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Hoya M, Matsunaga R, Nagatoishi S, Ide T, Kuroda D, Tsumoto K. Impact of single-residue mutations on protein thermal stability: The case of threonine 83 of BC2L-CN lectin. Int J Biol Macromol 2024; 272:132682. [PMID: 38815947 DOI: 10.1016/j.ijbiomac.2024.132682] [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] [Received: 10/11/2023] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 06/01/2024]
Abstract
The thermal stability of trimeric lectin BC2L-CN was investigated and found to be considerably altered when mutating residue 83, originally a threonine, located at the fucose-binding loop. Mutants were analyzed using differential scanning calorimetry and isothermal microcalorimetry. Although most mutations decreased the affinity of the protein for oligosaccharide H type 1, six mutations increased the melting temperature (Tm) by >5 °C; one mutation, T83P, increased the Tm value by 18.2 °C(T83P, Tm = 96.3 °C). In molecular dynamic simulations, the investigated thermostable mutants, T83P, T83A, and T83S, had decreased fluctuations in the loop containing residue 83. In the T83S mutation, the side-chain hydroxyl group of serine formed a hydrogen bond with a nearby residue, suggesting that the restricted movement of the side-chain resulted in fewer fluctuations and enhanced thermal stability. Residue 83 is located at the interface and near the upstream end of the equivalent loop in a different protomer; therefore, fluctuations by this residue likely propagate throughout the loop. Our study of the dramatic change in thermal stability by a single amino acid mutation provides useful insights into the rational design of protein structures, especially the structures of oligomeric proteins.
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Affiliation(s)
- Megumi Hoya
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; Sagami Chemical Research Institute, 2743-1 Hayakawa, Ayase, Kanagawa 252-1193, Japan
| | - Ryo Matsunaga
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Satoru Nagatoishi
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; Project Division of Advanced Biopharmaceutical Science, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
| | - Teruhiko Ide
- Tosoh Corporation, Hayakawa, 2743-1 Ayase, Kanagawa 252-1123, Japan
| | - Daisuke Kuroda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; Project Division of Advanced Biopharmaceutical Science, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
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Shi J, Mwabulili F, Xie Y, Yang Y, Sun S, Li Q, Ma W, Jia H. Characterization, Structural Analysis, and Thermal Stability Mutation of a New Zearalenone-Degrading Enzyme Mined from Bacillus subtilis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3025-3035. [PMID: 38300990 DOI: 10.1021/acs.jafc.3c06767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Zearalenone (ZEN) is a widespread mycotoxin that causes serious damage to animal husbandry and poses a threat to human health. A screen of ZEN-degrading soil bacteria yielded Bacillus subtilis YT-4, which yielded 80% ZEN degradation after 6 h and 95% after 36 h. The gene sequence encoding the degradative enzyme ZENY was mined from the genome of YT-4 and expressed in yeast. ZENY is an α/β-hydrolase with an optimal enzyme activity at 37 °C and pH 8. By breaking the lactone ring of ZEN, it produces ZENY-C18H24O5 with a molecular weight of 320.16 g/mol. Sequence comparison and molecular docking analyses identified the catalytic ZENY triad 99S-245H-123E and the primary ZEN-binding mode within the hydrophobic pocket of the enzyme. To improve the thermal stability of the enzyme for industrial applications, we introduced a mutation at the N-terminus, specifically replacing the fifth residue N with V, and achieved a 25% improvement in stability at 45 °C. These findings aim to achieve ZEN biodegradation and provide insight into the structure and function of ZEN hydrolases.
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Affiliation(s)
- Jinghao Shi
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001 , P. R. China
- Henan Key Laboratory of Cereal and Oil Food Safety Inspection and Control, Zhengzhou, Henan 450001, People's Republic of China
| | - Fred Mwabulili
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001 , P. R. China
- Henan Key Laboratory of Cereal and Oil Food Safety Inspection and Control, Zhengzhou, Henan 450001, People's Republic of China
| | - Yanli Xie
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001 , P. R. China
- Henan Key Laboratory of Cereal and Oil Food Safety Inspection and Control, Zhengzhou, Henan 450001, People's Republic of China
| | - Yuhui Yang
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001 , P. R. China
- Henan Key Laboratory of Cereal and Oil Food Safety Inspection and Control, Zhengzhou, Henan 450001, People's Republic of China
| | - Shumin Sun
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001 , P. R. China
- Henan Key Laboratory of Cereal and Oil Food Safety Inspection and Control, Zhengzhou, Henan 450001, People's Republic of China
| | - Qian Li
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001 , P. R. China
- Henan Key Laboratory of Cereal and Oil Food Safety Inspection and Control, Zhengzhou, Henan 450001, People's Republic of China
| | - Weibin Ma
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001 , P. R. China
- Henan Key Laboratory of Cereal and Oil Food Safety Inspection and Control, Zhengzhou, Henan 450001, People's Republic of China
| | - Hang Jia
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001 , P. R. China
- Henan Key Laboratory of Cereal and Oil Food Safety Inspection and Control, Zhengzhou, Henan 450001, People's Republic of China
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Ghaedizadeh S, Zeinali M, Dabirmanesh B, Rasekh B, Khajeh K, Banaei-Moghaddam AM. Rational design engineering of a more thermostable Sulfurihydrogenibium yellowstonense carbonic anhydrase for potential application in carbon dioxide capture technologies. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:140962. [PMID: 37716447 DOI: 10.1016/j.bbapap.2023.140962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/18/2023] [Accepted: 09/06/2023] [Indexed: 09/18/2023]
Abstract
Implementing hyperthermostable carbonic anhydrases into CO2 capture and storage technologies in order to increase the rate of CO2 absorption from the industrial flue gases is of great importance from technical and economical points of view. The present study employed a combination of in silico tools to further improve thermostability of a known thermostable carbonic anhydrase from Sulfurihydrogenibium yellowstonense. Experimental results showed that our rationally engineered K100G mutant not only retained the overall structure and catalytic efficiency but also showed a 3 °C increase in the melting temperature and a two-fold improvement in the enzyme half-life at 85 °C. Based on the molecular dynamics simulation results, rearrangement of salt bridges and hydrogen interactions network causes a reduction in local flexibility of the K100G variant. In conclusion, our study demonstrated that thermostability can be improved through imposing local structural rigidity by engineering a single-point mutation on the surface of the enzyme.
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Affiliation(s)
- Shima Ghaedizadeh
- Laboratory of Genomics and Epigenomics (LGE), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Majid Zeinali
- Microbiology and Biotechnology Research Group, Research Institute of Petroleum Industry (RIPI), Tehran, Iran.
| | - Bahareh Dabirmanesh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Behnam Rasekh
- Microbiology and Biotechnology Research Group, Research Institute of Petroleum Industry (RIPI), Tehran, Iran
| | - Khosrow Khajeh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ali Mohammad Banaei-Moghaddam
- Laboratory of Genomics and Epigenomics (LGE), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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Krishna Bhat S, Purushothaman K, Gopala Rao Appu Rao AR, Kini KR. Engineering non-conserved salt bridges in GH11 xylanase from Bacillus pumilus SSP34 for improved thermal stability: an in-silico evaluation. J Biomol Struct Dyn 2023; 41:792-804. [PMID: 34877909 DOI: 10.1080/07391102.2021.2012515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
GH11 xylanases are commercially important enzymes for degradation of xylan fibers. We have identified the presence of nine non-conserved and five conserved salt bridges in GH11 xylanase from Bacillus pumilus SSP34. We have designed two sets of mutants viz., (1) substitution mutants in which non-conserved charged amino acid residues have been replaced with appropriate hydrophobic residues based on side chain occupancy and hydrophobicity and (2) deletion mutants where non-conserved charged residues have been deleted. The stability of the mutants has been evaluated in-silico by analyzing the contributions of non-covalent interactions like hydrophobic interaction clusters and salt bridges. The stability of the resultant mutants was evaluated using parameters such as radius of gyration, solvent accessible surface area, root mean square deviation, root mean square fluctuations and protein unfolding measurements using molecular dynamic simulations. The deletion of certain charged residues resulted in mutants having lowered radius of gyration and decreased surface areas. However, RMSD and RMSF measurements indicated lowered stability in comparison to substitution mutants. Of the substitution mutants, the SBM 3 was the most stable mutant as indicated by Rg, SASA, RMSF and simulated protein unfolding measurements. The major contributing factors for improved stability could be strengthening of hydrophobic interactions in the GH11 xylanase from B. pumilus. These in-silico stability measurements of salt bridge mutants may lead to better design of GH11 xylanases for commercial applications.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sagar Krishna Bhat
- R&D Center, Kaypeeyes Biotech Pvt Ltd, Mysuru, Karnataka, India.,Department of Studies in Biotechnology, University of Mysore, Manasagangothri, Mysuru, Karnataka, India
| | | | | | - K Ramachandra Kini
- Department of Studies in Biotechnology, University of Mysore, Manasagangothri, Mysuru, Karnataka, India
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5
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Sürmeli Y, Şanlı-Mohamed G. Engineering of xylanases for the development of biotechnologically important characteristics. Biotechnol Bioeng 2023; 120:1171-1188. [PMID: 36715367 DOI: 10.1002/bit.28339] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/19/2022] [Accepted: 01/26/2023] [Indexed: 01/31/2023]
Abstract
Xylanases are the main biocatalysts used for the reduction of the xylan backbone from hemicellulose, randomly splitting off β-1,4-glycosidic linkages between xylopyranosyl residues. Xylanase market has been annually estimated at 500 million US Dollars and they are potentially used in broad industrial process ranges such as paper pulp biobleaching, xylo-oligosaccharide production, and biofuel manufacture from lignocellulose. The highly stable xylanases are preferred in the downstream procedure of industrial processes because they can tolerate severe conditions. Almost all native xylanases can not endure adverse conditions thus they are industrially not proper to be utilized. Protein engineering is a powerful technology for developing xylanases, which can effectively work in adverse conditions and can meet requirements for industrial processes. This study considered state-of-the-art strategies of protein engineering for creating the xylanase gene diversity, high-throughput screening systems toward upgraded traits of the xylanases, and the prediction and comprehensive analysis of the target mutations in xylanases by in silico methods. Also, key molecular factors have been elucidated for industrial characteristics (alkaliphilic enhancement, thermal stability, and catalytic performance) of GH11 family xylanases. The present review explores industrial characteristics improved by directed evolution, rational design, and semi-rational design as protein engineering approaches for pulp bleaching process, xylooligosaccharides production, and biorefinery & bioenergy production.
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Affiliation(s)
- Yusuf Sürmeli
- Department of Agricultural Biotechnology, Tekirdağ Namık Kemal University, Tekirdağ, Turkey
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6
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Kellock M, Rahikainen J, Borisova AS, Voutilainen S, Koivula A, Kruus K, Marjamaa K. Inhibitory effect of lignin on the hydrolysis of xylan by thermophilic and thermolabile GH11 xylanases. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:49. [PMID: 35568899 PMCID: PMC9107766 DOI: 10.1186/s13068-022-02148-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/30/2022] [Indexed: 11/10/2022]
Abstract
Abstract
Background
Enzymatic hydrolysis of lignocellulosic biomass into platform sugars can be enhanced by the addition of accessory enzymes, such as xylanases. Lignin from steam pretreated biomasses is known to inhibit enzymes by non-productively binding enzymes and limiting access to cellulose. The effect of enzymatically isolated lignin on the hydrolysis of xylan by four glycoside hydrolase (GH) family 11 xylanases was studied. Two xylanases from the mesophilic Trichoderma reesei, TrXyn1, TrXyn2, and two forms of a thermostable metagenomic xylanase Xyl40 were compared.
Results
Lignin isolated from steam pretreated spruce decreased the hydrolysis yields of xylan for all the xylanases at 40 and 50 °C. At elevated hydrolysis temperature of 50 °C, the least thermostable xylanase TrXyn1 was most inhibited by lignin and the most thermostable xylanase, the catalytic domain (CD) of Xyl40, was least inhibited by lignin. Enzyme activity and binding to lignin were studied after incubation of the xylanases with lignin for up to 24 h at 40 °C. All the studied xylanases bound to lignin, but the thermostable xylanases retained 22–39% of activity on the lignin surface for 24 h, whereas the mesophilic T. reesei xylanases become inactive. Removing of N-glycans from the catalytic domain of Xyl40 increased lignin inhibition in hydrolysis of xylan when compared to the glycosylated form. By comparing the 3D structures of these xylanases, features contributing to the increased thermal stability of Xyl40 were identified.
Conclusions
High thermal stability of xylanases Xyl40 and Xyl40-CD enabled the enzymes to remain partially active on the lignin surface. N-glycosylation of the catalytic domain of Xyl40 increased the lignin tolerance of the enzyme. Thermostability of Xyl40 was most likely contributed by a disulphide bond and salt bridge in the N-terminal and α-helix regions.
Graphical Abstract
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7
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Tian W, Zhang Z, Yang C, Li P, Xiao J, Wang R, Du P, Li N, Wang J. Engineering mesophilic GH11 xylanase from Cellulomonas flavigena by rational design of N-terminus substitution. Front Bioeng Biotechnol 2022; 10:1044291. [DOI: 10.3389/fbioe.2022.1044291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022] Open
Abstract
Xylanase, a glycoside hydrolase, is widely used in the food, papermaking, and textile industries; however, most xylanases are inactive at high temperatures. In this study, a xylanase gene, CFXyl3, was cloned from Cellulomonas flavigena and expressed in Escherichia coli BL21 (DE3). To improve the thermostability of xylanase, four hybrid xylanases with enhanced thermostability (designated EcsXyl1–4) were engineered from CFXyl3, guided by primary and 3D structure analyses. The optimal temperature of CFXyl3 was improved by replacing its N-terminus with the corresponding area of SyXyn11P, a xylanase that belongs to the hyperthermostable GH11 family. The optimal temperatures of the hybrid xylanases EcsXyl1–4 were 60, 60, 65, and 85°C, respectively. The optimal temperature of EcsXyl4 was 30 C higher than that of CFXyl3 (55°C) and its melting temperature was 34.5°C higher than that of CFXyl3. After the hydrolysis of beechwood xylan, the main hydrolysates were xylotetraose, xylotriose, and xylobiose; thus, these hybrid xylanases could be applied to prebiotic xylooligosaccharide manufacturing.
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Nezhad NG, Rahman RNZRA, Normi YM, Oslan SN, Shariff FM, Leow TC. Thermostability engineering of industrial enzymes through structure modification. Appl Microbiol Biotechnol 2022; 106:4845-4866. [PMID: 35804158 DOI: 10.1007/s00253-022-12067-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/25/2022] [Accepted: 07/02/2022] [Indexed: 01/14/2023]
Abstract
Thermostability is an essential requirement of enzymes in the industrial processes to catalyze the reactions at high temperatures; thus, enzyme engineering through directed evolution, semi-rational design and rational design are commonly employed to construct desired thermostable mutants. Several strategies are implemented to fulfill enzymes' thermostability demand including decreasing the entropy of the unfolded state through substitutions Gly → Xxx or Xxx → Pro, hydrogen bond, salt bridge, introducing two different simultaneous interactions through single mutant, hydrophobic interaction, filling the hydrophobic cavity core, decreasing surface hydrophobicity, truncating loop, aromatic-aromatic interaction and introducing positively charged residues to enzyme surface. In the current review, horizons about compatibility between secondary structures and substitutions at preferable structural positions to generate the most desirable thermostability in industrial enzymes are broadened. KEY POINTS: • Protein engineering is a powerful tool for generating thermostable industrial enzymes. • Directed evolution and rational design are practical approaches in enzyme engineering. • Substitutions in preferable structural positions can increase thermostability.
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Affiliation(s)
- Nima Ghahremani Nezhad
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Yahaya M Normi
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Siti Nurbaya Oslan
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Fairolniza Mohd Shariff
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia. .,Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia. .,Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
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Identification of a New Endo-β-1,4-xylanase Prospected from the Microbiota of the Termite Heterotermes tenuis. Microorganisms 2022; 10:microorganisms10050906. [PMID: 35630351 PMCID: PMC9143652 DOI: 10.3390/microorganisms10050906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 12/04/2022] Open
Abstract
Xylanases are hemicellulases that break down xylan to soluble pentoses. They are used for industrial purposes, such as paper whitening, beverage clarification, and biofuel production. The second-generation bioethanol production is hindered by the enzymatic hydrolysis step of the lignocellulosic biomass, due to the complex arrangement established among its constituents. Xylanases can potentially increase the production yield by improving the action of the cellulolytic enzyme complex. We prospected endo-β-1,4-xylanases from meta-transcriptomes of the termite Heterotermes tenuis. In silico structural characterization and functional analysis of an endo-β-1,4-xylanase from a symbiotic protist of H. tenuis indicate two active sites and a substrate-binding groove needed for the catalytic activity. No N-glycosylation sites were found. This endo-β-1,4-xylanase was recombinantly expressed in Pichia pastoris and Escherichia coli cells, presenting a molecular mass of approximately 20 kDa. Enzymatic activity assay using recombinant endo-β-1,4-xylanase was also performed on 1% xylan agar stained with Congo red at 30 °C and 40 °C. The enzyme expressed in both systems was able to hydrolyze the substrate xylan, becoming a promising candidate for further analysis aiming to determine its potential for application in industrial xylan degradation processes.
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Vanella R, Kovacevic G, Doffini V, Fernández de Santaella J, Nash MA. High-throughput screening, next generation sequencing and machine learning: advanced methods in enzyme engineering. Chem Commun (Camb) 2022; 58:2455-2467. [PMID: 35107442 PMCID: PMC8851469 DOI: 10.1039/d1cc04635g] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Enzyme engineering is an important biotechnological process capable of generating tailored biocatalysts for applications in industrial chemical conversion and biopharma. Typical enhancements sought in enzyme engineering and in vitro evolution campaigns include improved folding stability, catalytic activity, and/or substrate specificity. Despite significant progress in recent years in the areas of high-throughput screening and DNA sequencing, our ability to explore the vast space of functional enzyme sequences remains severely limited. Here, we review the currently available suite of modern methods for enzyme engineering, with a focus on novel readout systems based on enzyme cascades, and new approaches to reaction compartmentalization including single-cell hydrogel encapsulation techniques to achieve a genotype–phenotype link. We further summarize systematic scanning mutagenesis approaches and their merger with deep mutational scanning and massively parallel next-generation DNA sequencing technologies to generate mutability landscapes. Finally, we discuss the implementation of machine learning models for computational prediction of enzyme phenotypic fitness from sequence. This broad overview of current state-of-the-art approaches for enzyme engineering and evolution will aid newcomers and experienced researchers alike in identifying the important challenges that should be addressed to move the field forward. Enzyme engineering is an important biotechnological process capable of generating tailored biocatalysts for applications in industrial chemical conversion and biopharma.![]()
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Affiliation(s)
- Rosario Vanella
- Department of Chemistry, University of Basel, 4058 Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.
| | - Gordana Kovacevic
- Department of Chemistry, University of Basel, 4058 Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.
| | - Vanni Doffini
- Department of Chemistry, University of Basel, 4058 Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.
| | - Jaime Fernández de Santaella
- Department of Chemistry, University of Basel, 4058 Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.
| | - Michael A Nash
- Department of Chemistry, University of Basel, 4058 Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.
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11
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Wang Y, Wang J, Zhang Z, Yang J, Turunen O, Xiong H. High-temperature behavior of hyperthermostable Thermotoga maritima xylanase XYN10B after designed and evolved mutations. Appl Microbiol Biotechnol 2022; 106:2017-2027. [PMID: 35171339 DOI: 10.1007/s00253-022-11823-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/29/2022] [Accepted: 02/05/2022] [Indexed: 11/24/2022]
Abstract
A hyperthermostable xylanase XYN10B from Thermotoga maritima (PDB code 1VBR, GenBank accession number KR078269) was subjected to site-directed and error-prone PCR mutagenesis. From the selected five mutants, the two site-directed mutants (F806H and F806V) showed a 3.3-3.5-fold improved enzyme half-life at 100 °C. The mutant XYNA generated by error-prone PCR showed slightly improved stability at 100 °C and a lower Km. In XYNB and XYNC, the additional mutations over XYNA decreased the thermostability and temperature optimum, while elevating the Km. In XYNC, two large side-chains were introduced into the protein's interior. Micro-differential scanning calorimetry (DSC) showed that the melting temperature (Tm) dropped in XYNB and XYNC from 104.9 °C to 93.7 °C and 78.6 °C, respectively. The detrimental mutations showed that extremely thermostable enzymes can tolerate quite radical mutations in the protein's interior and still retain high thermostability. The analysis of mutations (F806H and F806V) in a hydrophobic area lining the substrate-binding region indicated that active site hydrophobicity is important for high activity at extreme temperatures. Although polar His at 806 provided higher stability, the hydrophobic Phe at 806 provided higher activity than His. This study generates an understanding of how extreme thermostability and high activity are formed in GH10 xylanases. KEY POINTS: • Characterization and molecular dynamics simulations of TmXYN10B and its mutants • Explanation of structural stability of GH10 xylanase.
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Affiliation(s)
- Yawei Wang
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430048, China
| | - Jing Wang
- College of Life Science, South-central University for Nationalities, Wuhan, 430074, China
| | - Zhongqiang Zhang
- College of Life Science, South-central University for Nationalities, Wuhan, 430074, China
| | - Jiangke Yang
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430048, China
| | - Ossi Turunen
- School of Forest Sciences, University of Eastern Finland, FI-80101, Joensuu, Finland.
| | - Hairong Xiong
- College of Life Science, South-central University for Nationalities, Wuhan, 430074, China.
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12
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Miao H, Ma Y, Zhe Y, Tang X, Wu Q, Huang Z, Han N. Improving the Thermostability of a Fungal GH11 Xylanase via Fusion of a Submodule (C2) from Hyperthermophilic CBM9_1-2. Int J Mol Sci 2021; 23:ijms23010463. [PMID: 35008888 PMCID: PMC8745443 DOI: 10.3390/ijms23010463] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/30/2021] [Accepted: 12/30/2021] [Indexed: 11/20/2022] Open
Abstract
Xylanases have been applied in many industrial fields. To improve the activity and thermostability of the xylanase CDBFV from Neocallimastix patriciarum (GenBank accession no. KP691331), submodule C2 from hyperthermophilic CBM9_1-2 was inserted into the N- and/or C-terminal regions of the CDBFV protein (producing C2-CDBFV, CDBFV-C2, and C2-CDBFV-C2) by genetic engineering. CDBFV and the hybrid proteins were successfully expressed in Escherichia coli BL21 (DE3). Enzymatic property analysis indicates that the C2 submodule had a significant effect on enhancing the thermostability of the CDBFV. At the optimal temperature (60.0 °C), the half-lives of the three chimeras C2-CDBFV, CDBFV-C2, and C2-CDBFV-C2 are 1.5 times (37.5 min), 4.9 times (122.2 min), and 3.8 times (93.1 min) longer than that of wild-type CDBFV (24.8 min), respectively. More importantly, structural analysis and molecular dynamics (MD) simulation revealed that the improved thermal stability of the chimera CDBFV-C2 was on account of the formation of four relatively stable additional hydrogen bonds (S42-S462, T59-E277, S41-K463, and S44-G371), which increased the protein structure’s stability. The thermostability characteristics of CDBFV-C2 make it a viable enzyme for industrial applications.
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Affiliation(s)
- Huabiao Miao
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming 650500, China; (H.M.); (X.T.); (Q.W.)
- School of Life Science, Yunnan Normal University, Kunming 650500, China; (Y.M.); (Y.Z.)
| | - Yu Ma
- School of Life Science, Yunnan Normal University, Kunming 650500, China; (Y.M.); (Y.Z.)
| | - Yuanyuan Zhe
- School of Life Science, Yunnan Normal University, Kunming 650500, China; (Y.M.); (Y.Z.)
| | - Xianghua Tang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming 650500, China; (H.M.); (X.T.); (Q.W.)
- School of Life Science, Yunnan Normal University, Kunming 650500, China; (Y.M.); (Y.Z.)
| | - Qian Wu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming 650500, China; (H.M.); (X.T.); (Q.W.)
- School of Life Science, Yunnan Normal University, Kunming 650500, China; (Y.M.); (Y.Z.)
| | - Zunxi Huang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming 650500, China; (H.M.); (X.T.); (Q.W.)
- School of Life Science, Yunnan Normal University, Kunming 650500, China; (Y.M.); (Y.Z.)
- Correspondence: (Z.H.); (N.H.); Tel.: +86-0871-5920830 (Z.H.); Fax: +86-0871-5920952 (Z.H.)
| | - Nanyu Han
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming 650500, China; (H.M.); (X.T.); (Q.W.)
- School of Life Science, Yunnan Normal University, Kunming 650500, China; (Y.M.); (Y.Z.)
- Correspondence: (Z.H.); (N.H.); Tel.: +86-0871-5920830 (Z.H.); Fax: +86-0871-5920952 (Z.H.)
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13
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Vucinic J, Novikov G, Montanier CY, Dumon C, Schiex T, Barbe S. A Comparative Study to Decipher the Structural and Dynamics Determinants Underlying the Activity and Thermal Stability of GH-11 Xylanases. Int J Mol Sci 2021; 22:ijms22115961. [PMID: 34073139 PMCID: PMC8199483 DOI: 10.3390/ijms22115961] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 11/23/2022] Open
Abstract
With the growing need for renewable sources of energy, the interest for enzymes capable of biomass degradation has been increasing. In this paper, we consider two different xylanases from the GH-11 family: the particularly active GH-11 xylanase from Neocallimastix patriciarum, NpXyn11A, and the hyper-thermostable mutant of the environmentally isolated GH-11 xylanase, EvXyn11TS. Our aim is to identify the molecular determinants underlying the enhanced capacities of these two enzymes to ultimately graft the abilities of one on the other. Molecular dynamics simulations of the respective free-enzymes and enzyme–xylohexaose complexes were carried out at temperatures of 300, 340, and 500 K. An in-depth analysis of these MD simulations showed how differences in dynamics influence the activity and stability of these two enzymes and allowed us to study and understand in greater depth the molecular and structural basis of these two systems. In light of the results presented in this paper, the thumb region and the larger substrate binding cleft of NpXyn11A seem to play a major role on the activity of this enzyme. Its lower thermal stability may instead be caused by the higher flexibility of certain regions located further from the active site. Regions such as the N-ter, the loops located in the fingers region, the palm loop, and the helix loop seem to be less stable than in the hyper-thermostable EvXyn11TS. By identifying molecular regions that are critical for the stability of these enzymes, this study allowed us to identify promising targets for engineering GH-11 xylanases. Eventually, we identify NpXyn11A as the ideal host for grafting the thermostabilizing traits of EvXyn11TS.
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Affiliation(s)
- Jelena Vucinic
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, ANITI, 31400 Toulouse, France; (J.V.); (G.N.); (C.Y.M.); (C.D.)
- Université Fédérale de Toulouse, ANITI, INRAE, UR 875, 31326 Toulouse, France;
| | - Gleb Novikov
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, ANITI, 31400 Toulouse, France; (J.V.); (G.N.); (C.Y.M.); (C.D.)
| | - Cédric Y. Montanier
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, ANITI, 31400 Toulouse, France; (J.V.); (G.N.); (C.Y.M.); (C.D.)
| | - Claire Dumon
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, ANITI, 31400 Toulouse, France; (J.V.); (G.N.); (C.Y.M.); (C.D.)
| | - Thomas Schiex
- Université Fédérale de Toulouse, ANITI, INRAE, UR 875, 31326 Toulouse, France;
| | - Sophie Barbe
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, ANITI, 31400 Toulouse, France; (J.V.); (G.N.); (C.Y.M.); (C.D.)
- Correspondence:
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14
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Bhat SK, Purushothaman K, Kini KR, Gopala Rao Appu Rao AR. Design of mutants of GH11 xylanase from Bacillus pumilus for enhanced stability by amino acid substitutions in the N-terminal region: an in silico analysis. J Biomol Struct Dyn 2021; 40:7666-7679. [PMID: 33749523 DOI: 10.1080/07391102.2021.1899988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
GH11 xylanases are versatile small-molecular-weight single-polypeptide chain monofunctional enzymes. This family of glycoside hydrolases has important applications in food, feed and chemical industries. We designed mutants for improved thermal stability with substitutions in the first six residues of the N-terminal region and evaluated the stability in silico. The first six residues RTITNN of native xylanase have been mutated accordingly to introduce β structure, increase hydrophobic clusters and enhance conformational rigidity in the molecule. To design stable mutants, the approach consisted of constructing root mean square fluctuation (RMSF) plots of both mesophilic and thermophilic xylanases to check the localized backbone displacement maxima, identify the hydrophobic interaction cluster in and around the peaks of interest, construct mutants by substituting appropriate residues based on beta propensity, hydrophobicity, side chain occupancy and conformational rigidity. This resulted in the decreased number of possible substitutions from 19 to 6 residues. Introduction of conformational rigidity by substitution of asparagine residues at 5th and 6th residue position with proline and valine enhanced the stability. Deletion of N-terminal region increased the stability probably by reducing entropic factors. The structure and stability of GH11 xylanase and resultant mutants were analyzed by root mean square deviation, RMSF, radius of gyration and solvent accessible surface area analysis. The stability of the mutants followed the order N-del > Y1P5 >Y1V5 > ATRLM. The contribution of N-terminal end to overall stability of the molecule is significant because of the proximity of the C-terminal end to the N-terminal end which reinforces long-range interactions. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - K Ramachandra Kini
- Department of Studies in Biotechnology, University of Mysore, Manasagangothri, Mysuru, Karnataka, India
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15
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Wang L, Gu J, Feng Y, Wang M, Tong Y, Liu Y, Lyu X, Yang R. Enhancement of the Isomerization Activity and Thermostability of Cellobiose 2-Epimerase from Caldicellulosiruptor saccharolyticus by Exchange of a Flexible Loop. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:1907-1915. [PMID: 33541071 DOI: 10.1021/acs.jafc.0c07073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Cellobiose 2-epimerase (CE) offers a promising enzymatic approach to produce lactulose. However, its application is limited by the unsatisfactory isomerization activity and thermostability. Our study attempted to optimize the catalytic performances of CEs by flexible loop exchange, for which four mutants were constructed using CsCE (CE from Caldicellulosiruptor saccharolyticus) as a template. As a result, all mutants maintained the same catalytic directions as the templates. Mutant RmC displayed a 2.2- and 1.34-fold increase in the isomerization activity and catalytic efficiency, respectively. According to the results of molecular dynamics (MD) simulations, it was revealed that the loop exchange in RmC enlarged the entrance of the active site for substrate binding and benefited proton transfer involved in the isomerization process. Besides, the t1/2 of mutant StC at 70 °C was increased from 29.07 to 38.29 h, owing to the abundance of rigid residues (proline) within the flexible loop of StC. Our work demonstrated that the isomerization activity and thermostability of CEs were closely related to the flexible loop surrounding the active site, which provides a new perspective to engineer CEs for higher lactulose production.
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Affiliation(s)
- Lu Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jiali Gu
- College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Yinghui Feng
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Mingming Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yanjun Tong
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yingjie Liu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiaomei Lyu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Ruijin Yang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
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16
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Xing H, Zou G, Liu C, Chai S, Yan X, Li X, Liu R, Yang Y, Zhou Z. Improving the thermostability of a GH11 xylanase by directed evolution and rational design guided by B-factor analysis. Enzyme Microb Technol 2020; 143:109720. [PMID: 33375980 DOI: 10.1016/j.enzmictec.2020.109720] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 10/20/2020] [Accepted: 11/26/2020] [Indexed: 01/19/2023]
Abstract
Operational stability under high temperature is required for enzyme application in industrial processes. Error-prone PCR and B-factor analysis were employed to enhance the thermostability of a xylanase from GH family 11 in this study. Based on the top 10 mutants screened from the random mutation libraries, mutant Xyn371 was derived from the optimal mutant Xyn370 by integrating the beneficial residues identified in the other 9 screened mutants. Subsequently, a best-saturation mutant Xyn372 originated from Xyn371 was selected with a 60-min half-life at 70 °C (0.5-min half-life for the wild-type enzyme). According to the site-saturated mutagenesis of 10 residues with higher B-factors in Xyn372, mutants Xyn375 and Xyn376 were screened; their half-lives at 70 °C were 410 and 360 min, respectively. The substituted residues located in the "palm" region of the N-terminus and the newly generated hydrogen bonds in the mutants might contribute to improved thermostability. The significantly improved thermostability of mutants will pave the way for applications in different industrial areas.
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Affiliation(s)
- Hongguan Xing
- CAS-key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Rd 300, Shanghai, 200032, China; Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Meilong Rd 130, Shanghai, 200237, China
| | - Gen Zou
- CAS-key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Rd 300, Shanghai, 200032, China
| | - Chunyan Liu
- CAS-key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Rd 300, Shanghai, 200032, China
| | - Shunxing Chai
- CAS-key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Rd 300, Shanghai, 200032, China
| | - Xing Yan
- CAS-key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Rd 300, Shanghai, 200032, China
| | - Xinliang Li
- CJ, Youtell (Shanghai) Biotech Co., Ltd, Ste 302, Bldg 7, 526 Ruiqing Rd, Shanghai 201201, China
| | - Rui Liu
- CJ, Youtell (Shanghai) Biotech Co., Ltd, Ste 302, Bldg 7, 526 Ruiqing Rd, Shanghai 201201, China
| | - Yi Yang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Meilong Rd 130, Shanghai, 200237, China
| | - Zhihua Zhou
- CAS-key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Rd 300, Shanghai, 200032, China.
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17
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Xylanases from marine microorganisms: A brief overview on scope, sources, features and potential applications. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140312. [DOI: 10.1016/j.bbapap.2019.140312] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/31/2019] [Accepted: 11/05/2019] [Indexed: 01/10/2023]
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18
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Han N, Ma Y, Mu Y, Tang X, Li J, Huang Z. Enhancing thermal tolerance of a fungal GH11 xylanase guided by B-factor analysis and multiple sequence alignment. Enzyme Microb Technol 2019; 131:109422. [DOI: 10.1016/j.enzmictec.2019.109422] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 08/24/2019] [Accepted: 09/03/2019] [Indexed: 11/24/2022]
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19
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Xiong K, Hou J, Jiang Y, Li X, Teng C, Li Q, Fan G, Yang R, Zhang C. Mutagenesis of N-terminal residues confer thermostability on a Penicillium janthinellum MA21601 xylanase. BMC Biotechnol 2019; 19:51. [PMID: 31345213 PMCID: PMC6659274 DOI: 10.1186/s12896-019-0541-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/05/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A mesophilic xylanase PjxA from Penicillium janthinellum MA21601 has high specific activity under acidic condition and holds great potential for applications in the animal feed industry. To enhance the thermostability of xylanase PjxA, two mutation strategies in the N-terminal region were examined and then integrated into the xylanase to further improvement. The recombinant xylanase PTxA-DB (The meaning of DB is disulfide-bridge.) was constructed by replacement of five residues in the mutated region in TfxA (T10Y, N11H, N12D, Y15F, N30 L), combined with an additional disulfide bridge in the N-terminal region. RESULTS The Tm value of mutant PTxA-DB was improved from 21.3 °C to 76.6 °C, and its half-life was found to be 53.6 min at 60 °C, 107-fold higher than the wild type strain. The location of the disulfide bridge (T2C-T29C) was between the irregular loop and the β-strand A2, accounting for most of the improvement in thermostability of PjxA. Further analysis indicated T2C, T29C, N30 L and Y15F lead to increase N-terminal hydrophobicity. Moreover, the specific activity and substrate affinity of PTxA-DB were also enhanced under the acidic pH values. CONCLUSIONS These results indicated PTxA-DB could be a prospective additive to industrial animal feeds.
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Affiliation(s)
- Ke Xiong
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, No 11 Fucheng Street, Haidian District, Beijing, 100084, China.,Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, No 11 Fucheng Street, Haidian District, Beijing, 100084, China.,Beijing Key Laboratory of Flavor Chemistry, Beijing Technology and Business University, No 11 Fucheng Street, Haidian District, Beijing, 100084, China
| | - Jie Hou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, No 11 Fucheng Street, Haidian District, Beijing, 100084, China.,Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, No 11 Fucheng Street, Haidian District, Beijing, 100084, China
| | - Yuefeng Jiang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, No 11 Fucheng Street, Haidian District, Beijing, 100084, China.,Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, No 11 Fucheng Street, Haidian District, Beijing, 100084, China
| | - Xiuting Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, No 11 Fucheng Street, Haidian District, Beijing, 100084, China. .,Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, No 11 Fucheng Street, Haidian District, Beijing, 100084, China. .,Beijing Key Laboratory of Flavor Chemistry, Beijing Technology and Business University, No 11 Fucheng Street, Haidian District, Beijing, 100084, China.
| | - Chao Teng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, No 11 Fucheng Street, Haidian District, Beijing, 100084, China.,Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, No 11 Fucheng Street, Haidian District, Beijing, 100084, China
| | - Qin Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, No 11 Fucheng Street, Haidian District, Beijing, 100084, China.,Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, No 11 Fucheng Street, Haidian District, Beijing, 100084, China
| | - Guangsen Fan
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, No 11 Fucheng Street, Haidian District, Beijing, 100084, China.,School of Food and Chemical Engineering, Beijing Technology and Business University, Beijing, 100048, China
| | - Ran Yang
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, No 11 Fucheng Street, Haidian District, Beijing, 100084, China.,Beijing Key Laboratory of Flavor Chemistry, Beijing Technology and Business University, No 11 Fucheng Street, Haidian District, Beijing, 100084, China.,School of Food and Chemical Engineering, Beijing Technology and Business University, Beijing, 100048, China
| | - Chengnan Zhang
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, No 11 Fucheng Street, Haidian District, Beijing, 100084, China.,Beijing Key Laboratory of Flavor Chemistry, Beijing Technology and Business University, No 11 Fucheng Street, Haidian District, Beijing, 100084, China.,School of Food and Chemical Engineering, Beijing Technology and Business University, Beijing, 100048, China
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20
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Hot CoFi Blot: A High-Throughput Colony-Based Screen for Identifying More Thermally Stable Protein Variants. Methods Mol Biol 2019. [PMID: 31267459 DOI: 10.1007/978-1-4939-9624-7_14] [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
Highly soluble and stable proteins are desirable for many different applications, from basic science to reaching a cancer patient in the form of a biological drug. For X-ray crystallography-where production of a protein crystal might take weeks and even months-a stable protein sample of high purity and concentration can greatly increase the chances of producing a well-diffracting crystal. For a patient receiving a specific protein drug, its safety, efficacy, and even cost are factors affected by its solubility and stability. Increased protein expression and protein stability can be achieved by randomly altering the coding sequence. As the number of mutants generated might be overwhelming, a powerful protein expression and stability screen is required. In this chapter, we describe a colony filtration technology, which allows us to screen random mutagenesis libraries for increased thermal stability-the Hot CoFi blot. We share how to create the random mutagenesis library, how to perform the Hot CoFi blot, and how to identify more thermally stable clones. We use the Tobacco Etch Virus protease as a target to exemplify the procedure.
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21
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Li JC, Nastertorabi F, Xuan W, Han GW, Stevens RC, Schultz PG. A Single Reactive Noncanonical Amino Acid Is Able to Dramatically Stabilize Protein Structure. ACS Chem Biol 2019; 14:1150-1153. [PMID: 31181898 DOI: 10.1021/acschembio.9b00002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A p-isothiocyanate phenylalanine mutant of the homodimeric protein homoserine o-succinyltransferase (MetA) was isolated in a temperature dependent selection from a library of metA mutants containing noncanonical amino acids. This mutant protein has a dramatic increase of 24 °C in thermal stability compared to the wild type protein. Peptide mapping experiments revealed that the isothiocyanate group forms a thiourea cross-link to the N terminal proline of the other monomer, despite the two positions being >30 Å apart in the X-ray crystal structure of the wild type protein. These results show that an expanded set of building blocks beyond the canonical 20 amino acids can lead to significant changes in the properties of proteins.
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Affiliation(s)
- Jack C. Li
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Fariborz Nastertorabi
- Department of Biological Sciences, Bridge Institute, Michaelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, United States
| | - Weimin Xuan
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Gye Won Han
- Department of Biological Sciences, Bridge Institute, Michaelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, United States
| | - Raymond C. Stevens
- Department of Biological Sciences, Bridge Institute, Michaelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, United States
| | - Peter G. Schultz
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
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22
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Li Q, Wu T, Duan Y, Pei J, Zhao L. Improving the Thermostability and pH Stability of Aspergillus niger Xylanase by Site-directed Mutagenesis. APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683819020108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Improving the thermostability and catalytic efficiency of GH11 xylanase PjxA by adding disulfide bridges. Int J Biol Macromol 2019; 128:354-362. [DOI: 10.1016/j.ijbiomac.2019.01.087] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/17/2019] [Accepted: 01/19/2019] [Indexed: 11/24/2022]
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24
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Sun Z, Liu Q, Qu G, Feng Y, Reetz MT. Utility of B-Factors in Protein Science: Interpreting Rigidity, Flexibility, and Internal Motion and Engineering Thermostability. Chem Rev 2019; 119:1626-1665. [PMID: 30698416 DOI: 10.1021/acs.chemrev.8b00290] [Citation(s) in RCA: 280] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Qian Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ge Qu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Chemistry Department, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
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25
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Li JC, Liu T, Wang Y, Mehta AP, Schultz PG. Enhancing Protein Stability with Genetically Encoded Noncanonical Amino Acids. J Am Chem Soc 2018; 140:15997-16000. [PMID: 30433771 DOI: 10.1021/jacs.8b07157] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ability to add noncanonical amino acids to the genetic code may allow one to evolve proteins with new or enhanced properties using a larger set of building blocks. To this end, we have been able to select mutant proteins with enhanced thermal properties from a library of E. coli homoserine O-succinyltransferase ( metA) mutants containing randomly incorporated noncanonical amino acids. Here, we show that substitution of Phe 21 with ( p-benzoylphenyl)alanine (pBzF), increases the melting temperature of E. coli metA by 21 °C. This dramatic increase in thermal stability, arising from a single mutation, likely results from a covalent adduct between Cys 90 and the keto group of pBzF that stabilizes the dimeric form of the enzyme. These experiments show that an expanded genetic code can provide unique solutions to the evolution of proteins with enhanced properties.
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Affiliation(s)
- Jack C Li
- Department of Chemistry and Skaggs Institute for Chemical Biology , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Tao Liu
- Department of Chemistry and Skaggs Institute for Chemical Biology , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Yan Wang
- Department of Chemistry and Skaggs Institute for Chemical Biology , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Angad P Mehta
- Department of Chemistry and Skaggs Institute for Chemical Biology , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Peter G Schultz
- Department of Chemistry and Skaggs Institute for Chemical Biology , The Scripps Research Institute , La Jolla , California 92037 , United States
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Han B, Hou Y, Jiang T, Lv B, Zhao L, Feng X, Li C. Computation-Aided Rational Deletion of C-Terminal Region Improved the Stability, Activity, and Expression Level of GH2 β-Glucuronidase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:11380-11389. [PMID: 30296070 DOI: 10.1021/acs.jafc.8b03449] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this study, computation-aided design on the basis of structural analysis was employed to rationally identify a highly dynamic C-terminal region that regulates the stability, expression level, and activity of a GH2 fungal glucuronidase from Aspergillus oryzae Li-3 (PGUS). Then, four mutants with a precisely truncated C-terminal region in different lengths were constructed; among them, mutant D591-604 with a 3.8-fold increase in half-life at 65 °C and a 6.8 kJ/mol increase in Gibbs free energy showed obviously improved kinetic and thermodynamic stability in comparison to PGUS. Mutants D590-604 and D591-604 both showed approximately 2.4-fold increases in the catalytic efficiency kcat/ Km and 1.8-fold increases in the expression level. Additionally, the expression level of PGUS was doubled through a C-terminal region swap with bacterial GUS from E. coli (EGUS). Finally, the robust PGUS mutants D590-604 and D591-604 were applied in the preparation of glycyrrhetinic acid with 4.0- and 4.4-fold increases in concentration through glycyrrhizin hydrolysis by a fed-batch process.
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Affiliation(s)
- Beijia Han
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , People's Republic of China
| | - Yuhui Hou
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , People's Republic of China
| | - Tian Jiang
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , People's Republic of China
| | - Bo Lv
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , People's Republic of China
| | - Lina Zhao
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety , Institute of High Energy Physics, Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Xudong Feng
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , People's Republic of China
| | - Chun Li
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , People's Republic of China
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Increase in the thermostability of Bacillus sp. strain TAR-1 xylanase using a site saturation mutagenesis library. Biosci Biotechnol Biochem 2018; 82:1715-1723. [DOI: 10.1080/09168451.2018.1495550] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
ABSTRACT
Site saturation mutagenesis library is a recently developed technique, in which any one out of all amino acid residues in a target region is substituted into other 19 amino acid residues. In this study, we used this technique to increase the thermostability of a GH10 xylanase, XynR, from Bacillus sp. strain TAR-1. We hypothesized that the substrate binding region of XynR is flexible, and that the thermostability of XynR will increase if the flexibility of the substrate binding region is decreased without impairing the substrate binding ability. Site saturation mutagenesis libraries of amino acid residues Tyr43–Lys115 and Ala300–Asn325 of XynR were constructed. By screening 480 clones, S92E was selected as the most thermostable one, exhibiting the residual activity of 80% after heat treatment at 80°C for 15 min in the hydrolysis of Remazol Brilliant Blue-xylan. Our results suggest that this strategy is effective for stabilization of GH10 xylanase.
Abbreviations: DNS: 3,5-dinitrosalicylic acid; RBB-xylan: Remazol Brilliant Blue-xylan
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28
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Qu W, Lin D, Zhang Z, Di W, Gao B, Zeng R. Metagenomics Investigation of Agarlytic Genes and Genomes in Mangrove Sediments in China: A Potential Repertory for Carbohydrate-Active Enzymes. Front Microbiol 2018; 9:1864. [PMID: 30177916 PMCID: PMC6109693 DOI: 10.3389/fmicb.2018.01864] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/25/2018] [Indexed: 12/31/2022] Open
Abstract
Monosaccharides and oligosaccharides produced by agarose degradation exhibit potential in the fields of bioenergy, medicine, and cosmetics. Mangrove sediments (MGSs) provide a special environment to enrich enzymes for agarose degradation. However, representative investigations of the agarlytic genes in MGSs have been rarely reported. In this study, agarlytic genes in MGSs were researched in detail from the aspects of diversity, abundance, activity, and location through deep metagenomics sequencing. Functional genes in MGSs were usually incomplete but were shown as results, which could cause virtually high number of results in previous studies because multiple fragmented sequences could originate from the same genes. In our work, only complete and nonredundant (CNR) genes were analyzed to avoid virtually high amount of the results. The number of CNR agarlytic genes in our datasets was significantly higher than that in the datasets of previous studies. Twenty-one recombinant agarases with agarose-degrading activity were detected using heterologous expression based on numerous complete open-reading frames, which are rarely obtained in metagenomics sequencing of samples with complex microbial communities, such as MGSs. Aga2, which had the highest crude enzyme activity among the 21 recombinant agarases, was further purified and subjected to enzymatic characterization. With its high agarose-degrading activity, resistance to temperature changes and chemical agents, Aga2 could be a suitable option for industrial production. The agarase ratio with signal peptides to that without signal peptides in our MGS datasets was lower than that of other reported agarases. Six draft genomes, namely, Clusters 1-6, were recovered from the datasets. The taxonomic annotation of these genomes revealed that Clusters 1, 3, 5, and 6 were annotated as Desulfuromonas sp., Treponema sp., Ignavibacteriales spp., and Polyangiaceae spp., respectively. Meanwhile, Clusters 2 and 4 were potential new species. All these genomes were first reported and found to have abilities of degrading various important polysaccharides. The metabolic pathway of agarose in Cluster 4 was also speculated. Our results showed the capacity and activity of agarases in the MGS microbiome, and MGSs exert potential as a repertory for mining not only agarlytic genes but also almost all genes of the carbohydrate-active enzyme family.
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Affiliation(s)
- Wu Qu
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Dan Lin
- Novogene Bioinformatics Technology Co. Ltd., Tianjin, China
| | - Zhouhao Zhang
- Novogene Bioinformatics Technology Co. Ltd., Tianjin, China
| | - Wenjie Di
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China
| | - Boliang Gao
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Runying Zeng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China.,Key Laboratory of Marine Genetic Resources, Xiamen, China
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29
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Watanabe M, Matsuzawa T, Yaoi K. Rational protein design for thermostabilization of glycoside hydrolases based on structural analysis. Appl Microbiol Biotechnol 2018; 102:8677-8684. [PMID: 30109396 DOI: 10.1007/s00253-018-9288-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/30/2018] [Accepted: 08/01/2018] [Indexed: 11/27/2022]
Abstract
Glycosidases are used in the food, chemical, and energy industries. These proteins are some of the most frequently used such enzymes, and their thermostability is essential for long-term and/or repeated use. In addition to thermostability, modification of the substrate selectivity and improvement of the glycosidase activities are also important. Thermostabilization of enzymes can be performed by directed evolution via random mutagenesis or by rational design via site-directed mutagenesis; each approach has advantages and disadvantages. In this paper, we introduce thermostabilization of glycoside hydrolases by rational protein design using site-directed mutagenesis along with X-ray crystallography and simulation modeling. We focus on the methods of thermostabilization of glycoside hydrolases by linking the N- and C-terminal ends, introducing disulfide bridges, and optimizing β-turn structures to promote hydrophobic interactions.
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Affiliation(s)
- Masahiro Watanabe
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32, Kagamiyama, Higashihiroshima, Hiroshima, 739-0046, Japan
| | - Tomohiko Matsuzawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Katsuro Yaoi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan.
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30
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Kötzler MP, Robinson K, Chen HM, Okon M, McIntosh LP, Withers SG. Modulating the Nucleophile of a Glycoside Hydrolase through Site-Specific Incorporation of Fluoroglutamic Acids. J Am Chem Soc 2018; 140:8268-8276. [DOI: 10.1021/jacs.8b04235] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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31
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Yang A, Cheng J, Liu M, Shangguan Y, Liu L. Sandwich fusion of CBM9_2 to enhance xylanase thermostability and activity. Int J Biol Macromol 2018; 117:586-591. [PMID: 29852224 DOI: 10.1016/j.ijbiomac.2018.05.199] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/25/2018] [Accepted: 05/26/2018] [Indexed: 12/16/2022]
Abstract
Used as model for sandwich fusion, a mesophilic Aspergillus niger GH11 xylanase (Xyn) was fused into C2-Xyn-C2 with a thermophilic Thermotaga maritima GH10 xylanase carbohydrate-binding module CBM9_2 (C2). Linearized plasmids C2-pET20b-C2-Xyn were amplified from template pET20b-Xyn-C2 with a 4.3 kb C2-pET20b megaprimer, ligated into circular plasmids in blunt-end ligation, and transformed into E. coli BL21 (DE3) cells. The C2-Xyn-C2 had optimum activity at 45 °C and pH 4.2, a 2.85 h thermal inactivation half-life at 80 °C and a 8.69 h at 50 °C, with the 8.69 h value 24.8-, 7.5-, and 7.1-fold longer than the Xyn and single terminal fusion enzymes Xyn-C2, and C2-Xyn. Thermodynamics showed that the enzyme had a 1.8 °C higher melting temperature, lower values ΔS, ΔΔG, and a denser structure than the Xyn. Kinetics showed that the C2-Xyn-C2 catalytic efficiency was 1.2-~6-fold and 2.7-~7.9-fold higher on beechwood and oat-spelt xylan than those of the enzymes Xyn, Xyn-C2, and C2-Xyn. The sandwich fusion evolved the xylanase with "armor-hands" to enhance simultaneously thermostability and activity in quality.
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Affiliation(s)
- Ang Yang
- the Life Science College, Henan Agricultural University, Zhengzhou 450002, China
| | - Jinsheng Cheng
- the Life Science College, Henan Agricultural University, Zhengzhou 450002, China
| | - Meng Liu
- the Life Science College, Henan Agricultural University, Zhengzhou 450002, China
| | - Yunjie Shangguan
- the Life Science College, Henan Agricultural University, Zhengzhou 450002, China
| | - Liangwei Liu
- the Life Science College, Henan Agricultural University, Zhengzhou 450002, China; The Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture, Henan Agricultural University, Zhengzhou 450002, China.
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32
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Censoni L, Dos Santos Muniz H, Martínez L. A network model predicts the intensity of residue-protein thermal coupling. Bioinformatics 2018; 33:2106-2113. [PMID: 28334219 DOI: 10.1093/bioinformatics/btx124] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 03/01/2017] [Indexed: 11/13/2022] Open
Abstract
Motivation The flow of vibrational energy in proteins has been shown not to obey expectations for isotropic media. The existence of preferential pathways for energy transport, with probable connections to allostery mechanisms, has been repeatedly demonstrated. Here, we investigate whether, by representing a set of protein structures as networks of interacting amino acid residues, we are able to model heat diffusion and predict residue-protein vibrational couplings, as measured by the Anisotropic Thermal Diffusion (ATD) computational protocol of modified molecular dynamics simulations. Results We revisit the structural rationales for the precise definition of a contact between amino acid residues. Using this definition to describe a set of proteins as contact networks where each node corresponds to a residue, we show that node centrality, particularly closeness centrality and eigenvector centrality , correlates to the strength of the vibrational coupling of each residue to the rest of the structure. We then construct an analytically solvable model of heat diffusion on a network, whose solution incorporates an explicit dependence on the connectivity of the heated node, as described by a perturbed graph Laplacian Matrix. Availability and Implementation An implementation of the described model is available at http://leandro.iqm.unicamp.br/atd-scripts . Contact leandro@iqm.unicamp.br.
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Affiliation(s)
- Luciano Censoni
- Institute of Chemistry, University of Campinas, Campinas, SP, Brazil
| | | | - Leandro Martínez
- Institute of Chemistry, University of Campinas, Campinas, SP, Brazil
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33
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Li C, Li J, Wang R, Li X, Li J, Deng C, Wu M. Substituting Both the N-Terminal and “Cord” Regions of a Xylanase from Aspergillus oryzae to Improve Its Temperature Characteristics. Appl Biochem Biotechnol 2018; 185:1044-1059. [DOI: 10.1007/s12010-017-2681-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 12/19/2017] [Indexed: 10/18/2022]
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Baslé A, Hewitt L, Koh A, Lamb HK, Thompson P, Burgess JG, Hall MJ, Hawkins AR, Murray H, Lewis RJ. Crystal structure of NucB, a biofilm-degrading endonuclease. Nucleic Acids Res 2018; 46:473-484. [PMID: 29165717 PMCID: PMC5758888 DOI: 10.1093/nar/gkx1170] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/13/2017] [Indexed: 01/23/2023] Open
Abstract
Bacterial biofilms are a complex architecture of cells that grow on moist interfaces, and are held together by a molecular glue of extracellular proteins, sugars and nucleic acids. Biofilms are particularly problematic in human healthcare as they can coat medical implants and are thus a potential source of disease. The enzymatic dispersal of biofilms is increasingly being developed as a new strategy to treat this problem. Here, we have characterized NucB, a biofilm-dispersing nuclease from a marine strain of Bacillus licheniformis, and present its crystal structure together with the biochemistry and a mutational analysis required to confirm its active site. Taken together, these data support the categorization of NucB into a unique subfamily of the ββα metal-dependent non-specific endonucleases. Understanding the structure and function of NucB will facilitate its future development into an anti-biofilm therapeutic agent.
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Affiliation(s)
- Arnaud Baslé
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Lorraine Hewitt
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Alan Koh
- Centre for Bacterial Cell Biology, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Heather K Lamb
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Paul Thompson
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - J Grant Burgess
- Marine Biology, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Michael J Hall
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Alastair R Hawkins
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Heath Murray
- Centre for Bacterial Cell Biology, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Richard J Lewis
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK,To whom correspondence should be addressed. Tel: +44 191 208 5482;
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Abstract
The dynamic native, functional folded forms of proteins are unstable mainly because they readily unfold into flexible unstructured forms.
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Affiliation(s)
- Romas Kazlauskas
- Department of Biochemistry, Molecular Biology and Biophysics
- University of Minnesota
- St Paul
- USA
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36
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Abstract
Directed evolution has emerged as one of the most effective protein engineering methods in basic research as well as in applications in synthetic organic chemistry and biotechnology. The successful engineering of protein activity, allostery, binding affinity, expression, folding, fluorescence, solubility, substrate scope, selectivity (enantio-, stereo-, and regioselectivity), and/or stability (temperature, organic solvents, pH) is just limited by the throughput of the genetic selection, display, or screening system that is available for a given protein. Sometimes it is possible to analyze millions of protein variants from combinatorial libraries per day. In other cases, however, only a few hundred variants can be screened in a single day, and thus the creation of smaller yet smarter libraries is needed. Different strategies have been developed to create these libraries. One approach is to perform mutational scanning or to construct "mutability landscapes" in order to understand sequence-function relationships that can guide the actual directed evolution process. Herein we provide a protocol for economically constructing scanning mutagenesis libraries using a cytochrome P450 enzyme in a high-throughput manner. The goal is to engineer activity, regioselectivity, and stereoselectivity in the oxidative hydroxylation of a steroid, a challenging reaction in synthetic organic chemistry. Libraries based on mutability landscapes can be used to engineer any fitness trait of interest. The protocol is also useful for constructing gene libraries for deep mutational scanning experiments.
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Affiliation(s)
- Carlos G Acevedo-Rocha
- Department of Biocatalysis, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany.
- Department of Chemistry, Philipps-Universität Marburg, Marburg, 35032, Germany.
- Biosyntia ApS, 2100, Copenhagen, Denmark.
| | - Matteo Ferla
- Department of Biochemistry, Oxford University, Oxford, OX1 3QU, UK
| | - Manfred T Reetz
- Department of Biocatalysis, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
- Department of Chemistry, Philipps-Universität Marburg, Marburg, 35032, Germany
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Li XQ, Wu Q, Hu D, Wang R, Liu Y, Wu MC, Li JF. Improving the temperature characteristics and catalytic efficiency of a mesophilic xylanase from Aspergillus oryzae, AoXyn11A, by iterative mutagenesis based on in silico design. AMB Express 2017; 7:97. [PMID: 28508385 PMCID: PMC5432455 DOI: 10.1186/s13568-017-0399-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 05/02/2017] [Indexed: 11/10/2022] Open
Abstract
To improve the temperature characteristics and catalytic efficiency of a glycoside hydrolase family (GHF) 11 xylanase from Aspergillus oryzae (AoXyn11A), its variants were predicted based on in silico design. Firstly, Gly21 with the maximum B-factor value, which was confirmed by molecular dynamics (MD) simulation on the three-dimensional structure of AoXyn11A, was subjected to site-saturation mutagenesis. Thus, one variant with the highest thermostability, AoXyn11AG21I, was selected from the mutagenesis library, E. coli/Aoxyn11AG21X (X: any one of 20 amino acids). Secondly, based on the primary structure multiple alignment of AoXyn11A with seven thermophilic GHF11 xylanases, AoXyn11AY13F or AoXyn11AG21I–Y13F, was designed by replacing Tyr13 in AoXyn11A or AoXyn11AG21I with Phe. Finally, three variant-encoding genes, Aoxyn11AG21I, Aoxyn11AY13F and Aoxyn11AG21I–Y13F, were constructed by two-stage whole-plasmid PCR method, and expressed in Pichia pastoris GS115, respectively. The temperature optimum (Topt) of recombinant (re) AoXyn11AG21I–Y13F was 60 °C, being 5 °C higher than that of reAoXyn11AG21I or reAoXyn11AY13F, and 10 °C higher than that of reAoXyn11A. The thermal inactivation half-life (t1/2) of reAoXyn11AG21I–Y13F at 50 °C was 240 min, being 40-, 3.4- and 2.5-fold longer than those of reAoXyn11A, reAoXyn11AG21I and reAoXyn11AY13F. The melting temperature (Tm) values of reAoXyn11A, reAoXyn11AG21I, reAoXyn11AY13F and reAoXyn11AG21I–Y13F were 52.3, 56.5, 58.6 and 61.3 °C, respectively. These findings indicated that the iterative mutagenesis of both Gly21Ile and Tyr13Phe improved the temperature characteristics of AoXyn11A in a synergistic mode. Besides those, the catalytic efficiency (kcat/Km) of reAoXyn11AG21I–Y13F was 473.1 mL mg−1 s−1, which was 1.65-fold higher than that of reAoXyn11A.
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Han Y, Yu R, Gao P, Lu X, Yu W. The hydrogen-bond network around Glu160 contributes to the structural stability of chitosanase CsnA from Renibacterium sp. QD1. Int J Biol Macromol 2017; 109:880-887. [PMID: 29155203 DOI: 10.1016/j.ijbiomac.2017.11.071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/31/2017] [Accepted: 11/10/2017] [Indexed: 10/18/2022]
Abstract
CsnA, a chitosanase from Renibacterium sp. QD1, has great potential for industrial applications due to its high yield and broad pH stability. In this study, a specific Glu160 in CsnA was identified by sequence alignment, and structural analysis and MD simulation predicted that Glu160 formed a hydrogen-bond network with Lys163 and Thr114. To evaluate the effect of the network, we constructed four mutants, including E160A, E160Q, K163A, and T114A, which partially or completely destroy this network. Characterization of these mutants demonstrated that the disruption of the network significantly decreased the enzyme thermostability. The underlying mechanisms responsible for the change of thermostability analyzed by circular dichroism spectroscopy revealed that the hydrogen-bond network conferred the structural stability of CsnA. Moreover, the length of the side chain of residue at 160 impacted conformational stability of the enzyme. Taken together, the hydrogen-bond network around Glu160 plays important roles in stabilization of CsnA.
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Affiliation(s)
- Yujuan Han
- Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Key Laboratory of Marine Drugs, Chinese Ministry of Education, Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Rilei Yu
- Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Key Laboratory of Marine Drugs, Chinese Ministry of Education, Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Peixin Gao
- Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Key Laboratory of Marine Drugs, Chinese Ministry of Education, Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Xinzhi Lu
- Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Key Laboratory of Marine Drugs, Chinese Ministry of Education, Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
| | - Wengong Yu
- Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Key Laboratory of Marine Drugs, Chinese Ministry of Education, Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
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Wu X, Tian Z, Jiang X, Zhang Q, Wang L. Enhancement in catalytic activity of Aspergillus niger XynB by selective site-directed mutagenesis of active site amino acids. Appl Microbiol Biotechnol 2017; 102:249-260. [DOI: 10.1007/s00253-017-8607-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 10/10/2017] [Accepted: 10/12/2017] [Indexed: 01/25/2023]
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40
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Site-directed mutagenesis of GH10 xylanase A from Penicillium canescens for determining factors affecting the enzyme thermostability. Int J Biol Macromol 2017. [DOI: 10.1016/j.ijbiomac.2017.06.079] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Boonyapakron K, Jaruwat A, Liwnaree B, Nimchua T, Champreda V, Chitnumsub P. Structure-based protein engineering for thermostable and alkaliphilic enhancement of endo-β-1,4-xylanase for applications in pulp bleaching. J Biotechnol 2017; 259:95-102. [DOI: 10.1016/j.jbiotec.2017.07.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 07/17/2017] [Accepted: 07/28/2017] [Indexed: 10/19/2022]
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Shah V, Pierre B, Kirtadze T, Shin S, Kim JR. Stabilization of Bacillus circulans xylanase by combinatorial insertional fusion to a thermophilic host protein. Protein Eng Des Sel 2017; 30:281-290. [PMID: 28100651 DOI: 10.1093/protein/gzw081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 12/21/2016] [Indexed: 11/15/2022] Open
Abstract
High thermostability of an enzyme is critical for its industrial application. While many engineering approaches such as mutagenesis have enhanced enzyme thermostability, they often suffer from reduced enzymatic activity. A thermally stabilized enzyme with unchanged amino acids is preferable for subsequent functional evolution necessary to address other important industrial needs. In the research presented here, we applied insertional fusion to a thermophilic maltodextrin-binding protein from Pyrococcus furiosus (PfMBP) in order to improve the thermal stability of Bacillus circulans xylanase (BCX). Specifically, we used an engineered transposon to construct a combinatorial library of randomly inserted BCX into PfMBP. The library was then subjected to functional screening to identify successful PfMBP-BCX insertion complexes, PfMBP-BCX161 and PfMBP-BCX165, displaying substantially improved kinetic stability at elevated temperatures compared to unfused BCX and other controls. Results from subsequent characterizations were consistent with the view that lowered aggregation of BCX and reduced conformational flexibility at the termini was responsible for increased thermal stability. Our stabilizing approach neither sacrificed xylanase activity nor required changes in the BCX amino acid sequence. Overall, the current study demonstrated the benefit of combinatorial insertional fusion to PfMBP as a systematic tool for the creation of enzymatically active and thermostable BCX variants.
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Affiliation(s)
- Vandan Shah
- Othmer-Jacobs Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY 11201, USA
| | - Brennal Pierre
- Othmer-Jacobs Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY 11201, USA
| | - Tamari Kirtadze
- Othmer-Jacobs Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY 11201, USA
| | - Seung Shin
- Othmer-Jacobs Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY 11201, USA
| | - Jin Ryoun Kim
- Othmer-Jacobs Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY 11201, USA
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Han N, Miao H, Ding J, Li J, Mu Y, Zhou J, Huang Z. Improving the thermostability of a fungal GH11 xylanase via site-directed mutagenesis guided by sequence and structural analysis. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:133. [PMID: 28546828 PMCID: PMC5442702 DOI: 10.1186/s13068-017-0824-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/17/2017] [Indexed: 05/28/2023]
Abstract
BACKGROUND Xylanases have been widely employed in many industrial processes, and thermophilic xylanases are in great demand for meeting the high-temperature requirements of biotechnological treatments. In this work, we aim to improve the thermostability of XynCDBFV, a glycoside hydrolase (GH) family 11 xylanase from the ruminal fungus Neocallimastix patriciarum, by site-directed mutagenesis. We report favorable mutations at the C-terminus from B-factor comparison and multiple sequence alignment. RESULTS C-terminal residues 207-NGGA-210 in XynCDBFV were discovered to exhibit pronounced flexibility based on comparison of normalized B-factors. Multiple sequence alignment revealed that beneficial residues 207-SSGS-210 are highly conserved in GH11 xylanases. Thus, a recombinant xylanase, Xyn-MUT, was constructed by substituting three residues (N207S, G208S, A210S) at the C-terminus of XynCDBFV. Xyn-MUT exhibited higher thermostability than XynCDBFV at ≥70 °C. Xyn-MUT showed promising improvement in residual activity with a thermal retention of 14% compared to that of XynCDBFV after 1 h incubation at 80 °C; Xyn-MUT maintained around 50% of the maximal activity after incubation at 95 °C for 1 h. Kinetic measurements showed that the recombinant Xyn-MUT had greater kinetic efficiency than XynCDBFV (Km, 0.22 and 0.59 µM, respectively). Catalytic efficiency values (kcat/Km) of Xyn-MUT also increased (1.64-fold) compared to that of XynCDBFV. Molecular dynamics simulations were performed to explore the improved catalytic efficiency and thermostability: (1) the substrate-binding cleft of Xyn-MUT prefers to open to a larger extent to allow substrate access to the active site residues, and (2) hydrogen bond pairs S208-N205 and S210-A55 in Xyn-MUT contribute significantly to the improved thermostability. In addition, three xylanases with single point mutations were tested, and temperature assays verified that the substituted residues S208 and S210 give rise to the improved thermostability. CONCLUSIONS This is the first report for GH11 recombinant with improved thermostability based on C-terminus replacement. The resulting Xyn-MUT will be an attractive candidate for industrial applications.
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Affiliation(s)
- Nanyu Han
- School of Life Sciences, Yunnan Normal University, Kunming, 650500 China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500 China
| | - Huabiao Miao
- School of Life Sciences, Yunnan Normal University, Kunming, 650500 China
| | - Junmei Ding
- School of Life Sciences, Yunnan Normal University, Kunming, 650500 China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500 China
| | - Junjun Li
- School of Life Sciences, Yunnan Normal University, Kunming, 650500 China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500 China
| | - Yuelin Mu
- School of Life Sciences, Yunnan Normal University, Kunming, 650500 China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500 China
| | - Junpei Zhou
- School of Life Sciences, Yunnan Normal University, Kunming, 650500 China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500 China
| | - Zunxi Huang
- School of Life Sciences, Yunnan Normal University, Kunming, 650500 China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500 China
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44
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Silva SB, Pinheiro MP, Fuzo CA, Silva SR, Ferreira TL, Lourenzoni MR, Nonato MC, Vieira DS, Ward RJ. The role of local residue environmental changes in thermostable mutants of the GH11 xylanase from Bacillus subtilis. Int J Biol Macromol 2017; 97:574-584. [DOI: 10.1016/j.ijbiomac.2017.01.054] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 01/09/2017] [Accepted: 01/11/2017] [Indexed: 12/24/2022]
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45
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Jiang X, Li W, Chen G, Wang L. Dynamic Perturbation of the Active Site Determines Reversible Thermal Inactivation in Glycoside Hydrolase Family 12. J Chem Inf Model 2017; 57:288-297. [DOI: 10.1021/acs.jcim.6b00692] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xukai Jiang
- State Key Laboratory
of Microbial
Technology, Shandong University, Jinan 250100, China
| | - Wen Li
- State Key Laboratory
of Microbial
Technology, Shandong University, Jinan 250100, China
| | - Guanjun Chen
- State Key Laboratory
of Microbial
Technology, Shandong University, Jinan 250100, China
| | - Lushan Wang
- State Key Laboratory
of Microbial
Technology, Shandong University, Jinan 250100, China
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46
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Hu D, Li J, Wu Q, Zang J, Cheng J, Wu M. Improved temperature characteristics of an Aspergillus oryzae GHF11 xylanase, by in silico design and site-directed mutagenesis. BIOTECHNOL BIOPROC E 2017. [DOI: 10.1007/s12257-016-0339-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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47
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Luo H, Zhu L, Chang Y, Liu X, Liu Z, Sun H, Li X, Yu H, Shen Z. Microenvironmental pH changes in immobilized cephalosporin C acylase during a proton-producing reaction and regulation by a two-stage catalytic process. BIORESOURCE TECHNOLOGY 2017; 223:157-165. [PMID: 27792925 DOI: 10.1016/j.biortech.2016.10.038] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 10/09/2016] [Accepted: 10/13/2016] [Indexed: 06/06/2023]
Abstract
Cephalosporin C acylase (CCA), a proton-producing enzyme, was covalently bound on an epoxy-activated porous support. The microenvironmental pH change in immobilized CCA during the reaction was detected using pH-sensitive fluorescein labeling. The high catalytic velocity of the initial stage of conversion resulted in a sharp intraparticle pH gradient, which was likely the key factor relating to low operational stability. Accordingly, a novel strategy for a two-stage catalytic process was developed to reduce the reaction rate of stage I at a low temperature to preserve enzymatic activity and to shorten the duration of catalysis at a high reaction temperature in stage II. The reaction using the two-stage catalytic process (10-37°C shift at 30min) showed significantly improved stability compared with that of the single-temperature reaction at 37°C (29 batches versus five batches, respectively) and a shorter catalytic period than the reaction at 10°C (40min versus 70min, respectively).
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Affiliation(s)
- Hui Luo
- Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing 100083, China.
| | - Linlin Zhu
- Department of Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China; Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, Beijing 100083, China
| | - Yanhong Chang
- Department of Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China; Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, Beijing 100083, China
| | - Xiuhong Liu
- Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing 100083, China; Department of Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Zijia Liu
- Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing 100083, China; Department of Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Hongxu Sun
- Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Xi Li
- Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Huimin Yu
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Zhongyao Shen
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
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48
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Bai W, Cao Y, Liu J, Wang Q, Jia Z. Improvement of alkalophilicity of an alkaline xylanase Xyn11A-LC from Bacillus sp. SN5 by random mutation and Glu135 saturation mutagenesis. BMC Biotechnol 2016; 16:77. [PMID: 27825339 PMCID: PMC5101721 DOI: 10.1186/s12896-016-0310-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 10/21/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Family 11 alkaline xylanases have great potential economic applications in the pulp and paper industry. In this study, we would improve the alkalophilicity of family 11 alkaline xylanase Xyn11A-LC from Bacillus sp. SN5, for the better application in this field. RESULTS A random mutation library of Xyn11A-LC with about 10,000 clones was constructed by error-prone PCR. One mutant, M52-C10 (V116A and E135V), with improved alkalophilicity was obtained from the library. Site-directed mutation showed that the mutation E135V was responsible for the alkalophilicity of the mutant. The variant E135V shifted the optimum pH of the wild-type enzyme from 7.5 to 8.0. Compared to the relative activities of the wild type enzyme, those of the mutant E135V increased by 17.5, 18.9, 14.3 and 9.5 % at pH 8.5, 9.0, 9.5 and 10.0, respectively. Furthermore, Glu135 saturation mutagenesis showed that the only mutant to have better alkalophilicity than E135V was E135R. The optimal pH of the mutant E135R was 8.5, 1.0 pH units higher than that of the wild-type. In addition, compared to the wild-type enzyme, the mutations E135V and E135R increased the catalytic efficiency (k cat/K m) by 57 and 37 %, respectively. Structural analysis showed that the residue at position 135, located in the eight-residue loop on the protein surface, might improve the alkalophilicity and catalytic activity by the elimination of the negative charge and the formation of salt-bridge. CONCLUSIONS Mutants E135V and E135R with improved alkalophilicity were obtained by directed evolution and site saturation mutagenesis. The residue at position 135 in the eight-residue loop on the protein surface was found to play an important role in the pH activity profile of family 11 xylanases. This study provided alkalophilic mutants for application in bleaching process, and it was also helpful to understand the alkaline adaptation mechanism of family 11 xylanases.
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Affiliation(s)
- Wenqin Bai
- Department of Strategic and Integrative Research, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China. .,College of Life Science, Shanxi Normal University, Linfen, 041004, China.
| | - Yufan Cao
- Department of Strategic and Integrative Research, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China.,College of Life Science, Shanxi Normal University, Linfen, 041004, China
| | - Jun Liu
- Department of Strategic and Integrative Research, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China.,College of Life Science, Shanxi Normal University, Linfen, 041004, China
| | - Qinhong Wang
- Department of Strategic and Integrative Research, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
| | - Zhenhu Jia
- College of Life Science, Shanxi Normal University, Linfen, 041004, China.
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49
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Zheng F, Huang H, Wang X, Tu T, Liu Q, Meng K, Wang Y, Su X, Xie X, Luo H. Improvement of the catalytic performance of a Bispora antennata cellulase by replacing the N-terminal semi-barrel structure. BIORESOURCE TECHNOLOGY 2016; 218:279-285. [PMID: 27372007 DOI: 10.1016/j.biortech.2016.06.094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 06/22/2016] [Accepted: 06/23/2016] [Indexed: 06/06/2023]
Abstract
The aim of this work was to study the contribution of the N-terminal structure to cellulase catalytic performance. A wild-type cellulase (BaCel5) of glycosyl hydrolase (GH) family 5 from Bispora antennata and two hybrid enzymes (BaCel5(127) and BaCel5(167)) with replacement of the N-terminal (βα)3 (127 residues) or (βα)4 (167 residues)-barrel with the corresponding sequences of TeEgl5A from Talaromyces emersonii were produced in Pichia pastoris and biochemically characterized. BaCel5 exhibited optimal activity at pH 5.0 and 50°C but had low catalytic efficiency (25.4±0.8mLs(-1)mg(-1)). In contrast, BaCel5(127) and BaCel5(167) showed similar enzymatic properties but improved catalytic performance. When using CMC-Na, barley β-glucan, lichenan, and cellooligosaccharides as substrates, BaCel5(127) and BaCel5(167) had increased specific activities and catalytic efficiencies by ∼1.8-6.7-fold and ∼1.0-4.7-fold, respectively. The catalytic efficiency of BaCel5(167) was even higher than that of parental proteins. The underlying mechanism was analyzed by molecular docking and molecular dynamic simulation.
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Affiliation(s)
- Fei Zheng
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, People's Republic of China; Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
| | - Huoqing Huang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
| | - Xiaoyu Wang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, People's Republic of China; Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
| | - Tao Tu
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
| | - Qiong Liu
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
| | - Kun Meng
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
| | - Yuan Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
| | - Xiaoyun Su
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
| | - Xiangming Xie
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, People's Republic of China
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China.
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50
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Yu T, Anbarasan S, Wang Y, Telli K, Aslan AS, Su Z, Zhou Y, Zhang L, Iivonen P, Havukainen S, Mentunen T, Hummel M, Sixta H, Binay B, Turunen O, Xiong H. Hyperthermostable Thermotoga maritima xylanase XYN10B shows high activity at high temperatures in the presence of biomass-dissolving hydrophilic ionic liquids. Extremophiles 2016; 20:515-24. [PMID: 27240671 PMCID: PMC4921120 DOI: 10.1007/s00792-016-0841-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/15/2016] [Indexed: 01/16/2023]
Abstract
The gene of Thermotoga maritima GH10 xylanase (TmXYN10B) was synthesised to study the extreme limits of this hyperthermostable enzyme at high temperatures in the presence of biomass-dissolving hydrophilic ionic liquids (ILs). TmXYN10B expressed from Pichia pastoris showed maximal activity at 100 °C and retained 92 % of maximal activity at 105 °C in a 30-min assay. Although the temperature optimum of activity was lowered by 1-ethyl-3-methylimidazolium acetate ([EMIM]OAc), TmXYN10B retained partial activity in 15-35 % hydrophilic ILs, even at 75-90 °C. TmXYN10B retained over 80 % of its activity at 90 °C in 15 % [EMIM]OAc and 15-25 % 1-ethyl-3-methylimidazolium dimethylphosphate ([EMIM]DMP) during 22-h reactions. [EMIM]OAc may rigidify the enzyme and lower V max. However, only minor changes in kinetic parameter K m showed that competitive inhibition by [EMIM]OAc of TmXYN10B is minimal. In conclusion, when extended enzymatic reactions under extreme conditions are required, TmXYN10B shows extraordinary potential.
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Affiliation(s)
- Tianyi Yu
- South-Central University for Nationalities, College of Life Science, Wuhan, 430074, China
| | - Sasikala Anbarasan
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Yawei Wang
- South-Central University for Nationalities, College of Life Science, Wuhan, 430074, China
| | - Kübra Telli
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Aşkın Sevinç Aslan
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Zhengding Su
- Hubei University of Technology, Wuhan, 430068, China
| | - Yin Zhou
- Wuhan Sunhy Biology Co., Ltd, Wuhan, 430074, China
| | - Li Zhang
- South-Central University for Nationalities, College of Life Science, Wuhan, 430074, China
| | - Piia Iivonen
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Sami Havukainen
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Tero Mentunen
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Michael Hummel
- Department of Forest Products Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Herbert Sixta
- Department of Forest Products Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Baris Binay
- Department of Bioengineering, Gebze Technical University, 41400, Gebze Kocaeli, Turkey
| | - Ossi Turunen
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland.
| | - Hairong Xiong
- South-Central University for Nationalities, College of Life Science, Wuhan, 430074, China.
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