [Indexed: 07/06/2023]
Abstract
Secretion of proteins into the extracellular space has great advantages for the production of recombinant proteins. Type 1 secretion systems (T1SS) are attractive candidates to be optimized for biotechnological applications, as they have a relatively simple architecture compared to other classes of secretion systems. A paradigm of T1SS is the hemolysin A type 1 secretion system (HlyA T1SS) from Escherichia coli harboring only three membrane proteins, which makes the plasmid-based expression of the system easy. Although for decades the HlyA T1SS has been successfully applied for secretion of a long list of heterologous proteins from different origins as well as peptides, but its utility at commercial scales is still limited mainly due to low secretion titers of the system. To address this drawback, we engineered the inner membrane complex of the system, consisting of HlyB and HlyD proteins, following KnowVolution strategy. The applied KnowVolution campaign in this study provided a novel HlyB variant containing four substitutions (T36L/F216W/S290C/V421I) with up to 2.5-fold improved secretion for two hydrolases, a lipase and a cutinase. KEY POINTS: • An improvement in protein secretion via the use of T1SS • Reaching almost 400 mg/L of soluble lipase into the supernatant • A step forward to making E. coli cells more competitive for applying as a secretion host.
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Affiliation(s)
- Zohreh N Pourhassan
- Institute of Biochemistry, Heinrich Heine University, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Haiyang Cui
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52056, Aachen, Germany
- Present Address: Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Neele Muckhoff
- Institute of Biochemistry, Heinrich Heine University, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Mehdi D Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich Heine University, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52056, Aachen, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University, Universitätsstr. 1, 40225, Düsseldorf, Germany.
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Figueroa W, Cazares A, Cazares D, Wu Y, de la Cruz A, Welch M, Kameyama L, Nobrega FL, Guarneros G. Distribution and molecular evolution of the anti-CRISPR family AcrIF7. PLoS Biol 2023; 21:e3002072. [PMID: 37083687 PMCID: PMC10155984 DOI: 10.1371/journal.pbio.3002072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/03/2023] [Accepted: 03/10/2023] [Indexed: 04/22/2023] Open
Abstract
Anti-clustered regularly interspaced short palindromic repeats (CRISPRs) are proteins capable of blocking CRISPR-Cas systems and typically their genes are located on mobile genetic elements. Since their discovery, numerous anti-CRISPR families have been identified. However, little is known about the distribution and sequence diversity of members within a family, nor how these traits influence the anti-CRISPR's function and evolution. Here, we use AcrIF7 to explore the dissemination and molecular evolution of an anti-CRISPR family. We uncovered 5 subclusters and prevalent anti-CRISPR variants within the group. Remarkably, AcrIF7 homologs display high similarity despite their broad geographical, ecological, and temporal distribution. Although mainly associated with Pseudomonas aeruginosa, AcrIF7 was identified in distinct genetic backgrounds indicating horizontal dissemination, primarily by phages. Using mutagenesis, we recreated variation observed in databases but also extended the sequence diversity of the group. Characterisation of the variants identified residues key for the anti-CRISPR function and other contributing to its mutational tolerance. Moreover, molecular docking revealed that variants with affected function lose key interactions with its CRISPR-Cas target. Analysis of publicly available data and the generated variants suggests that the dominant AcrIF7 variant corresponds to the minimal and optimal anti-CRISPR selected in the family. Our study provides a blueprint to investigate the molecular evolution of anti-CRISPR families.
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Affiliation(s)
- Wendy Figueroa
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Adrian Cazares
- EMBL's European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Daniel Cazares
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Yi Wu
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Ana de la Cruz
- Department of Genetics and Molecular Biology, Center for Research and Advanced Studies of the National Polytechnic Institute, Mexico City, Mexico
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Luis Kameyama
- Department of Genetics and Molecular Biology, Center for Research and Advanced Studies of the National Polytechnic Institute, Mexico City, Mexico
| | - Franklin L Nobrega
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Gabriel Guarneros
- Department of Genetics and Molecular Biology, Center for Research and Advanced Studies of the National Polytechnic Institute, Mexico City, Mexico
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5
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Cieh NL, Mokhtar MN, Baharuddin AS, Mohammed MAP, Wakisaka M. Progress on Lipase Immobilization Technology in Edible Oil and Fat Modifications. FOOD REVIEWS INTERNATIONAL 2023. [DOI: 10.1080/87559129.2023.2172427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- Ng Lin Cieh
- Department of Process and Food Engineering, Faculty of Engineering, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Mohd Noriznan Mokhtar
- Department of Process and Food Engineering, Faculty of Engineering, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Laboratory of Processing and Product Development, Institute of Plantation Studies, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Azhari Samsu Baharuddin
- Department of Process and Food Engineering, Faculty of Engineering, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Mohd Afandi P. Mohammed
- Department of Process and Food Engineering, Faculty of Engineering, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Minato Wakisaka
- Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
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El Harrar T, Davari MD, Jaeger KE, Schwaneberg U, Gohlke H. Critical assessment of structure-based approaches to improve protein resistance in aqueous ionic liquids by enzyme-wide saturation mutagenesis. Comput Struct Biotechnol J 2022; 20:399-409. [PMID: 35070165 PMCID: PMC8752993 DOI: 10.1016/j.csbj.2021.12.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 12/12/2022] Open
Abstract
Ionic liquids (IL) and aqueous ionic liquids (aIL) are attractive (co-)solvents for green industrial processes involving biocatalysts, but often reduce enzyme activity. Experimental and computational methods are applied to predict favorable substitution sites and, most often, subsequent site-directed surface charge modifications are introduced to enhance enzyme resistance towards aIL. However, almost no studies evaluate the prediction precision with random mutagenesis or the application of simple data-driven filtering processes. Here, we systematically and rigorously evaluated the performance of 22 previously described structure-based approaches to increase enzyme resistance to aIL based on an experimental complete site-saturation mutagenesis library of Bacillus subtilis Lipase A (BsLipA) screened against four aIL. We show that, surprisingly, most of the approaches yield low gain-in-precision (GiP) values, particularly for predicting relevant positions: 14 approaches perform worse than random mutagenesis. Encouragingly, exploiting experimental information on the thermostability of BsLipA or structural weak spots of BsLipA predicted by rigidity theory yields GiP = 3.03 and 2.39 for relevant variants and GiP = 1.61 and 1.41 for relevant positions. Combining five simple-to-compute physicochemical and evolutionary properties substantially increases the precision of predicting relevant variants and positions, yielding GiP = 3.35 and 1.29. Finally, combining these properties with predictions of structural weak spots identified by rigidity theory additionally improves GiP for relevant variants up to 4-fold to ∼10 and sustains or increases GiP for relevant positions, resulting in a prediction precision of ∼90% compared to ∼9% in random mutagenesis. This combination should be applicable to other enzyme systems for guiding protein engineering approaches towards improved aIL resistance.
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Affiliation(s)
- Till El Harrar
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
- John-von-Neumann-Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Mehdi D. Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, 52428 Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
- DWI – Leibniz Institute for Interactive Materials e.V., 52074 Aachen, Germany
| | - Holger Gohlke
- John-von-Neumann-Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
- Corresponding author at: John-von-Neumann-Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Str., 52428 Jülich, Germany.
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Recombination of Single Beneficial Substitutions Obtained from Protein Engineering by Computer-Assisted Recombination (CompassR). Methods Mol Biol 2022; 2461:9-18. [PMID: 35727441 DOI: 10.1007/978-1-0716-2152-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A large number of beneficial substitutions can be obtained from a successful directed enzyme evolution campaign and/or (semi)rational design. It is expected that the recombination of some beneficial substitutions leads to a much higher degree of performance through synergistic effect. However, systematic recombination studies show that poorly performing variants are often obtained after recombination of three to four individual beneficial substitutions and this limits protein engineers to exploit nature's potential in generating better performing enzymes. Computer-assisted Recombination (CompassR) strategy allows the recombination of identified beneficial substitutions in an effective and efficient manner in order to generate active enzymes with improved performance. Here, we describe in detail the CompassR procedure with an example of recombining four substitutions and discuss some important practical issues that should be considered (such as the selection of protein structures, number of FoldX runs, evaluation of calculations) for application of the CompassR rule. The core part of this protocol (system setup, ΔΔGfold calculation, and CompassR application) is transferable to other enzymes and any recombination of single beneficial substitutions.
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8
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Maldonado MR, Alnoch RC, de Almeida JM, Santos LAD, Andretta AT, Ropaín RDPC, de Souza EM, Mitchell DA, Krieger N. Key mutation sites for improvement of the enantioselectivity of lipases through protein engineering. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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9
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Enhancement of protein thermostability by three consecutive mutations using loop-walking method and machine learning. Sci Rep 2021; 11:11883. [PMID: 34088952 PMCID: PMC8178419 DOI: 10.1038/s41598-021-91339-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/25/2021] [Indexed: 01/22/2023] Open
Abstract
We developed a method to improve protein thermostability, “loop-walking method”. Three consecutive positions in 12 loops of Burkholderia cepacia lipase were subjected to random mutagenesis to make 12 libraries. Screening allowed us to identify L7 as a hot-spot loop having an impact on thermostability, and the P233G/L234E/V235M mutant was found from 214 variants in the L7 library. Although a more excellent mutant might be discovered by screening all the 8000 P233X/L234X/V235X mutants, it was difficult to assay all of them. We therefore employed machine learning. Using thermostability data of the 214 mutants, a computational discrimination model was constructed to predict thermostability potentials. Among 7786 combinations ranked in silico, 20 promising candidates were selected and assayed. The P233D/L234P/V235S mutant retained 66% activity after heat treatment at 60 °C for 30 min, which was higher than those of the wild-type enzyme (5%) and the P233G/L234E/V235M mutant (35%).
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10
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Menghiu G, Ostafe V, Prodanović R, Fischer R, Ostafe R. A High-Throughput Screening System Based on Fluorescence-Activated Cell Sorting for the Directed Evolution of Chitinase A. Int J Mol Sci 2021; 22:ijms22063041. [PMID: 33809788 PMCID: PMC8002391 DOI: 10.3390/ijms22063041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/10/2021] [Accepted: 03/12/2021] [Indexed: 12/13/2022] Open
Abstract
Chitinases catalyze the degradation of chitin, a polymer of N-acetylglucosamine found in crustacean shells, insect cuticles, and fungal cell walls. There is great interest in the development of improved chitinases to address the environmental burden of chitin waste from the food processing industry as well as the potential medical, agricultural, and industrial uses of partially deacetylated chitin (chitosan) and its products (chito-oligosaccharides). The depolymerization of chitin can be achieved using chemical and physical treatments, but an enzymatic process would be more environmentally friendly and more sustainable. However, chitinases are slow-acting enzymes, limiting their biotechnological exploitation, although this can be overcome by molecular evolution approaches to enhance the features required for specific applications. The two main goals of this study were the development of a high-throughput screening system for chitinase activity (which could be extrapolated to other hydrolytic enzymes), and the deployment of this new method to select improved chitinase variants. We therefore cloned and expressed the Bacillus licheniformis DSM8785 chitinase A (chiA) gene in Escherichia coli BL21 (DE3) cells and generated a mutant library by error-prone PCR. We then developed a screening method based on fluorescence-activated cell sorting (FACS) using the model substrate 4-methylumbelliferyl β-d-N,N′,N″-triacetyl chitotrioside to identify improved enzymes. We prevented cross-talk between emulsion compartments caused by the hydrophobicity of 4-methylumbelliferone, the fluorescent product of the enzymatic reaction, by incorporating cyclodextrins into the aqueous phases. We also addressed the toxicity of long-term chiA expression in E. coli by limiting the reaction time. We identified 12 mutants containing 2–8 mutations per gene resulting in up to twofold higher activity than wild-type ChiA.
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Affiliation(s)
- Gheorghita Menghiu
- Institute for Biology VII, Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany; (G.M.); (R.F.)
- Advanced Environmental Research Laboratories, Department of Biology–Chemistry, West University of Timisoara, Oituz 4, 300086 Timisoara, Romania;
| | - Vasile Ostafe
- Advanced Environmental Research Laboratories, Department of Biology–Chemistry, West University of Timisoara, Oituz 4, 300086 Timisoara, Romania;
| | - Radivoje Prodanović
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia;
| | - Rainer Fischer
- Institute for Biology VII, Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany; (G.M.); (R.F.)
- Departments of Biological Sciences and Chemistry, Purdue University, 207 S. Martin Jischke Dr., West Lafayette, IN 47907, USA
| | - Raluca Ostafe
- Institute for Biology VII, Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany; (G.M.); (R.F.)
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Molecular Evolution, Protein Engineering and Production, Purdue University, 207 S. Martin Jischke Dr., West Lafayette, IN 47907, USA
- Correspondence: ; Tel.: +1-317-765-496-4012
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Verma S, Meghwanshi GK, Kumar R. Current perspectives for microbial lipases from extremophiles and metagenomics. Biochimie 2021; 182:23-36. [PMID: 33421499 DOI: 10.1016/j.biochi.2020.12.027] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 12/21/2020] [Accepted: 12/31/2020] [Indexed: 01/21/2023]
Abstract
Microbial lipases are most broadly used biocatalysts for environmental and industrial applications. Lipases catalyze the hydrolysis and synthesis of long acyl chain esters and have a characteristic folding pattern of α/β hydrolase with highly conserved catalytic triad (Serine, Aspartic/Glutamic acid and Histidine). Mesophilic lipases (optimal activity in neutral pH range, mesophilic temperature range, atmospheric pressure, normal salinity, non-radio-resistant, and instability in organic solvents) have been in use for many industrial biotransformation reactions. However, lipases from extremophiles can be used to design biotransformation reactions with higher yields, less byproducts or useful side products and have been predicted to catalyze those reactions also, which otherwise are not possible with the mesophilic lipases. The extremophile lipase perform activity at extremes of temperature, pH, salinity, and pressure which can be screened from metagenome and de novo lipase design using computational approaches. Despite structural similarity, they exhibit great diversity at the sequence level. This diversity is broader when lipases from the bacterial, archaeal, plant, and animal domains/kingdoms are compared. Furthermore, a great diversity of novel lipases exists and can be discovered from the analysis of the dark matter - the unexplored nucleotide/metagenomic databases. This review is an update on extremophilic microbial lipases, their diversity, structure, and classification. An overview on novel lipases which have been detected through analysis of the genomic dark matter (metagenome) has also been presented.
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Affiliation(s)
- Swati Verma
- Department of Microbiology, Maharaja Ganga Singh University, Bikaner, 334004, India
| | | | - Rajender Kumar
- Department of Clinical Microbiology, Umeå University, SE-90185, Umeå, Sweden.
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Heckmann CM, Paradisi F. Looking Back: A Short History of the Discovery of Enzymes and How They Became Powerful Chemical Tools. ChemCatChem 2020; 12:6082-6102. [PMID: 33381242 PMCID: PMC7756376 DOI: 10.1002/cctc.202001107] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/02/2020] [Indexed: 12/20/2022]
Abstract
Enzymatic approaches to challenges in chemical synthesis are increasingly popular and very attractive to industry given their green nature and high efficiency compared to traditional methods. In this historical review we highlight the developments across several fields that were necessary to create the modern field of biocatalysis, with enzyme engineering and directed evolution at its core. We exemplify the modular, incremental, and highly unpredictable nature of scientific discovery, driven by curiosity, and showcase the resulting examples of cutting-edge enzymatic applications in industry.
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Affiliation(s)
- Christian M Heckmann
- School of Chemistry University of Nottingham University Park Nottingham NG7 2RD UK
| | - Francesca Paradisi
- School of Chemistry University of Nottingham University Park Nottingham NG7 2RD UK
- Department of Chemistry and Biochemistry University of Bern Freiestrasse 3 3012 Bern Switzerland
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13
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Enhancing promiscuous chemistries of a Schiff-base forming enzyme by divergent evolution. Methods Enzymol 2020. [PMID: 32943152 DOI: 10.1016/bs.mie.2020.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Directed evolution has emerged as a powerful technique for the rapid tailoring of enzymes toward particular synthetic demands, spawning a number of enzymes capable of complex chemical transformations. During random mutagenesis of a protein, changes in fitness must be assayed in order to quantify and understand the relative effect a given mutation has, and the assay employed must be carefully chosen to report directly on the transformation of interest. Here, we describe a series of medium-throughput screening techniques that have been utilized for the evolution and engineering of an artificial carboligase, RA95.5-8, resulting in improvement of catalytic efficiency of a number of promiscuous chemistries. The methods make use of common analytical chemistry equipment and low-cost materials, and may help inspire development of novel screening workflows for related transformations.
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14
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Abstract
Microbial lipases represent one of the most important groups of biotechnological biocatalysts. However, the high-level production of lipases requires an understanding of the molecular mechanisms of gene expression, folding, and secretion processes. Stable, selective, and productive lipase is essential for modern chemical industries, as most lipases cannot work in different process conditions. However, the screening and isolation of a new lipase with desired and specific properties would be time consuming, and costly, so researchers typically modify an available lipase with a certain potential for minimizing cost. Improving enzyme properties is associated with altering the enzymatic structure by changing one or several amino acids in the protein sequence. This review detailed the main sources, classification, structural properties, and mutagenic approaches, such as rational design (site direct mutagenesis, iterative saturation mutagenesis) and direct evolution (error prone PCR, DNA shuffling), for achieving modification goals. Here, both techniques were reviewed, with different results for lipase engineering, with a particular focus on improving or changing lipase specificity. Changing the amino acid sequences of the binding pocket or lid region of the lipase led to remarkable enzyme substrate specificity and enantioselectivity improvement. Site-directed mutagenesis is one of the appropriate methods to alter the enzyme sequence, as compared to random mutagenesis, such as error-prone PCR. This contribution has summarized and evaluated several experimental studies on modifying the substrate specificity of lipases.
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15
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Pulido IY, Prieto E, Pieffet GP, Méndez L, Jiménez-Junca CA. Functional Heterologous Expression of Mature Lipase LipA from Pseudomonas aeruginosa PSA01 in Escherichia coli SHuffle and BL21 (DE3): Effect of the Expression Host on Thermal Stability and Solvent Tolerance of the Enzyme Produced. Int J Mol Sci 2020; 21:E3925. [PMID: 32486240 PMCID: PMC7312249 DOI: 10.3390/ijms21113925] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/23/2020] [Accepted: 05/26/2020] [Indexed: 02/06/2023] Open
Abstract
This study aimed to express heterologously the lipase LipA from Pseudomonas aeruginosa PSA01 obtained from palm fruit residues. In previous approaches, LipA was expressed in Escherichia coli fused with its signal peptide and without its disulfide bond, displaying low activity. We cloned the mature LipA with its truncated chaperone Lif in a dual plasmid and overexpressed the enzyme in two E. coli strains: the traditional BL21 (DE3) and the SHuffle® strain, engineered to produce stable cytoplasmic disulfide bonds. We evaluated the effect of the disulfide bond on LipA stability using molecular dynamics. We expressed LipA successfully under isopropyl β-d-1-thio-galactopyranoside (IPTG) and slow autoinducing conditions. The SHuffle LipA showed higher residual activity at 45 °C and a greater hyperactivation after incubation with ethanol than the enzyme produced by E. coli BL21 (DE3). Conversely, the latter was slightly more stable in methanol 50% and 60% (t½: 49.5 min and 9 min) than the SHuffle LipA (t½: 31.5 min and 7.4 min). The molecular dynamics simulations showed that removing the disulfide bond caused some regions of LipA to become less flexible and some others to become more flexible, significantly affecting the closing lid and partially exposing the active site at all times.
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Affiliation(s)
- Ingrid Yamile Pulido
- Biosciences Doctoral Program, Universidad de La Sabana, km 7 Autopista Norte, Chía 250001, Colombia;
| | - Erlide Prieto
- Agro-industrial Processes Research Group, Engineering Faculty, Universidad de La Sabana, km 7 Autopista Norte, Chía, Cundinamarca 250001, Colombia; (E.P.); (L.M.)
| | - Gilles Paul Pieffet
- Science Faculty, Universidad Antonio Nariño, Calle 58 A # 37–94 Bogotá D.C.111511, Colombia;
| | - Lina Méndez
- Agro-industrial Processes Research Group, Engineering Faculty, Universidad de La Sabana, km 7 Autopista Norte, Chía, Cundinamarca 250001, Colombia; (E.P.); (L.M.)
| | - Carlos A. Jiménez-Junca
- Bioprospecting Research Group, Engineering Faculty, Universidad de La Sabana, km 7 Autopista Norte, Chía, Cundinamarca 250001, Colombia
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16
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Cui H, Cao H, Cai H, Jaeger K, Davari MD, Schwaneberg U. Computer-Assisted Recombination (CompassR) Teaches us How to Recombine Beneficial Substitutions from Directed Evolution Campaigns. Chemistry 2020; 26:643-649. [PMID: 31553080 PMCID: PMC7003928 DOI: 10.1002/chem.201903994] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Indexed: 01/09/2023]
Abstract
A main remaining challenge in protein engineering is how to recombine beneficial substitutions. Systematic recombination studies show that poorly performing variants are usually obtained after recombination of 3 to 4 beneficial substitutions. This limits researchers in exploiting nature's potential in generating better enzymes. The Computer-assisted Recombination (CompassR) strategy provides a selection guide for beneficial substitutions that can be recombined to gradually improve enzyme performance by analysis of the relative free energy of folding (ΔΔGfold ). The performance of CompassR was evaluated by analysis of 84 recombinants located on 13 positions of Bacillus subtilis lipase A. The finally obtained variant F17S/V54K/D64N/D91E had a 2.7-fold improved specific activity in 18.3 % (v/v) 1-butyl-3-methylimidazolium chloride ([BMIM][Cl]). In essence, the deducted CompassR rule allows recombination of beneficial substitutions in an iterative manner and empowers researchers to generate better enzymes in a time-efficient manner.
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Affiliation(s)
- Haiyang Cui
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
| | - Hao Cao
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
- Beijing Bioprocess Key Laboratory and College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijing100029P. R. China
| | - Haiying Cai
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
| | - Karl‐Erich Jaeger
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
- Institute of Molecular Enzyme TechnologyHeinrich Heine University Düsseldorf and Research Center Jülich, Wilhelm Johnen Strasse52426JülichGermany
| | - Mehdi D. Davari
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
| | - Ulrich Schwaneberg
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
- DWI Leibniz-Institute for Interactive MaterialsForckenbeckstrasse 5052074AachenGermany
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17
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Alfaro-Chávez AL, Liu JW, Stevenson BJ, Goldman A, Ollis DL. Evolving a lipase for hydrolysis of natural triglycerides along with enhanced tolerance towards a protease and surfactants. Protein Eng Des Sel 2019; 32:129-143. [PMID: 31504920 DOI: 10.1093/protein/gzz023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 06/30/2019] [Accepted: 07/04/2019] [Indexed: 11/15/2022] Open
Abstract
In the accompanying paper, we described evolving a lipase to the point where variants were soluble, stable and capable of degrading C8 TAG and C8 esters. These variants were tested for their ability to survive in an environment that might be encountered in a washing machine. Unfortunately, they were inactivated both by treatment with a protease used in laundry detergents and by very low concentrations of sodium dodecyl sulfate (SDS). In addition, all the variants had very low levels of activity with triglycerides with long aliphatic chains and with naturally occurring oils, like olive oil. Directed evolution was used to select variants with enhanced properties. In the first 10 rounds of evolution, the primary screen was selected for variants capable of hydrolyzing olive oil whereas the secondary screen was selected for enhanced tolerance towards a protease and SDS. In the final six rounds of evolution, the primary and secondary screens identified variants that retained activity after treatment with SDS. Sixteen cycles of evolution gave variants with greatly enhanced lipolytic activity on substrates that had both long (C16 and C18) as well as short (C3 and C8) chains. We found variants that were stable for more than 3 hours in protease concentrations that rapidly degrade the wild-type enzyme. Enhanced tolerance towards SDS was found in variants that could break down naturally occurring lipid and resist protease attack. The amino acid changes that gave enhanced properties were concentrated in the cap domain responsible for substrate binding.
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Affiliation(s)
- Ana L Alfaro-Chávez
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Jian-Wei Liu
- CSIRO Land and Water, Black Mountain, Canberra, ACT 2601, Australia
| | - Bradley J Stevenson
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Adrian Goldman
- School of Biomedical Sciences, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.,Molecular and Integrative Biosciences Program, University of Helsinki, Helsinki FIN-0018, Finland
| | - David L Ollis
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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18
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Brito e Cunha D, Bartkevihi L, Robert J, Cipolatti E, Ferreira A, Oliveira D, Gomes-Neto F, Almeida R, Fernandez-Lafuente R, Freire D, Anobom C. Structural differences of commercial and recombinant lipase B from Candida antarctica: An important implication on enzymes thermostability. Int J Biol Macromol 2019; 140:761-770. [DOI: 10.1016/j.ijbiomac.2019.08.148] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/08/2019] [Accepted: 08/17/2019] [Indexed: 01/29/2023]
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19
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Alfaro-Chávez AL, Liu JW, Porter JL, Goldman A, Ollis DL. Improving on nature’s shortcomings: evolving a lipase for increased lipolytic activity, expression and thermostability. Protein Eng Des Sel 2019; 32:13-24. [DOI: 10.1093/protein/gzz024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 06/30/2019] [Accepted: 07/07/2019] [Indexed: 01/18/2023] Open
Abstract
Abstract
An enzyme must be soluble, stable, active and easy to produce to be useful in industrial applications. Not all enzymes possess these attributes. We set out to determine how many changes are required to convert an enzyme with poor properties into one that has useful properties. Lipase Lip3 from Drosophila melanogaster had been previously optimised for expression in Escherichia coli. The expression levels were good, but Lip3 was mainly insoluble with poor activity. Directed evolution was used to identify variants with enhanced activity along with improved solubility. Five variants and the wild-type (wt) enzyme were purified and characterised. The yield of the wt enzyme was just 2.2 mg/L of culture, while a variant, produced under the same conditions, gave 351 mg. The improvement of activity of the best variant was 200 times higher than that of the wt when the crude lysates were analysed using pNP-C8, but with purified protein, the improvement observed was 1.5 times higher. This means that most of the increase of activity is due to increase in solubility and stability. All the purified variants showed increased thermal stability compared with the wt enzyme that had a T1/2 of 37°C, while the mutant with P291L of 42.2°C and the mutant R7_47D with five mutations had a value of 52.9°C, corresponding to an improvement of 16°C. The improved variants had between five and nine changes compared with the wt enzyme. There were four changes that were found in all 30 final round variants for which sequences were obtained; three of these changes were found in the substrate-binding domain.
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Affiliation(s)
- Ana L Alfaro-Chávez
- Research School of Chemistry, Australian National University, Canberra ACT 2601, Australia
| | - Jian-Wei Liu
- CSIRO Land and Water, Black Mountain, Canberra ACT 2601, Australia
| | - Joanne L Porter
- Research School of Chemistry, Australian National University, Canberra ACT 2601, Australia
| | - Adrian Goldman
- School of Biomedical Sciences, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- Molecular and Integrative Biosciences Program, University of Helsinki, Helsinki FIN-0018, Finland
| | - David L Ollis
- Research School of Chemistry, Australian National University, Canberra ACT 2601, Australia
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20
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Bornscheuer UT, Hauer B, Jaeger KE, Schwaneberg U. Gerichtete Evolution ermöglicht das Design von maßgeschneiderten Proteinen zur nachhaltigen Produktion von Chemikalien und Pharmazeutika. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201812717] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Uwe T. Bornscheuer
- Biotechnologie & Enzymkatalyse; Institut für Biochemie; Universität Greifswald; Felix-Hausdorff-Straße 4 17487 Greifswald Deutschland
| | - Bernhard Hauer
- Institut für Technische Biochemie; Universität Stuttgart; Allmandring 31 70569 Stuttgart Deutschland
| | - Karl Erich Jaeger
- Institut für Molekulare Enzymtechnologie; Heinrich-Heine-, Universität Düsseldorf & Forschungszentrum Jülich; Wilhelm-Johnen-Straße 52426 Jülich Deutschland
| | - Ulrich Schwaneberg
- ABBt-Institut für Biotechnologie; RWTH Aachen und DWI Leibniz-Institut für Interaktive Materialien; Worringer Weg 3 52074 Aachen Deutschland
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21
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Bornscheuer UT, Hauer B, Jaeger KE, Schwaneberg U. Directed Evolution Empowered Redesign of Natural Proteins for the Sustainable Production of Chemicals and Pharmaceuticals. Angew Chem Int Ed Engl 2018; 58:36-40. [DOI: 10.1002/anie.201812717] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Indexed: 01/22/2023]
Affiliation(s)
- Uwe T. Bornscheuer
- Biotechnology & Enzyme Catalysis; Institute of Biochemistry; Greifswald University; Felix Hausdorff Strasse 4 17487 Greifswald Germany
| | - Bernhard Hauer
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Karl Erich Jaeger
- Institute of Molecular Enzyme Technology; Heinrich Heine University Düsseldorf and Research Center Jülich; Wilhelm Johnen Strasse 52426 Jülich Germany
| | - Ulrich Schwaneberg
- ABBt-Institute of Biotechnology; RWTH Aachen University and DWI Leibniz Institute for, Interactive Materials; Worringer Weg 3 52074 Aachen Germany
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22
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Biodiesel production from microalgae oil by lipase from Pseudomonas aeruginosa displayed on yeast cell surface. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.09.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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23
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Masuno M, Molinski TF. Resolution of Atropisomeric Cyclic Catechol Monoether O-Sulfate Esters by a Molluscan Sulfatase. ACS OMEGA 2018; 3:7771-7775. [PMID: 30087921 PMCID: PMC6072249 DOI: 10.1021/acsomega.7b01899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/22/2018] [Indexed: 06/08/2023]
Abstract
Atropisomeric cyclic catechol ethers are notoriously difficult to resolve by classical chiral phase high-performance liquid chromatography. Here, we show the first application of sulfatase enzymes for the kinetic resolution of O-sulfato-catechol ethers with enantioselectivities ranging from 30 to 65% ee, as determined by preparation of their Marfey's ether derivatives. Substrate-structure dependence was briefly explored.
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Affiliation(s)
- Makoto
N. Masuno
- Department
of Chemistry, University of California, 1 Shields Avenue, Davis, California 95616, United States
| | - Tadeusz F. Molinski
- Department of Chemistry and Biochemistry and Skaggs School of Pharmacy and Pharmaceutical
Sciences, University of California, 9500 Gilman Drive 0358, La Jolla, San Diego, California 92093, United States
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24
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Wang XX, Lin CP, Zhang XJ, Liu ZQ, Zheng YG. Improvement of a newly cloned carbonyl reductase and its application to biosynthesize chiral intermediate of duloxetine. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.04.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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25
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Ma F, Chung MT, Yao Y, Nidetz R, Lee LM, Liu AP, Feng Y, Kurabayashi K, Yang GY. Efficient molecular evolution to generate enantioselective enzymes using a dual-channel microfluidic droplet screening platform. Nat Commun 2018; 9:1030. [PMID: 29531246 PMCID: PMC5847605 DOI: 10.1038/s41467-018-03492-6] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 02/19/2018] [Indexed: 01/01/2023] Open
Abstract
Directed evolution has long been a key strategy to generate enzymes with desired properties like high selectivity, but experimental barriers and analytical costs of screening enormous mutant libraries have limited such efforts. Here, we describe an ultrahigh-throughput dual-channel microfluidic droplet screening system that can be used to screen up to ~107 enzyme variants per day. As an example case, we use the system to engineer the enantioselectivity of an esterase to preferentially produce desired enantiomers of profens, an important class of anti-inflammatory drugs. Using two types of screening working modes over the course of five rounds of directed evolution, we identify (from among 5 million mutants) a variant with 700-fold improved enantioselectivity for the desired (S)-profens. We thus demonstrate that this screening platform can be used to rapidly generate enzymes with desired enzymatic properties like enantiospecificity, chemospecificity, and regiospecificity.
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Affiliation(s)
- Fuqiang Ma
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Meng Ting Chung
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yuan Yao
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Robert Nidetz
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Lap Man Lee
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Allen P Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Katsuo Kurabayashi
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Guang-Yu Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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26
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The molecular basis for lipase stereoselectivity. Appl Microbiol Biotechnol 2018; 102:3487-3495. [DOI: 10.1007/s00253-018-8858-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/11/2018] [Accepted: 02/12/2018] [Indexed: 01/13/2023]
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Engineering the Enantioselectivity and Thermostability of a (+)-γ-Lactamase from Microbacterium hydrocarbonoxydans for Kinetic Resolution of Vince Lactam (2-Azabicyclo[2.2.1]hept-5-en-3-one). Appl Environ Microbiol 2017; 84:AEM.01780-17. [PMID: 29054871 DOI: 10.1128/aem.01780-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 09/29/2017] [Indexed: 11/20/2022] Open
Abstract
To produce promising biocatalysts, natural enzymes often need to be engineered to increase their catalytic performance. In this study, the enantioselectivity and thermostability of a (+)-γ-lactamase from Microbacterium hydrocarbonoxydans as the catalyst in the kinetic resolution of Vince lactam (2-azabicyclo[2.2.1]hept-5-en-3-one) were improved. Enantiomerically pure (-)-Vince lactam is the key synthon in the synthesis of antiviral drugs, such as carbovir and abacavir, which are used to fight against HIV and hepatitis B virus. The work was initialized by using the combinatorial active-site saturation test strategy to engineer the enantioselectivity of the enzyme. The approach resulted in two mutants, Val54Ser and Val54Leu, which catalyzed the hydrolysis of Vince lactam to give (-)-Vince lactam, with 99.2% (enantiomeric ratio [E] > 200) enantiomeric excess (ee) and 99.5% ee (E > 200), respectively. To improve the thermostability of the enzyme, 11 residues with high temperature factors (B-factors) calculated by B-FITTER or high root mean square fluctuation (RMSF) values from the molecular dynamics simulation were selected. Six mutants with increased thermostability were obtained. Finally, the mutants generated with improved enantioselectivity and mutants evolved for enhanced thermostability were combined. Several variants showing (+)-selectivity (E value > 200) and improved thermostability were observed. These engineered enzymes are good candidates to serve as enantioselective catalysts for the preparation of enantiomerically pure Vince lactam.IMPORTANCE Enzymatic kinetic resolution of the racemic Vince lactam using (+)-γ-lactamase is the most often utilized means of resolving the enantiomers for the preparation of carbocyclic nucleoside compounds. The efficiency of the native enzymes could be improved by using protein engineering methods, such as directed evolution and rational design. In our study, two properties (enantioselectivity and thermostability) of a γ-lactamase identified from Microbacterium hydrocarbonoxydans were tackled using a semirational design. The protein engineering was initialized by combinatorial active-site saturation test to improve the enantioselectivity. At the same time, two strategies were applied to identify mutation candidates to enhance the thermostability based on calculations from both a static (B-FITTER based on the crystal structure) and a dynamic (root mean square fluctuation [RMSF] values based on molecular dynamics simulations) way. After combining the mutants, we successfully obtained the final mutants showing better properties in both properties. The engineered (+)-lactamase could be a candidate for the preparation of (-)-Vince lactam.
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Jones BJ, Bata Z, Kazlauskas RJ. Identical active sites in hydroxynitrile lyases show opposite enantioselectivity and reveal possible ancestral mechanism. ACS Catal 2017; 7:4221-4229. [PMID: 28798888 DOI: 10.1021/acscatal.7b01108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Evolutionarily related hydroxynitrile lyases from rubber tree (HbHNL) and from Arabidopsis thaliana (AtHNL) follow different catalytic mechanisms with opposite enantioselectivity toward mandelonitrile. We hypothesized that the HbHNL-like mechanism evolved from an enzyme with an AtHNL-like mechanism. We created ancestor-like composite active-sites in each scaffold to elucidate how this transition may have occurred. Surprisingly, a composite active site in HbHNL maintained (S)-selectivity, while the identical set of active site residues in AtHNL maintained (R)-selectivity. Composite active-site mutants that are (S)-selective without the Lys236 and Thr11 that are required for the classical (S)-HNL mechanism suggests a new mechanism. Modeling suggested a possibility for this new mechanism that does not exist in modern enzymes. Thus, the last common ancestor of HbHNL and AtHNL may have used an extinct mechanism, not the AtHNL-like mechanism. Multiple mechanisms are possible with the same catalytic residues and residues outside the active site strongly influence mechanism and enantioselectivity.
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Affiliation(s)
- Bryan J. Jones
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
| | - Zsófia Bata
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
- Department
of Organic Chemistry and Technology, Budapest University of Technology and Economics, 3 Műegyetem rkp, H-1111 Budapest, Hungary
| | - Romas J. Kazlauskas
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
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29
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Biocatalysts for the pharmaceutical industry created by structure-guided directed evolution of stereoselective enzymes. Bioorg Med Chem 2017; 26:1241-1251. [PMID: 28693917 DOI: 10.1016/j.bmc.2017.05.021] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 04/11/2017] [Accepted: 05/09/2017] [Indexed: 01/01/2023]
Abstract
Enzymes have been used for a long time as catalysts in the asymmetric synthesis of chiral intermediates needed in the production of therapeutic drugs. However, this alternative to man-made catalysts has suffered traditionally from distinct limitations, namely the often observed wrong or insufficient enantio- and/or regioselectivity, low activity, narrow substrate range, and insufficient thermostability. With the advent of directed evolution, these problems can be generally solved. The challenge is to develop and apply the most efficient mutagenesis methods which lead to highest-quality mutant libraries requiring minimal screening. Structure-guided saturation mutagenesis and its iterative form have emerged as the method of choice for evolving stereo- and regioselective mutant enzymes needed in the asymmetric synthesis of chiral intermediates. The number of (industrial) applications in the preparation of chiral pharmaceuticals is rapidly increasing. This review features and analyzes typical case studies.
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30
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Syal P, Gupta R. Heterologous expression of lipases YLIP4, YLIP5, YLIP7, YLIP13, and YLIP15 fromYarrowia lipolyticaMSR80 inEscherichia coli: Substrate specificity, kinetic comparison, and enantioselectivity. Biotechnol Appl Biochem 2017; 64:851-861. [DOI: 10.1002/bab.1542] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 10/16/2016] [Indexed: 01/14/2023]
Affiliation(s)
- Poonam Syal
- Department of Microbiology; University of Delhi South Campus; New Delhi India
| | - Rani Gupta
- Department of Microbiology; University of Delhi South Campus; New Delhi India
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31
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Heterologous production of an acidic thermostable lipase with broad-range pH activity from thermophilic fungus Neosartorya fischeri P1. J Biosci Bioeng 2016; 122:539-544. [DOI: 10.1016/j.jbiosc.2016.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 05/06/2016] [Accepted: 05/08/2016] [Indexed: 11/22/2022]
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Sun H, Wang H, Gao W, Chen L, Wu K, Wei D. Directed evolution of nitrilase PpL19 from Pseudomonas psychrotolerans L19 and identification of enantiocomplementary mutants toward mandelonitrile. Biochem Biophys Res Commun 2015; 468:820-5. [PMID: 26577409 DOI: 10.1016/j.bbrc.2015.11.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 11/07/2015] [Indexed: 10/22/2022]
Abstract
Nitrilase PpL19 from Pseudomonas psychrotolerans L19 can hydrolyze racemic mandelonitrile to (S)-mandelic acid with an enantiomeric excess (ee) value of 52.7%. In this study, random mutagenesis combined with site-directed mutagenesis was performed to identify the key residues responsible for nitrilase enantioselectivity. Five enzyme mutants exhibiting distinct selectivity were generated and four "hot spots" (M113, R128, A136, and I168) responsible for enantioselectivity toward mandelonitrile were identified and characterized. Furthermore, through saturation mutagenesis, positions 113 and 128 were confirmed to substantially influence the enantioselectivity of PpL19, and certain replacements of the methionine at position 113, in particular, were found to reverse the enantioselectivity of PpL19 from S- to R-selectivity. Two other single mutants of the enzyme, PpL19-A136Y and -I168Y, also showed reversed selectivity and preferentially produced (R)-mandelic acid (ee values: 66.7% and 74.3%, respectively). By combining the beneficial mutations, two enantiocomplementary nitrilase mutants, PpL19-LH and PpL19-GYY, were created, which exhibited high S- and R-selectivity toward mandelonitrile, respectively: PpL19-LH showed the highest S-selectivity toward mandelonitrile ever reported (91.1% ee), and, notably, the PpL19-GYY mutant was identified to be highly R-selective (90.1% ee) and thus an unexpected enantiocomplementary mutant for mandelonitrile.
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Affiliation(s)
- Huihui Sun
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, PR China
| | - Hualei Wang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, PR China.
| | - Wenyuan Gao
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, PR China
| | - Lifeng Chen
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, PR China
| | - Kai Wu
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, PR China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, PR China.
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Kawahara N, Asano Y. Mutagenesis of an Asn156 Residue in a Surface Region ofS-Selective Hydroxynitrile Lyase fromBaliospermum montanumEnhances Catalytic Efficiency and Enantioselectivity. Chembiochem 2015; 16:1891-1895. [DOI: 10.1002/cbic.201500225] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Indexed: 11/11/2022]
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Smith MR, Khera E, Wen F. Engineering Novel and Improved Biocatalysts by Cell Surface Display. Ind Eng Chem Res 2015; 54:4021-4032. [PMID: 29056821 PMCID: PMC5647830 DOI: 10.1021/ie504071f] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Biocatalysts, especially enzymes, have the ability to catalyze reactions with high product selectivity, utilize a broad range of substrates, and maintain activity at low temperature and pressure. Therefore, they represent a renewable, environmentally friendly alternative to conventional catalysts. Most current industrial-scale chemical production processes using biocatalysts employ soluble enzymes or whole cells expressing intracellular enzymes. Cell surface display systems differ by presenting heterologous enzymes extracellularly, overcoming some of the limitations associated with enzyme purification and substrate transport. Additionally, coupled with directed evolution, cell surface display is a powerful platform for engineering enzymes with enhanced properties. In this review, we will introduce the molecular and cellular principles of cell surface display and discuss how it has been applied to engineer enzymes with improved properties as well as to develop surface-engineered microbes as whole-cell biocatalysts.
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Affiliation(s)
- Mason R. Smith
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Eshita Khera
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Fei Wen
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
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Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
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Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
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Camacho-Ruiz MDLA, Mateos-Díaz JC, Carrière F, Rodriguez JA. A broad pH range indicator-based spectrophotometric assay for true lipases using tributyrin and tricaprylin. J Lipid Res 2015; 56:1057-67. [PMID: 25748441 DOI: 10.1194/jlr.d052837] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Indexed: 11/20/2022] Open
Abstract
A continuous assay is proposed for the screening of acidic, neutral, or alkaline lipases using microtiter plates, emulsified short- and medium-chain TGs, and a pH indicator. The lipase activity measurement is based on the decrease of the pH indicator optical density due to protonation which is caused by the release of FFAs during the hydrolysis of TGs and thus acidification. Purified lipases with distinct pH optima and an esterase were used to validate the method. The rate of lipolysis was found to be linear with time and proportional to the amount of enzyme added in each case. Specific activities measured with this microplate assay method were lower than those obtained by the pH-stat technique. Nevertheless, the pH-dependent profiles of enzymatic activity were similar with both assays. In addition, the substrate preference of each enzyme tested was not modified and this allowed discriminating lipase and esterase activities using tributyrin (low water solubility) and tricaprylin (not water soluble) as substrates. This continuous lipase assay is compatible with a high sample throughput and can be applied for the screening of lipases and lipase inhibitors from biological samples.
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Affiliation(s)
| | | | - Frédéric Carrière
- CNRS, Aix-Marseille Université, UMR 7282 Enzymologie Interfaciale et Physiologie de la Lipolyse, 13402 Marseille Cedex 20, France
| | - Jorge A Rodriguez
- Biotecnología Industrial, CIATEJ A.C., 44270 Guadalajara, Jalisco, Mexico
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Li J, Yue L, Li C, Pan Y, Yang L. Enantioselectivity and catalysis improvements of Pseudomonas cepacia lipase with Tyr and Asp modification. Catal Sci Technol 2015. [DOI: 10.1039/c5cy00110b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A concise strategy to improve the p-nitrophenyl palmitate catalytic activity and enantioselectivity towards secondary alcohols of PcL is described.
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Affiliation(s)
- Jing Li
- Institute of Biological Engineering
- Department of Chemical & Biological Engineering
- Zhejiang University
- Hangzhou 310027
- China
| | - Lei Yue
- Department of Chemistry
- Zhejiang University
- Hangzhou
- China
| | - Chang Li
- Department of Chemistry
- Zhejiang University
- Hangzhou
- China
| | - Yuanjiang Pan
- Department of Chemistry
- Zhejiang University
- Hangzhou
- China
| | - Lirong Yang
- Institute of Biological Engineering
- Department of Chemical & Biological Engineering
- Zhejiang University
- Hangzhou 310027
- China
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Min B, Park J, Sim YK, Jung S, Kim SH, Song JK, Kim BT, Park SY, Yun J, Park S, Lee H. Hydrogen-Bonding-Driven Enantioselective Resolution against the Kazlauskas Rule To Afford γ-Amino Alcohols byCandida rugosaLipase. Chembiochem 2014; 16:77-82. [DOI: 10.1002/cbic.201402563] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Indexed: 11/05/2022]
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Madan B, Mishra P. Directed evolution of Bacillus licheniformis lipase for improvement of thermostability. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2014.08.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Li XJ, Zheng RC, Ma HY, Huang JF, Zheng YG. Key residues responsible for enhancement of catalytic efficiency of Thermomyces lanuginosus lipase Lip revealed by complementary protein engineering strategy. J Biotechnol 2014; 188:29-35. [DOI: 10.1016/j.jbiotec.2014.08.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Revised: 07/25/2014] [Accepted: 08/01/2014] [Indexed: 01/13/2023]
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Chen H, Wu J, Yang L, Xu G. Characterization and structure basis of Pseudomonas alcaligenes lipase's enantiopreference towards d,l-menthyl propionate. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.01.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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43
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Anobom CD, Pinheiro AS, De-Andrade RA, Aguieiras ECG, Andrade GC, Moura MV, Almeida RV, Freire DM. From structure to catalysis: recent developments in the biotechnological applications of lipases. BIOMED RESEARCH INTERNATIONAL 2014; 2014:684506. [PMID: 24783219 PMCID: PMC3982246 DOI: 10.1155/2014/684506] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 02/17/2014] [Indexed: 12/23/2022]
Abstract
Microbial lipases are highly appreciated as biocatalysts due to their peculiar characteristics such as the ability to utilize a wide range of substrates, high activity and stability in organic solvents, and regio- and/or enantioselectivity. These enzymes are currently being applied in a variety of biotechnological processes, including detergent preparation, cosmetics and paper production, food processing, biodiesel and biopolymer synthesis, and the biocatalytic resolution of pharmaceutical derivatives, esters, and amino acids. However, in certain segments of industry, the use of lipases is still limited by their high cost. Thus, there is a great interest in obtaining low-cost, highly active, and stable lipases that can be applied in several different industrial branches. Currently, the design of specific enzymes for each type of process has been used as an important tool to address the limitations of natural enzymes. Nowadays, it is possible to "order" a "customized" enzyme that has ideal properties for the development of the desired bioprocess. This review aims to compile recent advances in the biotechnological application of lipases focusing on various methods of enzyme improvement, such as protein engineering (directed evolution and rational design), as well as the use of structural data for rational modification of lipases in order to create higher active and selective biocatalysts.
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Affiliation(s)
- Cristiane D. Anobom
- Departamento de Bioquímica, Universidade Federal do Rio de Janeiro, Avenida Athos da Silveira Ramos, 21941-909 Rio de Janeiro, RJ, Brazil
| | - Anderson S. Pinheiro
- Departamento de Bioquímica, Universidade Federal do Rio de Janeiro, Avenida Athos da Silveira Ramos, 21941-909 Rio de Janeiro, RJ, Brazil
| | - Rafael A. De-Andrade
- Departamento de Bioquímica, Universidade Federal do Rio de Janeiro, Avenida Athos da Silveira Ramos, 21941-909 Rio de Janeiro, RJ, Brazil
| | - Erika C. G. Aguieiras
- Departamento de Bioquímica, Universidade Federal do Rio de Janeiro, Avenida Athos da Silveira Ramos, 21941-909 Rio de Janeiro, RJ, Brazil
| | - Guilherme C. Andrade
- Departamento de Bioquímica, Universidade Federal do Rio de Janeiro, Avenida Athos da Silveira Ramos, 21941-909 Rio de Janeiro, RJ, Brazil
| | - Marcelo V. Moura
- Departamento de Bioquímica, Universidade Federal do Rio de Janeiro, Avenida Athos da Silveira Ramos, 21941-909 Rio de Janeiro, RJ, Brazil
| | - Rodrigo V. Almeida
- Departamento de Bioquímica, Universidade Federal do Rio de Janeiro, Avenida Athos da Silveira Ramos, 21941-909 Rio de Janeiro, RJ, Brazil
| | - Denise M. Freire
- Departamento de Bioquímica, Universidade Federal do Rio de Janeiro, Avenida Athos da Silveira Ramos, 21941-909 Rio de Janeiro, RJ, Brazil
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Abstract
Pseudomonas aeruginosa is a versatile human opportunistic pathogen that produces and secretes an arsenal of enzymes, proteins and small molecules many of which serve as virulence factors. Notably, about 40 % of P. aeruginosa genes code for proteins of unknown function, among them more than 80 encoding putative, but still unknown lipolytic enzymes. This group of hydrolases (EC 3.1.1) is known already for decades, but only recently, several of these enzymes have attracted attention as potential virulence factors. Reliable and reproducible enzymatic activity assays are crucial to determine their physiological function and particularly assess their contribution to pathogenicity. As a consequence of the unique biochemical properties of lipids resulting in the formation of micellar structures in water, the reproducible preparation of substrate emulsions is strongly dependent on the method used. Furthermore, the physicochemical properties of the respective substrate emulsion may drastically affect the activities of the tested lipolytic enzymes. Here, we describe common methods for the activity determination of lipase, esterase, phospholipase, and lysophospholipase. These methods cover lipolytic activity assays carried out in vitro, with cell extracts or separated subcellular compartments and with purified enzymes. We have attempted to describe standardized protocols, allowing the determination and comparison of enzymatic activities of lipolytic enzymes from different sources. These methods should also encourage the Pseudomonas community to address the wealth of still unexplored lipolytic enzymes encoded and produced by P. aeruginosa.
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Affiliation(s)
- Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Research Centre Juelich Heinrich-Heine-University of Duesseldorf, D-52426, Juelich, Germany,
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Chen H, Wu J, Yang L, Xu G. A combination of site-directed mutagenesis and chemical modification to improve diastereopreference of Pseudomonas alcaligenes lipase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2494-501. [DOI: 10.1016/j.bbapap.2013.08.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 08/26/2013] [Accepted: 08/27/2013] [Indexed: 11/29/2022]
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Timm M, Görl J, Kraus M, Kralj S, Hellmuth H, Beine R, Buchholz K, Dijkhuizen L, Seibel J. An Unconventional Glycosyl Transfer Reaction: Glucansucrase GTFA Functions as an Allosyltransferase Enzyme. Chembiochem 2013; 14:2423-6. [DOI: 10.1002/cbic.201300392] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Indexed: 11/12/2022]
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Reetz MT. Biocatalysis in organic chemistry and biotechnology: past, present, and future. J Am Chem Soc 2013; 135:12480-96. [PMID: 23930719 DOI: 10.1021/ja405051f] [Citation(s) in RCA: 522] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Enzymes as catalysts in synthetic organic chemistry gained importance in the latter half of the 20th century, but nevertheless suffered from two major limitations. First, many enzymes were not accessible in large enough quantities for practical applications. The advent of recombinant DNA technology changed this dramatically in the late 1970s. Second, many enzymes showed a narrow substrate scope, often poor stereo- and/or regioselectivity and/or insufficient stability under operating conditions. With the development of directed evolution beginning in the 1990s and continuing to the present day, all of these problems can be addressed and generally solved. The present Perspective focuses on these and other developments which have popularized enzymes as part of the toolkit of synthetic organic chemists and biotechnologists. Included is a discussion of the scope and limitation of cascade reactions using enzyme mixtures in vitro and of metabolic engineering of pathways in cells as factories for the production of simple compounds such as biofuels and complex natural products. Future trends and problems are also highlighted, as is the discussion concerning biocatalysis versus nonbiological catalysis in synthetic organic chemistry. This Perspective does not constitute a comprehensive review, and therefore the author apologizes to those researchers whose work is not specifically treated here.
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Affiliation(s)
- Manfred T Reetz
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein Strasse, 35032 Marburg, Germany.
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49
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Tielen P, Kuhn H, Rosenau F, Jaeger KE, Flemming HC, Wingender J. Interaction between extracellular lipase LipA and the polysaccharide alginate of Pseudomonas aeruginosa. BMC Microbiol 2013; 13:159. [PMID: 23848942 PMCID: PMC3733896 DOI: 10.1186/1471-2180-13-159] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 07/08/2013] [Indexed: 12/21/2022] Open
Abstract
Background As an opportunistic human pathogen Pseudomonas aeruginosa is able to cause acute and chronic infections. The biofilm mode of life significantly contributes to the growth and persistence of P. aeruginosa during an infection process and mediates the pathogenicity of the bacterium. Within a biofilm mucoid strains of P. aeruginosa simultaneously produce and secrete several hydrolytic enzymes and the extracellular polysaccharide alginate. The focus of the current study was the interaction between extracellular lipase LipA and alginate, which may be physiologically relevant in biofilms of mucoid P. aeruginosa. Results Fluorescence microscopy of mucoid P. aeruginosa biofilms were performed using fluorogenic lipase substrates. It showed a localization of the extracellular enzyme near the cells. A microtiter plate-based binding assay revealed that the polyanion alginate is able to bind LipA. A molecular modeling approach showed that this binding is structurally based on electrostatic interactions between negatively charged residues of alginate and positively charged amino acids of the protein localized opposite of the catalytic centre. Moreover, we showed that the presence of alginate protected the lipase activity by protection from heat inactivation and from degradation by the endogenous, extracellular protease elastase LasB. This effect was influenced by the chemical properties of the alginate molecules and was enhanced by the presence of O-acetyl groups in the alginate chain. Conclusion We demonstrate that the extracellular lipase LipA from P. aeruginosa interacts with the polysaccharide alginate in the self-produced extracellular biofilm matrix of P. aeruginosa via electrostatic interactions suggesting a role of this interaction for enzyme immobilization and accumulation within biofilms. This represents a physiological advantage for the cells. Especially in the biofilm lifestyle, the enzyme is retained near the cell surface, with the catalytic centre exposed towards the substrate and is protected from denaturation and proteolytic degradation.
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Affiliation(s)
- Petra Tielen
- Department of Aquatic Microbiology, University of Duisburg-Essen, Faculty of Chemistry, Biofilm Centre, Essen, Germany.
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Akbulut N, Tuzlakoğlu Öztürk M, Pijning T, İşsever Öztürk S, Gümüşel F. Improved activity and thermostability of Bacillus pumilus lipase by directed evolution. J Biotechnol 2013; 164:123-9. [DOI: 10.1016/j.jbiotec.2012.12.016] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 12/20/2012] [Accepted: 12/21/2012] [Indexed: 11/27/2022]
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