1
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Xing H, Wang P, Yan X, Yang Y, Li X, Liu R, Zhou Z. Thermostability enhancement of Escherichia coli phytase by error-prone polymerase chain reaction (epPCR) and site-directed mutagenesis. Front Bioeng Biotechnol 2023; 11:1167530. [PMID: 37064242 PMCID: PMC10101328 DOI: 10.3389/fbioe.2023.1167530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/20/2023] [Indexed: 03/31/2023] Open
Abstract
Phytase efficiently hydrolyzes phytate to phosphate; thus, it is widely used to increase phosphorus availability in animal feeds and reduce phosphorus pollution through excretion. Phytase is easily inactivated during feed pelleting at high temperature, and sufficient thermostability of phytase is essential for industrial applications. In this study, directed evolution was performed to enhance phytase thermostability. Variants were initially expressed in Escherichia coli BL21 for screening, then in Pichia pastoris for characterization. Over 19,000 clones were generated from an error-prone Polymerase Chain Reaction (epPCR) library; 5 mutants (G10, D7, E3, F8, and F9) were obtained with approximately 9.6%, 10.6%, 11.5%, 11.6%, and 12.2% higher residual activities than the parent after treatment at 99°C for 60 min. Three of these mutants, D7, E3, and F8, exhibited 79.8%, 73.2%, and 92.6% increases in catalytic efficiency (kcat/Km), respectively. In addition, the specific activities of D7, E3, and F8 were 2.33-, 1.98-, and 2.02-fold higher than parental phytase; they were also higher than the activities of all known thermostable phytases. Sequence analysis revealed that all mutants were substituted at residue 75 and was confirmed that the substitution of cysteine at position 75 was the main contribution to the improvement of thermostability of mutants by saturation mutagenesis, indicating that this amino acid is crucial for the stability and catalytic efficiency of phytase. Docking structure analysis revealed that substitution of the C75 residue allowed the mutants to form additional hydrogen bonds in the active pocket, thereby facilitating binding to the substrate. In addition, we confirmed that the intrinsic C77-C108 disulfide bond in E. coli phytase is detrimental to its stability.
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Affiliation(s)
- Hongguan Xing
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Pingping Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xing Yan
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yi Yang
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xinliang Li
- CJ Youtell (Shanghai) Biotech Co., Ltd., Shanghai, China
| | - Rui Liu
- CJ Youtell (Shanghai) Biotech Co., Ltd., Shanghai, China
| | - Zhihua Zhou
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Zhihua Zhou,
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2
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Sürmeli Y, Şanlı-Mohamed G. Engineering of xylanases for the development of biotechnologically important characteristics. Biotechnol Bioeng 2023; 120:1171-1188. [PMID: 36715367 DOI: 10.1002/bit.28339] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/19/2022] [Accepted: 01/26/2023] [Indexed: 01/31/2023]
Abstract
Xylanases are the main biocatalysts used for the reduction of the xylan backbone from hemicellulose, randomly splitting off β-1,4-glycosidic linkages between xylopyranosyl residues. Xylanase market has been annually estimated at 500 million US Dollars and they are potentially used in broad industrial process ranges such as paper pulp biobleaching, xylo-oligosaccharide production, and biofuel manufacture from lignocellulose. The highly stable xylanases are preferred in the downstream procedure of industrial processes because they can tolerate severe conditions. Almost all native xylanases can not endure adverse conditions thus they are industrially not proper to be utilized. Protein engineering is a powerful technology for developing xylanases, which can effectively work in adverse conditions and can meet requirements for industrial processes. This study considered state-of-the-art strategies of protein engineering for creating the xylanase gene diversity, high-throughput screening systems toward upgraded traits of the xylanases, and the prediction and comprehensive analysis of the target mutations in xylanases by in silico methods. Also, key molecular factors have been elucidated for industrial characteristics (alkaliphilic enhancement, thermal stability, and catalytic performance) of GH11 family xylanases. The present review explores industrial characteristics improved by directed evolution, rational design, and semi-rational design as protein engineering approaches for pulp bleaching process, xylooligosaccharides production, and biorefinery & bioenergy production.
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Affiliation(s)
- Yusuf Sürmeli
- Department of Agricultural Biotechnology, Tekirdağ Namık Kemal University, Tekirdağ, Turkey
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3
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Chai S, Zhu Z, Tian E, Xiao M, Wang Y, Zou G, Zhou Z. Building a Versatile Protein Production Platform Using Engineered Trichoderma reesei. ACS Synth Biol 2022; 11:486-496. [PMID: 34928572 DOI: 10.1021/acssynbio.1c00570] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Trichoderma reesei has an extremely high capacity for synthesizing and secreting proteins, thus exhibiting promise as an expression platform for heterologous proteins. However, T. reesei secretes large amounts of native proteins, which hinders its widespread application for heterologous protein production. Here, we designed and built a series of T. reesei chassis using an iterative gene deletion approach based on an efficient genome editing system. Donor DNAs with specially designed construct facilitated screening of positive deletion strains without ectopic insertion. Finally, marker-free T. reesei chassis with lower rates of native protein secretion and low levels of extracellular protease activity were constructed after 11 consecutive rounds of gene deletion. Higher production levels of three heterologous proteins─a bacterial xylanase XYL7, a fungal immunomodulatory protein LZ8, and the human serum albumin HSA─were achieved with these chassis using the cbh1 promoter. It is possible that diverse high-value proteins might be produced at a high yield using this engineered platform.
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Affiliation(s)
- Shunxing Chai
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
- University of Chinese Academy of Sciences, 19(A) Yuquan Rd, Beijing 100049, China
| | - Zhihua Zhu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
- University of Chinese Academy of Sciences, 19(A) Yuquan Rd, Beijing 100049, China
| | - Ernuo Tian
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
| | - Meili Xiao
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
- University of Chinese Academy of Sciences, 19(A) Yuquan Rd, Beijing 100049, China
| | - Yan Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
| | - Gen Zou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, 1000 Jinqi Rd, Shanghai 201403, China
| | - Zhihua Zhou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
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4
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Madhavan A, Arun KB, Binod P, Sirohi R, Tarafdar A, Reshmy R, Kumar Awasthi M, Sindhu R. Design of novel enzyme biocatalysts for industrial bioprocess: Harnessing the power of protein engineering, high throughput screening and synthetic biology. BIORESOURCE TECHNOLOGY 2021; 325:124617. [PMID: 33450638 DOI: 10.1016/j.biortech.2020.124617] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/19/2020] [Accepted: 12/22/2020] [Indexed: 05/13/2023]
Abstract
Biocatalysts have wider applications in various industries. Biocatalysts are generating bigger attention among researchers due to their unique catalytic properties like activity, specificity and stability. However the industrial use of many enzymes is hindered by low catalytic efficiency and stability during industrial processes. Properties of enzymes can be altered by protein engineering. Protein engineers are increasingly study the structure-function characteristics, engineering attributes, design of computational tools for enzyme engineering, and functional screening processes to improve the design and applications of enzymes. The potent and innovative techniques of enzyme engineering deliver outstanding opportunities for tailoring industrially important enzymes for the versatile production of biochemicals. An overview of the current trends in enzyme engineering is explored with important representative examples.
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Affiliation(s)
- Aravind Madhavan
- Rajiv Gandhi Centre for Biotechnology, Trivandrum 695 014, India
| | - K B Arun
- Rajiv Gandhi Centre for Biotechnology, Trivandrum 695 014, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, India
| | - Ranjna Sirohi
- The Center for Energy and Environmental Sustainability, Lucknow 226 010, Uttar Pradesh, India
| | - Ayon Tarafdar
- Division of Livestock Production and Management, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly 243 122, Uttar Pradesh, India
| | - R Reshmy
- Post Graduate and Research Department of Chemistry, Bishop Moore College, Mavelikara 690 110, Kerala, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, North West A & F University, Yangling, Shaanxi 712 100, China
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, India.
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5
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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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6
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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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7
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Xing H, Zou G, Liu C, Chai S, Yan X, Li X, Liu R, Yang Y, Zhou Z. Improving the thermostability of a GH11 xylanase by directed evolution and rational design guided by B-factor analysis. Enzyme Microb Technol 2020; 143:109720. [PMID: 33375980 DOI: 10.1016/j.enzmictec.2020.109720] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 10/20/2020] [Accepted: 11/26/2020] [Indexed: 01/19/2023]
Abstract
Operational stability under high temperature is required for enzyme application in industrial processes. Error-prone PCR and B-factor analysis were employed to enhance the thermostability of a xylanase from GH family 11 in this study. Based on the top 10 mutants screened from the random mutation libraries, mutant Xyn371 was derived from the optimal mutant Xyn370 by integrating the beneficial residues identified in the other 9 screened mutants. Subsequently, a best-saturation mutant Xyn372 originated from Xyn371 was selected with a 60-min half-life at 70 °C (0.5-min half-life for the wild-type enzyme). According to the site-saturated mutagenesis of 10 residues with higher B-factors in Xyn372, mutants Xyn375 and Xyn376 were screened; their half-lives at 70 °C were 410 and 360 min, respectively. The substituted residues located in the "palm" region of the N-terminus and the newly generated hydrogen bonds in the mutants might contribute to improved thermostability. The significantly improved thermostability of mutants will pave the way for applications in different industrial areas.
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Affiliation(s)
- Hongguan Xing
- CAS-key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Rd 300, Shanghai, 200032, China; Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Meilong Rd 130, Shanghai, 200237, China
| | - Gen Zou
- CAS-key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Rd 300, Shanghai, 200032, China
| | - Chunyan Liu
- CAS-key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Rd 300, Shanghai, 200032, China
| | - Shunxing Chai
- CAS-key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Rd 300, Shanghai, 200032, China
| | - Xing Yan
- CAS-key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Rd 300, Shanghai, 200032, China
| | - Xinliang Li
- CJ, Youtell (Shanghai) Biotech Co., Ltd, Ste 302, Bldg 7, 526 Ruiqing Rd, Shanghai 201201, China
| | - Rui Liu
- CJ, Youtell (Shanghai) Biotech Co., Ltd, Ste 302, Bldg 7, 526 Ruiqing Rd, Shanghai 201201, China
| | - Yi Yang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Meilong Rd 130, Shanghai, 200237, China
| | - Zhihua Zhou
- CAS-key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Rd 300, Shanghai, 200032, China.
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8
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Verma D, Satyanarayana T. Xylanolytic Extremozymes Retrieved From Environmental Metagenomes: Characteristics, Genetic Engineering, and Applications. Front Microbiol 2020; 11:551109. [PMID: 33042057 PMCID: PMC7527525 DOI: 10.3389/fmicb.2020.551109] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 08/21/2020] [Indexed: 01/29/2023] Open
Abstract
Xylanolytic enzymes have extensive applications in paper, food, and feed, pharmaceutical, and biofuel industries. These industries demand xylanases that are functional under extreme conditions, such as high temperature, acidic/alkaline pH, and others, which are prevailing in bioprocessing industries. Despite the availability of several xylan-hydrolyzing enzymes from cultured microbes, there is a huge gap between what is available and what industries require. DNA manipulations as well as protein-engineering techniques are also not quite satisfactory in generating xylan-hydrolyzing extremozymes. With a compound annual growth rate of 6.6% of xylan-hydrolyzing enzymes in the global market, there is a need for xylanolytic extremozymes. Therefore, metagenomic approaches have been employed to uncover hidden xylanolytic genes that were earlier inaccessible in culture-dependent approaches. Appreciable success has been achieved in retrieving several unusual xylanolytic enzymes with novel and desirable characteristics from different extreme environments using functional and sequence-based metagenomic approaches. Moreover, the Carbohydrate Active Enzymes database includes approximately 400 GH-10 and GH-11 unclassified xylanases. This review discusses sources, characteristics, and applications of xylanolytic enzymes obtained through metagenomic approaches and their amelioration by genetic engineering techniques.
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Affiliation(s)
- Digvijay Verma
- Department of Microbiology, Babasaheb Bhimrao Ambedkar (Central) University, Lucknow, India
| | - Tulasi Satyanarayana
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
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9
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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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10
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Cai L, Zhang M, Shao T, He Y, Li J, Ren B, Zhou C. Effect of introducing disulfide bridges in C-terminal structure on the thermostability of xylanase XynZF-2 from Aspergillus niger. J GEN APPL MICROBIOL 2019; 65:240-245. [PMID: 30905899 DOI: 10.2323/jgam.2018.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In this study, a mutant xylanase of high thermostability was obtained by site-directed mutagenesis. The homologous 3D structure of xylanase was successfully modeled and the mutation sites were predicted using bioinformatics software. Two amino acids of XynZF-2 were respectively substituted by cysteines (T205C and A52C) and a disulfide bridge was introduced into the C-terminal of XynZF-2. The mutant gene xynZFTA was cloned into pPIC9K and expressed in P. pastoris. The optimum temperature of the variant XynZFTA was improved from 45°C to 60°C, and XynZFTA retained greater than 90.0% activity (XynZF-2 retained only 50.0% activity) after treatment at 50°C for 5 min. The optimum pH of mutant xylanase was similar to XynZF-2 (pH = 5.0). The pH stability span (5.0~7.0) of the mutant xylanase was increased to 3.0~9.0. Overall, the results implied that the introduction of a disulfide bridge in the C-terminal structure improved the thermostability and pH stability of XynZF-2.
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Affiliation(s)
- Liutengzi Cai
- School of Life Science and Technology, Xinxiang Medical University.,Synthetic Biology Engineering Lab of Henan Province
| | - Mishuai Zhang
- School of Life Science and Technology, Xinxiang Medical University.,Synthetic Biology Engineering Lab of Henan Province
| | - Tianci Shao
- School of Life Science and Technology, Xinxiang Medical University.,Synthetic Biology Engineering Lab of Henan Province
| | - You He
- School of Life Science and Technology, Xinxiang Medical University.,Synthetic Biology Engineering Lab of Henan Province
| | - Jingyi Li
- School of Life Science and Technology, Xinxiang Medical University.,Synthetic Biology Engineering Lab of Henan Province
| | - Bingjie Ren
- School of Life Science and Technology, Xinxiang Medical University.,Synthetic Biology Engineering Lab of Henan Province
| | - Chenyan Zhou
- School of Life Science and Technology, Xinxiang Medical University.,Synthetic Biology Engineering Lab of Henan Province
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11
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Characterization of CBM36-containing GH11 endoxylanase NtSymX11 from the hindgut metagenome of higher termite Nasutitermes takasagoensis displaying prominent catalytic activity. Carbohydr Res 2019; 474:1-7. [DOI: 10.1016/j.carres.2019.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 01/05/2019] [Accepted: 01/06/2019] [Indexed: 11/17/2022]
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12
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Sun Z, Liu Q, Qu G, Feng Y, Reetz MT. Utility of B-Factors in Protein Science: Interpreting Rigidity, Flexibility, and Internal Motion and Engineering Thermostability. Chem Rev 2019; 119:1626-1665. [PMID: 30698416 DOI: 10.1021/acs.chemrev.8b00290] [Citation(s) in RCA: 278] [Impact Index Per Article: 55.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Qian Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ge Qu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Chemistry Department, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
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13
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Liu N, Li H, Chevrette MG, Zhang L, Cao L, Zhou H, Zhou X, Zhou Z, Pope PB, Currie CR, Huang Y, Wang Q. Functional metagenomics reveals abundant polysaccharide-degrading gene clusters and cellobiose utilization pathways within gut microbiota of a wood-feeding higher termite. THE ISME JOURNAL 2019; 13:104-117. [PMID: 30116044 PMCID: PMC6298952 DOI: 10.1038/s41396-018-0255-1] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/16/2018] [Accepted: 07/20/2018] [Indexed: 12/27/2022]
Abstract
Plant cell-wall polysaccharides constitute the most abundant but recalcitrant organic carbon source in nature. Microbes residing in the digestive tract of herbivorous bilaterians are particularly efficient at depolymerizing polysaccharides into fermentable sugars and play a significant support role towards their host's lifestyle. Here, we combine large-scale functional screening of fosmid libraries, shotgun sequencing, and biochemical assays to interrogate the gut microbiota of the wood-feeding "higher" termite Globitermes brachycerastes. A number of putative polysaccharide utilization gene clusters were identified with multiple fibrolytic genes. Our large-scale functional screening of 50,000 fosmid clones resulted in 464 clones demonstrating plant polysaccharide-degrading activities, including 267 endoglucanase-, 24 exoglucanase-, 72 β-glucosidase-, and 101 endoxylanase-positive clones. We sequenced 173 functionally active clones and identified ~219 genes encoding putative carbohydrate-active enzymes (CAZymes) targeting cellulose, hemicellulose and pectin. Further analyses revealed that 68 of 154 contigs encode one or more CAZyme, which includes 35 examples of putative saccharolytic operons, suggesting that clustering of CAZymes is common in termite gut microbial inhabitants. Biochemical characterization of a representative xylanase cluster demonstrated that constituent enzymes exhibited complementary physicochemical properties and saccharolytic capabilities. Furthermore, diverse cellobiose-metabolizing enzymes include β-glucosidases, cellobiose phosphorylases, and phopho-6-β-glucosidases were identified and functionally verified, indicating that the termite gut micro-ecosystem utilizes diverse metabolic pathways to interconnect hydrolysis and central metabolism. Collectively, these results provide an in-depth view of the adaptation and digestive strategies employed by gut microbiota within this tiny-yet-efficient host-associated ecosystem.
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Affiliation(s)
- Ning Liu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hongjie Li
- Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, USA
- Department Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Marc G Chevrette
- Department Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Lei Zhang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lin Cao
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Haokui Zhou
- Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, USA
| | - Zhihua Zhou
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Phillip B Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Cameron R Currie
- Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, USA
- Department Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Yongping Huang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Qian Wang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China.
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14
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Kötzler MP, Robinson K, Chen HM, Okon M, McIntosh LP, Withers SG. Modulating the Nucleophile of a Glycoside Hydrolase through Site-Specific Incorporation of Fluoroglutamic Acids. J Am Chem Soc 2018; 140:8268-8276. [DOI: 10.1021/jacs.8b04235] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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15
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Kumar V, Dangi AK, Shukla P. Engineering Thermostable Microbial Xylanases Toward its Industrial Applications. Mol Biotechnol 2018; 60:226-235. [DOI: 10.1007/s12033-018-0059-6] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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16
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Berini F, Casciello C, Marcone GL, Marinelli F. Metagenomics: novel enzymes from non-culturable microbes. FEMS Microbiol Lett 2017; 364:4329276. [DOI: 10.1093/femsle/fnx211] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/02/2017] [Indexed: 01/02/2023] Open
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17
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Coyotzi S, Pratscher J, Murrell JC, Neufeld JD. Targeted metagenomics of active microbial populations with stable-isotope probing. Curr Opin Biotechnol 2016; 41:1-8. [DOI: 10.1016/j.copbio.2016.02.017] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 02/09/2016] [Accepted: 02/13/2016] [Indexed: 02/02/2023]
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18
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Li G, Zhang H, Sun Z, Liu X, Reetz MT. Multiparameter Optimization in Directed Evolution: Engineering Thermostability, Enantioselectivity, and Activity of an Epoxide Hydrolase. ACS Catal 2016. [DOI: 10.1021/acscatal.6b01113] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guangyue Li
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich
Chemie der Philipps-Universität, Hans-Meerwein-Strasse, 35032 Marburg, Germany
| | - Hui Zhang
- State
Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, 300071 Tianjin, People’s Republic of China
| | - Zhoutong Sun
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich
Chemie der Philipps-Universität, Hans-Meerwein-Strasse, 35032 Marburg, Germany
| | - Xinqi Liu
- State
Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, 300071 Tianjin, People’s Republic of China
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich
Chemie der Philipps-Universität, Hans-Meerwein-Strasse, 35032 Marburg, Germany
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19
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Xu X, Liu MQ, Huo WK, Dai XJ. Obtaining a mutant of Bacillus amyloliquefaciens xylanase A with improved catalytic activity by directed evolution. Enzyme Microb Technol 2016; 86:59-66. [DOI: 10.1016/j.enzmictec.2016.02.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 02/03/2016] [Accepted: 02/07/2016] [Indexed: 12/29/2022]
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20
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Kumar V, Marín-Navarro J, Shukla P. Thermostable microbial xylanases for pulp and paper industries: trends, applications and further perspectives. World J Microbiol Biotechnol 2016; 32:34. [PMID: 26754672 DOI: 10.1007/s11274-015-2005-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 12/23/2015] [Indexed: 10/22/2022]
Abstract
Xylanases are enzymes with biotechnological relevance in a number of fields, including food, feed, biofuel, and textile industries. Their most significant application is in the paper and pulp industry, where they are used as a biobleaching agent, showing clear economic and environmental advantages over chemical alternatives. Since this process requires high temperatures and alkali media, the identification of thermostable and alkali stable xylanases represents a major biotechnological goal in this field. Moreover, thermostability is a desirable property for many other applications of xylanases. The review makes an overview of xylanase producing microorganisms and their current implementation in paper biobleaching. Future perspectives are analyzed focusing in the efforts carried out to generate thermostable enzymes by means of modern biotechnological tools, including metagenomic analysis, enzyme molecular engineering and nanotechnology. Furthermore, structural and mutagenesis studies have revealed critical sites for stability of xylanases from glycoside hydrolase families GH10 and GH11, which constitute the main classes of these enzymes. The overall conclusions of these works are summarized here and provide relevant information about putative weak spots within xylanase structures to be targeted in future protein engineering approaches.
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Affiliation(s)
- Vishal Kumar
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Julia Marín-Navarro
- Instituto de Agroquímica y Tecnología de Alimentos, C.S.I.C., Av. Catedrático Agustín Escardino, 7, E6980, Paterna, Valencia, Spain
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India.
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21
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Zhou CY, Li TB, Wang YT, Zhu XS, Kang J. Exploration of a N-terminal disulfide bridge to improve the thermostability of a GH11 xylanase from Aspergillus niger. J GEN APPL MICROBIOL 2016; 62:83-9. [DOI: 10.2323/jgam.62.83] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Chen-Yan Zhou
- School of Life Science and Technology, Xinxiang Medical University
| | - Tong-Biao Li
- School of Life Science and Technology, Xinxiang Medical University
| | - Yong-Tao Wang
- The First Affiliated Hospital, Xinxiang Medical University
| | - Xin-Shu Zhu
- School of Life Science and Technology, Xinxiang Medical University
| | - Jing Kang
- School of Life Science and Technology, Xinxiang Medical University
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22
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Gu X, Wang S, Wang S, Zhao LX, Cao M, Feng Z. Identification and Characterization of Two Novel Esterases from a Metagenomic Library. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2015. [DOI: 10.3136/fstr.21.649] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Xinqi Gu
- College of Food Science and Technology, Nanjing Agricultural University
| | - Shilin Wang
- College of Food Science and Technology, Nanjing Agricultural University
| | - Shaochen Wang
- College of Food Science and Technology, Nanjing Agricultural University
| | - Li-Xing Zhao
- Key Laboratory of Medicinal chemistry for Natural Resource, Ministry of Education, School of Chemical Science and Technology, Yunnan University
| | - Mingming Cao
- College of Food Science and Technology, Nanjing Agricultural University
| | - Zhiyang Feng
- College of Food Science and Technology, Nanjing Agricultural University
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