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Pitchayatanakorn P, Suwan E, Kongsaeree PT. Characterization of BrGH3A, a bovine rumen-derived glycoside hydrolase family 3 β-glucosidase with a permuted domain arrangement. PLoS One 2024; 19:e0305817. [PMID: 38980877 PMCID: PMC11233000 DOI: 10.1371/journal.pone.0305817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 06/05/2024] [Indexed: 07/11/2024] Open
Abstract
The bovine rumen contains a large consortium of residential microbes that release a variety of digestive enzymes for feed degradation. However, the utilization of these microbial enzymes is still limited because these rumen microorganisms are mostly anaerobes and are thus unculturable. Therefore, we applied a sequence-based metagenomic approach to identify a novel 2,445-bp glycoside hydrolase family 3 β-glucosidase gene known as BrGH3A from the metagenome of bovine ruminal fluid. BrGH3A β-glucosidase is a 92-kDa polypeptide composed of 814 amino acid residues. Unlike most glycoside hydrolases in the same family, BrGH3A exhibited a permuted domain arrangement consisting of an (α/β)6 sandwich domain, a fibronectin type III domain and a (β/α)8 barrel domain. BrGH3A exhibited greater catalytic efficiency toward laminaribiose than cellobiose. We proposed that BrGH3A is an exo-acting β-glucosidase from Spirochaetales bacteria that is possibly involved in the intracellular degradation of β-1,3-/1,4-mixed linkage glucans that are present in grass cell walls. BrGH3A exhibits rich diversity in rumen hydrolytic enzymes and may represent a member of a new clan with a permuted domain topology within the large family.
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Affiliation(s)
| | - Eukote Suwan
- Department of Veterinary Technology, Faculty of Veterinary Technology, Kasetsart University, Bangkok, Thailand
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2
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Chettri D, Verma AK. Statistical optimization of cellulase production from Bacillus sp. YE16 isolated from yak dung of the Sikkim Himalayas for its application in bioethanol production using pretreated sugarcane bagasse. Microbiol Res 2024; 281:127623. [PMID: 38301380 DOI: 10.1016/j.micres.2024.127623] [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: 07/06/2023] [Revised: 11/03/2023] [Accepted: 01/13/2024] [Indexed: 02/03/2024]
Abstract
Cellulolytic bacteria were isolated from yak dung samples collected from different habitats of Sikkim, India. Isolate YE16 from the Yumthang Valley sample showed highest enzyme activity of 7.68 U/mL and was identified as Bacillus sp., which has a sequence similarity of 96.15% with B. velezensis. One factor at a time (OFAT) analysis revealed that an acidic pH of 5 with 37 °C temperature was optimum for maximum enzyme production after 36 hrs of incubation (13.88 U/mL), which was further increased after statistical optimization (34.70 U/mL). Media optimization based on response surface methodology predicted that Carboxymethyl cellulose (CMC) and MgSO4 at concentrations of 30 g/L and 0.525 g/L, respectively, at pH 5.5 to show CMCase activity of 30.612 U/mL, which was consistent with the observed value of 30.25 U/mL and confirmed the model. The crude enzyme also efficiently hydrolyzed alkaline pretreated sugarcane bagasse, releasing 7.09 g/L of glucose equivalent with an ethanol production of 3.05 g.
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Affiliation(s)
- Dixita Chettri
- Department of Microbiology, Sikkim University, Gangtok 737102, Sikkim, India
| | - Anil Kumar Verma
- Department of Microbiology, Sikkim University, Gangtok 737102, Sikkim, India.
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3
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Huang YY, Lv ZH, Zheng HZ, Zhu Q, Liu MT, Sang P, Wang F, Zhu D, Xian WD, Yin YR. Characterization of a thermophilic and glucose-tolerant GH1 β-glucosidase from hot springs and its prospective application in corn stover degradation. Front Microbiol 2023; 14:1286682. [PMID: 38179451 PMCID: PMC10764553 DOI: 10.3389/fmicb.2023.1286682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/05/2023] [Indexed: 01/06/2024] Open
Abstract
Introduction β-Glucosidase serves as the pivotal rate-limiting enzyme in the cellulose degradation process, facilitating the hydrolysis of cellobiose and cellooligosaccharides into glucose. However, the widespread application of numerous β-glucosidases is hindered by their limited thermostability and low glucose tolerance, particularly in elevated-temperature and high-glucose environments. Methods This study presents an analysis of a β-glucosidase gene belonging to the GH1 family, denoted lqbg8, which was isolated from the metagenomic repository of Hehua hot spring located in Tengchong, China. Subsequently, the gene was cloned and heterologously expressed in Escherichia coli BL21(DE3). Post expression, the recombinant β-glucosidase (LQBG8) underwent purification through a Ni affinity chromatography column, thereby enabling the in-depth exploration of its enzymatic properties. Results LQBG8 had an optimal temperature of 70°C and an optimum pH of 5.6. LQBG8 retained 100 and 70% of its maximum activity after 2-h incubation periods at 65°C and 70°C, respectively. Moreover, even following exposure to pH ranges of 3.0-10.0 for 24 h, LQBG8 retained approximately 80% of its initial activity. Notably, the enzymatic prowess of LQBG8 remained substantial at glucose concentrations of up to 3 M, with a retention of over 60% relative activity. The kinetic parameters of LQBG8 were characterized using cellobiose as substrate, with Km and Vmax values of 28 ± 1.9 mg/mL and 55 ± 3.2 μmol/min/mg, respectively. Furthermore, the introduction of LQBG8 (at a concentration of 0.03 mg/mL) into a conventional cellulase reaction system led to an impressive 43.7% augmentation in glucose yield from corn stover over a 24-h period. Molecular dynamics simulations offered valuable insights into LQBG8's thermophilic nature, attributing its robust stability to reduced fluctuations, conformational changes, and heightened structural rigidity in comparison to mesophilic β-glucosidases. Discussion In summation, its thermophilic, thermostable, and glucose-tolerant attributes, render LQBG8 ripe for potential applications across diverse domains encompassing food, feed, and the production of lignocellulosic ethanol.
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Affiliation(s)
- Yu-Ying Huang
- College of Agriculture and Biological Science, Dali University, Dali, China
| | - Zhi-Hua Lv
- College of Agriculture and Biological Science, Dali University, Dali, China
| | - Hong-Zhao Zheng
- College of Agriculture and Biological Science, Dali University, Dali, China
| | - Qian Zhu
- College of Agriculture and Biological Science, Dali University, Dali, China
| | - Meng-Ting Liu
- College of Agriculture and Biological Science, Dali University, Dali, China
- Key Laboratory of Bioinformatics and Computational Biology, Department of Education of Yunnan Province, Dali University, Dali, China
| | - Peng Sang
- College of Agriculture and Biological Science, Dali University, Dali, China
- Key Laboratory of Bioinformatics and Computational Biology, Department of Education of Yunnan Province, Dali University, Dali, China
| | - Fei Wang
- College of Agriculture and Biological Science, Dali University, Dali, China
| | - Dan Zhu
- College of Agriculture and Biological Science, Dali University, Dali, China
| | - Wen-Dong Xian
- Marine Microorganism Ecological and Application Lab, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Yi-Rui Yin
- College of Agriculture and Biological Science, Dali University, Dali, China
- Key Laboratory of Bioinformatics and Computational Biology, Department of Education of Yunnan Province, Dali University, Dali, China
- Cangshan Forest Ecosystem Observation and Research Station of Yunnan Province, Dali University, Dali, China
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Kaenying W, Tagami T, Suwan E, Pitsanuwong C, Chomngam S, Okuyama M, Kongsaeree P, Kimura A, Kongsaeree PT. Structural and mutational analysis of glycoside hydrolase family 1 Br2 β-glucosidase derived from bovine rumen metagenome. Heliyon 2023; 9:e21923. [PMID: 38034805 PMCID: PMC10685196 DOI: 10.1016/j.heliyon.2023.e21923] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 08/21/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023] Open
Abstract
Ruminant animals rely on the activities of β-glucosidases from residential microbes to convert feed fibers into glucose for further metabolic uses. In this report, we determined the structures of Br2, which is a glycoside hydrolase family 1 β-glucosidase from the bovine rumen metagenome. Br2 folds into a classical (β/α)8-TIM barrel domain but displays unique structural features at loop β5→α5 and α-helix 5, resulting in different positive subsites from those of other GH1 enzymes. Br2 exhibited the highest specificity toward laminaritriose, suggesting its involvement in β-glucan hydrolysis in digested feed. We then substituted the residues at subsites +1 and + 2 of Br2 with those of Halothermothrix orenii β-glucosidase. The C170E and C221T mutations provided favorable interactions with glucooligosaccharide substrates at subsite +2, while the A219N mutation probably improved the substrate preference for cellobiose and gentiobiose relative to laminaribiose at subsite +1. The N407Y mutation increased the affinity toward cellooligosaccharides. These results give further insights into the molecular determinants responsible for substrate specificity in GH1 β-glucosidases and may provide a basis for future enzyme engineering applications.
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Affiliation(s)
- Wilaiwan Kaenying
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Takayoshi Tagami
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Eukote Suwan
- Department of Veterinary Technology, Faculty of Veterinary Technology, Kasetsart University, Bangkok 10900, Thailand
| | - Chariwat Pitsanuwong
- Faculty of Science and Technology, Suan Sunandha Rajabhat University, Bangkok 10300, Thailand
| | - Sinchai Chomngam
- Department of Chemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Masayuki Okuyama
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Palangpon Kongsaeree
- Department of Chemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Atsuo Kimura
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
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Li N, Zhang R, Zhou J, Huang Z. Structures, Biochemical Characteristics, and Functions of β-Xylosidases. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:7961-7976. [PMID: 37192316 DOI: 10.1021/acs.jafc.3c01425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The complete degradation of abundant xylan derived from plants requires the participation of β-xylosidases to produce the xylose which can be converted to xylitol, ethanol, and other valuable chemicals. Some phytochemicals can also be hydrolyzed by β-xylosidases into bioactive substances, such as ginsenosides, 10-deacetyltaxol, cycloastragenol, and anthocyanidins. On the contrary, some hydroxyl-containing substances such as alcohols, sugars, and phenols can be xylosylated by β-xylosidases into new chemicals such as alkyl xylosides, oligosaccharides, and xylosylated phenols. Thus, β-xylosidases shows great application prospects in food, brewing, and pharmaceutical industries. This review focuses on the molecular structures, biochemical properties, and bioactive substance transformation function of β-xylosidases derived from bacteria, fungi, actinomycetes, and metagenomes. The molecular mechanisms of β-xylosidases related to the properties and functions are also discussed. This review will serve as a reference for the engineering and application of β-xylosidases in food, brewing, and pharmaceutical industries.
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Affiliation(s)
- Na Li
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, People's Republic of China
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming 650500, People's Republic of China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Kunming 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 650500, People's Republic of China
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming 650500, People's Republic of China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Kunming 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 650500, People's Republic of China
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming 650500, People's Republic of China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Kunming 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 650500, People's Republic of China
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming 650500, People's Republic of China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Kunming 650500, People's Republic of China
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Ariaeenejad S, Motamedi E, Kavousi K, Ghasemitabesh R, Goudarzi R, Salekdeh GH, Zolfaghari B, Roy S. Enhancing the ethanol production by exploiting a novel metagenomic-derived bifunctional xylanase/β-glucosidase enzyme with improved β-glucosidase activity by a nanocellulose carrier. Front Microbiol 2023; 13:1056364. [PMID: 36687660 PMCID: PMC9845577 DOI: 10.3389/fmicb.2022.1056364] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/21/2022] [Indexed: 01/06/2023] Open
Abstract
Some enzymes can catalyze more than one chemical conversion for which they are physiologically specialized. This secondary function, which is called underground, promiscuous, metabolism, or cross activity, is recognized as a valuable feature and has received much attention for developing new catalytic functions in industrial applications. In this study, a novel bifunctional xylanase/β-glucosidase metagenomic-derived enzyme, PersiBGLXyn1, with underground β-glucosidase activity was mined by in-silico screening. Then, the corresponding gene was cloned, expressed and purified. The PersiBGLXyn1 improved the degradation efficiency of organic solvent pretreated coffee residue waste (CRW), and subsequently the production of bioethanol during a separate enzymatic hydrolysis and fermentation (SHF) process. After characterization, the enzyme was immobilized on a nanocellulose (NC) carrier generated from sugar beet pulp (SBP), which remarkably improved the underground activity of the enzyme up to four-fold at 80°C and up to two-fold at pH 4.0 compared to the free one. The immobilized PersiBGLXyn1 demonstrated 12 to 13-fold rise in half-life at 70 and 80°C for its underground activity. The amount of reducing sugar produced from enzymatic saccharification of the CRW was also enhanced from 12.97 g/l to 19.69 g/l by immobilization of the enzyme. Bioethanol production was 29.31 g/l for free enzyme after 72 h fermentation, while the immobilized PersiBGLXyn1 showed 51.47 g/l production titre. Overall, this study presented a cost-effective in-silico metagenomic approach to identify novel bifunctional xylanase/β-glucosidase enzyme with underground β-glucosidase activity. It also demonstrated the improved efficacy of the underground activities of the bifunctional enzyme as a promising alternative for fermentable sugars production and subsequent value-added products.
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Affiliation(s)
- Shohreh Ariaeenejad
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran,*Correspondence: Shohreh Ariaeenejad, ;
| | - Elaheh Motamedi
- Department of Nanotechnology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Kaveh Kavousi
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Rezvaneh Ghasemitabesh
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Razieh Goudarzi
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran,Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia,Ghasem Hosseini Salekdeh,
| | - Behrouz Zolfaghari
- Department of Integrated Art and Sciences, Faculty of Education, Waseda University, Tokyo, Japan
| | - Swapnoneel Roy
- School of Computing, University of North Florida, Jacksonville, FL, United States
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7
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Zhang Z, Zhang Z, Yu Z, Chen S, Zhang M, Zhang T, Luo X, Zhao J, Li Z. Simultaneous Improvement of Final Product-Tolerance and Thermostability of GH39 Xylosidase for Prebiotic Production by Directed Evolution. Foods 2022; 11:foods11193039. [PMID: 36230114 PMCID: PMC9563585 DOI: 10.3390/foods11193039] [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: 08/28/2022] [Revised: 09/16/2022] [Accepted: 09/27/2022] [Indexed: 11/29/2022] Open
Abstract
Xylosidases are widely used for the production of prebiotics and the transformation of natural active substances in the food industry. However, xylosidases with excellent thermostability and product tolerance are required for industrial applications. In this study, the thermostability and final-product tolerance of the previously reported robust xylosidase Xyl21 were further improved via directed evolution. The triple mutant variant Xyl21-A16 (K16R, L94I, and K262N) showed significantly enhanced xylose tolerance, ethanol tolerance, and thermostability with no apparent changes in the specific activity, optimum pH, and temperature compared with the wild type. Single site mutations suggested that variant Xyl21-A16 is the cumulative result of three mutated sites, which indicated that K16 and L94 play important roles in enzyme characteristics. Moreover, a comparison of the predicted protein structures of Xyl21 and its variant indicated that additional molecular interactions formed by K16R and K262N might directly improve the rigidity of the protein structure, therefore contributing to the increased thermostability and product tolerance. The variant Xyl21-A16 developed in this study has great application potential in the production of prebiotics, and also provides a useful reference for the future engineering of other xylosidases.
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Affiliation(s)
- Zirui Zhang
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zhengjie Zhang
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zhao Yu
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Shiheng Chen
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Mengwei Zhang
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Tongcun Zhang
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xuegang Luo
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Junqi Zhao
- School of Chemical and Biological Engineering, Qilu Institute of Technology, Jinan 250200, China
- Correspondence: (J.Z.); (Z.L.)
| | - Zhongyuan Li
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
- Correspondence: (J.Z.); (Z.L.)
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8
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Pan K, Liu Z, Zhang Z, Jin S, Yu Z, Liu T, Zhang T, Zhao J, Li Z. Improving the Specific Activity and Thermostability of Psychrophilic Xylosidase AX543 by Comparative Mutagenesis. Foods 2022; 11:foods11162463. [PMID: 36010463 PMCID: PMC9407119 DOI: 10.3390/foods11162463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/21/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
Improving the specific activity and thermostability of psychrophilic xylosidase is important for improving its enzymatic performance and promoting its industrial application. Herein, a psychrophilic xylosidase AX543 exhibited activity in the temperature range between 0 and 35 °C, with optimum activity at 20 °C, which is lower than that of other reported psychrophilic xylosidases. The thermostability, specific activity, and catalytic efficiency of the site-directed variants G110S, Q201R, and L2 were significantly enhanced, without affecting the optimal reaction temperature. Comparative protein structural analysis and molecular dynamics simulation indicated that these improvements might be the result of the increased hydrogen bonds interaction and improved structural rigidity. Furthermore, homologous module substitution with four segments demonstrated that the psychrophilic characteristics of AX543 are the results of the whole protein structure, and the C-terminal segment A4 appears to be more essential in determining psychrophilic characteristics, exhibiting potentiality to produce more psychrophilic xylosidases. This study provides valuable structural information on psychrophilic xylosidases and also offers attractive modification strategies to modify catalytic activity, thermostability, and optimal reaction temperature.
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Affiliation(s)
- Kungang Pan
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zhongqi Liu
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zhengjie Zhang
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Shanzheng Jin
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zhao Yu
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Tianhui Liu
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Tongcun Zhang
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Junqi Zhao
- School of Chemical and Biological Engineering, Qilu Institute of Technology, Jinan 250200, China
- Correspondence: (J.Z.); (Z.L.)
| | - Zhongyuan Li
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
- Correspondence: (J.Z.); (Z.L.)
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9
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Murguiondo C, Mestre A, Méndez-Líter JA, Nieto-Domínguez M, de Eugenio LI, Molina-Gutiérrez M, Martínez MJ, Prieto A. Enzymatic glycosylation of bioactive acceptors catalyzed by an immobilized fungal β-xylosidase and its multi-glycoligase variant. Int J Biol Macromol 2020; 167:245-254. [PMID: 33217466 DOI: 10.1016/j.ijbiomac.2020.11.069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 10/23/2022]
Abstract
A recombinant β-xylosidase (rBxTW1) from the ascomycete Talaromyces amestolkiae and a mutant derived from it, with mostly synthetic activity, have been immobilized as magnetic cross-linked enzyme aggregates (mCLEAs). The mCLEAs of rBxTW1 kept the excellent hydrolytic and O-transxylosylating activities of the free enzyme and had improved thermal and pH stability. The mCLEAs of the mutant also maintained or improved the catalytic properties of the soluble enzyme, synthetizing the O-xylosides of vanillin and (-)-epigallocatechin gallate, and the N- and S-xyloside of 3,5-dibromo-1,2,4-triazole and thiophenol, respectively. The mCLEAs were recyclable across 4 cycles of synthesis of the O-xylosides through a green and highly selective process. The magnetic properties of the scaffold used for immobilization may allow the easy recovery and reuse of the biocatalyst even from reactions containing insoluble lignocellulosic biomass.
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Affiliation(s)
- Carlos Murguiondo
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), c/Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Anna Mestre
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), c/Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Juan A Méndez-Líter
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), c/Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Manuel Nieto-Domínguez
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), c/Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Laura I de Eugenio
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), c/Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - María Molina-Gutiérrez
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), c/Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - María Jesús Martínez
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), c/Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Alicia Prieto
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), c/Ramiro de Maeztu 9, 28040 Madrid, Spain.
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10
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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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11
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Simultaneous Enhancement of Thermostability and Catalytic Activity of a Metagenome-Derived β-Glucosidase Using Directed Evolution for the Biosynthesis of Butyl Glucoside. Int J Mol Sci 2019; 20:ijms20246224. [PMID: 31835569 PMCID: PMC6940790 DOI: 10.3390/ijms20246224] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/08/2019] [Accepted: 12/08/2019] [Indexed: 01/16/2023] Open
Abstract
Butyl glucoside synthesis using bioenzymatic methods at high temperatures has gained increasing interest. Protein engineering using directed evolution of a metagenome-derived β-glucosidase of Bgl1D was performed to identify enzymes with improved activity and thermostability. An interesting mutant Bgl1D187 protein containing five amino acid substitutions (S28T, Y37H, D44E, R91G, and L115N), showed catalytic efficiency (kcat/Km of 561.72 mM−1 s−1) toward ρ-nitrophenyl-β-d-glucopyranoside (ρNPG) that increased by 23-fold, half-life of inactivation by 10-fold, and further retained transglycosidation activity at 50 °C as compared with the wild-type Bgl1D protein. Site-directed mutagenesis also revealed that Asp44 residue was essential to β-glucosidase activity of Bgl1D. This study improved our understanding of the key amino acids of the novel β-glucosidases and presented a raw material with enhanced catalytic activity and thermostability for the synthesis of butyl glucosides.
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12
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β-Xylosidases: Structural Diversity, Catalytic Mechanism, and Inhibition by Monosaccharides. Int J Mol Sci 2019; 20:ijms20225524. [PMID: 31698702 PMCID: PMC6887791 DOI: 10.3390/ijms20225524] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/02/2019] [Accepted: 11/04/2019] [Indexed: 12/20/2022] Open
Abstract
Xylan, a prominent component of cellulosic biomass, has a high potential for degradation into reducing sugars, and subsequent conversion into bioethanol. This process requires a range of xylanolytic enzymes. Among them, β-xylosidases are crucial, because they hydrolyze more glycosidic bonds than any of the other xylanolytic enzymes. They also enhance the efficiency of the process by degrading xylooligosaccharides, which are potent inhibitors of other hemicellulose-/xylan-converting enzymes. On the other hand, the β-xylosidase itself is also inhibited by monosaccharides that may be generated in high concentrations during the saccharification process. Structurally, β-xylosidases are diverse enzymes with different substrate specificities and enzyme mechanisms. Here, we review the structural diversity and catalytic mechanisms of β-xylosidases, and discuss their inhibition by monosaccharides.
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13
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Morlighem JÉRL, Radis-Baptista G. The Place for Enzymes and Biologically Active Peptides from Marine Organisms for Application in Industrial and Pharmaceutical Biotechnology. Curr Protein Pept Sci 2019; 20:334-355. [PMID: 30255754 DOI: 10.2174/1389203719666180926121722] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/10/2018] [Accepted: 09/15/2018] [Indexed: 01/07/2023]
Abstract
Since the beginning of written history, diverse texts have reported the use of enzymatic preparations in food processing and have described the medicinal properties of crude and fractionated venoms to treat various diseases and injuries. With the biochemical characterization of enzymes from distinct sources and bioactive polypeptides from animal venoms, the last sixty years have testified the advent of industrial enzymology and protein therapeutics, which are currently applicable in a wide variety of industrial processes, household products, and pharmaceuticals. Bioprospecting of novel biocatalysts and bioactive peptides is propelled by their unsurpassed properties that are applicable for current and future green industrial processes, biotechnology, and biomedicine. The demand for both novel enzymes with desired characteristics and novel peptides that lead to drug development, has experienced a steady increase in response to the expanding global market for industrial enzymes and peptidebased drugs. Moreover, although largely unexplored, oceans and marine realms, with their unique ecosystems inhabited by a large variety of species, including a considerable number of venomous animals, are recognized as untapped reservoirs of molecules and macromolecules (enzymes and bioactive venom-derived peptides) that can potentially be converted into highly valuable biopharmaceutical products. In this review, we have focused on enzymes and animal venom (poly)peptides that are presently in biotechnological use, and considering the state of prospection of marine resources, on the discovery of useful industrial biocatalysts and drug leads with novel structures exhibiting selectivity and improved performance.
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Affiliation(s)
- Jean-Étienne R L Morlighem
- Institute for Marine Sciences, Federal University of Ceara, Av da Abolicao 3207. Fortaleza/CE. 60165081, Brazil
| | - Gandhi Radis-Baptista
- Institute for Marine Sciences, Federal University of Ceara, Av da Abolicao 3207. Fortaleza/CE. 60165081, Brazil
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14
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Affiliation(s)
- Tomohiko Matsuzawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
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15
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Alves LDF, Meleiro LP, Silva RN, Westmann CA, Guazzaroni ME. Novel Ethanol- and 5-Hydroxymethyl Furfural-Stimulated β-Glucosidase Retrieved From a Brazilian Secondary Atlantic Forest Soil Metagenome. Front Microbiol 2018; 9:2556. [PMID: 30420843 PMCID: PMC6215845 DOI: 10.3389/fmicb.2018.02556] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 10/08/2018] [Indexed: 11/13/2022] Open
Abstract
Beta-glucosidases are key enzymes involved in lignocellulosic biomass degradation for bioethanol production, which complete the final step during cellulose hydrolysis by converting cellobiose into glucose. Currently, industry requires enzymes with improved catalytic performance or tolerance to process-specific parameters. In this sense, metagenomics has become a powerful tool for accessing and exploring the biochemical biodiversity present in different natural environments. Here, we report the identification of a novel β-glucosidase from metagenomic DNA isolated from soil samples enriched with decaying plant matter from a Secondary Atlantic Forest region. For this, we employed a functional screening approach using an optimized and synthetic broad host-range vector for library production. The novel β-glucosidase – named Lfa2 – displays three GH3-family conserved domains and conserved catalytic amino acids D283 and E487. The purified enzyme was most active in pH 5.5 and at 50°C, and showed hydrolytic activity toward several pNP synthetic substrates containing β-glucose, β-galactose, β-xylose, β-fucose, and α-arabinopyranose, as well as toward cellobiose. Lfa2 showed considerable glucose tolerance, exhibiting an IC50 of 300 mM glucose and 30% of remaining activity in 600 mM glucose. In addition, Lfa2 retained full or slightly enhanced activity in the presence of several metal ions. Further, β-glucosidase activity was increased by 1.7-fold in the presence of 10% (v/v) ethanol, a concentration that can be reached in conventional fermentation processes. Similarly, Lfa2 showed 1.7-fold enhanced activity at high concentrations of 5-hydroxymethyl furfural, one of the most important cellulase inhibitors in pretreated sugarcane bagasse hydrolysates. Moreover, the synergistic effect of Lfa2 on Bacillus subtilis GH5-CBM3 endoglucanase activity was demonstrated by the increased production of glucose (1.6-fold). Together, these results indicate that β-glucosidase Lfa2 is a promissory enzyme candidate for utilization in diverse industrial applications, such as cellulosic biomass degradation or flavor enhancement in winemaking and grape processing.
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Affiliation(s)
- Luana de Fátima Alves
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Luana Parras Meleiro
- Department of Chemistry, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Roberto N Silva
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Cauã Antunes Westmann
- Department of Cellular and Molecular Biology, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - María-Eugenia Guazzaroni
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
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16
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Sato M, Suda M, Okuma J, Kato T, Hirose Y, Nishimura A, Kondo Y, Shibata D. Isolation of highly thermostable β-xylosidases from a hot spring soil microbial community using a metagenomic approach. DNA Res 2018; 24:649-656. [PMID: 29106502 PMCID: PMC5726482 DOI: 10.1093/dnares/dsx032] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 07/31/2017] [Indexed: 11/24/2022] Open
Abstract
The DNA extracted from a high-temperature environment in which micro-organisms are living will be a good source for the isolation of thermostable enzymes. Using a metagenomic approach, we aimed to isolate thermostable β-xylosidases that will be exploited for biofuel production from lignocellulosic biomass. DNA samples obtained from the soil near a spout of a hot spring (70°C, pH7.2) were subjected to sequencing, which generated a total of 84.2 Gbp with 967,925 contigs of >500 bp in length. Similarity search for β-xylosidase in the contigs revealed the presence of 168 candidate sequences, each of which may have arisen from more than one gene. Individual genes were amplified by PCR using sequence-specific primers. The resultant DNA fragments were cloned and introduced into Escherichia coli BL21 Star(DE3). Consequently, 269 proteins were successfully expressed in the E. coli cells and then examined for β-xylosidase activity. A total of 82 proteins exhibited β-xylosidase activity at 50°C, six of which retained the activity even at 90°C. Out of the six, three proteins were originated from a single candidate sequence, AR19M-311. An amino acid sequence comparison suggested the amino acid residues that appeared to be crucial for thermal stability of the enzymes.
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Affiliation(s)
- Masaru Sato
- Department of Biotechnology Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Migiwa Suda
- Department of Biotechnology Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Jiro Okuma
- Honda Research Institute Japan Co., Ltd., Wako, Saitama 351-0188, Japan
| | - Tomohiko Kato
- Department of Biotechnology Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Yoshitsugu Hirose
- Honda Research Institute Japan Co., Ltd., Wako, Saitama 351-0188, Japan
| | - Asuka Nishimura
- Honda Research Institute Japan Co., Ltd., Wako, Saitama 351-0188, Japan
| | - Yasuhiko Kondo
- Honda Research Institute Japan Co., Ltd., Wako, Saitama 351-0188, Japan
| | - Daisuke Shibata
- Department of Biotechnology Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
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17
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Singhania RR, Patel AK, Pandey A, Ganansounou E. Genetic modification: A tool for enhancing beta-glucosidase production for biofuel application. BIORESOURCE TECHNOLOGY 2017; 245:1352-1361. [PMID: 28596076 DOI: 10.1016/j.biortech.2017.05.126] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/17/2017] [Accepted: 05/19/2017] [Indexed: 05/25/2023]
Abstract
Beta-glucosidase (BGL) is a rate-limiting enzyme for cellulose hydrolysis as it acts in the final step of lignocellulosic biomass conversion to convert cellobiose into glucose, the final end product. Most of the fungal strains used for cellulase production are deficient in BGL hence BGL is supplemented into cellulases to have an efficient biomass conversion. Genetic engineering has enabled strain modification to produce BGL optimally with desired properties to be employed for biofuel applications. It has been cloned either directly into the host strains lacking BGL or into another expression system, to be overexpressed so as to be blended into BGL deficient cellulases. In this article, role of genetic engineering to overcome BGL limitations in the cellulase cocktail and its significance for biofuel applications has been critically reviewed.
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Affiliation(s)
- Reeta Rani Singhania
- DBT-IOC Advanced Bio-Energy Research Centre, Indian Oil Corporation; R&D Centre, Sector-13, Faridabad 121007, India
| | - Anil Kumar Patel
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu 96822, HI, United States.
| | - Ashok Pandey
- Center of Innovative and Applied Bioprocessing, Sector 81, Knowledge City PO Manauli, SAS Nagar, Mohali 140306, Punjab, India
| | - Edgard Ganansounou
- Bioenergy and Energy Planning Research Group, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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18
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Purification and characterization of novel bi-functional GH3 family β-xylosidase/β-glucosidase from Aspergillus niger ADH-11. Int J Biol Macromol 2017; 109:1260-1269. [PMID: 29174354 DOI: 10.1016/j.ijbiomac.2017.11.132] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 11/18/2017] [Accepted: 11/20/2017] [Indexed: 11/22/2022]
Abstract
β-Xylosidase plays an important role in xylan degradation by relieving the end product inhibition of endo-xylanase caused by xylo-oligosaccharides. β-Xylosidase has a wide range of applications in food, feed, paper and pulp, pharmaceutical industries and in bioconversion of lignocellulosic biomass. Hence, in the present study focused on purification, biochemical characterization and partial sequencing of purified β-xylosidase from xylanolytic strain Aspergillus niger ADH-11. Acetone precipitation followed by GPC using Sephacryl S-200 yielded 20.59-fold purified β-xylosidase with 58.30% recovery. SDS-PAGE analysis of purified β-xylosidase relieved a monomeric subunit with a molecular weight 120.48kDa. Kinetic parameters of purified β-xylosidase viz Km, Vmax, Kcat and catalytic efficiency were assessed. Purified β-xylosidase was additionally active on p-nitrophenyl-β-d-glucopyranoside substrate also. Moreover, peptide mass fingerprinting analysis support our biochemical studies and showed that the purified protein is a novel β-xylosidase with β-glucosidase activity and belongs to the bi-functional GH3 superfamily. Besides, tolerance of purified β-xylosidase towards glucose and xylose was also assessed.
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19
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Effect of Feedstock Concentration on Biogas Production by Inoculating Rumen Microorganisms in Biomass Solid Waste. Appl Biochem Biotechnol 2017; 184:1219-1231. [PMID: 28983796 DOI: 10.1007/s12010-017-2615-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 09/20/2017] [Indexed: 01/16/2023]
Abstract
A methane production system with continuous stirred-tank reactor, rumen liquid as inoculate microorganisms, and paper mill excess sludge (PES) as feedstock was studied. The work mainly focused on revealing the effect of feedstock concentration on the biogas production, which was seldom reported previously for the current system. The optimal fermentation conditions were found as follows: pH = 7, T = 39 ± 1 °C, sludge retention time is 20 days, sludge with total solids (TS) are 1, 2, 3.5, 5, 10, and 13% in weight. Daily gas yields were measured, and biogas compositions were analyzed by gas chromatograph. Under such conditions, the optimum input TS was 10 wt%, and the biogas yield and volume gas productivity were 280.2 mL/g·TS and 1188.4 mL L-1·d-1, respectively. The proportions of CH4 and CO2 in the biogas were 65.1 and 34.2%. The CH4 yield reached 182.7 mL/g VS (volatile suspended solid), which was higher than previously reported values. The findings of this work have a significant effect on promoting the application of digesting PES by rumen microorganisms and further identified the technical parameter.
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20
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Zang X, Liu M, Wang H, Fan Y, Zhang H, Liu J, Xing E, Xu X, Li H. The distribution of active β-glucosidase-producing microbial communities in composting. Can J Microbiol 2017; 63:998-1008. [PMID: 28892642 DOI: 10.1139/cjm-2017-0368] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The composting ecosystem is a suitable source for the discovery of novel microorganisms and secondary metabolites. Cellulose degradation is an important part of the global carbon cycle, and β-glucosidases complete the final step of cellulose hydrolysis by converting cellobiose to glucose. This work analyzes the succession of β-glucosidase-producing microbial communities that persist throughout cattle manure - rice straw composting, and evaluates their metabolic activities and community advantage during the various phases of composting. Fungal and bacterial β-glucosidase genes belonging to glycoside hydrolase families 1 and 3 (GH1 and GH3) amplified from DNA were classified and gene abundance levels were analyzed. The major reservoirs of β-glucosidase genes were the fungal phylum Ascomycota and the bacterial phyla Firmicutes, Actinobacteria, Proteobacteria, and Deinococcus-Thermus. This indicates that a diverse microbial community utilizes cellobiose. The succession of dominant bacteria was also detected during composting. Firmicutes was the dominant bacteria in the thermophilic phase of composting; there was a shift to Actinomycetes in the maturing stage. Proteobacteria accounted for the highest proportions during the heating and thermophilic phases of composting. By contrast, the fungal phylum Ascomycota was a minor microbial community constituent in thermophilic phase of composting. Combined with the analysis of the temperature, cellulose degradation rate and the carboxymethyl cellulase and β-glucosidase activities showed that the bacterial GH1 family β-glucosidase genes make greater contribution in cellulose degradation at the later thermophilic stage of composting. In summary, even GH1 bacteria families β-glucosidase genes showing low abundance in DNA may be functionally important in the later thermophilic phase of composting. The results indicate that a complex community of bacteria and fungi expresses β-glucosidases in compost. Several β-glucosidase-producing bacteria and fungi identified in this study may represent potential indicators of composting in cellulose degradation.
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Affiliation(s)
- Xiangyun Zang
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Meiting Liu
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.,College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Han Wang
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.,College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Yihong Fan
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.,College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Haichang Zhang
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.,College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Jiawen Liu
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.,College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Enlu Xing
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.,College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Xiuhong Xu
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.,College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Hongtao Li
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.,College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China
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21
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Suwan E, Arthornthurasuk S, Kongsaeree PT. A metagenomic approach to discover a novel β-glucosidase from bovine rumens. PURE APPL CHEM 2017. [DOI: 10.1515/pac-2016-0924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstractβ-Glucosidases play an important role in biomass degradation as they hydrolyze cellobiose to glucose in a final step of cellulolysis. In particular, ruminant animals rely onβ-glucosidases from rumen microorganisms for conversion of plant cellulosic materials into glucose. In this study, we are interested in characterization of a novelβ-glucosidase from rumen microorganisms. However, most rumen microorganisms are obligate anaerobes, which require special cultivation conditions. Presently, the metagenomic techniques, which enable isolation and characterization of microbial genes directly from environmental samples, have been applied to overcome these problems. In this study, the sequence-based screening approach was successfully applied to identify a novelβ-glucosidase gene,Br2, from a bovine rumen metagenomic sample. A 1338-bp complete coding sequence ofBr2encodes a 51-kDa GH1β-glucosidase of 445 amino acid residues with 59% sequence identity to aβ-glucosidase fromCellulosilyticum ruminicolaJCM 14822. The recombinantly expressed Br2 exhibited an optimal activity at pH 6.5 and 40°C, reflecting its rumen bacterial origin, and relatively higher catalytic efficiencies toward glucoside and fucoside substrates than other glycosides, similar to many previously reported bacterialβ-glucosidases. Our sequence-based screening approach can be applied to identify other genes of interest from environmental samples.
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22
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Wang L, Chen Y. Efficient Biotransformation of Astragaloside IV to Cycloastragenol by Bacillus sp. LG-502. Appl Biochem Biotechnol 2017; 183:1488-1502. [DOI: 10.1007/s12010-017-2517-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 05/19/2017] [Indexed: 10/19/2022]
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Enhanced Production of Gypenoside LXXV Using a Novel Ginsenoside-Transforming β-Glucosidase from Ginseng-Cultivating Soil Bacteria and Its Anti-Cancer Property. Molecules 2017; 22:molecules22050844. [PMID: 28534845 PMCID: PMC6153937 DOI: 10.3390/molecules22050844] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 05/07/2017] [Accepted: 05/12/2017] [Indexed: 11/16/2022] Open
Abstract
Minor ginsenosides, such as compound K, Rg3(S), which can be produced by deglycosylation of ginsenosides Rb1, showed strong anti-cancer effects. However, the anticancer effects of gypenoside LXXV, which is one of the deglycosylated shapes of ginsenoside Rb1, is still unknown due to the rarity of its content in plants. Here, we cloned and characterized a novel ginsenoside-transforming β-glucosidase (BglG167b) derived from Microbacterium sp. Gsoil 167 which can efficiently hydrolyze gypenoside XVII into gypenoside LXXV, and applied it to the production of gypenoside LXXV at the gram-scale with high specificity. In addition, the anti-cancer activity of gypenoside LXXV was investigated against three cancer cell lines (HeLa, B16, and MDA-MB231) in vitro. Gypenoside LXXV significantly reduced cell viability, displaying an enhanced anti-cancer effect compared to gypenoside XVII and Rb1. Taken together, this enzymatic method would be useful in the preparation of gypenoside LXXV for the functional food and pharmaceutical industries.
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Wallace RJ, Snelling TJ, McCartney CA, Tapio I, Strozzi F. Application of meta-omics techniques to understand greenhouse gas emissions originating from ruminal metabolism. Genet Sel Evol 2017; 49:9. [PMID: 28093073 PMCID: PMC5240273 DOI: 10.1186/s12711-017-0285-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 01/06/2017] [Indexed: 12/13/2022] Open
Abstract
Methane emissions from ruminal fermentation contribute significantly to total anthropological greenhouse gas (GHG) emissions. New meta-omics technologies are beginning to revolutionise our understanding of the rumen microbial community structure, metabolic potential and metabolic activity. Here we explore these developments in relation to GHG emissions. Microbial rumen community analyses based on small subunit ribosomal RNA sequence analysis are not yet predictive of methane emissions from individual animals or treatments. Few metagenomics studies have been directly related to GHG emissions. In these studies, the main genes that differed in abundance between high and low methane emitters included archaeal genes involved in methanogenesis, with others that were not apparently related to methane metabolism. Unlike the taxonomic analysis up to now, the gene sets from metagenomes may have predictive value. Furthermore, metagenomic analysis predicts metabolic function better than only a taxonomic description, because different taxa share genes with the same function. Metatranscriptomics, the study of mRNA transcript abundance, should help to understand the dynamic of microbial activity rather than the gene abundance; to date, only one study has related the expression levels of methanogenic genes to methane emissions, where gene abundance failed to do so. Metaproteomics describes the proteins present in the ecosystem, and is therefore arguably a better indication of microbial metabolism. Both two-dimensional polyacrylamide gel electrophoresis and shotgun peptide sequencing methods have been used for ruminal analysis. In our unpublished studies, both methods showed an abundance of archaeal methanogenic enzymes, but neither was able to discriminate high and low emitters. Metabolomics can take several forms that appear to have predictive value for methane emissions; ruminal metabolites, milk fatty acid profiles, faecal long-chain alcohols and urinary metabolites have all shown promising results. Rumen microbial amino acid metabolism lies at the root of excessive nitrogen emissions from ruminants, yet only indirect inferences for nitrogen emissions can be drawn from meta-omics studies published so far. Annotation of meta-omics data depends on databases that are generally weak in rumen microbial entries. The Hungate 1000 project and Global Rumen Census initiatives are therefore essential to improve the interpretation of sequence/metabolic information.
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Affiliation(s)
- Robert J Wallace
- Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, AB16 5BD, UK.
| | - Timothy J Snelling
- Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, AB16 5BD, UK
| | - Christine A McCartney
- Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, AB16 5BD, UK
| | - Ilma Tapio
- Green Technology, Natural Resources Institute Finland, Jokioinen, Finland
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25
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Mhetras N, Liddell S, Gokhale D. Purification and characterization of an extracellular β-xylosidase from Pseudozyma hubeiensis NCIM 3574 (PhXyl), an unexplored yeast. AMB Express 2016; 6:73. [PMID: 27637943 PMCID: PMC5023640 DOI: 10.1186/s13568-016-0243-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 09/07/2016] [Indexed: 11/22/2022] Open
Abstract
This paper reports on the production of β-xylosidase from an unexplored yeast, Pseudozyma hubeinsis. The expression of this enzyme could be induced by beech wood xylan when the yeast was grown at 27 °C. The enzyme was purified to homogeneity as a glycoprotein with 23 % glycosylation. The purification protocol involved ammonium sulphate precipitation, QAE-Sephadex A50 ion exchange chromatography and sephacryl-200 column chromatography which resulted in 8.3-fold purification with 53.12 % final recovery. The purified enzyme showed prominent single band on SDS-PAGE. It is a monomeric protein of 110 kDa molecular weight confirmed by SDS-PAGE followed by MALDI-TOF mass spectrometry (112.3 kDa). The enzyme was optimally active at 60 °C and pH 4.5 and stable at pH range (4–9) and at 50 °C for 4 h. Chemical modification studies revealed that active site of the purified enzyme comprised of carboxyl, tyrosine and tryptophan residues. The carboxyl residue is involved in catalysis and tryptophan residue is solely involved in substrate binding. The best match from the search of the NCBInr database was with gi|808364558 glycoside hydrolase of Pseudozyma hubeiensis SY62 with 26 % sequence coverage confirming that it is a glycoside hydrolase/beta-glucosidase. From the search of customized SWISSPROT database, it was revealed that SWISSPROT does not contain any entries that are similar to the purified enzyme.
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Nieto-Domínguez M, Prieto A, Fernández de Toro B, Cañada FJ, Barriuso J, Armstrong Z, Withers SG, de Eugenio LI, Martínez MJ. Enzymatic fine-tuning for 2-(6-hydroxynaphthyl) β-D-xylopyranoside synthesis catalyzed by the recombinant β-xylosidase BxTW1 from Talaromyces amestolkiae. Microb Cell Fact 2016; 15:171. [PMID: 27716291 PMCID: PMC5050587 DOI: 10.1186/s12934-016-0568-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 09/23/2016] [Indexed: 02/02/2023] Open
Abstract
Background Glycosides are compounds displaying crucial biological roles and plenty of applications. Traditionally, these molecules have been chemically obtained, but its efficient production is limited by the lack of regio- and stereo-selectivity of the chemical synthesis. As an interesting alternative, glycosidases are able to catalyze the formation of glycosides in a process considered green and highly selective. In this study, we report the expression and characterization of a fungal β-xylosidase in Pichia pastoris. The transglycosylation potential of the enzyme was evaluated and its applicability in the synthesis of a selective anti-proliferative compound demonstrated. Results The β-xylosidase BxTW1 from the ascomycete fungus Talaromyces amestolkiae was cloned and expressed in Pichia pastoris GS115. The yeast secreted 8 U/mL of β-xylosidase that was purified by a single step of cation-exchange chromatography. rBxTW1 in its active form is an N-glycosylated dimer of about 200 kDa. The enzyme was biochemically characterized displaying a Km and kcat against p-nitrophenyl-β-d-xylopyranoside of 0.20 mM and 69.3 s−1 respectively, and its maximal activity was achieved at pH 3 and 60 °C. The glycan component of rBxTW1 was also analyzed in order to interpret the observed loss of stability and maximum velocity when compared with the native enzyme. A rapid screening of aglycone specificity was performed, revealing a remarkable high number of potential transxylosylation acceptors for rBxTW1. Based on this analysis, the enzyme was successfully tested in the synthesis of 2-(6-hydroxynaphthyl) β-d-xylopyranoside, a well-known selective anti-proliferative compound, enzymatically obtained for the first time. The application of response surface methodology, following a Box-Behnken design, enhanced this production by eightfold, fitting the reaction conditions into a multiparametric model. The naphthyl derivative was purified and its identity confirmed by NMR. Conclusions A β-xylosidase from T. amestolkiae was produced in P. pastoris and purified. The final yields were much higher than those attained for the native protein, although some loss of stability and maximum velocity was observed. rBxTW1 displayed remarkable acceptor versatility in transxylosylation, catalyzing the synthesis of a selective antiproliferative compound, 2-(6-hydroxynaphthyl) β-d-xylopyranoside. These results evidence the interest of rBxTW1 for transxylosylation of relevant products with biotechnological interest. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0568-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Manuel Nieto-Domínguez
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Alicia Prieto
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Beatriz Fernández de Toro
- Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Francisco Javier Cañada
- Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Jorge Barriuso
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Zach Armstrong
- Department of Chemistry, Centre for High-Throughput Biology, University of British Columbia, Vancouver, Canada
| | - Stephen G Withers
- Department of Chemistry, Centre for High-Throughput Biology, University of British Columbia, Vancouver, Canada
| | - Laura I de Eugenio
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain.
| | - María Jesús Martínez
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain.
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Matsuzawa T, Kimura N, Suenaga H, Yaoi K. Screening, identification, and characterization of α-xylosidase from a soil metagenome. J Biosci Bioeng 2016; 122:393-9. [PMID: 27074950 DOI: 10.1016/j.jbiosc.2016.03.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Revised: 03/04/2016] [Accepted: 03/17/2016] [Indexed: 10/22/2022]
Abstract
A novel α-xylosidase, MeXyl31, was isolated and characterized from a soil metagenomic library. The amino acid sequence of MeXyl31 showed a slight homology with other characterized α-xylosidases. The optimal pH and temperature of recombinant MeXyl31 were pH 5.5 and 45°C, respectively. Recombinant MeXyl31 had a higher α-xylosidase activity toward pNP α-d-xylopyranoside than pNP α-d-glucopyranoside, isoprimeverose, and other xyloglucan oligosaccharides. The kcat/Km value toward pNP α-d-xylopyranoside was about 750-fold higher than that of isoprimeverose. MeXyl31 activity was strongly inactivated in the presence of zinc and copper ions. MeXyl31 is the first α-xylosidase isolated from the metagenome and, relative to other xyloglucan oligosaccharides, shows higher activity toward pNP α-d-xylopyranoside.
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Affiliation(s)
- Tomohiko Matsuzawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Nobutada Kimura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Hikaru Suenaga
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Katsuro Yaoi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
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Fungal Biotechnology for Industrial Enzyme Production: Focus on (Hemi)cellulase Production Strategies, Advances and Challenges. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Contemporary molecular tools in microbial ecology and their application to advancing biotechnology. Biotechnol Adv 2015; 33:1755-73. [DOI: 10.1016/j.biotechadv.2015.09.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 09/19/2015] [Accepted: 09/20/2015] [Indexed: 12/30/2022]
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Wallace RJ, Rooke JA, McKain N, Duthie CA, Hyslop JJ, Ross DW, Waterhouse A, Watson M, Roehe R. The rumen microbial metagenome associated with high methane production in cattle. BMC Genomics 2015; 16:839. [PMID: 26494241 PMCID: PMC4619255 DOI: 10.1186/s12864-015-2032-0] [Citation(s) in RCA: 218] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 10/08/2015] [Indexed: 02/01/2023] Open
Abstract
Background Methane represents 16 % of total anthropogenic greenhouse gas emissions. It has been estimated that ruminant livestock produce ca. 29 % of this methane. As individual animals produce consistently different quantities of methane, understanding the basis for these differences may lead to new opportunities for mitigating ruminal methane emissions. Metagenomics is a powerful new tool for understanding the composition and function of complex microbial communities. Here we have applied metagenomics to the rumen microbial community to identify differences in the microbiota and metagenome that lead to high- and low-methane-emitting cattle phenotypes. Methods Four pairs of beef cattle were selected for extreme high and low methane emissions from 72 animals, matched for breed (Aberdeen-Angus or Limousin cross) and diet (high or medium concentrate). Community analysis was carried out by qPCR of 16S and 18S rRNA genes and by alignment of Illumina HiSeq reads to the GREENGENES database. Total genomic reads were aligned to the KEGG genes databasefor functional analysis. Results Deep sequencing produced on average 11.3 Gb per sample. 16S rRNA gene abundances indicated that archaea, predominantly Methanobrevibacter, were 2.5× more numerous (P = 0.026) in high emitters, whereas among bacteria Proteobacteria, predominantly Succinivibrionaceae, were 4-fold less abundant (2.7 vs. 11.2 %; P = 0.002). KEGG analysis revealed that archaeal genes leading directly or indirectly to methane production were 2.7-fold more abundant in high emitters. Genes less abundant in high emitters included acetate kinase, electron transport complex proteins RnfC and RnfD and glucose-6-phosphate isomerase. Sequence data were assembled de novo and over 1.5 million proteins were annotated on the subsequent metagenome scaffolds. Less than half of the predicted genes matched matched a domain within Pfam. Amongst 2774 identified proteins of the 20 KEGG orthologues that correlated with methane emissions, only 16 showed 100 % identity with a publicly available protein sequence. Conclusions The abundance of archaeal genes in ruminal digesta correlated strongly with differing methane emissions from individual animals, a finding useful for genetic screening purposes. Lower emissions were accompanied by higher Succinovibrionaceae abundance and changes in acetate and hydrogen production leading to less methanogenesis, as similarly postulated for Australian macropods. Large numbers of predicted protein sequences differed between high- and low-methane-emitting cattle. Ninety-nine percent were unknown, indicating a fertile area for future exploitation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2032-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- R John Wallace
- Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen, AB21 9SB, UK.
| | | | - Nest McKain
- Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen, AB21 9SB, UK.
| | | | | | | | | | - Mick Watson
- Edinburgh Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.
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Novel pH-Stable Glycoside Hydrolase Family 3 β-Xylosidase from Talaromyces amestolkiae: an Enzyme Displaying Regioselective Transxylosylation. Appl Environ Microbiol 2015; 81:6380-92. [PMID: 26150469 DOI: 10.1128/aem.01744-15] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 07/01/2015] [Indexed: 11/20/2022] Open
Abstract
This paper reports on a novel β-xylosidase from the hemicellulolytic fungus Talaromyces amestolkiae. The expression of this enzyme, called BxTW1, could be induced by beechwood xylan and was purified as a glycoprotein from culture supernatants. We characterized the gene encoding this enzyme as an intronless gene belonging to the glycoside hydrolase gene family 3 (GH3). BxTW1 exhibited transxylosylation activity in a regioselective way. This feature would allow the synthesis of oligosaccharides or other compounds not available from natural sources, such as alkyl glycosides displaying antimicrobial or surfactant properties. Regioselective transxylosylation, an uncommon combination, makes the synthesis reproducible, which is desirable for its potential industrial application. BxTW1 showed high pH stability and Cu(2+) tolerance. The enzyme displayed a pI of 7.6, a molecular mass around 200 kDa in its active dimeric form, and Km and Vmax values of 0.17 mM and 52.0 U/mg, respectively, using commercial p-nitrophenyl-β-d-xylopyranoside as the substrate. The catalytic efficiencies for the hydrolysis of xylooligosaccharides were remarkably high, making it suitable for different applications in food and bioenergy industries.
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Wang M, Lai GL, Nie Y, Geng S, Liu L, Zhu B, Shi Z, Wu XL. Synergistic function of four novel thermostable glycoside hydrolases from a long-term enriched thermophilic methanogenic digester. Front Microbiol 2015; 6:509. [PMID: 26052323 PMCID: PMC4441150 DOI: 10.3389/fmicb.2015.00509] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 05/08/2015] [Indexed: 12/25/2022] Open
Abstract
In biofuel production from lignocellulose, low thermostability and product inhibition strongly restrict the enzyme activities and production process. Application of multiple thermostable glycoside hydrolases, forming an enzyme "cocktail", can result in a synergistic action and therefore improve production efficiency and reduce operational costs. Therefore, increasing enzyme thermostabilities and compatibility are important for the biofuel industry. In this study, we reported the screening, cloning and biochemical characterization of four novel thermostable lignocellulose hydrolases from a metagenomic library of a long-term dry thermophilic methanogenic digester community, which were highly compatible with optimal conditions and specific activities. The optimal temperatures of the four enzymes, β-xylosidase, xylanase, β-glucosidase, and cellulase ranged from 60 to 75°C, and over 80% residual activities were observed after 2 h incubation at 50°C. Mixtures of these hydrolases retained high residual synergistic activities after incubation with cellulose, xylan, and steam-exploded corncob at 50°C for 72 h. In addition, about 55% dry weight of steam-exploded corncob was hydrolyzed to glucose and xylose by the synergistic action of the four enzymes at 50°C for 48 h. This work suggested that since different enzymes from a same ecosystem could be more compatible, screening enzymes from a long-term enriching community could be a favorable strategy.
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Affiliation(s)
- Meng Wang
- School of Biotechnology, Jiangnan University Wuxi, China ; Department of Energy and Resources Engineering, College of Engineering, Peking University Beijing, China
| | - Guo-Li Lai
- Department of Energy and Resources Engineering, College of Engineering, Peking University Beijing, China ; Institute of Engineering (Baotou), College of Engineering, Peking University Baotou, China
| | - Yong Nie
- Department of Energy and Resources Engineering, College of Engineering, Peking University Beijing, China ; Institute of Engineering (Baotou), College of Engineering, Peking University Baotou, China
| | - Shuang Geng
- Department of Energy and Resources Engineering, College of Engineering, Peking University Beijing, China
| | - Liming Liu
- School of Biotechnology, Jiangnan University Wuxi, China
| | - Baoli Zhu
- Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - Zhongping Shi
- School of Biotechnology, Jiangnan University Wuxi, China
| | - Xiao-Lei Wu
- Department of Energy and Resources Engineering, College of Engineering, Peking University Beijing, China ; Institute of Engineering (Baotou), College of Engineering, Peking University Baotou, China
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Matsuzawa T, Kaneko S, Yaoi K. Screening, identification, and characterization of a GH43 family β-xylosidase/α-arabinofuranosidase from a compost microbial metagenome. Appl Microbiol Biotechnol 2015; 99:8943-54. [DOI: 10.1007/s00253-015-6647-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 04/09/2015] [Accepted: 04/19/2015] [Indexed: 01/09/2023]
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Matsumoto T, Shimada S, Hata Y, Tanaka T, Kondo A. Multi-functional glycoside hydrolase: Blon_0625 from Bifidobacterium longum subsp. infantis ATCC 15697. Enzyme Microb Technol 2014; 68:10-4. [PMID: 25435500 DOI: 10.1016/j.enzmictec.2014.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 10/14/2014] [Accepted: 10/14/2014] [Indexed: 10/24/2022]
Abstract
We here describe a unique β-D-glucosidase (BGL; Blon_0625) derived from Bifidobacterium longum subsp. infantis ATCC 15697. The Blon_0625 gene was expressed by recombinant Escherichia coli. Purified recombinant Blon_0625 retains hydrolyzing activity against both p-nitrophenyl-β-D-glucopyranoside (pNPG; 17.3±0.24Umg(-1)) and p-nitrophenyl-β-D-xylopyranoside (pNPX; 16.7±0.32Umg(-1)) at pH 6.0, 30°C. To best of our knowledge, no previously described BGL retains the same level of both pNPGase and pNPXase activity. Furthermore, Blon_0625 also retains the activity against 4-nitrophenyl-α-l-arabinofranoside (pNPAf; 5.6±0.09Umg(-1)). In addition, the results of the degradation of phosphoric acid swollen cellulose (PASC) or xylan using endoglucanase from Thermobifida fusca YX (Tfu_0901) or xylanase from Kitasatospora setae KM-6054 (KSE_59480) show that Blon_0625 acts as a BGL and as a β-D-xylosidase (XYL) for hydrolyzing oligosaccharides. These results clearly indicate that Blon_0625 is a multi-functional glycoside hydrolase which retains the activity of BGL, XYL, and also α-l-arabinofuranosidase. Therefore, the utilization of multi-functional Blon_0625 may contribute to facilitating the efficient degradation of lignocellulosic materials and help enhance bioconversion processes.
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Affiliation(s)
- Takuya Matsumoto
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan
| | - Shota Shimada
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan
| | - Yuto Hata
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan
| | - Tsutomu Tanaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan.
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan
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Li Y, Liu N, Yang H, Zhao F, Yu Y, Tian Y, Lu X. Cloning and characterization of a new β-glucosidase from a metagenomic library of rumen of cattle feeding with Miscanthus sinensis. BMC Biotechnol 2014; 14:85. [PMID: 25274487 PMCID: PMC4287584 DOI: 10.1186/1472-6750-14-85] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 09/24/2014] [Indexed: 11/22/2022] Open
Abstract
Background The study on the second generation bio-fuel is a hot area of current research of renewable energy. Among series of key points in this area, the role of β-glucosidase in the degradation of intermediate gluco-oligosaccharides limits the rate of the complete saccharification of lignocellulose. Results In this study, a new β-glucosidase gene, unglu135B12, which was isolated from a metagenomic library of rumen of cattle feeding with Miscanthus sinensis by the function-based screening, encodes a 779 amino acid polypeptide that contains a catalytic domain belonging to glycoside hydrolase family 3 (GH3). It was recombinantly expressed, purified and biochemically characterized. The recombinant β-glucosidase, unglu135B12, displayed optimum enzymatic activity at pH 5.0 at 38°C, and showed the highest specific activity of 2.5 × 103 U/mg under this optimal condition to p-nitrophenyl-β-D-glucopyranoside (pNPG), and its Km and Vmax values were 0.309 mmol/L and 7.292 μmol/min, respectively. In addition, the presence of Ca2+, K+, Na+ slightly improved β-glucosidase activity of unglu135B12 by about 5%, while about 10 ~ 85% loss of β-glucosidase activity was induced by addition of Mn2+, Fe3+, Zn2+, Cu2+. Interestingly, unglu135B12 was activated by glucose at the concentration lower than 40 mM. Conclusions Our findings indicate that unglu135B12 is a new β-glucosidase derived from rumen of cattle, and it might be a potent candidate for saccharification of lignocellulose in industrial application. Electronic supplementary material The online version of this article (doi:10.1186/1472-6750-14-85) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Yun Tian
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China.
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Banka AL, Guralp SA, Gulari E. Secretory expression and characterization of two hemicellulases, xylanase, and β-xylosidase, isolated from Bacillus subtilis M015. Appl Biochem Biotechnol 2014; 174:2702-10. [PMID: 25224913 PMCID: PMC4237932 DOI: 10.1007/s12010-014-1219-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 09/02/2014] [Indexed: 11/23/2022]
Abstract
Microbial hydrolysis of lignocellulosic biomass is becoming increasingly important for the production of renewable biofuels to address global energy concerns. Hemicellulose is the second most abundant lignocellulosic biopolymer consisting of mostly xylan and other polysaccharides. A variety of enzymes is involved in complete hydrolysis of xylan into its constituent sugars for subsequent biofuel fermentation. Two enzymes, endo-β-xylanase and β-xylosidase, are particularly important in hydrolyzing the xylan backbone into xylooligosaccharides and individual xylose units. In this study, we describe the cloning, expression, and characterization of xylanase and β-xylosidase isolated from Bacillus subtilis M015 in Escherichia coli. The genes were identified to encode a 213 amino acid protein for xylanase (glycoside hydrolase (GH) family 11) and a 533 amino acid protein for β-xylosidase (GH family 43). Recombinant enzymes were produced by periplasmic-leaky E. coli JE5505 and therefore secreted into the supernatant during growth. Temperature and pH optima were determined to be 50 °C and 5.5–6 for xylanase and 35 °C and 7.0–7.5 for β-xylosidase using beech wood xylan and p-nitrophenyl-β-D-xylopyranoside as the substrates, respectively. We have also investigated the synergy of two enzymes on xylan hydrolysis and observed 90 % increase in total sugar release (composed of xylose, xylobiose, xylotriose, and xylotetraose) for xylanase/β-xylosidase combination as opposed to xylanase alone.
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Affiliation(s)
- Alison L Banka
- Department of Chemical Engineering, University of Michigan, 3074 H.H.Dow Buil., 2300 Hayward St, Ann Arbor, MI, 48109, USA
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Bergmann JC, Costa OYA, Gladden JM, Singer S, Heins R, D'haeseleer P, Simmons BA, Quirino BF. Discovery of two novel β-glucosidases from an Amazon soil metagenomic library. FEMS Microbiol Lett 2013; 351:147-55. [PMID: 24236615 DOI: 10.1111/1574-6968.12332] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 11/07/2013] [Accepted: 11/07/2013] [Indexed: 11/30/2022] Open
Abstract
An Amazon soil microbial community metagenomic fosmid library was functionally screened for β-glucosidase activity. Contig analysis of positive clones revealed the presence of two ORFs encoding novel β-glucosidases, AmBGL17 and AmBGL18, from the GH3 and GH1 families, respectively. Both AmBGL17 and AmBGL18 were functionally identified as β-glucosidases. The enzymatic activity of AmBGL17 was further characterized. AmBGL17 was tested with different substrates and showed highest activity on pNPβG substrate with an optimum temperature of 45 °C and an optimum pH of 6. AmBGL17 showed a Vmax of 116 mM s(-1) and Km of 0.30 ± 0.017 mM. This is the first report of β-glucosidases from an Amazon soil microbial community using a metagenomic approach.
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Affiliation(s)
- Jessica C Bergmann
- Genomic Sciences and Biotechnology Program, Universidade Católica de Brasília, Brasília, Brazil
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Gruninger RJ, Gong X, Forster RJ, McAllister TA. Biochemical and kinetic characterization of the multifunctional β-glucosidase/β-xylosidase/α-arabinosidase, Bgxa1. Appl Microbiol Biotechnol 2013; 98:3003-12. [DOI: 10.1007/s00253-013-5191-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 08/06/2013] [Accepted: 08/11/2013] [Indexed: 12/28/2022]
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Cloning and characterization of a new broadspecific β-glucosidase from Lactococcus sp. FSJ4. World J Microbiol Biotechnol 2013; 30:213-23. [PMID: 23892562 DOI: 10.1007/s11274-013-1444-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Accepted: 07/19/2013] [Indexed: 10/26/2022]
Abstract
A β-glucosidase gene bglX was cloned from Lactococcus sp. FSJ4 by the method of shotgun. The bglX open reading frame consisted of 1,437 bp, encoding 478 amino acids. SDS-PAGE showed a recombinant bglX monomer of 54 kDa. Substrate specificity study revealed that the enzyme exhibited multifunctional catalysis activity against pNPG, pNPX and pNPGal. This enzyme shows higher activity against aryl glycosides of xylose than those of glucose or galactose. The enzyme exhibited the maximal activity at 40 °C, and the optimal pH was 6.0 with pNPG and 6.5 with pNPX as the substrates. Molecular modeling and substrate docking showed that there should be one active center responsible for the mutifuntional activity in this enzyme, since the active site pocket was substantially wide to allow the entry of pNPG, pNPX and pNPGal, which elucidated the structure-function relationship in substrate specificities. Substrate docking results indicated that Glu180 and Glu377 were the essential catalytic residues of the enzyme. The CDOCKER_ENERGY values obtained by substrate docking indicated that the enzyme has higher activity against pNPX than those of pNPG and pNPGal. These observations are in conformity with the results obtained from experimental investigation. Therefore, such substrate specificity makes this β-glucosidase of great interest for further study on physiological and catalytic reaction processes.
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Li H, Xu X, Chen H, Zhang Y, Xu J, Wang J, Lu X. Molecular analyses of the functional microbial community in composting by PCR-DGGE targeting the genes of the β-glucosidase. BIORESOURCE TECHNOLOGY 2013; 134:51-8. [PMID: 23500559 DOI: 10.1016/j.biortech.2013.01.077] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 01/12/2013] [Accepted: 01/16/2013] [Indexed: 05/06/2023]
Abstract
The study investigated the β-glucosidase-producing microbial communities and the enzymatic dynamics of CMCase and β-glucosidase during the process of cattle manure-rice straw composting. In order to analyze the succession of functional community by PCR-denaturing gradient gel electrophoresis (DGGEs), three sets of PCR primers were designed to amplify the family 1 and 3 β-glucosidase genes from both bacteria and fungi. The results showed in general that the stable functional community composition as well as for the high level enzymatic activities of both cellulase and β-glucosidase occurred during the last phase (days 14-31) of composting. In the process of composting, that functional groups were determined by the stable bands (GH1-F, GH1-H, GH1-G, GH3E-D and GH3E-E) may significantly contribute to the increase of β-glucosidase activities in the later phase. Especially, the bands from the family 1 β-glucosidase genes were appeared before that from the family 3 β-glucosidase genes from fungi, then the former was substituted for the latter gradually in the cooling phase. We found significant correlations between the β-glucosidase activity and the communities of the functional bacteria and fungi. The results indicated that different β-glucosidase-producing microbe release different amounts or activities of β-glucosidase, and that the composition of microbial communities may play a major role in determining overall β-glucosidase activity during the composting process.
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Affiliation(s)
- Hongtao Li
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, China
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Singhania RR, Patel AK, Sukumaran RK, Larroche C, Pandey A. Role and significance of beta-glucosidases in the hydrolysis of cellulose for bioethanol production. BIORESOURCE TECHNOLOGY 2013; 127:500-7. [PMID: 23069613 DOI: 10.1016/j.biortech.2012.09.012] [Citation(s) in RCA: 323] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 09/05/2012] [Accepted: 09/05/2012] [Indexed: 05/02/2023]
Abstract
One of the major challenges in the bioconversion of lignocellulosic biomass into liquid biofuels includes the search for a glucose tolerant beta-gulucosidase. Beta-glucosidase is the key enzyme component present in cellulase and completes the final step during cellulose hydrolysis by converting the cellobiose to glucose. This reaction is always under control as it gets inhibited by its product glucose. It is a major bottleneck in the efficient biomass conversion by cellulase. To circumvent this problem several strategies have been adopted which we have discussed in the article along with its production strategies and general properties. It plays a very significant role in bioethanol production from biomass through enzymatic route. Hence several amendments took place in the commercial preparation of cellulase for biomass hydrolysis, which contains higher and improved beta-glucosidase for efficient biomass conversion. This article presents beta-glucosidase as the key component for bioethanol from biomass through enzymatic route.
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Affiliation(s)
- Reeta Rani Singhania
- Laboratoire de Génie Chimique et Biochimique, Université Blaise Pascal, Polytech Clermont-Ferrand, Aubiere cedex, France.
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Divalent metal activation of a GH43 β-xylosidase. Enzyme Microb Technol 2012; 52:84-90. [PMID: 23273276 DOI: 10.1016/j.enzmictec.2012.10.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 10/06/2012] [Accepted: 10/26/2012] [Indexed: 11/21/2022]
Abstract
Depolymerization of xylan, a major fraction of lignocellulosic biomass, releases xylose which can be converted into transportation fuels and chemical feedstocks. A requisite enzyme for the breakdown of xylan is β-xylosidase. A gene encoding the 324-amino acid β-xylosidase, RS223-BX, was cloned from an anaerobic mixed microbial culture. This glycoside hydrolase belongs to family 43. Unlike other GH43 enzymes, RS223-BX can be strongly activated by exogenously supplied Ca(2+), Co(2+), Fe(2+), Mg(2+), Mn(2+) and Ni(2+) (e.g., 28-fold by Mg(2+)) and it is inhibited by Cu(2+) or Zn(2+). Sedimentation equilibrium centrifugation experiments indicated that the divalent metal cations mediate multimerization of the enzyme from a dimeric to a tetrameric state, which have equal catalytic activity on an active-site basis. Compared to the determined active sites of other GH43 β-xylosidases, the predicted active site of RS223-BX contains two additional amino acids with carboxylated side chains that provide potential sites for divalent metal cations to reside. Thus, the divalent metal cations likely occupy the active site and participate in the catalytic mechanism. RS223-BX accepts as substrate xylobiose, arabinobiose, 4-nitrophenyl-β-D-xylopyranoside, and 4-nitrophenyl-α-L-arabinofuranoside. Additionally, the enzyme has good pH and temperature stabilities and a large K(i) for D-glucose (1.3 M), favorable properties for performance in saccharification reactors.
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Li G, Jiang Y, Fan XJ, Liu YH. Molecular cloning and characterization of a novel β-glucosidase with high hydrolyzing ability for soybean isoflavone glycosides and glucose-tolerance from soil metagenomic library. BIORESOURCE TECHNOLOGY 2012; 123:15-22. [PMID: 22940294 DOI: 10.1016/j.biortech.2012.07.083] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 07/17/2012] [Accepted: 07/23/2012] [Indexed: 05/18/2023]
Abstract
A novel β-glucosidase (Bgl1269) was identified from a metagenomic library of mangrove soil by activity-based functional screening. Sequence analysis revealed that Bgl1269 encodes a protein of 422 amino acids. After being overexpressed in Escherichia coli and purified, the enzymatic properties of Bgl1269 were investigated. The recombinant enzyme displayed a pH optimum of 6.0 and a temperature optimum of 40°C, and the addition of most common metal ions (1 or 10mM) increased the enzymatic activity evidently. In addition, the enzyme showed high hydrolyzing ability for soybean isoflavone glycosides, and 0.8unit of enzyme could completely converted daidzin and genistin (0.5mg/mL) to daidzein and genistein at 40°C for 0.5h. Interestingly, Bgl1269 also exhibited a very high glucose-tolerance, with the highest inhibition constant K(i) (4.28M) among β-glucosidases reported so far. These properties make it a good candidate in the production of soybean isoflavone aglycones after further study.
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Affiliation(s)
- Gang Li
- School of life science, Sun Yat-sen University, Guangzhou 510275, PR China
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Mutations in the substrate entrance region of -glucosidase from Trichoderma reesei improve enzyme activity and thermostability. Protein Eng Des Sel 2012; 25:733-40. [DOI: 10.1093/protein/gzs073] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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