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Duan S, Wu Y, Chao T, Zhang N, Wei Z, Ji R. Improving the catalytic activity and thermostability of Aspergillus niger xylanase through computational design. Protein Expr Purif 2024; 223:106561. [PMID: 39094812 DOI: 10.1016/j.pep.2024.106561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2024] [Revised: 07/26/2024] [Accepted: 07/30/2024] [Indexed: 08/04/2024]
Abstract
Xylanase plays the most important role in catalyzing xylan to xylose moieties. GH11 xylanases have been widely used in many fields, but most GH11 xylanases are mesophilic enzymes. To improve the catalytic activity and thermostability of Aspergillus niger xylanase (Xyn-WT), we predicted potential key mutation sites of Xyn-WT through multiple computer-aided enzyme engineering strategies. We introduce a simple and economical Ni affinity chromatography purification method to obtain high-purity xylanase and its mutants. Ten mutants (Xyn-A, Xyn-B, Xyn-C, E45T, Q93R, E45T/Q93R, A161P, Xyn-D, Xyn-E, Xyn-F) were identified. Among the ten mutants, four (Xyn-A, Xyn-C, A161P, Xyn-F) presented improved thermal stability and activity, with Xyn-F(A161P/E45T/Q93R) being the most thermally stable and active. Compared with Xyn-WT, after heat treatment at 55°C and 60°C for 10 min, the remaining enzyme activity of Xyn-F was 12 and 6 times greater than that of Xyn-WT, respectively, and Xyn-F was approximately 1.5 times greater than Xyn-WT when not heat treated. The pH adaptation of Xyn-F was also significantly enhanced. In summary, an improved catalytic activity and thermostability of the design variant Xyn-F has been reported.
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Affiliation(s)
- Shuyan Duan
- College of Food Science and Pharmaceutical Engineering, Zaozhuang University, Zaozhuang, Shandong 277160, China.
| | - Yaoyao Wu
- College of Food Science and Pharmaceutical Engineering, Zaozhuang University, Zaozhuang, Shandong 277160, China
| | - Tianzhu Chao
- College of Food Science and Pharmaceutical Engineering, Zaozhuang University, Zaozhuang, Shandong 277160, China
| | - Nan Zhang
- College of Food Science and Pharmaceutical Engineering, Zaozhuang University, Zaozhuang, Shandong 277160, China
| | - Zhaoyi Wei
- College of Food Science and Pharmaceutical Engineering, Zaozhuang University, Zaozhuang, Shandong 277160, China
| | - Rui Ji
- Shandong Academy of Pharmaceutical Sciences, Key Laboratory of Biopharmaceuticals, Jinan, 250101, China
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2
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Nakamura T, Takita T, Kuwata K, Mizutani K, Mikami B, Nakamura S, Yasukawa K. Activity-stability trade-off observed in variants at position 315 of the GH10 xylanase XynR. Sci Rep 2024; 14:7767. [PMID: 38565938 PMCID: PMC10987496 DOI: 10.1038/s41598-024-57819-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/21/2024] [Indexed: 04/04/2024] Open
Abstract
XynR is a thermostable alkaline GH10 xylanase, for which we have previously examined the effects of saturation mutagenesis at position 315 on enzyme alkaliphily, and found that at pH 10, the activities of variants could be ordered as follows: T315Q > T315S = T315N > T315H = wild-type XynR (WT) > 15 other variants. In this study, we sought to elucidate the mechanisms underlying the variable activity of these different variants. Crystallographic analysis revealed that the Ca2+ ion near position 315 in WT was absent in the T315Q variant. We accordingly hypothesized that the enhancement of alkaliphily in T315Q, and probably also in the T315H, T315N, and T315S variants, could be ascribed to an activity-stability trade-off associated with a reduction in stability due to the lack of this Ca2+ ion. Consistent with expectations, the alkaline resistance of T315H, T315N, T315Q, and T315S, evaluated through the pH-dependence of stability at 0 mM CaCl2 under alkaline conditions, was found to be lower than that of WT: the residual activity at pH 11 of WT was 78% while those of T315H, T315N, T315Q, and T315S were 0, 9, 0, and 43%, respectively. In addition, the thermostabilities of these four variants, as assessed using the denaturing temperatures (Tm) at 0 mM CaCl2 based on ellipticity at 222 nm in circular dichroism measurements, were lower than that of WT by 2-8 °C. Furthermore, the Tm values of WT and variants at 5 mM CaCl2 were higher than those at 0 mM CaCl2 by 6-11 °C. Collectively, our findings in this study indicate that mutation of the T residue at position 315 of XynR to H, N, Q, and S causes an increase in the alkaliphily of this enzyme, thereby reducing its stability.
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Affiliation(s)
- Tomoka Nakamura
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kohei Kuwata
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kimihiko Mizutani
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Bunzo Mikami
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, 611-0011, Japan
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Satoshi Nakamura
- Department of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, 226-8501, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan.
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Li S, Shao Z, Lu C, Duan D. Isolation and functional verification of an aspartate aminotransferase gene from Neoporphyra haitanensis. BMC PLANT BIOLOGY 2023; 23:150. [PMID: 36941626 PMCID: PMC10029208 DOI: 10.1186/s12870-023-04158-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/08/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Neoporphyra haitanensis is a commercial laver species in China. Aspartic acid is an important flavor amino acid, and aspartate aminotransferase (AAT) is a crucial enzyme in its biosynthesis. In this study, we cloned one AAT gene (NhAAT) from the red alga N. haitanensis and investigated its sequence structure, transcriptional expression and enzymatic characteristics. The purpose of our research is to obtain a functional AAT responsible for the biosynthesis of aspartic acid from red seaweeds, which has the potential to influence the flavor of N. haitanensis. RESULTS Sequence analysis showed that NhAAT contains a conserved domain of Aminotran_1_2, which belongs to the transaminase superfamily. The secondary structure of NhAAT is dominated by α-helix. The results of enzymatic characterization illustrated that the NhAAT has highest catalytic activity at 45 °C and pH 7.5 in both forward and reverse reactions. The calculated Km values of NhAAT was 5.67 and 6.16 mM for L-glutamic acid and L-aspartic acid, respectively. Quantitative analysis showed that the NhAAT expression of N. haitanensis collected in late harvest (Dec) was 4.5 times that of N. haitanensis collected in early harvest (Oct), while the aspartic acid content of N. haitanensis collected in late harvest (Dec) was 1.2 times that of N. haitanensis collected in early harvest (Oct). CONCLUSION The results of enzyme kinetics indicated that NhAAT prefers to catalyze the reaction in the direction of aspartic acid production. Moreover, the trend of NhAAT expression level was consistent with that of aspartic acid content in N. haitanensis in different harvest periods. Our research is helpful to understand the accumulation and regulation of amino acids in N. haitanensis in different habitats and the taste difference of N. haitanensis in different harvest periods.
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Affiliation(s)
- Shuang Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhanru Shao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Chang Lu
- Department of Biological Engineering, College of Life Science, Yantai University, Yantai, 264005, P. R. China
| | - Delin Duan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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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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5
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Verma D. Extremophilic Prokaryotic Endoxylanases: Diversity, Applicability, and Molecular Insights. Front Microbiol 2021; 12:728475. [PMID: 34566933 PMCID: PMC8458939 DOI: 10.3389/fmicb.2021.728475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/06/2021] [Indexed: 11/13/2022] Open
Abstract
Extremophilic endoxylanases grabbed attention in recent years due to their applicability under harsh conditions of several industrial processes. Thermophilic, alkaliphilic, and acidophilic endoxylanases found their employability in bio-bleaching of paper pulp, bioconversion of lignocellulosic biomass into xylooligosaccharides, bioethanol production, and improving the nutritious value of bread and other bakery products. Xylanases obtained from extremophilic bacteria and archaea are considered better than fungal sources for several reasons. For example, enzymatic activity under broad pH and temperature range, low molecular weight, cellulase-free activity, and longer stability under extreme conditions of prokaryotic derived xylanases make them a good choice. In addition, a short life span, easy cultivation/harvesting methods, higher yield, and rapid DNA manipulations of bacterial and archaeal cells further reduces the overall cost of the product. This review focuses on the diversity of prokaryotic endoxylanases, their characteristics, and their functional attributes. Besides, the molecular mechanisms of their extreme behavior have also been presented here.
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Affiliation(s)
- Digvijay Verma
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
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6
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Kuwata K, Suzuki M, Takita T, Yatsunami R, Nakamura S, Yasukawa K. The mutation of Thr315 to Asn of GH10 xylanase XynR increases the alkaliphily but decreases the alkaline resistance. Biosci Biotechnol Biochem 2021; 85:1853-1860. [PMID: 34077498 DOI: 10.1093/bbb/zbab102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/26/2021] [Indexed: 11/13/2022]
Abstract
XynR is a thermophilic and alkaline GH10 xylanase, identified in the culture broth of alkaliphilic and thermophilic Bacillus sp. strain TAR-1. We previously selected S92E as a thermostable variant from a site saturation mutagenesis library. Here, we attempted to select the alkaliphilic XynR variant from the library and isolated T315N. In the hydrolysis of beechwood xylan, T315N and S92E/T315N exhibited a broader bell-shaped pH-dependent activity than the wild-type (WT) XynR and S92E. The optimal pH values of T315N and S92E/T315N were 6.5-9.5 while those of WT and S92E were 6.5-8.5. On the other hand, T315N and S92E/T315N exhibited a narrower bell-shaped pH dependence of stability: the pHs at which the activity was stable after the incubation at 37 °C for 24 h were 6.0-8.5 for T315N and S92E/T315N, but 6.0-10.0 for WT and S92E. These results indicated that the mutation of Thr315 to Asn increased the alkaliphily but decreased the alkaline resistance.
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Affiliation(s)
- Kohei Kuwata
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Manami Suzuki
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Rie Yatsunami
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama, Japan
| | - Satoshi Nakamura
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama, Japan.,National Institute of Technology, Numazu College, Ooka, Numazu, Shizuoka, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
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7
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Suzuki M, Takita T, Kuwata K, Nakatani K, Li T, Katano Y, Kojima K, Mizutani K, Mikami B, Yatsunami R, Nakamura S, Yasukawa K. Insight into the mechanism of thermostabilization of GH10 xylanase from Bacillus sp. strain TAR-1 by the mutation of S92 to E. Biosci Biotechnol Biochem 2021; 85:386-390. [PMID: 33604642 DOI: 10.1093/bbb/zbaa003] [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] [Received: 07/22/2020] [Accepted: 09/02/2020] [Indexed: 11/12/2022]
Abstract
The mechanism of thermostabilization of GH10 xylanase, XynR, from Bacillus sp. strain TAR-1 by the mutation of S92 to E was investigated. Thermodynamic analysis revealed that thermostabilization was driven by the decrease in entropy change of activation for thermal inactivation. Crystallographic analysis suggested that this mutation suppressed the fluctuation of the amino acid residues at position 92-95.
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Affiliation(s)
- Manami Suzuki
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kohei Kuwata
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kota Nakatani
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Tongyang Li
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yuta Katano
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kenji Kojima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kimihiko Mizutani
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Bunzo Mikami
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.,Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Rie Yatsunami
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Satoshi Nakamura
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.,National Institute of Technology, Numazu College, Ooka, Numazu, Shizuoka 410-8501, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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Takita T, Nakatani K, Katano Y, Suzuki M, Kojima K, Saka N, Mikami B, Yatsunami R, Nakamura S, Yasukawa K. Increase in the thermostability of GH11 xylanase XynJ from Bacillus sp. strain 41M-1 using site saturation mutagenesis. Enzyme Microb Technol 2019; 130:109363. [DOI: 10.1016/j.enzmictec.2019.109363] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/29/2019] [Accepted: 06/17/2019] [Indexed: 10/26/2022]
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9
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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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10
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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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11
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Heterologous expression in Pichia pastoris and characterization of a novel GH11 xylanase from saline-alkali soil with excellent tolerance to high pH, high salt concentrations and ethanol. Protein Expr Purif 2017; 139:71-77. [DOI: 10.1016/j.pep.2017.06.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 05/17/2017] [Accepted: 06/06/2017] [Indexed: 11/22/2022]
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12
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Laboratory Evolution of Bacillus circulans Xylanase Inserted into Pyrococcus furiosus Maltodextrin-Binding Protein for Increased Xylanase Activity and Thermal Stability Toward Alkaline pH. Appl Biochem Biotechnol 2017; 184:1232-1246. [DOI: 10.1007/s12010-017-2619-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 09/27/2017] [Indexed: 12/26/2022]
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13
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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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14
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Xu Y, Liu Y, Rasool A, E W, Li C. Sequence editing strategy for improving performance of β-glucuronidase from Aspergillus terreus. Chem Eng Sci 2017. [DOI: 10.1016/j.ces.2017.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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15
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Wang G, Wu J, Yan R, Lin J, Ye X. A Novel Multi-domain High Molecular, Salt-Stable Alkaline Xylanase from Alkalibacterium sp. SL3. Front Microbiol 2017; 7:2120. [PMID: 28101084 PMCID: PMC5209378 DOI: 10.3389/fmicb.2016.02120] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 12/15/2016] [Indexed: 11/13/2022] Open
Abstract
A novel multi-domain high molecular xylanase coding gene (xynSL3) was cloned from Alkalibacterium sp. SL3, an alkaliphilic bacterial strain isolated from the sediment of soda lake Dabusu. The deduced XynSL3 is composed of a putative signal peptide, three tandem domains of carbohydrate binding module (CBM) family 22, a catalytic domain of glycosyl hydrolase (GH) family 10 and a domain of CBM9. XynSL3 shares the highest identity of 66% to a hypothetical protein from Alkalibacterium sp. AK22 and has low identities (33-45%) with other functionally characterized xylanases. The gene xynSL3 was expressed heterologously in Escherichia coli and the recombinant enzyme demonstrated some particular characteristics. Purified recombinant XynSL3 (rXynSL3) was highly active and stable over the neutral and alkaline pH ranges from 7.0 to 12.0, with maximum activity at pH 9.0 and around 45% activity at pH 12.0. It had an apparent temperature optimum of 55°C and was stable at 50°C. The rXynSL3 was highly halotolerant, retaining more than 60% activity with 3 M NaCl and was stable at up to a 4 M concentration of NaCl. The hydrolysis products of rXynSL3 from corncob xylan were mainly xylobiose and xylotetraose. The activity of rXynSL3 was enhanced by Ca2+ and it has strong resistance to sodium dodecyl sulfate (SDS). This multi-domain, alkaline and salt-tolerant enzyme has great potential for basic research and industrial applications such as the biobleaching of paper pulp and production of xylo-oligosaccharides (XOS).
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Affiliation(s)
- Guozeng Wang
- Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou UniversityFuzhou, China; College of Biological Science and Technology, Fuzhou UniversityFuzhou, China
| | - Jingjing Wu
- Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou UniversityFuzhou, China; College of Biological Science and Technology, Fuzhou UniversityFuzhou, China
| | - Renxiang Yan
- College of Biological Science and Technology, Fuzhou University Fuzhou, China
| | - Juan Lin
- Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou UniversityFuzhou, China; College of Biological Science and Technology, Fuzhou UniversityFuzhou, China
| | - Xiuyun Ye
- Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou UniversityFuzhou, China; College of Biological Science and Technology, Fuzhou UniversityFuzhou, China
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16
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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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Niu C, Zhu L, Xu X, Li Q. Rational design of thermostability in bacterial 1,3-1,4-β-glucanases through spatial compartmentalization of mutational hotspots. Appl Microbiol Biotechnol 2016; 101:1085-1097. [DOI: 10.1007/s00253-016-7826-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 08/15/2016] [Accepted: 08/22/2016] [Indexed: 11/28/2022]
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18
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Niu C, Zhu L, Xu X, Li Q. Rational Design of Disulfide Bonds Increases Thermostability of a Mesophilic 1,3-1,4-β-Glucanase from Bacillus terquilensis. PLoS One 2016; 11:e0154036. [PMID: 27100881 PMCID: PMC4839689 DOI: 10.1371/journal.pone.0154036] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/07/2016] [Indexed: 11/19/2022] Open
Abstract
1,3-1,4-β-glucanase is an important biocatalyst in brewing industry and animal feed industry, while its low thermostability often reduces its application performance. In this study, the thermostability of a mesophilic β-glucanase from Bacillus terquilensis was enhanced by rational design and engineering of disulfide bonds in the protein structure. Protein spatial configuration was analyzed to pre-exclude the residues pairs which negatively conflicted with the protein structure and ensure the contact of catalytic center. The changes in protein overall and local flexibility among the wild-type enzyme and the designated mutants were predicted to select the potential disulfide bonds for enhancement of thermostability. Two residue pairs (N31C-T187C and P102C-N125C) were chosen as engineering targets and both of them were proved to significantly enhance the protein thermostability. After combinational mutagenesis, the double mutant N31C-T187C/P102C-N125C showed a 48.3% increase in half-life value at 60°C and a 4.1°C rise in melting temperature (Tm) compared to wild-type enzyme. The catalytic property of N31C-T187C/P102C-N125C mutant was similar to that of wild-type enzyme. Interestingly, the optimal pH of double mutant was shifted from pH6.5 to pH6.0, which could also increase its industrial application. By comparison with mutants with single-Cys substitutions, the introduction of disulfide bonds and the induced new hydrogen bonds were proved to result in both local and overall rigidification and should be responsible for the improved thermostability. Therefore, the introduction of disulfide bonds for thermostability improvement could be rationally and highly-effectively designed by combination with spatial configuration analysis and molecular dynamics simulation.
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Affiliation(s)
- Chengtuo Niu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of biotechnology, Jiangnan University, Wuxi, China
| | - Linjiang Zhu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of biotechnology, Jiangnan University, Wuxi, China
| | - Xin Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of biotechnology, Jiangnan University, Wuxi, China
| | - Qi Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of biotechnology, Jiangnan University, Wuxi, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- * E-mail:
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Biochemical characterization of an acidophilic β-mannanase from Gloeophyllum trabeum CBS900.73 with significant transglycosylation activity and feed digesting ability. Food Chem 2016; 197:474-81. [DOI: 10.1016/j.foodchem.2015.10.115] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 09/06/2015] [Accepted: 10/24/2015] [Indexed: 02/05/2023]
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20
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Bai W, Zhou C, Zhao Y, Wang Q, Ma Y. Structural Insight into and Mutational Analysis of Family 11 Xylanases: Implications for Mechanisms of Higher pH Catalytic Adaptation. PLoS One 2015; 10:e0132834. [PMID: 26161643 PMCID: PMC4498622 DOI: 10.1371/journal.pone.0132834] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/18/2015] [Indexed: 11/25/2022] Open
Abstract
To understand the molecular basis of higher pH catalytic adaptation of family 11 xylanases, we compared the structures of alkaline, neutral, and acidic active xylanases and analyzed mutants of xylanase Xyn11A-LC from alkalophilic Bacillus sp. SN5. It was revealed that alkaline active xylanases have increased charged residue content, an increased ratio of negatively to positively charged residues, and decreased Ser, Thr, and Tyr residue content relative to non-alkaline active counterparts. Between strands β6 and β7, alkaline xylanases substitute an α-helix for a coil or turn found in their non-alkaline counterparts. Compared with non-alkaline xylanases, alkaline active enzymes have an inserted stretch of seven amino acids rich in charged residues, which may be beneficial for xylanase function in alkaline conditions. Positively charged residues on the molecular surface and ionic bonds may play important roles in higher pH catalytic adaptation of family 11 xylanases. By structure comparison, sequence alignment and mutational analysis, six amino acids (Glu16, Trp18, Asn44, Leu46, Arg48, and Ser187, numbering based on Xyn11A-LC) adjacent to the acid/base catalyst were found to be responsible for xylanase function in higher pH conditions. Our results will contribute to understanding the molecular mechanisms of higher pH catalytic adaptation in family 11 xylanases and engineering xylanases to suit industrial applications.
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Affiliation(s)
- Wenqin Bai
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Engineering Laboratory for Industrial Enzymes, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- School of Life Science, Shanxi Normal University, Linfen, 041004, China
- * E-mail: (YHM); (WQB)
| | - Cheng Zhou
- National Engineering Laboratory for Industrial Enzymes, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yueju Zhao
- Institute of Agro-Products Processing Science and Technology, Chinese Academy of Agriculture Sciences, Beijing, 100193, China
| | - Qinhong Wang
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Yanhe Ma
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Engineering Laboratory for Industrial Enzymes, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- * E-mail: (YHM); (WQB)
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Cheng YS, Chen CC, Huang JW, Ko TP, Huang Z, Guo RT. Improving the catalytic performance of a GH11 xylanase by rational protein engineering. Appl Microbiol Biotechnol 2015; 99:9503-10. [DOI: 10.1007/s00253-015-6712-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 05/18/2015] [Accepted: 05/21/2015] [Indexed: 11/28/2022]
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22
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Li H, Turunen O. Effect of acidic amino acids engineered into the active site cleft ofThermopolyspora flexuosaGH11 xylanase. Biotechnol Appl Biochem 2015; 62:433-40. [DOI: 10.1002/bab.1288] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 09/02/2014] [Indexed: 11/07/2022]
Affiliation(s)
- He Li
- Department of Biotechnology and Chemical Technology; School of Chemical Technology; Aalto University; Aalto 00076 Finland
| | - Ossi Turunen
- Department of Biotechnology and Chemical Technology; School of Chemical Technology; Aalto University; Aalto 00076 Finland
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Bai W, Xue Y, Zhou C, Ma Y. Cloning, expression, and characterization of a novel alkali-tolerant xylanase from alkaliphilicBacillussp. SN5. Biotechnol Appl Biochem 2014; 62:208-17. [DOI: 10.1002/bab.1265] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 06/18/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Wenqin Bai
- National Engineering Lab for Industrial Enzymes, Institute of Microbiology; Chinese Academy of Sciences; Beijing People's Republic of China
- National Engineering Lab for Industrial Enzymes; Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin People's Republic of China
- College of Life Science; Shanxi Normal University; Linfen People's Republic of China
| | - Yanfen Xue
- National Engineering Lab for Industrial Enzymes, Institute of Microbiology; Chinese Academy of Sciences; Beijing People's Republic of China
| | - Cheng Zhou
- National Engineering Lab for Industrial Enzymes, Institute of Microbiology; Chinese Academy of Sciences; Beijing People's Republic of China
| | - Yanhe Ma
- National Engineering Lab for Industrial Enzymes, Institute of Microbiology; Chinese Academy of Sciences; Beijing People's Republic of China
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Zouari Ayadi D, Hmida Sayari A, Ben Hlima H, Ben Mabrouk S, Mezghani M, Bejar S. Improvement of Trichoderma reesei xylanase II thermal stability by serine to threonine surface mutations. Int J Biol Macromol 2014; 72:163-70. [PMID: 25158289 DOI: 10.1016/j.ijbiomac.2014.08.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/04/2014] [Accepted: 08/05/2014] [Indexed: 10/24/2022]
Abstract
Three simple mutants, S80T, S146T, and S149T, and a double mutant, S80T-S149T, were constructed and expressed in Escherichia coli to replace Serine on the surface of the Trichoderma reesei xylanase protein with Threonine residues. While the Wild-type (WT) xylanase showed a half-life time (t1/2) of 20 min at 55 °C, the double mutant was more thermostable exhibiting a t1/2 value of 37 min, followed by the S80T and S149T mutants whose t1/2 values were 25 and 23 min, respectively. At 55 °C, the S146T mutant showed a decrease in thermostability with a t1/2 value of 3 min. While the WT enzyme retained only 32% of residual activity after incubation for 5 min at 60°C, the S80T, S149T, and the S80T-S149T mutant enzymes retained 45%, 41%, and 60%, respectively. Molecular modeling attributed the increase in the thermostability of the S80T and S149T mutants to a new hydrogen bond formation and a packing effect, respectively.
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Affiliation(s)
- Dorra Zouari Ayadi
- Laboratory of Microorganisms and Biomolecules (LMB), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, PO Box 1177, Sfax 3018, Tunisia
| | - Aida Hmida Sayari
- Laboratory of Microorganisms and Biomolecules (LMB), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, PO Box 1177, Sfax 3018, Tunisia
| | - Hajer Ben Hlima
- Laboratory of Microorganisms and Biomolecules (LMB), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, PO Box 1177, Sfax 3018, Tunisia
| | - Sameh Ben Mabrouk
- Laboratory of Microorganisms and Biomolecules (LMB), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, PO Box 1177, Sfax 3018, Tunisia
| | - Monia Mezghani
- Laboratory of Microorganisms and Biomolecules (LMB), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, PO Box 1177, Sfax 3018, Tunisia
| | - Samir Bejar
- Laboratory of Microorganisms and Biomolecules (LMB), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, PO Box 1177, Sfax 3018, Tunisia.
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Three-dimensional structure of an alkaline xylanase Xyn11A-LC from alkalophilic Bacillus sp. SN5 and improvement of its thermal performance by introducing arginines substitutions. Biotechnol Lett 2014; 36:1495-501. [PMID: 24682788 DOI: 10.1007/s10529-014-1512-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 03/04/2014] [Indexed: 10/25/2022]
Abstract
The alkaline xylanase Xyn11A-LC from the alkalophilic Bacillus sp. SN5 was expressed in E. coli, purified and crystallized. The crystal structure was determined at a resolution of 1.49 Å. Xyn11A-LC has the β-jelly roll structure typical of family 11 xylanases. To improve its thermostability and thermophilicity, a mutant SB3 was constructed by introducing three arginines on the different sides of the protein surface. SB3 increased the optimum temperature by 5 °C. The wild type and SB3 had the half-lives of 22 and 68 min at 65 °C at pH 8.0 (Tris/HCl buffer), respectively. CD spectroscopy revealed that the melting temperature (T m) of the wild type and SB3 were 55.3 and 66.9 °C, respectively. These results showed that the introduction of arginines enhance the thermophilicity and thermostability of Xyn11A-LC.
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26
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Zheng H, Liu Y, Sun M, Han Y, Wang J, Sun J, Lu F. Improvement of alkali stability and thermostability of Paenibacillus campinasensis Family-11 xylanase by directed evolution and site-directed mutagenesis. ACTA ACUST UNITED AC 2014; 41:153-62. [DOI: 10.1007/s10295-013-1363-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 10/05/2013] [Indexed: 11/30/2022]
Abstract
Abstract
The extreme process condition of high temperature and high alkali limits the applications of most of natural xylanases in pulp and paper industry. Recently, various methods of protein engineering have been used to improve the thermal and alkalic tolerance of xylanases. In this work, directed evolution and site-directed mutagenesis were performed to obtain a mutant xylanase improved both on alkali stability and thermostability from the native Paenibacillus campinasensis Family-11 xylanase (XynG1-1). Mutant XynG1-1B43 (V90R/P172H) with two units increased in the optimum pH (pH 7.0–pH 9.0) and significant improvement on alkali stability was selected from the second round of epPCR library. And the further thermoduric mutant XynG1-1B43cc16 (V90R/P172H/T84C-T182C/D16Y) with 10 °C increased in the optimum temperature (60–70 °C) was then obtained by introducing a disulfide bridge (T84C-T182C) and a single amino acid substitution (D16Y) to XynG1-1B43 using site-directed mutagenesis. XynG1-1B43cc16 also showed higher thermostability and catalytic efficiency (k cat/K m) than that of wild-type (XynG1-1) and XynG1-1B43. The attractive improved properties make XynG1-1B43cc16 more suitable for bioleaching of cotton stalk pulp under the extreme process condition of high temperature (70 °C) and high alkali (pH 9.0).
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Affiliation(s)
- Hongchen Zheng
- grid.419897.a 000000040369313X Key Laboratory of Industrial Fermentation Microbiology Education Ministry of China 300457 Tianjin China
- grid.413109.e 0000000097356249 Industrial Microbiology Laboratory, College of Biotechnology Tianjin University of Science & Technology No. 29, 13th Avenue, Tianjin Economic and Technological Development Area 300457 Tianjin China
- grid.469560.8 Chinese Academy of Agricultural Engineering 100125 Beijing China
| | - Yihan Liu
- grid.419897.a 000000040369313X Key Laboratory of Industrial Fermentation Microbiology Education Ministry of China 300457 Tianjin China
- Tianjin Key Laboratory of Industrial Microbiology 300457 Tianjin China
- grid.413109.e 0000000097356249 Industrial Microbiology Laboratory, College of Biotechnology Tianjin University of Science & Technology No. 29, 13th Avenue, Tianjin Economic and Technological Development Area 300457 Tianjin China
| | - Mingzhe Sun
- National Engineering Laboratory for Industrial Enzymes (NELIE) 300457 Tianjin China
- grid.413109.e 0000000097356249 Industrial Microbiology Laboratory, College of Biotechnology Tianjin University of Science & Technology No. 29, 13th Avenue, Tianjin Economic and Technological Development Area 300457 Tianjin China
| | - Yang Han
- grid.419897.a 000000040369313X Key Laboratory of Industrial Fermentation Microbiology Education Ministry of China 300457 Tianjin China
- grid.413109.e 0000000097356249 Industrial Microbiology Laboratory, College of Biotechnology Tianjin University of Science & Technology No. 29, 13th Avenue, Tianjin Economic and Technological Development Area 300457 Tianjin China
| | - Jianling Wang
- Tianjin Key Laboratory of Industrial Microbiology 300457 Tianjin China
- grid.413109.e 0000000097356249 Industrial Microbiology Laboratory, College of Biotechnology Tianjin University of Science & Technology No. 29, 13th Avenue, Tianjin Economic and Technological Development Area 300457 Tianjin China
| | - Junshe Sun
- grid.469560.8 Chinese Academy of Agricultural Engineering 100125 Beijing China
| | - Fuping Lu
- grid.419897.a 000000040369313X Key Laboratory of Industrial Fermentation Microbiology Education Ministry of China 300457 Tianjin China
- National Engineering Laboratory for Industrial Enzymes (NELIE) 300457 Tianjin China
- grid.413109.e 0000000097356249 Industrial Microbiology Laboratory, College of Biotechnology Tianjin University of Science & Technology No. 29, 13th Avenue, Tianjin Economic and Technological Development Area 300457 Tianjin China
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In silico rational design and systems engineering of disulfide bridges in the catalytic domain of an alkaline α-amylase from Alkalimonas amylolytica to improve thermostability. Appl Environ Microbiol 2013; 80:798-807. [PMID: 24212581 DOI: 10.1128/aem.03045-13] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
High thermostability is required for alkaline α-amylases to maintain high catalytic activity under the harsh conditions used in textile production. In this study, we attempted to improve the thermostability of an alkaline α-amylase from Alkalimonas amylolytica through in silico rational design and systems engineering of disulfide bridges in the catalytic domain. Specifically, 7 residue pairs (P35-G426, Q107-G167, G116-Q120, A147-W160, G233-V265, A332-G370, and R436-M480) were chosen as engineering targets for disulfide bridge formation, and the respective residues were replaced with cysteines. Three single disulfide bridge mutants-P35C-G426C, G116C-Q120C, and R436C-M480C-of the 7 showed significantly enhanced thermostability. Combinational mutations were subsequently assessed, and the triple mutant P35C-G426C/G116C-Q120C/R436C-M480C showed a 6-fold increase in half-life at 60°C and a 5.2°C increase in melting temperature compared with the wild-type enzyme. Interestingly, other biochemical properties of this mutant also improved: the optimum temperature increased from 50°C to 55°C, the optimum pH shifted from 9.5 to 10.0, the stable pH range extended from 7.0 to 11.0 to 6.0 to 12.0, and the catalytic efficiency (kcat/Km) increased from 1.8 × 10(4) to 2.4 × 10(4) liters/g · min. The possible mechanism responsible for these improvements was explored through comparative analysis of the model structures of wild-type and mutant enzymes. The disulfide bridge engineering strategy used in this work may be applied to improve the thermostability of other industrial enzymes.
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29
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Torres-Bacete J, Sinha PK, Sato M, Patki G, Kao MC, Matsuno-Yagi A, Yagi T. Roles of subunit NuoK (ND4L) in the energy-transducing mechanism of Escherichia coli NDH-1 (NADH:quinone oxidoreductase). J Biol Chem 2012; 287:42763-72. [PMID: 23105119 DOI: 10.1074/jbc.m112.422824] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The bacterial H(+)-translocating NADH:quinone oxidoreductase (NDH-1) catalyzes electron transfer from NADH to quinone coupled with proton pumping across the cytoplasmic membrane. The NuoK subunit (counterpart of the mitochondrial ND4L subunit) is one of the seven hydrophobic subunits in the membrane domain and bears three transmembrane segments (TM1-3). Two glutamic residues located in the adjacent transmembrane helices of NuoK are important for the energy coupled activity of NDH-1. In particular, mutation of the highly conserved carboxyl residue ((K)Glu-36 in TM2) to Ala led to a complete loss of the NDH-1 activities. Mutation of the second conserved carboxyl residue ((K)Glu-72 in TM3) moderately reduced the activities. To clarify the contribution of NuoK to the mechanism of proton translocation, we relocated these two conserved residues. When we shifted (K)Glu-36 along TM2 to positions 32, 38, 39, and 40, the mutants largely retained energy transducing NDH-1 activities. According to the recent structural information, these positions are located in the vicinity of (K)Glu-36, present in the same helix phase, in an immediately before and after helix turn. In an earlier study, a double mutation of two arginine residues located in a short cytoplasmic loop between TM1 and TM2 (loop-1) showed a drastic effect on energy transducing activities. Therefore, the importance of this cytosolic loop of NuoK ((K)Arg-25, (K)Arg-26, and (K)Asn-27) for the energy transducing activities was extensively studied. The probable roles of subunit NuoK in the energy transducing mechanism of NDH-1 are discussed.
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Affiliation(s)
- Jesus Torres-Bacete
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
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30
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Baek CU, Lee SG, Chung YR, Cho I, Kim JH. Cloning of a Family 11 Xylanase Gene from Bacillus amyloliquefaciens CH51 Isolated from Cheonggukjang. Indian J Microbiol 2012; 52:695-700. [PMID: 24293733 DOI: 10.1007/s12088-012-0260-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2012] [Accepted: 03/01/2012] [Indexed: 10/28/2022] Open
Abstract
Bacillus amyloliquefaciens CH51, an isolate from cheonggukjang, Korean fermented soyfood, secretes several enzymes into culture medium. A gene encoding 19 kDa xylanase was cloned by PCR. Sequencing showed that the gene encoded a glycohydrolase family 11 xylanase and named xynA. xynAHis, xynA with additional codons for his-tag, was overexpressed in Escherichia coli BL21(DE3) using pET-26b(+). XynAHis was purified using HisTrap affinity column. Km and Vmax of XynAHis were 0.363 mg/ml and 701.1 μmol/min/mg, respectively with birchwood xylan as a substrate. The optimum pH and temperature were pH 4 and 25 °C, respectively. When xynA was introduced into Bacillus subtilis WB600, active XynA was secreted into culture medium.
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Affiliation(s)
- C U Baek
- Division of Applied Life Science (Bk21), Graduate School, Research Institute of Life Sciences, Gyeongsang National University, Jinju, Korea
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Paës G, Berrin JG, Beaugrand J. GH11 xylanases: Structure/function/properties relationships and applications. Biotechnol Adv 2011; 30:564-92. [PMID: 22067746 DOI: 10.1016/j.biotechadv.2011.10.003] [Citation(s) in RCA: 284] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 10/06/2011] [Accepted: 10/13/2011] [Indexed: 01/02/2023]
Abstract
For technical, environmental and economical reasons, industrial demands for process-fitted enzymes have evolved drastically in the last decade. Therefore, continuous efforts are made in order to get insights into enzyme structure/function relationships to create improved biocatalysts. Xylanases are hemicellulolytic enzymes, which are responsible for the degradation of the heteroxylans constituting the lignocellulosic plant cell wall. Due to their variety, xylanases have been classified in glycoside hydrolase families GH5, GH8, GH10, GH11, GH30 and GH43 in the CAZy database. In this review, we focus on GH11 family, which is one of the best characterized GH families with bacterial and fungal members considered as true xylanases compared to the other families because of their high substrate specificity. Based on an exhaustive analysis of the sequences and 3D structures available so far, in relation with biochemical properties, we assess biochemical aspects of GH11 xylanases: structure, catalytic machinery, focus on their "thumb" loop of major importance in catalytic efficiency and substrate selectivity, inhibition, stability to pH and temperature. GH11 xylanases have for a long time been used as biotechnological tools in various industrial applications and represent in addition promising candidates for future other uses.
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Affiliation(s)
- Gabriel Paës
- INRA, UMR614 FARE, 2 esplanade Roland-Garros, F-51686 Reims, France.
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Fushinobu S, Uno T, Kitaoka M, Hayashi K, Matsuzawa H, Wakagi T. Mutational Analysis of Fungal Family 11 Xylanases on pH Optimum Determination. J Appl Glycosci (1999) 2011. [DOI: 10.5458/jag.jag.jag-2011_001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Gibbs M, Reeves R, Hardiman E, Choudhary P, Daniel R, Bergquist P. The activity of family 11 xylanases at alkaline pH. N Biotechnol 2010; 27:795-802. [DOI: 10.1016/j.nbt.2010.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Accepted: 06/09/2010] [Indexed: 11/30/2022]
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Structural insights into the acidophilic pH adaptation of a novel endo-1,4-β-xylanase from Scytalidium acidophilum. Biochimie 2010; 92:1407-15. [DOI: 10.1016/j.biochi.2010.07.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Accepted: 07/02/2010] [Indexed: 11/22/2022]
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35
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Jordan DB, Wagschal K. Properties and applications of microbial β-D-xylosidases featuring the catalytically efficient enzyme from Selenomonas ruminantium. Appl Microbiol Biotechnol 2010; 86:1647-58. [DOI: 10.1007/s00253-010-2538-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Revised: 03/02/2010] [Accepted: 03/03/2010] [Indexed: 11/28/2022]
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Umemoto H, Yazawa R, Takakura J, Yatsunami R, Fukui T, Nakamura S. Analysis of Functional Domains and Improvement of Alkaliphily of an Alkaline Xylanase on the Basis of Its Three-dimensional Structure. J Appl Glycosci (1999) 2010. [DOI: 10.5458/jag.57.145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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