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Abe I, Tagami U, Kashiwagi T, Sugiyama M, Suzuki SI, Takagi H, Yokozeki K. Screening of α-amino acid ester acyl transferase variant with improved activity by combining rational and random mutagenesis. J Biochem 2022; 173:43-52. [PMID: 36260086 DOI: 10.1093/jb/mvac083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/21/2022] [Accepted: 10/04/2022] [Indexed: 12/29/2022] Open
Abstract
Random and rational mutagenesis of an α-amino acid ester acyl transferase from Sphingobacterium siyangensis AJ2458 (SAET) was conducted to examine the production of aspartame, an α-l-aspartyl-l-phenylalanine methyl ester. We previously reported aspartame production via combination of enzymatic and chemical methods. However, the productivity of the aspartame intermediate by SAET was approximately one-fifth that of l-alanyl-l-glutamine (Ala-Gln), whose production method has already been established. Here, to improve the enzymatic activity of SAET, we performed random mutagenesis in the gene encoding SAET and obtained 10 mutations that elevated the enzymatic activity (1.2- to 1.7-fold increase) relative to that of wild-type SAET. To further improve the activity, we performed mutagenesis to optimize the combination of the obtained mutations and finally selected one SAET variant with 10 amino acid substitutions (M35-4 SAET). An Escherichia coli strain overexpressing M35-4 SAET displayed a 5.7-fold higher activity than that of the wild-type SAET, which was almost equal to that of Ala-Gln by an E. coli strain overexpressing wild-type SAET. The Vmax value of M35-4 SAET was 2.0-fold greater, and its thermostability was higher than those of wild-type SAET. These results suggest that the obtained SAET variants contribute to improvement in aspartame production.
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Affiliation(s)
- Isao Abe
- Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co., Inc., Kawasaki 210-8681, Japan.,Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara 630-0192, Japan
| | - Uno Tagami
- Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co., Inc., Kawasaki 210-8681, Japan
| | - Tatsuki Kashiwagi
- Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co., Inc., Kawasaki 210-8681, Japan
| | - Masakazu Sugiyama
- Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co., Inc., Kawasaki 210-8681, Japan
| | - Shun-Ichi Suzuki
- Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co., Inc., Kawasaki 210-8681, Japan
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara 630-0192, Japan
| | - Kenzo Yokozeki
- Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co., Inc., Kawasaki 210-8681, Japan
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Tian L, Zhou J, Lv Q, Liu F, Yang T, Zhang X, Xu M, Rao Z. Rational engineering of the Plasmodium falciparuml-lactate dehydrogenase loop involved in catalytic proton transfer to improve chiral 2-hydroxybutyric acid production. Int J Biol Macromol 2021; 179:71-79. [PMID: 33631263 DOI: 10.1016/j.ijbiomac.2021.02.144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/13/2021] [Accepted: 02/19/2021] [Indexed: 12/29/2022]
Abstract
l-lactate dehydrogenases (LDHs) has been widely studied for their ability to reduce 2-keto acids for the production of 2-hydroxy acids, whereby 2-hydroxybutyric acids (2-HBA) is among the most important fundamental building blocks for synthesizing pharmaceuticals and biodegradable materials. However, LDHs usually show low activity towards 2-keto acids with longer side chain such as 2-oxobutyric acid (2-OBA). Here rational engineering of the Plasmodium falciparum LDH loop with residue involved in the catalytic proton transfer was initially studied. By combining homology alignment and structure-based design approach, we found that changing the charge characteristics or hydrogen bond network interactions of this loop could improve enzymatic catalytic activities and stabilities towards 2-OBA. Compared with wild type, variant N197Dldh showed 1.15 times higher activity and 2.73 times higher Kcat/Km. The half-life of variant N197Dldh at 40 °C increased to 77.9 h compared with 50.4 h of wild type. Furthermore, asymmetric synthesis of (S)-2-HBA with coenzyme regeneration revealed 95.8 g/L production titer within 12 h for variant N197Dldh, 2.05 times higher than using wild type. Our study indicated the importance of loop with residues involved in the catalytic proton transfer process, and the engineered LDH would be more suitable for (S)-2-HBA production.
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Affiliation(s)
- Lingzhi Tian
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, China
| | - Junping Zhou
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, China
| | - Qinglan Lv
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, China
| | - Fei Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, China
| | - Taowei Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, China
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, China.
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, China.
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Azouz RAM, Hegazy UM, Said MM, Bassuiny RI, Salem AM, Fahmy AS. Improving the catalytic efficiency of thermostable Geobacillus stearothermophilus xylanase XT6 by single-amino acid substitution. J Biochem 2020; 167:203-215. [PMID: 31617574 DOI: 10.1093/jb/mvz086] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/02/2019] [Indexed: 01/09/2023] Open
Abstract
Directed evolution using error-prone polymerase chain reaction was employed in the current study to enhance the catalytic efficiency of a thermostable Geobacillus stearothermophilus xylanase XT6 parent. High-throughput screening identified two variants with enhanced activity. Sequencing analysis revealed the presence of a single-amino acid substitution (P209L or V161L) in each variant. The maximum activity of mutant V161L and P209L was at 85°C and 70°C, respectively. Both mutants exhibited maximum activity at pH 7. The thermal and alkaline tolerance of mutant V161L only were markedly improved. The two mutants were more resistant to ethanol inhibition than the parent. Substrate specificity of the two mutants was shifted from beechwood xylan to birchwood xylan. The potential of the two mutants to hydrolyze rice straw and sugarcane bagasse increased. Both turnover number (kcat) and catalytic efficiency (kcat/kM) increased 12.2- and 5.7-folds for variant P209L and 13- and 6.5-folds for variant V161L, respectively, towards birchwood xylan. Based on the previously published crystal structure of extracellular G. stearothermophilus xylanase XT6, V161L and P209L mutation locate on βα-loops. Conformational changes of the respective loops could potentiate the loop swinging, product release and consequently result in enhancement of the catalytic performance.
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Affiliation(s)
- Rasha A M Azouz
- Genetic Engineering and Biotechnology Research Division, Molecular Biology Department, National Research Centre, El-Behouth Street, Dokki, 12622 Giza, Egypt
| | - Usama M Hegazy
- Genetic Engineering and Biotechnology Research Division, Molecular Biology Department, National Research Centre, El-Behouth Street, Dokki, 12622 Giza, Egypt
| | - Mahmoud M Said
- Faculty of Science, Department of Biochemistry, Ain Shams University, El-Khalyfa El-Mamoun Street, Abbasya, 11566 Cairo, Egypt
| | - Roqaya I Bassuiny
- Genetic Engineering and Biotechnology Research Division, Molecular Biology Department, National Research Centre, El-Behouth Street, Dokki, 12622 Giza, Egypt
| | - Ahmed M Salem
- Faculty of Science, Department of Biochemistry, Ain Shams University, El-Khalyfa El-Mamoun Street, Abbasya, 11566 Cairo, Egypt
| | - Afaf S Fahmy
- Genetic Engineering and Biotechnology Research Division, Molecular Biology Department, National Research Centre, El-Behouth Street, Dokki, 12622 Giza, Egypt
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Current situation of biofuel production and its enhancement by CRISPR/Cas9-mediated genome engineering of microbial cells. Microbiol Res 2019; 219:1-11. [DOI: 10.1016/j.micres.2018.10.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 10/10/2018] [Accepted: 10/30/2018] [Indexed: 12/26/2022]
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Payal D, Prateek K, Munendra K, Renu S, Monisha KK. Purification and molecular characterization of chitinases from soil actinomycetes. ACTA ACUST UNITED AC 2017. [DOI: 10.5897/ajmr2017.8612] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Anné J, Vrancken K, Van Mellaert L, Van Impe J, Bernaerts K. Protein secretion biotechnology in Gram-positive bacteria with special emphasis on Streptomyces lividans. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1750-61. [PMID: 24412306 DOI: 10.1016/j.bbamcr.2013.12.023] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 12/26/2013] [Accepted: 12/31/2013] [Indexed: 02/07/2023]
Abstract
Proteins secreted by Gram-positive bacteria are released into the culture medium with the obvious benefit that they usually retain their native conformation. This property makes these host cells potentially interesting for the production of recombinant proteins, as one can take full profit of established protocols for the purification of active proteins. Several state-of-the-art strategies to increase the yield of the secreted proteins will be discussed, using Streptomyces lividans as an example and compared with approaches used in some other host cells. It will be shown that approaches such as increasing expression and translation levels, choice of secretion pathway and modulation of proteins thereof, avoiding stress responses by changing expression levels of specific (stress) proteins, can be helpful to boost production yield. In addition, the potential of multi-omics approaches as a tool to understand the genetic background and metabolic fluxes in the host cell and to seek for new targets for strain and protein secretion improvement is discussed. It will be shown that S. lividans, along with other Gram-positive host cells, certainly plays a role as a production host for recombinant proteins in an economically viable way. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Jozef Anné
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Laboratory of Molecular Bacteriology, Herestraat 49, box 1037, B-3000 Leuven, Belgium.
| | - Kristof Vrancken
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Laboratory of Molecular Bacteriology, Herestraat 49, box 1037, B-3000 Leuven, Belgium.
| | - Lieve Van Mellaert
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Laboratory of Molecular Bacteriology, Herestraat 49, box 1037, B-3000 Leuven, Belgium.
| | - Jan Van Impe
- Chemical and Biochemical Process Technology and Control Section (BioTeC), Department of Chemical Engineering, KU Leuven, Willem de Croylaan 46 box 2423, B-3001 Leuven, Belgium.
| | - Kristel Bernaerts
- Chemical and Biochemical Process Technology and Control Section (BioTeC), Department of Chemical Engineering, KU Leuven, Willem de Croylaan 46 box 2423, B-3001 Leuven, Belgium.
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Enhancing catalytic activity of a hybrid xylanase through single substitution of Leu to Pro near the active site. World J Microbiol Biotechnol 2011; 28:929-35. [PMID: 22805813 DOI: 10.1007/s11274-011-0890-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 09/10/2011] [Indexed: 12/21/2022]
Abstract
A modified error-prone PCR and high-throughout screening system based on 96-well plate were employed to improve catalytic activity of a hybrid xylanase (ATx). The mutant (FSI-A124) with enhanced activity was further heterologously expressed in Pichia pastoris under the control of GAP promoter. The recombinant xylanase driven by the Saccharomyces cerevisiae α-mating factor was secreted into culture medium. After growth in YPD medium for 96 h, xylanase activity in the culture supernatant reached 66.1 U ml(-1), which was 2.92 times as that of its parent. 6 × His-tagged purification increased the specific activity to 1557.61 U mg(-1). The optimum temperature and pH of recombinant xylanase were 55°C and 6.0, respectively. A single amino acid substitution (L49P) was observed within sequence of the mutant. Insight of the three dimensional structure revealed that proline possibly produced weaker hydrogen bond, van der Waals force and hydrophobic interaction with other residues nearby than leucine, especially for V174, contributing to the flexibility of catalytic residue E177. In this study, FSI-A124 exhibited higher xylanase activity but poorer thermostability than its parent, indicating that activity and stability might be negatively correlated.
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Yang H, Wang K, Song X, Xu F. Production of xylooligosaccharides by xylanase from Pichia stipitis based on xylan preparation from triploid Populas tomentosa. BIORESOURCE TECHNOLOGY 2011; 102:7171-7176. [PMID: 21565493 DOI: 10.1016/j.biortech.2011.03.110] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 03/31/2011] [Accepted: 03/31/2011] [Indexed: 05/30/2023]
Abstract
Xylooligosaccharides (XOS) with DP 2-4 are important synbiotics used as food ingredients based on its prebiotic characteristics. In this work, the production of XOS from lignocellulosic material was performed by combined chemical-enzymatic methods. Xylan was prepared from triploid Populas tomentosa, and bioconverted into XOS by crude xylanase solution obtained from Pichia stipitis. The effects of reaction time, temperature, enzyme dosage, and pH value on the production of XOS were fully evaluated. Under the optimal condition (25U g(-1) substrate, pH 5.4 and 50°C), 36.8% of the xylan preparation was converted to XOS, equivalent to 3.95 mg/mL of the hydrolyzate. Xylobiose, xylotriose and xylotetrose were analyzed to be the main products of the enzymatic hydrolyzate, which together accounted for over 95% of the released oligosaccharides. Meanwhile, the effect of sonication pretreatment on the conversion efficiency of the xylan preparation was also investigated.
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Affiliation(s)
- Haiyan Yang
- Institute of Biomass Chemistry and Technology, College of Material Science and Technology, Beijing Forestry University, Beijing, 100083, China
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Hawwa R, Larsen SD, Ratia K, Mesecar AD. Structure-Based and Random Mutagenesis Approaches Increase the Organophosphate-Degrading Activity of a Phosphotriesterase Homologue from Deinococcus radiodurans. J Mol Biol 2009; 393:36-57. [DOI: 10.1016/j.jmb.2009.06.083] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2009] [Revised: 06/13/2009] [Accepted: 06/15/2009] [Indexed: 10/20/2022]
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Maki M, Leung KT, Qin W. The prospects of cellulase-producing bacteria for the bioconversion of lignocellulosic biomass. Int J Biol Sci 2009; 5:500-16. [PMID: 19680472 PMCID: PMC2726447 DOI: 10.7150/ijbs.5.500] [Citation(s) in RCA: 261] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Accepted: 07/21/2009] [Indexed: 11/05/2022] Open
Abstract
Lignocellulosic biomass is a renewable and abundant resource with great potential for bioconversion to value-added bioproducts. However, the biorefining process remains economically unfeasible due to a lack of biocatalysts that can overcome costly hurdles such as cooling from high temperature, pumping of oxygen/stirring, and, neutralization from acidic or basic pH. The extreme environmental resistance of bacteria permits screening and isolation of novel cellulases to help overcome these challenges. Rapid, efficient cellulase screening techniques, using cellulase assays and metagenomic libraries, are a must. Rare cellulases with activities on soluble and crystalline cellulose have been isolated from strains of Paenibacillus and Bacillus and shown to have high thermostability and/or activity over a wide pH spectrum. While novel cellulases from strains like Cellulomonas flavigena and Terendinibacter turnerae, produce multifunctional cellulases with broader substrate utilization. These enzymes offer a framework for enhancement of cellulases including: specific activity, thermalstability, or end-product inhibition. In addition, anaerobic bacteria like the clostridia offer potential due to species capable of producing compound multienzyme complexes called cellulosomes. Cellulosomes provide synergy and close proximity of enzymes to substrate, increasing activity towards crystalline cellulose. This has lead to the construction of designer cellulosomes enhanced for specific substrate activity. Furthermore, cellulosome-producing Clostridium thermocellum and its ability to ferment sugars to ethanol; its amenability to co-culture and, recent advances in genetic engineering, offer a promising future in biofuels. The exploitation of bacteria in the search for improved enzymes or strategies provides a means to upgrade feasibility for lignocellulosic biomass conversion, ultimately providing means to a 'greener' technology.
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Affiliation(s)
- Miranda Maki
- Biorefining Research Initiative, Lakehead University, Thunder Bay, Ontario, Canada
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