1
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Pasin TM, Lucas RC, de Oliveira TB, McLeish MJ, Polizeli MDLTM. A new halotolerant xylanase from Aspergillus clavatus expressed in Escherichia coli with catalytic efficiency improved by site-directed mutagenesis. 3 Biotech 2024; 14:178. [PMID: 38855145 PMCID: PMC11156621 DOI: 10.1007/s13205-024-04021-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 05/27/2024] [Indexed: 06/11/2024] Open
Abstract
Daily agro-industrial waste, primarily cellulose, lignin, and hemicellulose, poses a significant environmental challenge. Harnessing lignocellulolytic enzymes, particularly endo-1,4-β-xylanases, for efficient saccharification is a cost-effective strategy, transforming biomass into high-value products. This study focuses on the cloning, expression, site-directed mutagenesis, purification, three-dimensional modeling, and characterization of the recombinant endo-1,4-β-xylanase (XlnA) from Aspergillus clavatus in Escherichia coli. This work includes evaluation of the stability at varied NaCl concentrations, determining kinetic constants, and presenting the heterologous expression of XlnAΔ36 using pET22b(+). The expression led to purified enzymes with robust stability across diverse pH levels, exceptional thermostability at 50 °C, and 96-100% relative stability after 24 h in 3.0 M NaCl. Three-dimensional modeling reveals a GH11 architecture with catalytic residues Glu 132 and 22. XlnAΔ36 demonstrates outstanding kinetic parameters compared to other endo-1,4-β-xylanases, indicating its potential for industrial enzymatic cocktails, enhancing saccharification. Moreover, its ability to yield high-value compounds, such as sugars, suggests a promising and ecologically positive alternative for the food and biotechnology industries.
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Affiliation(s)
- Thiago M. Pasin
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900 Brazil
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202 USA
- Department of Chemistry, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249 USA
| | - Rosymar C. Lucas
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900 Brazil
- Department of Biochemistry, Institute of Biomedical Sciences, Federal University of Alfenas, Alfenas, MG 37130-001 Brazil
| | - Tássio B. de Oliveira
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP 14040-901 Brazil
- Department of Systematics and Ecology, Center for Exact and Nature Sciences, Federal University of Paraíba, João Pessoa, PB 58051-900 Brazil
| | - Michael J. McLeish
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202 USA
| | - Maria de Lourdes T. M. Polizeli
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900 Brazil
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP 14040-901 Brazil
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2
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Zhu X, Zhao YF, Wen HJ, Lu Y, You S, Herman RA, Wang J. Silkworm pupae protein co-degradation by magnetic nanoparticles immobilized proteinase K and Mucor circinelloides aspartic protease for further utilization of sericulture by-products. ENVIRONMENTAL RESEARCH 2024; 249:118385. [PMID: 38331140 DOI: 10.1016/j.envres.2024.118385] [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: 12/09/2023] [Revised: 01/18/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024]
Abstract
Silkworm pupae, by-product of sericulture industry, is massively discarded. The degradation rate of silkworm pupae protein is critical to further employment, which reduces the impact of waste on the environment. Herein, magnetic Janus mesoporous silica nanoparticles immobilized proteinase K mutant T206M and Mucor circinelloides aspartic protease were employed in the co-degradation. The thermostability of T206M improved by enhancing structural rigidity (t1/2 by 30 min and T50 by 5 °C), prompting the degradation efficiency. At 65 °C and pH 7, degradation rate reached the highest of 61.7%, which improved by 26% compared with single free protease degradation. Besides, the immobilized protease is easy to separate and reuse, which maintains 50% activity after 10 recycles. Therefore, immobilized protease co-degradation was first applied to the development and utilization of silkworm pupae resulting in the release of promising antioxidant properties and reduces the environmental impact by utilizing a natural and renewable resource.
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Affiliation(s)
- Xuan Zhu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
| | - Yi-Fan Zhao
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
| | - Hong-Jian Wen
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
| | - Yu Lu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
| | - Shuai You
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212100, China
| | - Richard Ansah Herman
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212100, China
| | - Jun Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212100, China.
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3
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Hu G, Hong X, Zhu M, Lei L, Han Z, Meng Y, Yang J. Improving the Quality of Wheat Flour Bread by a Thermophilic Xylanase with Ultra Activity and Stability Reconstructed by Ancestral Sequence and Computational-Aided Analysis. Molecules 2024; 29:1895. [PMID: 38675714 PMCID: PMC11054572 DOI: 10.3390/molecules29081895] [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: 03/20/2024] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Xylanase is an essential component used to hydrolyze the xylan in wheat flour to enhance the quality of bread. Presently, cold-activated xylanase is popularly utilized to aid in the development of dough. In this study, ancestral sequence reconstruction and molecular docking of xylanase and wheat xylan were used to enhance the activity and stability of a thermophilic xylanase. The results indicated that the ancestral enzyme TmxN3 exhibited significantly improved activity and thermal stability. The Vmax increased by 2.7 times, and the catalytic efficiency (Kcat/Km) increased by 1.7 times in comparison to TmxB. After being incubated at 100 °C for 120 min, it still retained 87.3% of its activity, and the half-life in 100 °C was 330 min, while the wild type xylanase was only 55 min. This resulted in an improved shelf life of bread, while adding TmxN3 considerably enhanced its quality with excellent volume and reduced hardness, chewiness, and gumminess. The results showed that the hardness was reduced by 55.2%, the chewiness was reduced by 40.11%, and the gumminess was reduced by 53.52%. To facilitate its industrial application, we further optimized the production conditions in a 5L bioreactor, and the xylanase activity reached 1.52 × 106 U/mL culture.
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Affiliation(s)
- Guoshuai Hu
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, College of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China; (G.H.); (M.Z.)
| | - Xizhi Hong
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, College of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China; (G.H.); (M.Z.)
| | - Meixin Zhu
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, College of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China; (G.H.); (M.Z.)
| | - Lei Lei
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, College of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China; (G.H.); (M.Z.)
| | - Zhenggang Han
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, College of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China; (G.H.); (M.Z.)
| | - Yong Meng
- Mianyang Habio Bioengineering Co., Ltd., Mianyang 621000, China;
| | - Jiangke Yang
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, College of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China; (G.H.); (M.Z.)
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4
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Yang Y, Zhang C, Lu H, Wu Q, Wu Y, Li W, Li X. Improvement of thermostability and catalytic efficiency of xylanase from Myceliophthora thermophilar by N-terminal and C-terminal truncation. Front Microbiol 2024; 15:1385329. [PMID: 38659990 PMCID: PMC11039872 DOI: 10.3389/fmicb.2024.1385329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 03/27/2024] [Indexed: 04/26/2024] Open
Abstract
Introduction Extracting xylanase from thermophilic filamentous fungi is a feasible way to obtain xylanase with good thermal stability. Methods The transcriptomic data of Myceliophthora thermophilic destructive ATCC42464 were differentially expressed and enriched. By comparing the sequences of Mtxylan2 and more than 10 xylanases, the N-terminal and C-terminal of Mtxylan2 were truncated, and three mutants 28N, 28C and 28NC were constructed. Results and discussion GH11 xylan Mtxylan2 was identified by transcriptomic analysis, the specific enzyme activity of Mtxylan2 was 104.67 U/mg, and the optimal temperature was 65°C. Molecular modification of Mtxylan2 showed that the catalytic activity of the mutants was enhanced. Among them, the catalytic activity of 28C was increased by 9.3 times, the optimal temperature was increased by 5°C, and the residual enzyme activity remained above 80% after 30 min at 50-65°C, indicating that redundant C-terminal truncation can improve the thermal stability and catalytic performance of GH11 xylanase.
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Affiliation(s)
- Yue Yang
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing, China
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing, China
| | - Chengnan Zhang
- Department of Exercise Biochemistry, Exercise Science School, Beijing Sport University, Beijing, China
| | - Hongyun Lu
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing, China
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing, China
| | - QiuHua Wu
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing, China
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing, China
| | - Yanfang Wu
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing, China
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing, China
| | - Weiwei Li
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing, China
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing, China
| | - Xiuting Li
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing, China
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing, China
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5
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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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6
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Tai H, Guo Q, Zhao J, Liu Y, Yu H, Liu Y, Qu Y, Du G, Li R. A thermostable xylanase hydrolyzes several polysaccharides from Bacillus altitudinis JYY-02 showing promise for industrial applications. Carbohydr Res 2024; 538:109080. [PMID: 38513464 DOI: 10.1016/j.carres.2024.109080] [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: 01/26/2024] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/23/2024]
Abstract
Polysaccharides have attracted immense attention as the largest source of bioactive compounds. Its bioavailability and bioactivity can be improved by utilizing degradation enzymes to reduce their molecular weight and viscosity. In this study, a 654 bp gene encoding xylanase was screened from the genome of Bacillus altitudinis JYY-02 and overexpressed in Escherichia coli Rosetta (DE3). The recombinant xylanase with a molecular weight of 27.98 kDa was purified (11.7-fold) using Ni-NTA affinity chromatography, with a 43.6% final yield. Through molecular docking, Glu, Arg, Tyr, and Trp were found to be the main amino acids involved in the interaction between xylanase and xylobiose. The effects of pH, temperature, metal ions, and substrates on xylanase activity were determined, and the results showed that the highest catalytic activity was displayed at pH 6.5, 50 °C temperature, with Cu2+ as an activator and xylan as the substrate. The Km (substrate concentration that yields a half-maximal velocity) and Vmax (maximum velocity) of recombinant xylanase were 6.876 mg/mL and 10984.183 μmol/mg∙pr/min, respectively. The recombinant xylanase was thermostable, with 85% and 39% of the enzymatic activity retained after 1 h at 60 °C and 1 h at 90 °C, respectively. The recombinant xylanase demonstrated a significant clarifying effect on fruit juices.
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Affiliation(s)
- Hongzheng Tai
- College of Life Sciences, Qingdao University, Qingdao, 266071, PR China
| | - Qunqun Guo
- College of Life Sciences, Qingdao University, Qingdao, 266071, PR China
| | - Jiamin Zhao
- College of Life Sciences, Qingdao University, Qingdao, 266071, PR China
| | - Yandong Liu
- College of Life Sciences, Qingdao University, Qingdao, 266071, PR China
| | - Hao Yu
- College of Life Sciences, Qingdao University, Qingdao, 266071, PR China
| | - Yili Liu
- College of Life Sciences, Qingdao University, Qingdao, 266071, PR China
| | - Yifan Qu
- College of Life Sciences, Qingdao University, Qingdao, 266071, PR China
| | - Guicai Du
- College of Life Sciences, Qingdao University, Qingdao, 266071, PR China.
| | - Ronggui Li
- College of Life Sciences, Qingdao University, Qingdao, 266071, PR China.
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7
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Ma L, Li G, Liu Y, Li Z, Miao Y, Wan Q, Liu D, Zhang R. Investigating the effect of substrate binding on the catalytic activity of xylanase. Appl Microbiol Biotechnol 2023; 107:6873-6886. [PMID: 37715802 DOI: 10.1007/s00253-023-12774-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/28/2023] [Accepted: 09/03/2023] [Indexed: 09/18/2023]
Abstract
XynAF1 from Aspergillus fumigatus Z5 is an efficient thermophilic xylanase belonging to glycoside hydrolase family 10 (GH10). The non-catalytic amino acids N179 and R246 in its catalytic center formed one and three intermolecular H-bonds with the substrate in the aglycone region, respectively. Here we purified XynAF1-N179S and XynAF1-R246K, and obtained the protein-product complex structures by X-ray diffraction. The snapshots indicated that mutations at N179 and R246 had decreased the substrate-binding ability in the aglycone region. XynAF1-N179S, XynAF1-R246K, and XynAF1-N179S-R246K lost one, three, and four H-bonds with the substrate in comparison with the wild-type XynAF1, respectively, but this had little influence on the protein structure. As expected, N179S, R246K, and N179S-R246K led to a gradual decrease of substrate affinity of XynAF1. Interestingly, the enzyme assay showed that N179S increased catalytic efficiency, while both R246K and N179S-R246K had decreased catalytic efficiency. KEY POINTS: • The non-catalytic amino acids of XynAF1 could form H-bonds with the substrate. • The protein-product complex structures were obtained by X-ray diffraction. • The enzyme-substrate-binding capacity could affect enzyme catalytic efficiency.
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Affiliation(s)
- Lei Ma
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, 467000, Henan, People's Republic of China
| | - Guangqi Li
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Yunpeng Liu
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Zhihong Li
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Youzhi Miao
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Qun Wan
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Dongyang Liu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Ruifu Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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Cao L, Xue D, Liu X, Wang C, Fang D, Zhang J, Gong C. Ferulic acid production from wheat bran by integration of enzymatic pretreatment and a cold-adapted carboxylesterase catalysis. BIORESOURCE TECHNOLOGY 2023; 385:129435. [PMID: 37399964 DOI: 10.1016/j.biortech.2023.129435] [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: 05/17/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/05/2023]
Abstract
High-value chemical production from natural lignocellulose transformation is a reliable waste utilization approach. A gene encoding cold-adapted carboxylesterase in Arthrobacter soli Em07 was identified. The gene was cloned and expressed in Escherichia coli to obtain a carboxylesterase enzyme with a molecular weight of 37.2 KDa. The activity of the enzyme was determined using α-naphthyl acetate as substrate. Results showed that the optimum enzyme activity of carboxylesterase was at 10 °C and pH 7.0. It was also found that the enzyme could degrade 20 mg enzymatic pretreated de-starched wheat bran (DSWB) to produce 235.8 μg of ferulic acid under the same conditions, which was 5.6 times more than the control. Compared to the chemical strategy, enzymatic pretreatment is advantageous because it is environmentally friendly, and the by-products can be easily treated. Therefore, this strategy provides an effective method for high-value utilization of biomass waste in agriculture and industry.
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Affiliation(s)
- Liping Cao
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, PR China
| | - Dongsheng Xue
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, PR China
| | - Xiaoji Liu
- CECEP (Feixi) WTE CO., LTD. Hefei 230001, PR China
| | - Chongju Wang
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, PR China
| | - Donglai Fang
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, PR China
| | - Jiaqi Zhang
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, PR China
| | - Chunjie Gong
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, PR China.
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9
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Satvati S, Ghasemi Y, Najafipour S, Eskandari S, Mahmoodi S, Nezafat N, Hashemzaei M. Finding and engineering the newly found bacterial superoxide dismutase enzyme to increase its thermostability and decrease the immunogenicity: a computational and experimental research. Arch Microbiol 2023; 205:260. [PMID: 37291420 DOI: 10.1007/s00203-023-03601-0] [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: 04/03/2023] [Revised: 05/23/2023] [Accepted: 05/29/2023] [Indexed: 06/10/2023]
Abstract
Superoxide dismutase (SOD) is one of the most important antioxidant enzymes that can reduce oxidative stress in the cell environment. Nowadays, bacterial sources of enzyme are commercially applicable in the cosmetics and pharmaceutical industries, but the allergenic effect of proteins from non-human sources has been mentioned as disadvantage of these kinds of enzymes. In this study, to find the suitable bacterial SOD candidate for decreasing immunogenicity, the sequences of five thermophilic bacteria were selected as reference species. Then, linear and conformational B-cell epitopes of the SOD were analyzed by different servers. The stability and immunogenicity of mutant positions were also evaluated. The mutant gene was inserted into the pET-23a expression vector and transformed into E. Coli BL21 (DE3) for expression of the recombinant enzyme. Afterward, the expression of the mutant enzyme was evaluated by SDS-PAGE analysis and the recombinant enzyme activity was assessed. Anoxybacillus gonensis was selected as a reasonable SOD source according to BLAST search, physicochemical properties analysis, and prediction of allergenic features. Regarding our results, five residues including E84, E142, K144, G147, and M148 were predicted as candidates for mutagenesis. Finally, the K144A was chosen as the final modification due to the increase in the stability of the enzyme and decreased immunogenicity of the enzyme as well. The enzyme activity was 240 U/ml at room temperature. Alternation in K144 to alanine caused increased stability of the enzyme. In silico studies confirmed non-antigenic protein after mutation.
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Affiliation(s)
- Saha Satvati
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Computational vaccine and Drug Design Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sohrab Najafipour
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, Iran
- Department of Tissue Engineering, School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Sedigheh Eskandari
- Computational vaccine and Drug Design Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shirin Mahmoodi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, Iran.
| | - Navid Nezafat
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
- Computational vaccine and Drug Design Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
- Pharmaceutical Science Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Masoud Hashemzaei
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Computational vaccine and Drug Design Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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10
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Alwakeel S, Alothman N, Ameen F, Alotaibi M, Mohammed AE, Alhomaidi E. Stress-driven metabolites of desert soil fungi. Biotechnol Genet Eng Rev 2023:1-14. [PMID: 36852923 DOI: 10.1080/02648725.2023.2182537] [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: 12/15/2022] [Accepted: 01/17/2023] [Indexed: 03/01/2023]
Abstract
Microorganisms produce secondary metabolites to survive under stressful conditions. The effect of drought and heat stress on fungi isolated from Arabian desert soil during the hot (ca 40°C) and cool (ca 10°C) seasons was studied using the genome mining approach. The presence of three stress-related genes (calmodulin, polyketide synthase and beta tubulin) was analyzed molecularly using specific primers. The presence of the genes in desert fungi was compared to their antimicrobial (ten bacterial or fungal pathogens) and anticancer (liver, cervical and breast) properties and the production of thermostable enzymes (phytase and xylanase). The genes appeared to be present in the fungal sequence obtained during the summer, while none of the genes were present during winter. Appreciable differences were observed in enzyme activities, with summer activities high and winter low. The antagonistic activities of A. niger were relatively stable and varying, while those of P. chrysogenum were consistently higher in summer than in winter. The presence of the three genes seemed to correlate with the highly antagonistic activities of P. chrysogenum, while A. niger had relatively active winter isolates without any of the genes. The hot season in deserts yields fungal isolates with biological activities useful in biotechnological solutions.
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Affiliation(s)
- Suaad Alwakeel
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Nouf Alothman
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Fuad Ameen
- Department of Botany & Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Modhi Alotaibi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Afrah E Mohammed
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Eman Alhomaidi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
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11
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Ketsakhon P, Thammasittirong A, Thammasittirong SNR. Adding value to rice straw waste for high-level xylanase production using a new isolate of Bacillus altitudinis RS3025. Folia Microbiol (Praha) 2023; 68:87-99. [PMID: 35945409 DOI: 10.1007/s12223-022-00998-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 07/27/2022] [Indexed: 11/04/2022]
Abstract
An investigation was carried out using rice straw as a low-cost substrate to study the optimization of xylanase production using a newly identified endospore-forming bacterium, Bacillus altitudinis RS3025. The highest xylanase activity was achieved using 2% rice straw (pretreated with 2% NaOH at 100 °C) at pH 7.0, 37 °C temperature, and with 72-h incubation time. Under the optimized conditions, xylanase activity reached 2518.51 U/mL, which was 11.56-fold higher than the activity under the initial conditions using untreated rice straw as substrate. Enzymatic hydrolysis of the rice straw using crude xylanase of B. altitudinis RS3025 demonstrated the hydrolyzation efficiency of the rice straw waste, especially alkaline rice straw. The highest level of released reducing sugars was 149.78 mg/g substrate. The study demonstrated the successful utilization of rice straw waste for high-level xylanase production using B. altitudinis RS3025 and reducing sugar production using low-cost crude enzyme, which has the advantages of reducing the processing cost and environmental concerns associated with rice straw waste management.
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Affiliation(s)
- Punpaporn Ketsakhon
- Department of Microbiology, Faculty of Liberal Arts and Science, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand
| | - Anon Thammasittirong
- Department of Microbiology, Faculty of Liberal Arts and Science, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand.,Microbial Biotechnology Unit, Faculty of Liberal Arts and Science, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand
| | - Sutticha Na-Ranong Thammasittirong
- Department of Microbiology, Faculty of Liberal Arts and Science, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand. .,Microbial Biotechnology Unit, Faculty of Liberal Arts and Science, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand.
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12
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Tyagi JL, Sharma M, Gulati K, Kairamkonda M, Kumar D, Poluri KM. Engineering of a T7 Bacteriophage Endolysin Variant with Enhanced Amidase Activity. Biochemistry 2023; 62:330-344. [PMID: 35060722 DOI: 10.1021/acs.biochem.1c00710] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The therapeutic use of bacteriophage-encoded endolysins as enzybiotics has increased significantly in recent years due to the emergence of antibiotic resistant bacteria. Phage endolysins lyse the bacteria by targeting their cell wall. Various engineering strategies are commonly used to modulate or enhance the utility of therapeutic enzymes. This study employed a structure-guided mutagenesis approach to engineer a T7 bacteriophage endolysin (T7L) with enhanced amidase activity and lysis potency via replacement of a noncatalytic gating residue (His 37). Two H37 variants (H37A and H37K) were designed and characterized comprehensively using integrated biophysical and biochemical techniques to provide mechanistic insights into their structure-stability-dynamics-activity paradigms. Among the studied proteins, cell lysis data suggested that the obtained H37A variant exhibits amidase activity (∼35%) enhanced compared to that of wild-type T7 endolysin (T7L-WT). In contrast to this, the H37K variant is highly unstable, prone to aggregation, and less active. Comparison of the structure and dynamics of the H37A variant to those of T7L-WT evidenced that the alteration at the site of H37 resulted in long-range structural perturbations, attenuated the conformational heterogeneity, and quenched the microsecond to millisecond time scale motions. Stability analysis confirmed the altered stability of H37A compared to that of its WT counterpart. All of the obtained results established that the H37A variant enhances the lysis activity by regulating the stability-activity trade-off. This study provided deeper atomic level insights into the structure-function relationships of endolysin proteins, thus aiding researchers in the rational design of engineered endolysins with enhanced therapeutic properties.
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Affiliation(s)
- Jaya Lakshmi Tyagi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Meenakshi Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Khushboo Gulati
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Manikyaprabhu Kairamkonda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Dinesh Kumar
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow 226014, Uttar Pradesh, India
| | - Krishna Mohan Poluri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India.,Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
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13
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Saavedra-Bouza A, Escuder-Rodríguez JJ, deCastro ME, Becerra M, González-Siso MI. Xylanases from thermophilic archaea: a hidden treasure. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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14
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Escuder-Rodríguez JJ, González-Suarez M, deCastro ME, Saavedra-Bouza A, Becerra M, González-Siso MI. Characterization of a novel thermophilic metagenomic GH5 endoglucanase heterologously expressed in Escherichia coli and Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:76. [PMID: 35799200 PMCID: PMC9264688 DOI: 10.1186/s13068-022-02172-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/24/2022] [Indexed: 01/05/2023]
Abstract
Background Endoglucanases from thermophilic microorganisms are a valuable resource as they can be used in a wide variety of biotechnological applications including the valorisation of biomass and the production of biofuels. In the present work we analysed the metagenome from the hot spring Muiño da Veiga, located in the northwest of Spain (in the Galicia region), in search for novel thermostable endoglucanases. Results Sequence analysis of the metagenome revealed a promising enzyme (Cel776). Predictions on protein structure and conserved amino acid sequences were conducted, as well as expression in heterologous systems with Escherichia coli and Saccharomyces cerevisiae as the host. Cel776Ec was correctly expressed and purified by taking advantage of the His-Tag system, with a yield of 0.346 U/mL in the eluted fraction. Cel776Sc was expressed extracellulary and was easily recovered from the supernatant without the need of further purification, requiring only a concentration step by ultrafiltration, with a significantly higher yield of 531.95 U/mL, revealing a much more suitable system for production of large amounts of the enzyme. Their biochemical characterization revealed biotechnologically interesting enzymes. Both Cel776Ec and Cel776Sc had an optimal temperature of 80 °C and optimal pH of 5. Cel776Ec exhibited high thermostability maintaining its activity for 24 h at 60 °C and maintained its activity longer than Cel776Sc at increasing incubation temperatures. Moreover, its substrate specificity allowed the degradation of both cellulose and xylan. Whereas Cel776Ec was more active in the presence of calcium and magnesium, manganese was found to increase Cel776Sc activity. A stronger inhibitory effect was found for Cel776Ec than Cel776Sc adding detergent SDS to the reaction mix, whereas EDTA only significantly affected Cel776Sc activity. Conclusions Our study reports the discovery of a new promising biocatalyst for its application in processes, such as the production of biofuel and the saccharification of plant biomass, due to its bifunctional enzymatic activity as an endoglucanase and as a xylanase, as well as highlights the advantages of a yeast expression system over bacteria. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02172-4.
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Affiliation(s)
- Juan-José Escuder-Rodríguez
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071, A Coruña, Spain
| | - María González-Suarez
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071, A Coruña, Spain
| | - María-Eugenia deCastro
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071, A Coruña, Spain
| | - Almudena Saavedra-Bouza
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071, A Coruña, Spain
| | - Manuel Becerra
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071, A Coruña, Spain.
| | - María-Isabel González-Siso
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071, A Coruña, Spain.
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15
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Pereira de Almeida A, Vargas IP, Marciano CL, Zanoelo FF, Giannesi GC, Moraes Polizeli MDLTD, Jorge JA, Furriel RDPM, Ruller R, Masui DC. Investigation of biochemical and biotechnological potential of a thermo-halo-alkali-tolerant endo-xylanase (GH11) from Humicola brevis var. thermoidea for lignocellulosic valorization of sugarcane biomass. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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16
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Cloning, expression, and characterization of a recombinant xylanase from Bacillus sonorensis T6. PLoS One 2022; 17:e0265647. [PMID: 35298551 PMCID: PMC8929556 DOI: 10.1371/journal.pone.0265647] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/05/2022] [Indexed: 11/19/2022] Open
Abstract
Xylanase is one of industrial enzymes with diverse applications including the paper-bleaching industry and feed additives. Here, a strain having xylanolytic activity and identified as Bacillus sonorensis T6 was isolated from soil. A secretory enzyme was identified by mass-spectrometry as a xylanase of glycosyl hydrolase family 11, with a molecular weight of 23.3 kDa. The xylanase gene of Bacillus sonorensis T6 was cloned and expressed in Escherichia coli (yielding an enzyme designated as rXynT6-E) and in Pichia pastoris (yielding rXynT6-P). The recombinant xylanases were found to have optimal activity at 47–55°C and pH 6.0–7.0. The recombinant xylanase expressed in P. pastoris has 40% higher thermal stability than that expressed in E. coli. The recombinant xylanases retained 100% of activity after 10 h incubation in the pH range 3–11 and 68% of activity after 1 h at pH 2.0. The xylanase activities of rXynT6-E and rXynT6-P under optimal conditions were 1030.2 and 873.8 U/mg, respectively. The good stability in a wide range of pH and moderate temperatures may make the xylanase from Bacillus sonorensis T6 useful for various biotechnological applications, e.g., as an enzyme additive in the feed industry.
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17
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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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18
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Dong R, Liu X, Wang Y, Qin X, Wang X, Zhang H, Wang Y, Luo H, Yao B, Bai Y, Tu T. Fusion of a proline-rich oligopeptide to the C-terminus of a ruminal xylanase improves catalytic efficiency. Bioengineered 2022; 13:10482-10492. [PMID: 35441569 PMCID: PMC9161913 DOI: 10.1080/21655979.2022.2061290] [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] [Indexed: 11/25/2022] Open
Abstract
Xylanases are widely used in the degradation of lignocellulose and are important industrial enzymes. Therefore, increasing the catalytic activity of xylanases can improve their efficiency and performance. In this study, we introduced the C-terminal proline-rich oligopeptide of the rumen-derived XynA into XylR, a GH10 family xylanase. The optimum temperature and pH of the fused enzyme (XylR-Fu) were consistent with those of XylR; however, its catalytic efficiency was 2.48-fold higher than that of XylR. Although the proline-rich oligopeptide did not change the enzyme hydrolysis mode, the amount of oligosaccharides released from beechwood xylan by XylR-Fu was 17% higher than that released by XylR. This increase may be due to the abundance of proline in the oligopeptide, which plays an important role in substrate binding. Furthermore, circular dichroism analysis indicated that the proline-rich oligopeptide might increase the rigidity of the overall structure, thereby enhancing the affinity to the substrate and catalytic activity of the enzyme. Our study shows that the proline-rich oligopeptide enhances the catalytic efficiency of GH10 xylanases and provides a better understanding of the C-terminal oligopeptide-function relationships. This knowledge can guide the rational design of GH10 xylanases to improve their catalytic activity and provides clues for further applications of xylanases in industry.
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Affiliation(s)
- Ruyue Dong
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoqing Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yaru Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xing Qin
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaolu Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Honglian Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuan Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yingguo Bai
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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19
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Raghav D, Jyoti A, Siddiqui AJ, Saxena J. Plant associated endophytic fungi as potential bio-factories for extracellular enzymes: Progress, Challenges and Strain improvement with precision approaches. J Appl Microbiol 2022; 133:287-310. [PMID: 35396804 DOI: 10.1111/jam.15574] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 03/04/2022] [Accepted: 04/04/2022] [Indexed: 11/29/2022]
Abstract
There is an intricate network of relations between endophytic fungi and their hosts that affects the production of various bioactive compounds. Plant-associated endophytic contain industrially important enzymes and have the potential to fulfill their rapid demand in the international market to boost business in technology. Being safe and metabolically active, they have replaced the usage of toxic and harmful chemicals and hold a credible application in biotransformation, bioremediation, and industrial processes. Despite these, there are limited reports on fungal endophytes that can directly cater to the demand and supply of industrially stable enzymes. The underlying reasons include low endogenous production and secretion of enzymes from fungal endophytes which have raised concern for widely accepted applications. Hence it is imperative to augment the biosynthetic and secretory potential of fungal endophytes. Modern state-of-the-art biotechnological technologies aiming at strain improvement using cell factory engineering as well as precise gene editing like Clustered Regularly Interspaced Palindromic Repeats (CRISPR) and its Associated proteins (Cas) systems which can provide a boost in fungal endophyte enzyme production. Additionally, it is vital to characterize optimum conditions to grow one strain with multiple enzymes (OSME). The present review encompasses various plants-derived endophytic fungal enzymes and their applications in various sectors. Further, we postulate the feasibility of new precision approaches with an aim for strain improvement and enhanced enzyme production.
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Affiliation(s)
- Divyangi Raghav
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh, India
| | - Anupam Jyoti
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh, India.,Department of Biotechnology, University Institute of Biotechnology, Chandigarh University, SAS, Nagar, Punjab
| | - Arif Jamal Siddiqui
- Department of Biology, College of Science, University of Ha'il, Ha'il, P O Box, Saudi Arabia
| | - Juhi Saxena
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh, India.,Department of Biotechnology, University Institute of Biotechnology, Chandigarh University, SAS, Nagar, Punjab
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20
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Teufl M, Zajc CU, Traxlmayr MW. Engineering Strategies to Overcome the Stability-Function Trade-Off in Proteins. ACS Synth Biol 2022; 11:1030-1039. [PMID: 35258287 PMCID: PMC8938945 DOI: 10.1021/acssynbio.1c00512] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
In addition to its
biological function, the stability of a protein
is a major determinant for its applicability. Unfortunately, engineering
proteins for improved functionality usually results in destabilization
of the protein. This so-called stability–function trade-off
can be explained by the simple fact that the generation of a novel
protein function—or the improvement of an existing one—necessitates
the insertion of mutations, i.e., deviations from
the evolutionarily optimized wild-type sequence. In fact, it was demonstrated
that gain-of-function mutations are not more destabilizing than other
random mutations. The stability–function trade-off is a universal
phenomenon during protein evolution that has been observed with completely
different types of proteins, including enzymes, antibodies, and engineered
binding scaffolds. In this review, we discuss three types of strategies
that have been successfully deployed to overcome this omnipresent
obstacle in protein engineering approaches: (i) using highly stable
parental proteins, (ii) minimizing the extent of destabilization during
functional engineering (by library optimization and/or coselection
for stability and function), and (iii) repairing damaged mutants through
stability engineering. The implementation of these strategies in protein
engineering campaigns will facilitate the efficient generation of
protein variants that are not only functional but also stable and
therefore better-suited for subsequent applications.
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Affiliation(s)
- Magdalena Teufl
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
- CD Laboratory for Next Generation CAR T Cells, 1190 Vienna, Austria
| | - Charlotte U. Zajc
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
- CD Laboratory for Next Generation CAR T Cells, 1190 Vienna, Austria
| | - Michael W. Traxlmayr
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
- CD Laboratory for Next Generation CAR T Cells, 1190 Vienna, Austria
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21
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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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22
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Paramjeet S, Manasa P, Korrapati N. Biochemical Characterization of Low Molecular Weight Thermostable Xylanase from Aspergillus fumigatus JCM 10253. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821100094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Improved Production of Streptomyces sp. FA1 Xylanase in a Dual-Plasmid Pichia pastoris System. Curr Issues Mol Biol 2021; 43:2289-2304. [PMID: 34940135 PMCID: PMC8928940 DOI: 10.3390/cimb43030161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/16/2021] [Accepted: 12/16/2021] [Indexed: 12/18/2022] Open
Abstract
Methanol is considered as a potential hazard in the methanol-induced yeast expression of food-related enzymes. To increase the production efficiency of recombinant proteins in Pichia pastoris without methanol induction, a novel dual-plasmid system was constructed, for the first time, by a combining the strategies of genomic integration and episomal expression. To obtain a high copy number of the target gene, the autonomously replicating sequence derived from Kluyveromyces lactis (PARS) was used to construct episomal vectors carrying the constitutive promoters PGAP and PGCW14. In addition, an integrative vector carrying the PGCW14 promoter was constructed by replacing the PGAP promoter sequence with a partial PGCW14 promoter. Next, using xylanase XynA from Streptomyces sp. FA1 as the model enzyme, recombination strains were transformed with different combinations of integrating and episomal vectors that were constructed to investigate the changes in the protein yield. Results in shake flasks indicated that the highest enzyme yield was achieved when integrated PGAP and episomal PGCW14 were simultaneously transformed into the host strain. Meanwhile, the copy number of xynA increased from 1.14 ± 0.46 to 3.06 ± 0.35. The yield of XynA was successfully increased to 3925 U·mL-1 after 102 h of fermentation in a 3.6 L fermenter, which was 16.7-fold and 2.86-fold of the yields that were previously reported for the constitutive expression and methanol-induced expression of the identical protein, respectively. Furthermore, the high-cell-density fermentation period was shortened from 132 h to 102 h compared to that of methanol-induced system. Since the risk of methanol toxicity is removed, this novel expression system would be suitable for the production of proteins related to the food and pharmaceutical industries.
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You S, Li J, Zhang F, Bai ZY, Shittu S, Herman RA, Zhang WX, Wang J. Loop engineering of a thermostable GH10 xylanase to improve low-temperature catalytic performance for better synergistic biomass-degrading abilities. BIORESOURCE TECHNOLOGY 2021; 342:125962. [PMID: 34563821 DOI: 10.1016/j.biortech.2021.125962] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
Lignocellulosic biorefining for producing biofuels poses technical challenges. It is usually conducted over a long time using heat, making it energy intensive. In this study, we lowered the energy consumption of this process through an optimized enzyme and pretreatment strategy. First, the dominant mutant M137E/N269G of Bispora sp. MEY-1XYL10C_ΔN was obtained by directed evolution with highcatalytic efficiency (970 mL/s∙mg)and specific activity (2090 U/mg)at 37 °C, and thermostability was improved (T50 increased by5 °C). After pretreatment with seawater immersionfollowing steam explosion,bagasse was co-treated with cellulase and M137E/N269G under mild conditions (37 °C), the resulting highest yield of fermentable sugars reached 219 µmol/g of bagasse,46% higher than that of the non-seawater treatment group, with the highest degree of synergy of 2.0. Pretreatment with seawater following steam explosion and synergistic hydrolysis through high activity xylanase and cellulase helped to achieve low energy degradation of lignocellulosic biomass.
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Affiliation(s)
- Shuai You
- Jiangsu Key Laboratory of Sericutural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, PR China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu 212100, PR China
| | - Jing Li
- Department of Nephrology, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, PR China
| | - Fang Zhang
- Jiangsu Key Laboratory of Sericutural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, PR China
| | - Zhi-Yuan Bai
- Jiangsu Key Laboratory of Sericutural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, PR China
| | - Saidi Shittu
- Jiangsu Key Laboratory of Sericutural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, PR China
| | - Richard-Ansah Herman
- Jiangsu Key Laboratory of Sericutural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, PR China
| | - Wen-Xin Zhang
- Jiangsu Key Laboratory of Sericutural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, PR China
| | - Jun Wang
- Jiangsu Key Laboratory of Sericutural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, PR China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu 212100, PR China.
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25
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Dotsenko AS, Denisenko YA, Rozhkova AM, Zorov IN, Korotkova OG, Sinitsyn AP. Enhancement of thermostability of GH10 xylanase E Penicillium canescens directed by ΔΔG calculations and structure analysis. Enzyme Microb Technol 2021; 152:109938. [PMID: 34753033 DOI: 10.1016/j.enzmictec.2021.109938] [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: 06/29/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 11/26/2022]
Abstract
Hydrolytic enzymes are highly demanded in the industry. Thermostability is an important property of enzymes that affects the economic costs of the industrial processes. The rational design of GH10 xylanase E (XylE) Penicillium canescens for the thermostability improvement was directed by ΔΔG calculations and structure analysis. Amino acid substitutions with stabilizing values of ΔΔG and providing an increase in side-chain volume of buried residues were performed experimentally. From the six designed substitutions, four substitutions appeared to be stabilizing, one - destabilizing, and one - neutral. For the improved XylE variants, values of Tm were increased by 1.1-3.1 °C, and times of half-life at 70 °C were increased in 1.3-1.7-times. Three of the four stabilizing substitutions were located in the N- or the C-terminus region. This highlights the importance of N- and C-terminus for the thermostability of GH10 xylanases and also enzymes with (β/α)8 TIM barrel type of structure. The criteria of stabilizing values of ΔΔG and increased side-chain volume of buried residues for selection of substitutions may be applied in the rational design for thermostability improvement.
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Affiliation(s)
- Anna S Dotsenko
- Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow 119071, Russia.
| | - Yury A Denisenko
- Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow 119071, Russia.
| | - Aleksandra M Rozhkova
- Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow 119071, Russia.
| | - Ivan N Zorov
- Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow 119071, Russia; Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia.
| | - Olga G Korotkova
- Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow 119071, Russia
| | - Arkady P Sinitsyn
- Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow 119071, Russia; Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia.
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Tang K, Cui Y, Xiao J, Ding M, Chao H, Wu J, Han Z, Liu J, Li X, Yan D. Molecular cloning and characterization of a novel xylanase from Microbacterium imperiale YD-01. J Food Biochem 2021; 45:e13988. [PMID: 34730252 DOI: 10.1111/jfbc.13988] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/25/2021] [Accepted: 10/13/2021] [Indexed: 11/27/2022]
Abstract
Xylaneses are very common xylanolytic enzymes, which are widely used in food, papermaking, and other industries. In this study, a xylanase-encoding gene xyn1923, which encodes a protein of 1352 amino acids, was identified through the whole genome analysis of Microbacterium imperiale YD-01. Bioinformatics analysis showed that Xyn1923 only had maximum similarity of 37% with the reported xylanase from Alkalihalobacillus halodurans C-125, indicating that Xyn1923 was a novel xylanase. The enzymatic properties of Xyn1923 were systematically analyzed after purification. The results showed that the specific activity of the enzyme was 10.582 ± 0.413 U/mg, while the optimum pH and temperature of the enzyme were 7.0 and 70°C, respectively. The enzyme is stable in the pH range of 6.0-9.0, and the enzyme activity could maintain more than 85% of the original activity after 16 hr incubation at pH 9.0. The enzyme activity is relatively stable in the range of 30-60°C, and its enzyme activity could maintain more than 89% of the original activity after treatment at 60°C for 30 min. Low concentrations (≤1 mM) of Co2+ , Ba2+ , Fe2+ , and Fe3+ metal ions exerted a stimulatory effect on the activity of Xyn1923. And in contrast, high concentrations (≥2 mM) of the above metal ions inhibit the activity of Xyn1923. Mg2+ , Ag+ , Cu2+ , Ca2+ , Mn2+ , and Pb2+ ions showed a negative effect on the activity of Xyn1923. Enzyme kinetic studies showed that Km and Vmax values for xylan were 7.842 ± 0.538 mg/ml and 15.208 ± 0.822 U/mg, respectively. Xyn1923 was found to be a weakly alkaline thermophilic xylanase through an enzymatic property analysis. PRACTICAL APPLICATIONS: Xylanases are widely used in food and feed, biofuels, papermaking, and other industries. However, their use is limited by poor performance under the conditions of pH and temperature. Therefore, the discovery of xylanases with the capability of working efficiently at alkaline pH and high temperature is the priority for its industrial applications. In this study, a novel xylanase-encoding gene xyn1923 from Microbacterium imperiale YD-01 was cloned and heterologously expressed in Escherichia coli. Enzymatic properties of this novel xylanase were investigated, indicating that the robust thermal stability and alkali resistance of Xyn1923 make it a potential candidate for the food and paper industries.
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Affiliation(s)
- Keqin Tang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,School of life science and technology, Wuhan Polytechnic University, Wuhan, China
| | - Yin Cui
- School of life science and technology, Wuhan Polytechnic University, Wuhan, China
| | - Jingyi Xiao
- City University of Hong Kong, Kowloon, China
| | - Mengyao Ding
- School of life science and technology, Wuhan Polytechnic University, Wuhan, China
| | - Hongjun Chao
- School of life science and technology, Wuhan Polytechnic University, Wuhan, China
| | - Jing Wu
- School of life science and technology, Wuhan Polytechnic University, Wuhan, China
| | - Zhenggang Han
- School of life science and technology, Wuhan Polytechnic University, Wuhan, China
| | - Jun Liu
- School of life science and technology, Wuhan Polytechnic University, Wuhan, China
| | - Xin Li
- School of life science and technology, Wuhan Polytechnic University, Wuhan, China
| | - Dazhong Yan
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,School of life science and technology, Wuhan Polytechnic University, Wuhan, China
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Min K, Kim H, Park HJ, Lee S, Jung YJ, Yoon JH, Lee JS, Park K, Yoo YJ, Joo JC. Improving the catalytic performance of xylanase from Bacillus circulans through structure-based rational design. BIORESOURCE TECHNOLOGY 2021; 340:125737. [PMID: 34426235 DOI: 10.1016/j.biortech.2021.125737] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
Endo-1,4-β-xylanase is one of the most important enzymes employed in biorefineries for obtaining fermentable sugars from hemicellulosic components. Herein, we aimed to improve the catalytic performance of Bacillus circulans xylanase (Bcx) using a structure-guided rational design. A systematic analysis of flexible motions revealed that the R49 component of Bcx (i) constrains the global conformational changes essential for substrate binding and (ii) is involved in modulating flexible motion. Site-saturated mutagenesis of the R49 residue led to the engineering of the active mutants with the trade-off between flexibility and rigidity. The most active mutant R49N improved the catalytic performance, including its catalytic efficiency (7.51-fold), conformational stability (0.7 °C improvement), and production of xylose oligomers (2.18-fold higher xylobiose and 1.72-fold higher xylotriose). The results discussed herein can be applied to enhance the catalytic performance of industrially important enzymes by controlling flexibility.
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Affiliation(s)
- Kyoungseon Min
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea
| | - Hoyong Kim
- Center for Bio-Based Chemistry, Korea Research Institute of Chemical Technology, Ulsan 44429, Republic of Korea
| | - Hyun June Park
- Department of Biotechnology, Duksung Women's University, Seoul 01369, Republic of Korea
| | - Siseon Lee
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si, Gyeonggi-do 14662, Republic of Korea
| | - Ye Jean Jung
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si, Gyeonggi-do 14662, Republic of Korea; Department of Biological and Chemical Engineering, Hongik University, Sejong Ro 2639, Jochiwon, Sejong City, Republic of Korea
| | - Ji Hyun Yoon
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si, Gyeonggi-do 14662, Republic of Korea
| | - Jin-Suk Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea
| | - Kyoungmoon Park
- Department of Biological and Chemical Engineering, Hongik University, Sejong Ro 2639, Jochiwon, Sejong City, Republic of Korea
| | - Young Je Yoo
- School of Chemical and Biological Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Jeong Chan Joo
- Center for Bio-Based Chemistry, Korea Research Institute of Chemical Technology, Ulsan 44429, Republic of Korea; Department of Biotechnology, The Catholic University of Korea, Bucheon-si, Gyeonggi-do 14662, Republic of Korea.
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You S, Zha Z, Li J, Zhang W, Bai Z, Hu Y, Wang X, Chen Y, Chen Z, Wang J, Luo H. Improvement of XYL10C_∆N catalytic performance through loop engineering for lignocellulosic biomass utilization in feed and fuel industries. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:195. [PMID: 34598723 PMCID: PMC8487158 DOI: 10.1186/s13068-021-02044-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/23/2021] [Indexed: 06/01/2023]
Abstract
BACKGROUND Xylanase, an important accessory enzyme that acts in synergy with cellulase, is widely used to degrade lignocellulosic biomass. Thermostable enzymes with good catalytic activity at lower temperatures have great potential for future applications in the feed and fuel industries, which have distinct demands; however, the potential of the enzymes is yet to be researched. RESULTS In this study, a structure-based semi-rational design strategy was applied to enhance the low-temperature catalytic performance of Bispora sp. MEY-1 XYL10C_∆N wild-type (WT). Screening and comparisons were performed for the WT and mutant strains. Compared to the WT, the mutant M53S/F54L/N207G exhibited higher specific activity (2.9-fold; 2090 vs. 710 U/mg) and catalytic efficiency (2.8-fold; 1530 vs. 550 mL/s mg) at 40 °C, and also showed higher thermostability (the melting temperature and temperature of 50% activity loss after 30 min treatment increased by 7.7 °C and 3.5 °C, respectively). Compared with the cellulase-only treatment, combined treatment with M53S/F54L/N207G and cellulase increased the reducing sugar contents from corn stalk, wheat bran, and corn cob by 1.6-, 1.2-, and 1.4-folds, with 1.9, 1.2, and 1.6 as the highest degrees of synergy, respectively. CONCLUSIONS This study provides useful insights into the underlying mechanism and methods of xylanase modification for industrial utilization. We identified loop2 as a key functional area affecting the low-temperature catalytic efficiency of GH10 xylanase. The thermostable mutant M53S/F54L/N207G was selected for the highest low-temperature catalytic efficiency and reducing sugar yield in synergy with cellulase in the degradation of different types of lignocellulosic biomass.
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Affiliation(s)
- Shuai You
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018 People’s Republic of China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212018 People’s Republic of China
| | - Ziqian Zha
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018 People’s Republic of China
| | - Jing Li
- Department of Nephrology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001 People’s Republic of China
| | - Wenxin Zhang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018 People’s Republic of China
| | - Zhiyuan Bai
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018 People’s Republic of China
| | - Yanghao Hu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018 People’s Republic of China
| | - Xue Wang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018 People’s Republic of China
| | - Yiwen Chen
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018 People’s Republic of China
| | - Zhongli Chen
- Xinyuan Cocoon Silk Group Co., Ltd., Nantong, 226600 People’s Republic of China
| | - Jun Wang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018 People’s Republic of China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212018 People’s Republic of China
| | - Huiying Luo
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 People’s Republic of China
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Gupta GK, Dixit M, Kapoor RK, Shukla P. Xylanolytic Enzymes in Pulp and Paper Industry: New Technologies and Perspectives. Mol Biotechnol 2021; 64:130-143. [PMID: 34580813 DOI: 10.1007/s12033-021-00396-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/08/2021] [Indexed: 11/26/2022]
Abstract
The pulp and paper industry discharges massive amount of wastewater containing hazardous organochlorine compounds released during different processing stages. Therefore, some cost-effective and nonpolluting practices such as enzymatic treatments are required for the potential mitigation of effluents released in the environment. Various xylanolytic enzymes such as xylanases, laccases, cellulases and hemicellulases are used to hydrolyse raw materials in the paper manufacturing industry. These enzymes are used either individually or in combination, which has the efficient potential to be considered for bio-deinking and bio-bleaching components. They are highly dynamic, renewable, and high in specificity for enhancing paper quality. The xylanase act on the xylan and cellulases act on the cellulose fibers, and thus increase the bleaching efficacy of paper. Similarly, hemicellulase enzyme like endo-xylanases, arabinofuranosidase and β-D-xylosidases have been described as functional properties towards the biodegradation of biomass. In contrast, laccase enzymes act as multi-copper oxidoreductases, bleaching the paper by the oxidation and reduction process. Laccases possess low redox potential compared to other enzymes, which need some redox mediators to catalyze. The enzymatic process can be affected by various factors such as pH, temperature, metal ions, incubation periods, etc. These factors can either increase or decrease the efficiency of the enzymes. This review draws attention to the xylanolytic enzyme-based advanced technologies for pulp bleaching in the paper industry.
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Affiliation(s)
- Guddu Kumar Gupta
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Mandeep Dixit
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Rajeev Kumar Kapoor
- Enzyme and Fermentation Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India.
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.
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30
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Cao L, Zhang R, Zhou J, Huang Z. Biotechnological Aspects of Salt-Tolerant Xylanases: A Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:8610-8624. [PMID: 34324332 DOI: 10.1021/acs.jafc.1c03192] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
β-1,4-Xylan is the main component of hemicelluloses in land plant cell walls, whereas β-1,3-xylan is widely found in seaweed cell walls. Complete hydrolysis of xylan requires a series of synergistically acting xylanases. High-saline environments, such as saline-alkali lands and oceans, frequently occur in nature and are also involved in a broad range of various industrial processes. Thus, salt-tolerant xylanases may contribute to high-salt and marine food processing, aquatic feed production, industrial wastewater treatment, saline-alkali soil improvement, and global carbon cycle, with great commercial and environmental benefits. This review mainly introduces the definition, sources, classification, biochemical and molecular characteristics, adaptation mechanisms, and biotechnological applications of salt-tolerant xylanases. The scope of development for salt-tolerant xylanases is also discussed. It is anticipated that this review would serve as a reference for further development and utilization of salt-tolerant xylanases and other salt-tolerant enzymes.
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Affiliation(s)
- Lijuan Cao
- College of Life Sciences, Yunnan Normal University, Kunming, Yunnan 650500, People's Republic of China
| | - Rui Zhang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, Yunnan 650500, People's Republic of China
- College of Life Sciences, Yunnan Normal University, Kunming, Yunnan 650500, People's Republic of China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan 650500, People's Republic of China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming, Yunnan 650500, People's Republic of China
| | - Junpei Zhou
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, Yunnan 650500, People's Republic of China
- College of Life Sciences, Yunnan Normal University, Kunming, Yunnan 650500, People's Republic of China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan 650500, People's Republic of China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming, Yunnan 650500, People's Republic of China
| | - Zunxi Huang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, Yunnan 650500, People's Republic of China
- College of Life Sciences, Yunnan Normal University, Kunming, Yunnan 650500, People's Republic of China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan 650500, People's Republic of China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming, Yunnan 650500, People's Republic of China
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Li G, Zhou X, Li Z, Liu Y, Liu D, Miao Y, Wan Q, Zhang R. Significantly improving the thermostability of a hyperthermophilic GH10 family xylanase XynAF1 by semi-rational design. Appl Microbiol Biotechnol 2021; 105:4561-4576. [PMID: 34014347 DOI: 10.1007/s00253-021-11340-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/16/2021] [Accepted: 05/09/2021] [Indexed: 11/28/2022]
Abstract
Xylanases have a broad range of applications in industrial biotechnologies, which require the enzymes to resist the high-temperature environments. The majority of xylanases have maximum activity at moderate temperatures, which limited their potential applications in industries. In this study, a thermophilic GH10 family xylanase XynAF1 from the high-temperature composting strain Aspergillus fumigatus Z5 was characterized and engineered to further improve its thermostability. XynAF1 has the optimal reaction temperature of 90 °C. The crystal structure of XynAF1 was obtained by X-ray diffraction after heterologous expression, purification, and crystallization. The high-resolution X-ray crystallographic structure of the protein-product complex was obtained by soaking the apo-state crystal with xylotetraose. Structure analysis indicated that XynAF1 has a rigid skeleton, which helps to maintain the hyperthermophilic characteristic. The homologous structure analysis and the catalytic center mutant construction of XynAF1 indicated the conserved catalytic center contributed to the high optimum catalytic temperature. The amino acids in the surface of xylanase XynAF1 which might influence the enzyme thermostability were identified by the structure analysis. Combining the rational design with the saturation mutation at the high B-value regions, the integrative mutant XynAF1-AC with a 6-fold increase of thermostability was finally obtained. This study efficiently improved the thermostability of a GH10 family xylanase by semi-rational design, which provided a new biocatalyst for high-temperature biotechnological applications. KEY POINTS: • Obtained the crystal structure of GH10 family hyperthermophilic xylanase XynAF1. • Shed light on the understanding of the GH10 family xylanase thermophilic mechanism. • Constructed a 6-fold increased thermostability recombinant xylanase.
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Affiliation(s)
- Guangqi Li
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.,Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Xuan Zhou
- National Agricultural Technology Extension and Service Center, Beijing, 100125, People's Republic of China
| | - Zhihong Li
- College of Science, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yunpeng Liu
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Dongyang Liu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Youzhi Miao
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Qun Wan
- College of Science, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China. .,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
| | - Ruifu Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China. .,Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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Zhang S, Zhao S, Shang W, Yan Z, Wu X, Li Y, Chen G, Liu X, Wang L. Synergistic mechanism of GH11 xylanases with different action modes from Aspergillus niger An76. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:118. [PMID: 33971954 PMCID: PMC8112042 DOI: 10.1186/s13068-021-01967-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/03/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND Xylan is the most abundant hemicellulose polysaccharide in nature, which can be converted into high value-added products. However, its recalcitrance to breakdown requires the synergistic action of multiple enzymes. Aspergillus niger, possessing numerous xylan degrading isozyme-encoding genes, are highly effective xylan degraders in xylan-rich habitats. Therefore, it is necessary to explore gene transcription, the mode of action and cooperation mechanism of different xylanase isozymes to further understand the efficient xylan-degradation by A. niger. RESULTS Aspergillus niger An76 encoded a comprehensive set of xylan-degrading enzymes, including five endo-xylanases (one GH10 and four GH11). Quantitative transcriptional analysis showed that three xylanase genes (xynA, xynB and xynC) were up-regulated by xylan substrates, and the order and amount of enzyme secretion differed. Specifically, GH11 xylanases XynA and XynB were initially secreted successively, followed by GH10 xylanase XynC. Biochemical analyses displayed that three GH11 xylanases (XynA, XynB and XynD) showed differences in catalytic performance and product profiles, possibly because of intricate hydrogen bonding between substrates and functional residues in the active site architectures impacted their binding capacity. Among these, XynB had the best performance in the degradation of xylan and XynE had no catalytic activity. Furthermore, XynA and XynB showed synergistic effects during xylan degradation. CONCLUSIONS The sequential secretion and different action modes of GH11 xylanases were essential for the efficient xylan degradation by A. niger An76. The elucidation of the degradation mechanisms of these xylanase isozymes further improved our understanding of GH-encoding genes amplification in filamentous fungi and may guide the design of the optimal enzyme cocktails in industrial applications.
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Affiliation(s)
- Shu Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 Shandong China
| | - Sha Zhao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 Shandong China
- School of Life Sciences, Shandong University, Qingdao, 266237 Shandong China
| | - Weihao Shang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 Shandong China
| | - Zijuan Yan
- School of Life Sciences, Shandong University, Qingdao, 266237 Shandong China
| | - Xiuyun Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 Shandong China
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, 250353 Shandong China
| | - Yingjie Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 Shandong China
| | - Guanjun Chen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 Shandong China
| | - Xinli Liu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, 250353 Shandong China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 Shandong China
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Chhe C, Uke A, Baramee S, Ungkulpasvich U, Tachaapaikoon C, Pason P, Waeonukul R, Ratanakhanokchai K, Kosugi A. Draft genome sequence data of the facultative, thermophilic, xylanolytic bacterium Paenibacillus sp. strain DA-C8. Data Brief 2021; 35:106784. [PMID: 33553530 PMCID: PMC7859314 DOI: 10.1016/j.dib.2021.106784] [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: 12/11/2020] [Revised: 01/17/2021] [Accepted: 01/19/2021] [Indexed: 11/24/2022] Open
Abstract
Thermophilic, facultatively anaerobic, xylanolytic bacterial strain DA-C8 (=JCM34211 =DSM111723), newly isolated from compost, shows strong beechwood xylan degradation ability. Whole-genome sequencing of strain DA-C8 on the Ion GeneStudio S5 system yielded 69 contigs with a total size of 3,110,565 bp, 2,877 protein-coding sequences, and a G+C content of 52.3 mol%. Genome annotation revealed that strain DA-C8 possesses debranching enzymes, such as β-L-arabinofuranosidase and polygalacturonase, that are important for efficient degradation of xylan. As inferred from 16S rRNA sequences and average nucleotide identity values, the closest relatives of strain DA-C8 are Paenibacillus cisolokensis and P. chitinolyticus. The genomic data have been deposited at the National Center for Biotechnology Information (NCBI) under accession number BMAQ00000000.
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Affiliation(s)
- Chinda Chhe
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Ayaka Uke
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Sirilak Baramee
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Umbhorn Ungkulpasvich
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Chakrit Tachaapaikoon
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Patthra Pason
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Rattiya Waeonukul
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Khanok Ratanakhanokchai
- Enzyme Technology Laboratory, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Akihiko Kosugi
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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Wang J, Liang J, Li Y, Tian L, Wei Y. Characterization of efficient xylanases from industrial-scale pulp and paper wastewater treatment microbiota. AMB Express 2021; 11:19. [PMID: 33464408 PMCID: PMC7815853 DOI: 10.1186/s13568-020-01178-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 12/31/2020] [Indexed: 02/08/2023] Open
Abstract
Xylanases are widely used enzymes in the food, textile, and paper industries. Most efficient xylanases have been identified from lignocellulose-degrading microbiota, such as the microbiota of the cow rumen and the termite hindgut. Xylanase genes from efficient pulp and paper wastewater treatment (PPWT) microbiota have been previously recovered by metagenomics, assigning most of the xylanase genes to the GH10 family. In this study, a total of 40 GH10 family xylanase genes derived from a certain PPWT microbiota were cloned and expressed in Escherichia coli BL21 (DE3). Among these xylanase genes, 14 showed xylanase activity on beechwood substrate. Two of these, PW-xyl9 and PW-xyl37, showed high activities, and were purified to evaluate their xylanase properties. Values of optimal pH and temperature for PW-xyl9 were pH 7 and 60 ℃, respectively, while those for PW-xyl37 were pH 7 and 55 ℃, respectively; their specific xylanase activities under optimal conditions were 470.1 U/mg protein and 113.7 U/mg protein, respectively. Furthermore, the Km values of PW-xyl9 and PW-xyl37 were determined as 8.02 and 18.8 g/L, respectively. The characterization of these two xylanases paves the way for potential application in future pulp and paper production and other industries, indicating that PPWT microbiota has been an undiscovered reservoir of efficient lignocellulase genes. This study demonstrates that a metagenomic approach has the potential to screen efficient xylanases of uncultured microorganisms from lignocellulose-degrading microbiota. In a similar way, other efficient lignocellulase genes might be identified from PPWT treatment microbiota in the future.
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Jaiswal S, Kumar Gupta G, Panchal K, Mandeep, Shukla P. Synthetic Organic Compounds From Paper Industry Wastes: Integrated Biotechnological Interventions. Front Bioeng Biotechnol 2021; 8:592939. [PMID: 33490048 PMCID: PMC7820897 DOI: 10.3389/fbioe.2020.592939] [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: 08/08/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022] Open
Abstract
Synthetic organic compounds (SOCs) are reported as xenobiotics compounds contaminating the environment from various sources including waste from the pulp and paper industries: Since the demand and production of paper is growing increasingly, the release of paper and pulp industrial waste consisting of SOCs is also increasing the SOCs' pollution in natural reservoirs to create environmental pollution. In pulp and paper industries, the SOCs viz. phenol compounds, furans, dioxins, benzene compounds etc. are produced during bleaching phase of pulp treatment and they are principal components of industrial discharge. This review gives an overview of various biotechnological interventions for paper mill waste effluent management and elimination strategies. Further, the review also gives the insight overview of various ways to restrict SOCs release in natural reservoirs, its limitations and integrated approaches for SOCs bioremediation using engineered microbial approaches. Furthermore, it gives a brief overview of the sustainable remediation of SOCs via genetically modified biological agents, including bioengineering system innovation at industry level before waste discharge.
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Affiliation(s)
- Shweta Jaiswal
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Guddu Kumar Gupta
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Kusum Panchal
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Mandeep
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
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Santibáñez L, Henríquez C, Corro-Tejeda R, Bernal S, Armijo B, Salazar O. Xylooligosaccharides from lignocellulosic biomass: A comprehensive review. Carbohydr Polym 2021; 251:117118. [DOI: 10.1016/j.carbpol.2020.117118] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/22/2020] [Accepted: 09/04/2020] [Indexed: 02/04/2023]
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Lai Z, Zhou C, Ma X, Xue Y, Ma Y. Enzymatic characterization of a novel thermostable and alkaline tolerant GH10 xylanase and activity improvement by multiple rational mutagenesis strategies. Int J Biol Macromol 2020; 170:164-177. [PMID: 33352153 DOI: 10.1016/j.ijbiomac.2020.12.137] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/08/2020] [Accepted: 12/17/2020] [Indexed: 11/15/2022]
Abstract
Thermo-alkaline xylanases are widely applied in paper pulping industry. In this study, a novel thermostable and alkaline tolerant GH10 xylanase (Xyn30Y5) gene from alkaliphilic Bacillus sp. 30Y5 was cloned and the surface-layer homology (SLH) domains truncated enzyme (Xyn30Y5-SLH) was expressed in Escherichia coli. The purified Xyn30Y5-SLH was most active at 70 °C and pH 7.0 and showed the highest specific activity of 349.4 U mg-1. It retained more than 90% activity between pH 6.0 to 9.5 and was stable at pH 6.0-10.0. To improve the activity, 47 mutants were designed based on eight rational strategies and 21 mutants showed higher activity. By combinatorial mutagenesis, the best mutant 3B demonstrated specific activity of 1016.8 U mg-1 with a doubled catalytic efficiency (kcat/Km) and RA601/2h value, accompanied by optimal pH shift to 8.0. The molecular dynamics simulation analysis indicated that the increase of flexibility of α5 helix and loop7 located near to the catalytic residues is likely responsible for its activity improvement. And the decrease of flexibility of the most unstable regions is vital for the thermostablity improvement. This work provided not only a novel thermostable and alkaline tolerant xylanase with industrial application potential but also an effective mutagenesis strategy for xylanase activity improvement.
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Affiliation(s)
- Zhihua Lai
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Cheng Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Xiaochen Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanfen Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanhe Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; National Engineering Laboratory for Industrial Enzymes, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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Talens-Perales D, Sánchez-Torres P, Marín-Navarro J, Polaina J. In silico screening and experimental analysis of family GH11 xylanases for applications under conditions of alkaline pH and high temperature. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:198. [PMID: 33372612 PMCID: PMC7720462 DOI: 10.1186/s13068-020-01842-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Xylanases are one of the most extensively used enzymes for biomass digestion. However, in many instances, their use is limited by poor performance under the conditions of pH and temperature required by the industry. Therefore, the search for xylanases able to function efficiently at alkaline pH and high temperature is an important objective for different processes that use lignocellulosic substrates, such as the production of paper pulp and biofuels. RESULTS A comprehensive in silico analysis of family GH11 sequences from the CAZY database allowed their phylogenetic classification in a radial cladogram in which sequences of known or presumptive thermophilic and alkalophilic xylanases appeared in three clusters. Eight sequences from these clusters were selected for experimental analysis. The coding DNA was synthesized, cloned and the enzymes were produced in E. coli. Some of these showed high xylanolytic activity at pH values > 8.0 and temperature > 80 °C. The best enzymes corresponding to sequences from Dictyoglomus thermophilum (Xyn5) and Thermobifida fusca (Xyn8). The addition of a carbohydrate-binding module (CBM9) to Xyn5 increased 4 times its activity at 90 °C and pH > 9.0. The combination of Xyn5 and Xyn8 was proved to be efficient for the saccharification of alkali pretreated rice straw, yielding xylose and xylooligosaccharides. CONCLUSIONS This study provides a fruitful approach for the selection of enzymes with suitable properties from the information contained in extensive databases. We have characterized two xylanases able to hydrolyze xylan with high efficiency at pH > 8.0 and temperature > 80 °C.
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Affiliation(s)
- David Talens-Perales
- Department of Food Biotechnology. Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Paloma Sánchez-Torres
- Department of Food Biotechnology. Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Julia Marín-Navarro
- Department of Food Biotechnology. Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Paterna, Valencia, Spain
- Department of Biochemistry and Molecular Biology, University of Valencia, Valencia, Spain
| | - Julio Polaina
- Department of Food Biotechnology. Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Paterna, Valencia, Spain.
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Liu H, Luo J, Shukla P. Effluents detoxification from pulp and paper industry using microbial engineering and advanced oxidation techniques. JOURNAL OF HAZARDOUS MATERIALS 2020; 398:122998. [PMID: 32502804 DOI: 10.1016/j.jhazmat.2020.122998] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/11/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
Due to the high demand of paper and related items, pulp and paper industry is flourishing day by day. With increased production, come the hazards associated with the toxic elements present in the effluents. Various microorganisms are currently employed in the remediation of these toxic effluents. In addition, various techniques like ozonation, electrocoagulation, UV treatment, Fenton's reagent, and photo-Fenton based techniques are used in advanced oxidation processes to reduce these toxins from effluents. This review highlights various above mentioned advanced techniques and innovative processes along with the biological remediation of these toxic effluents with the help of some potential microbial consortia or their combinatory effects. Moreover, the present review will also disclose the ideas on utilizing the tools of metabolic engineering, systems biology, and artificial intelligence towards microbial engineering for relatively better bioremediation processes. In the future, these techniques might be helpful in increasing the capability of microbial consortia towards detoxification of effluents to make them environmentally safe. Finally, this review gives well-synchronized approaches to get more insights into these innovative methodologies and techniques and their use for various industrial applications.
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Affiliation(s)
- Hao Liu
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640, PR China
| | - Jianfei Luo
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India.
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Boonyapakron K, Chitnumsub P, Kanokratana P, Champreda V. Enhancement of catalytic performance of a metagenome-derived thermophilic oligosaccharide-specific xylanase by binding module removal and random mutagenesis. J Biosci Bioeng 2020; 131:13-19. [PMID: 33067124 DOI: 10.1016/j.jbiosc.2020.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 10/23/2022]
Abstract
Xylo-oligosaccharide (XO) is a promising pre-biotic with applications in food, feed and healthcare products. XO can be produced by enzymatic digestion of xylan with xylanase. In this study, we aimed to improve the biochemical properties relevant to catalysis and kinetics of X11, a thermophilic glycosyl hydrolase (GH) family 11 endo-β-1,4-xylanase derived from a metagenomic library isolated from sugarcane bagasse, under high-temperature conditions preferred for XO synthesis. Removal of a carbohydrate-binding module (X11C) resulted in 6.5 fold greater catalytic efficiency. X11C was further improved by a Pro71Thr mutation in the X11P variant obtained from a random mutagenesis library, which exhibited 15.9 fold greater catalytic efficiency compared with wild-type X11 under the enzyme's optimal conditions of 80°C and pH 6.0. Homology modeling suggested that the improved performance of X11P could be attributed to formation of an extra H-bond between Thr71 and Ser75, which stabilizes the key catalytic residue Glu180 at the active pocket and β-sheet layers and agrees with the respective increase in melting temperature (Tm) where X11P >X11C >X11 as determined by differential scanning fluorimetry. The X11P variant was tested for hydrolysis of beechwood xylan, which showed X6 as the major product followed by X3 and X4 XOs. The highest yield of 5.5 g total XOs product/mg enzyme was observed for X11P, equivalent to 3.7 fold higher than that of wild-type with XO production of >800 mg/g xylan. The X11P enzyme could be developed as a thermophilic biocatalyst for XO synthesis in biorefineries.
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Affiliation(s)
- Katewadee Boonyapakron
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Penchit Chitnumsub
- Biomolecular Analysis and Application Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Pattanop Kanokratana
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Verawat Champreda
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand.
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Shi Z, Han C, Zhang X, Tian L, Wang L. Novel Synergistic Mechanism for Lignocellulose Degradation by a Thermophilic Filamentous Fungus and a Thermophilic Actinobacterium Based on Functional Proteomics. Front Microbiol 2020; 11:539438. [PMID: 33042052 PMCID: PMC7518101 DOI: 10.3389/fmicb.2020.539438] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 08/24/2020] [Indexed: 11/13/2022] Open
Abstract
Effective artificial microbial consortia containing microorganisms with desired biological functions have the potential to optimize the lignocellulose-based bioindustry. Thermobifida fusca was a dominant actinobacterium in high-temperature corn stalk composts, but it was unable to grow alone in corn stalk solid medium. Interestingly, T. fusca showed good growth and secreted enzymes when cocultured with Thermomyces lanuginosus. T. lanuginosus grew firstly during the initial stage, whereas T. fusca dominated the system subsequently during cocultivation. The secretome indicated that T. lanuginosus mainly degraded xylan by expressing a GH11 xylanase (g4601.t1, GenBank AAB94633.1; with relative secretion of 4.95 ± 0.65%). T. fusca was induced by xylan mainly to secrete a xylanase from GH11 family (W8GGR4, GenBank AHK22788.1; with relative secretion of 8.71 ± 3.83%) which could rapidly degrade xylan to xylo-oligosaccharide (XOS) and xylose within 2 min, while high concentrations (>0.5%, w/v) of XOS or xylose suppressed the growth of T. fusca; which may be the reason why T. fusca unable to grow alone in corn stalk solid medium. However, T. lanuginosus could utilize the XOS and xylose produced by xylanases secreted by T. fusca. During the synergistic degradation of lignocellulose by T. lanuginosus and T. fusca, xylan was rapidly consumed by T. lanuginosus, the residual cellulose could specifically induced T. fusca to express a GH10 xylanase with a CBM2 domain (Q47KR6, GenBank AAZ56956.1; with relative secretion of 5.03 ± 1.33%) and 6 cellulases (2 exocellulases and 4 endocellulases). Moreover, T. lanuginosus increased the secretion of cellulases from T. fusca by 19-25%. The order of T. lanuginosus and T. fusca was consistent with the multilayered structures of lignocellulose and could be regulated by different concentrations of XOS and xylose. The novel synergism of T. lanuginosus and T. fusca gave a new sight for revealing more synergetic relationships in natural environments and exploring efficient microbial inoculants and enzyme cocktails for lignocellulose degradation.
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Affiliation(s)
- Zelu Shi
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Chao Han
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Xiujun Zhang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Li Tian
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
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Yang J, Ma T, Shang-Guan F, Han Z. Improving the catalytic activity of thermostable xylanase from Thermotoga maritima via mutagenesis of non-catalytic residues at glycone subsites. Enzyme Microb Technol 2020; 139:109579. [PMID: 32732029 DOI: 10.1016/j.enzmictec.2020.109579] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/31/2020] [Accepted: 04/14/2020] [Indexed: 10/24/2022]
Abstract
Endo-β-1,4-xylanase from Thermotoga maritima, TmxB, is an industrially attractive enzyme due to its extreme thermostability. To improve its application value, four variants were designed on the basis of multiple sequence and three-dimensional structure alignments. Wild-type TmxB (wt-TmxB) and its mutants were produced via a Pichia pastoris expression system. Among four single-site mutants, the tyrosine substitution of a threonine residue (T74Y) at putative -3/-4 subsite led to a 1.3-fold increase in specific activity at 40 °C - 100 °C and pH 5 for 5 min, with beechwood xylan as the substrate. T74Y had an improved catalytic efficiency (kcat/Km), being 1.6 times that of wt-TmxB. Variants DY (two amino acid insertions) and N68Q displayed a slight increase (1.2 fold) and dramatic decline (1.7 fold) in catalytic efficiency, respectively. Mutant E67Y was totally inactive under all test conditions. Structural modeling and docking simulation elucidated structural insights into the molecular mechanism of activity changes for these TmxB variants. This study helps in further understanding the roles of the non-catalytic amino acids at the glycone subsites of xylanases from glycoside hydrolase family 10.
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Affiliation(s)
- Jiangke Yang
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Tengfei Ma
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Fang Shang-Guan
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Zhenggang Han
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, China.
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Efficient xylan-to-sugar biotransformation using an engineered xylanase in hyperthermic environment. Int J Biol Macromol 2020; 157:17-23. [DOI: 10.1016/j.ijbiomac.2020.04.145] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/11/2020] [Accepted: 04/18/2020] [Indexed: 11/30/2022]
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A thermophilic and thermostable xylanase from Caldicoprobacter algeriensis: Recombinant expression, characterization and application in paper biobleaching. Int J Biol Macromol 2020; 164:808-817. [PMID: 32698070 DOI: 10.1016/j.ijbiomac.2020.07.162] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/23/2020] [Accepted: 07/14/2020] [Indexed: 01/11/2023]
Abstract
A novel xylanase gene xynBCA, encoding a polypeptide of 439 residues (XynBCA), was cloned from Caldicoprobacter algeriensis genome and recombinantly expressed in Escherichia coli BL21(DE3). The amino acid sequence analysis showed that XynBCA belongs to the glycoside hydrolase family 10. The purified recombinant enzyme has a monomeric structure of 52 kDa. It is active and stable in a wide range of pH from 3 to 10 with a maximum activity at 6.5. Interestingly, XynBCA was highly thermoactive with an optimum temperature of 80 °C, thermostable with a half-life of 20 min at 80 °C. The specific activity was 117 U mg-1, while the Km and Vmax were 1.247 mg ml-1, and 114.7 μmol min-1 mg-1, respectively. The investigation of XynBCA in kraft pulp biobleaching experiments showed effectiveness in releasing reducing sugars and chromophores, with best achievements at 100 U g-1 of pulp and 1 h of incubation. The comparative molecular modeling studies with the less thermostable Xylanase B from Clostridium stercorarium, revealed extra charged residues at the surface of XynBCA potentially participating in the formation of intermolecular hydrogen bonds with solvent molecules or generating salt bridges, therefore contributing to the higher thermal stability.
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Improving the catalytic thermostability of Bacillus altitudinis W3 ω-transaminase by proline substitutions. 3 Biotech 2020; 10:323. [PMID: 32656056 DOI: 10.1007/s13205-020-02321-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/24/2020] [Indexed: 01/10/2023] Open
Abstract
As a green biocatalyst, transaminase with high thermostability can be better employed to synthesize many pharmaceutical intermediates in industry. To improve the thermostability of (R)-selective amine transaminase from Bacillus altitudinis W3, related mutation sites were determined by multiple amino acid sequence alignment between wild-type ω-transaminase and four potential thermophilic ω-transaminases, followed by replacement of the related amino acid residues with proline by site-directed mutagenesis. Three stabilized mutants (D192P, T237P, and D192P/T237P) showing the highest stability were obtained and used for further analysis. Comparison with the wild-type enzyme revealed that the double mutant D192P/T237P exhibited the largest shift in thermostability, with a 2.5-fold improvement of t 1/2 at 40 °C, and a 6.3 °C increase in T 50 15, and a 5 °C higher optimal catalytic temperature. Additionally, this mutant exhibited an increase in catalytic efficiency (k cat/K m) relative to the wild-type enzyme. Modeling analysis indicated that the improved thermostability of the mutants could be associated with newly formed hydrophobic interactions and hydrogen bonds. This study shown that proline substitutions guided by sequence alignment to improve the thermostability of (R)-selective amine transaminase was effective and this method can also be used to engineering other enzymes.
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Differential antioxidant activity of glucuronoxylooligosaccharides (UXOS) and arabinoxylooligosaccharides (AXOS) produced by two novel xylanases. Int J Biol Macromol 2020; 155:1075-1083. [DOI: 10.1016/j.ijbiomac.2019.11.073] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/24/2019] [Accepted: 11/07/2019] [Indexed: 01/09/2023]
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Jaiswal S, Shukla P. Alternative Strategies for Microbial Remediation of Pollutants via Synthetic Biology. Front Microbiol 2020; 11:808. [PMID: 32508759 PMCID: PMC7249858 DOI: 10.3389/fmicb.2020.00808] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/06/2020] [Indexed: 12/13/2022] Open
Abstract
Continuous contamination of the environment with xenobiotics and related recalcitrant compounds has emerged as a serious pollution threat. Bioremediation is the key to eliminating persistent contaminants from the environment. Traditional bioremediation processes show limitations, therefore it is necessary to discover new bioremediation technologies for better results. In this review we provide an outlook of alternative strategies for bioremediation via synthetic biology, including exploring the prerequisites for analysis of research data for developing synthetic biological models of microbial bioremediation. Moreover, cell coordination in synthetic microbial community, cell signaling, and quorum sensing as engineered for enhanced bioremediation strategies are described, along with promising gene editing tools for obtaining the host with target gene sequences responsible for the degradation of recalcitrant compounds. The synthetic genetic circuit and two-component regulatory system (TCRS)-based microbial biosensors for detection and bioremediation are also briefly explained. These developments are expected to increase the efficiency of bioremediation strategies for best results.
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Jacomini D, Bussler L, Corrêa JM, Kadowaki MK, Maller A, da-Conceição Silva JL, Simão RDCG. Cloning, expression and characterization of C. crescentus xynA2 gene and application of Xylanase II in the deconstruction of plant biomass. Mol Biol Rep 2020; 47:4427-4438. [PMID: 32424521 DOI: 10.1007/s11033-020-05507-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 05/08/2020] [Indexed: 11/24/2022]
Abstract
Biotechnology offers innovative alternatives for industrial bioprocesses mainly because it uses enzymes that biodegrade the hemicellulose releasing fermentable sugars. Caulobacter crescentus (C. crescentus) has seven genes responsible for xylanolytic cleavage, 5 to β-xylosidases (EC 3.2.1.37) and 2 for endoxylanases, like xynA2 (CCNA_03137) that encodes Xylanase II (EC 3.2.1.8) of the glycohydrolases-GH10 group. The xynA2 gene was amplified by PCR, cloned into the pTrcHisA vector e efficiently overexpressed in E. coli providing a His-tag fusion protein. Recombinant xylanase (XynA2) was purified by affinity chromatography using a nickel sepharose column and exhibited a single 43 kDa band on SDS-PAGE gel. XynA2 showed an optimum alkaline pH (8) and stability at alkaline pH for 24 h. Although C. crescentus is mesophilic, XynA2 has optimum temperature of 60 °C and is thermo-resistance at 65 °C. XynA maintains 66% of the enzymatic activity at high temperatures (90 °C) without being denatured.The enzyme displayed a xylanolitic activity free of cellulase to xylan from beechwood and it was not inhibited in the presence of 50 μmol mL-1 of xylose. In addition, dithiothreitol (DTT) induced XynA2 activity, as it improved its kinetic parameters by lowering the KM (5.78 μmol mL-1) and increasing the KCat/KM ratio (1.63 U s-1). Finally, C. crescentus XynA2 efficiently hydrolyzed corn straw with high release of reducing sugars that can be applied in different branches of the industry.
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Affiliation(s)
- Débora Jacomini
- Laboratório de Bioquímica Molecular, Centro de Ciências Exatas e Tecnológicas, Universidade Estadual do Oeste do Paraná, Cascavel,, Paraná, 85814-110, Brazil
| | - Larissa Bussler
- Laboratório de Bioquímica Molecular, Centro de Ciências Exatas e Tecnológicas, Universidade Estadual do Oeste do Paraná, Cascavel,, Paraná, 85814-110, Brazil
| | - Juliana Moço Corrêa
- Laboratório de Bioquímica Molecular, Centro de Ciências Médicas e Farmacêuticas, Universidade Estadual do Oeste do Paraná, Rua Universitária, 2069, Cascavel, PR, 85814-110, Brazil
| | - Marina Kimiko Kadowaki
- Laboratório de Bioquímica Molecular, Centro de Ciências Médicas e Farmacêuticas, Universidade Estadual do Oeste do Paraná, Rua Universitária, 2069, Cascavel, PR, 85814-110, Brazil
| | - Alexandre Maller
- Laboratório de Bioquímica Molecular, Centro de Ciências Médicas e Farmacêuticas, Universidade Estadual do Oeste do Paraná, Rua Universitária, 2069, Cascavel, PR, 85814-110, Brazil
| | - José Luis da-Conceição Silva
- Laboratório de Bioquímica Molecular, Centro de Ciências Médicas e Farmacêuticas, Universidade Estadual do Oeste do Paraná, Rua Universitária, 2069, Cascavel, PR, 85814-110, Brazil
| | - Rita de Cássia Garcia Simão
- Laboratório de Bioquímica Molecular, Centro de Ciências Exatas e Tecnológicas, Universidade Estadual do Oeste do Paraná, Cascavel,, Paraná, 85814-110, Brazil. .,Laboratório de Bioquímica Molecular, Centro de Ciências Médicas e Farmacêuticas, Universidade Estadual do Oeste do Paraná, Rua Universitária, 2069, Cascavel, PR, 85814-110, Brazil.
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Wu X, Zhang Q, Zhang L, Liu S, Chen G, Zhang H, Wang L. Insights Into the Role of Exposed Surface Charged Residues in the Alkali-Tolerance of GH11 Xylanase. Front Microbiol 2020; 11:872. [PMID: 32457729 PMCID: PMC7225583 DOI: 10.3389/fmicb.2020.00872] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/14/2020] [Indexed: 11/29/2022] Open
Abstract
Thermostable and alkaline- or acid-stable xylanases are more advantageous in agricultural and industrial fields. In this study, a rational structure-based design was conducted based on a thermostable GH11 xylanase TlXynA from Thermomyces lanuginosus to improved pH-tolerance. Four mutant enzymes (P1, P2, P3, and P4) and five variants (N1, N2, N3, N4, and N5) were constructed by substituting surface charged residue combinations using site-directed mutagenesis. Compared to the native enzyme, two mutants P1 and P2 showed higher acid tolerance, especially at pH 3.0, presented 50 and 40% of their maximum activity, respectively. In addition, four mutants N1, N2, N3 and N4 had higher tolerance than the native enzyme to alkaline environments (pH 7.0-9.0). At pH 9.0, the residual activities of N1, N2, N3, and N4 were 86, 78, 77, and 66%, respectively. In summary, an improved pH-tolerance design principle is being reported.
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Affiliation(s)
- Xiuyun Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Qun Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Lanzeng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Shijia Liu
- Taishan College, Shandong University, Jinan, China
| | - Guanjun Chen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Huaiqiang Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
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Hamann PR, Gomes TC, de M.B.Silva L, Noronha EF. Influence of lignin-derived phenolic compounds on the Clostridium thermocellum endo-β-1,4-xylanase XynA. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.02.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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