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Zhang D, Zhu Z, Su X, Gao T, Li N, Huang W, Wu M. Cloning and characterization of a novel mesophilic xylanase gene Fgxyn3 from Fusarium graminearum Z-1. 3 Biotech 2024; 14:162. [PMID: 38803445 PMCID: PMC11127905 DOI: 10.1007/s13205-024-03973-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/01/2024] [Indexed: 05/29/2024] Open
Abstract
In order to search for high specific activity and the resistant xylanases to XIP-I and provide more alternative xylanases for industrial production, a strain of Fusarium graminearum from Triticum aestivum grains infected with filamentous fungus produced xylanases was isolated and identified. Three xylanase genes from Fusarium graminearum Z-1 were cloned and successfully expressed in E. coli and P. pastoris, respectively. The specific activities of Fgxyn1, EFgxyn2 and EFgxyn3 for birchwood xylan were 38.79, 0.85 and 243.83 U/mg in E. coli, and 40.11, 0 and 910.37 U/mg in P. pastoris, respectively. EFgxyn3 and PFgxyn3 had the similar optimum pH at 6.0 and pH stability at 5.0-9.0. However, they had different optimum temperature and thermal stability, with 30 °C for EFgxyn3 and 40 °C for PFgxyn3, and 4-35 °C for EFgxyn3 and 4-40 °C for PFgxyn3, respectively. The substrate spectrum and the kinetic parameters showed that the two xylanases also exhibited the highest xylanase activity and catalytic efficiency (kcat/km) toward birchwood xylan, with 243.83 U/mg and 61.44 mL/mg/s for EFgxyn3 and 910.37 U/mg and 910.37 mL/mg/s for PFgxyn3, respectively. This study provided a novel mesophilic xylanase with high specific activity and catalytic efficiency, thus making it a promising candidate for extensive applications in animal feed and food industry. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-03973-0.
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Affiliation(s)
- Dong Zhang
- Wuxi School of Medicine, Jiangnan University, Wuxi, 214122 China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Zhu Zhu
- Science Island Branch of Graduate, University of Science and Technology of China, Hefei, 230026 China
| | - Xiaoya Su
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Tiecheng Gao
- Guangzhou Puratos Food Co., Ltd., Guangzhou, 511400 China
| | - Ning Li
- Guangzhou Puratos Food Co., Ltd., Guangzhou, 511400 China
| | - Weining Huang
- State Key Laboratory of Food Science and Technology, and the Laboratory of Baking and Fermentation Science, Cereals/Sourdough and Ingredient Functionality Research, School of Food Science and Technology, Jiangnan University, Wuxi, 214122 China
| | - Minchen Wu
- Wuxi School of Medicine, Jiangnan University, Wuxi, 214122 China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
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2
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MacDonald ME, Wells NGM, Hassan BA, Dudley JA, Walters KJ, Korzhnev DM, Aramini JM, Smith CA. Effects of Xylanase A double mutation on substrate specificity and structural dynamics. J Struct Biol 2024; 216:108082. [PMID: 38438058 DOI: 10.1016/j.jsb.2024.108082] [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: 12/16/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
While protein activity is traditionally studied with a major focus on the active site, the activity of enzymes has been hypothesized to be linked to the flexibility of adjacent regions, warranting more exploration into how the dynamics in these regions affects catalytic turnover. One such enzyme is Xylanase A (XylA), which cleaves hemicellulose xylan polymers by hydrolysis at internal β-1,4-xylosidic linkages. It contains a "thumb" region whose flexibility has been suggested to affect the activity. The double mutation D11F/R122D was previously found to affect activity and potentially bias the thumb region to a more open conformation. We find that the D11F/R122D double mutation shows substrate-dependent effects, increasing activity on the non-native substrate ONPX2 but decreasing activity on its native xylan substrate. To characterize how the double mutant causes these kinetics changes, nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulations were used to probe structural and flexibility changes. NMR chemical shift perturbations revealed structural changes in the double mutant relative to the wild-type, specifically in the thumb and fingers regions. Increased slow-timescale dynamics in the fingers region was observed as intermediate-exchange line broadening. Lipari-Szabo order parameters show negligible changes in flexibility in the thumb region in the presence of the double mutation. To help understand if there is increased energetic accessibility to the open state upon mutation, alchemical free energy simulations were employed that indicated thumb opening is more favorable in the double mutant. These studies aid in further characterizing how flexibility in adjacent regions affects the function of XylA.
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Affiliation(s)
- Meagan E MacDonald
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, United States; Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, United States
| | - Nicholas G M Wells
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, United States
| | - Bakar A Hassan
- Protein Processing Section, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, United States
| | - Joshua A Dudley
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, United States
| | - Kylie J Walters
- Protein Processing Section, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, United States
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030, United States
| | - James M Aramini
- Structural Biology Initiative, Advanced Science Research Center, The City University of New York, New York, NY 10031, United States
| | - Colin A Smith
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, United States.
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Sardiña-Peña AJ, Mesa-Ramos L, Iglesias-Figueroa BF, Ballinas-Casarrubias L, Siqueiros-Cendón TS, Espinoza-Sánchez EA, Flores-Holguín NR, Arévalo-Gallegos S, Rascón-Cruz Q. Analyzing Current Trends and Possible Strategies to Improve Sucrose Isomerases' Thermostability. Int J Mol Sci 2023; 24:14513. [PMID: 37833959 PMCID: PMC10572972 DOI: 10.3390/ijms241914513] [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: 09/01/2023] [Revised: 09/10/2023] [Accepted: 09/10/2023] [Indexed: 10/15/2023] Open
Abstract
Due to their ability to produce isomaltulose, sucrose isomerases are enzymes that have caught the attention of researchers and entrepreneurs since the 1950s. However, their low activity and stability at temperatures above 40 °C have been a bottleneck for their industrial application. Specifically, the instability of these enzymes has been a challenge when it comes to their use for the synthesis and manufacturing of chemicals on a practical scale. This is because industrial processes often require biocatalysts that can withstand harsh reaction conditions, like high temperatures. Since the 1980s, there have been significant advancements in the thermal stabilization engineering of enzymes. Based on the literature from the past few decades and the latest achievements in protein engineering, this article systematically describes the strategies used to enhance the thermal stability of sucrose isomerases. Additionally, from a theoretical perspective, we discuss other potential mechanisms that could be used for this purpose.
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Affiliation(s)
- Amado Javier Sardiña-Peña
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico; (A.J.S.-P.); (B.F.I.-F.); (L.B.-C.); (T.S.S.-C.); (E.A.E.-S.); (S.A.-G.)
| | - Liber Mesa-Ramos
- Laboratorio de Microbiología III, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico;
| | - Blanca Flor Iglesias-Figueroa
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico; (A.J.S.-P.); (B.F.I.-F.); (L.B.-C.); (T.S.S.-C.); (E.A.E.-S.); (S.A.-G.)
| | - Lourdes Ballinas-Casarrubias
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico; (A.J.S.-P.); (B.F.I.-F.); (L.B.-C.); (T.S.S.-C.); (E.A.E.-S.); (S.A.-G.)
| | - Tania Samanta Siqueiros-Cendón
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico; (A.J.S.-P.); (B.F.I.-F.); (L.B.-C.); (T.S.S.-C.); (E.A.E.-S.); (S.A.-G.)
| | - Edward Alexander Espinoza-Sánchez
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico; (A.J.S.-P.); (B.F.I.-F.); (L.B.-C.); (T.S.S.-C.); (E.A.E.-S.); (S.A.-G.)
| | - Norma Rosario Flores-Holguín
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua 31136, Mexico;
| | - Sigifredo Arévalo-Gallegos
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico; (A.J.S.-P.); (B.F.I.-F.); (L.B.-C.); (T.S.S.-C.); (E.A.E.-S.); (S.A.-G.)
| | - Quintín Rascón-Cruz
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico; (A.J.S.-P.); (B.F.I.-F.); (L.B.-C.); (T.S.S.-C.); (E.A.E.-S.); (S.A.-G.)
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4
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Structural and biochemical analysis reveals how ferulic acid improves catalytic efficiency of Humicola grisea xylanase. Sci Rep 2022; 12:11409. [PMID: 35794132 PMCID: PMC9259647 DOI: 10.1038/s41598-022-15175-w] [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: 01/14/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Humicolagrisea var. thermoidea is an aerobic and thermophilic fungus that secretes the GH11 xylanase HXYN2 in the presence of sugarcane bagasse. In this study, HXYN2 was expressed in Pichiapastoris and characterized biochemically and structurally in the presence of beechwood xylan substrate and ferulic acid (FA). HXYN2 is a thermally stable protein, as indicated by circular dichroism, with greater activity in the range of 40–50 °C and pH 5.0–9.0, with optimal temperature and pH of 50 °C and 6.0, respectively. FA resulted in a 75% increase in enzyme activity and a 2.5-fold increase in catalytic velocity, catalytic efficiency, and catalytic rate constant (kcat), with no alteration in enzyme affinity for the substrate. Fluorescence quenching indicated that FA forms a complex with HXYN2 interacting with solvent-exposed tryptophan residues. The binding constants ranged from moderate (pH 7.0 and 9.0) to strong (pH 4.0) affinity. Isothermal titration calorimetry, structural models and molecular docking suggested that hydrogen bonds and hydrophobic interactions occur in the aglycone region inducing conformational changes in the active site driven by initial and final enthalpy- and entropy processes, respectively. These results indicate a potential for biotechnological application for HXYN2, such as in the bioconversion of plant residues rich in ferulic acid.
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Min K, Kim H, Park HJ, Lee S, Jung YJ, Yoon JH, Lee JS, Park K, Yoo YJ, Joo JC. Improving the catalytic performance of xylanase from Bacillus circulans through structure-based rational design. BIORESOURCE TECHNOLOGY 2021; 340:125737. [PMID: 34426235 DOI: 10.1016/j.biortech.2021.125737] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
Endo-1,4-β-xylanase is one of the most important enzymes employed in biorefineries for obtaining fermentable sugars from hemicellulosic components. Herein, we aimed to improve the catalytic performance of Bacillus circulans xylanase (Bcx) using a structure-guided rational design. A systematic analysis of flexible motions revealed that the R49 component of Bcx (i) constrains the global conformational changes essential for substrate binding and (ii) is involved in modulating flexible motion. Site-saturated mutagenesis of the R49 residue led to the engineering of the active mutants with the trade-off between flexibility and rigidity. The most active mutant R49N improved the catalytic performance, including its catalytic efficiency (7.51-fold), conformational stability (0.7 °C improvement), and production of xylose oligomers (2.18-fold higher xylobiose and 1.72-fold higher xylotriose). The results discussed herein can be applied to enhance the catalytic performance of industrially important enzymes by controlling flexibility.
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Affiliation(s)
- Kyoungseon Min
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea
| | - Hoyong Kim
- Center for Bio-Based Chemistry, Korea Research Institute of Chemical Technology, Ulsan 44429, Republic of Korea
| | - Hyun June Park
- Department of Biotechnology, Duksung Women's University, Seoul 01369, Republic of Korea
| | - Siseon Lee
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si, Gyeonggi-do 14662, Republic of Korea
| | - Ye Jean Jung
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si, Gyeonggi-do 14662, Republic of Korea; Department of Biological and Chemical Engineering, Hongik University, Sejong Ro 2639, Jochiwon, Sejong City, Republic of Korea
| | - Ji Hyun Yoon
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si, Gyeonggi-do 14662, Republic of Korea
| | - Jin-Suk Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea
| | - Kyoungmoon Park
- Department of Biological and Chemical Engineering, Hongik University, Sejong Ro 2639, Jochiwon, Sejong City, Republic of Korea
| | - Young Je Yoo
- School of Chemical and Biological Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Jeong Chan Joo
- Center for Bio-Based Chemistry, Korea Research Institute of Chemical Technology, Ulsan 44429, Republic of Korea; Department of Biotechnology, The Catholic University of Korea, Bucheon-si, Gyeonggi-do 14662, Republic of Korea.
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6
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Safitri E, Hanifah, Previta, Sudarko, Ni Nyoman Tri Puspaningsih, Istri Ratnadewi AA. Cloning, purification, and characterization of recombinant endo- β-1,4-D-xylanase of Bacillus sp. From soil termite abdomen. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2020.101877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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7
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High-resolution crystal structure and biochemical characterization of a GH11 endoxylanase from Nectria haematococca. Sci Rep 2020; 10:15658. [PMID: 32973265 PMCID: PMC7519127 DOI: 10.1038/s41598-020-72644-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/28/2020] [Indexed: 11/08/2022] Open
Abstract
Enzymatic degradation of vegetal biomass offers versatile procedures to improve the production of alternative fuels and other biomass-based products. Here we present the three-dimensional structure of a xylanase from Nectria haematococca (NhGH11) at 1.0 Å resolution and its functional properties. The atomic resolution structure provides details and insights about the complex hydrogen bonding network of the active site region and allowed a detailed comparison with homologous structures. Complementary biochemical studies showed that the xylanase can catalyze the hydrolysis of complex xylan into simple xylose aldopentose subunits of different lengths. NhGH11 can catalyze the efficient breakdown of beechwood xylan, xylan polysaccharide, and wheat arabinoxylan with turnover numbers of 1730.6 ± 318.1 min-1, 1648.2 ± 249.3 min-1 and 2410.8 ± 517.5 min-1 respectively. NhGH11 showed maximum catalytic activity at pH 6.0 and 45 °C. The mesophilic character of NhGH11 can be explained by distinct structural features in comparison to thermophilic GH11 enzymes, including the number of hydrogen bonds, side chain interactions and number of buried water molecules. The enzymatic activity of NhGH11 is not very sensitive to metal ions and chemical reagents that are typically present in associated industrial production processes. The data we present highlights the potential of NhGH11 to be applied in industrial biomass degradation processes.
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Knapik K, Becerra M, González-Siso MI. Microbial diversity analysis and screening for novel xylanase enzymes from the sediment of the Lobios Hot Spring in Spain. Sci Rep 2019; 9:11195. [PMID: 31371784 PMCID: PMC6671963 DOI: 10.1038/s41598-019-47637-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/11/2019] [Indexed: 01/28/2023] Open
Abstract
Here, we describe the metagenome composition of a microbial community in a hot spring sediment as well as a sequence-based and function-based screening of the metagenome for identification of novel xylanases. The sediment was collected from the Lobios Hot Spring located in the province of Ourense (Spain). Environmental DNA was extracted and sequenced using Illumina technology, and a total of 3.6 Gbp of clean paired reads was produced. A taxonomic classification that was obtained by comparison to the NCBI protein nr database revealed a dominance of Bacteria (93%), followed by Archaea (6%). The most abundant bacterial phylum was Acidobacteria (25%), while Thaumarchaeota (5%) was the main archaeal phylum. Reads were assembled into contigs. Open reading frames (ORFs) predicted on these contigs were searched by BLAST against the CAZy database to retrieve xylanase encoding ORFs. A metagenomic fosmid library of approximately 150,000 clones was constructed to identify functional genes encoding thermostable xylanase enzymes. Function-based screening revealed a novel xylanase-encoding gene (XynA3), which was successfully expressed in E. coli BL21. The resulting protein (41 kDa), a member of glycoside hydrolase family 11 was purified and biochemically characterized. The highest activity was measured at 80 °C and pH 6.5. The protein was extremely thermostable and showed 94% remaining activity after incubation at 60 °C for 24 h and over 70% remaining activity after incubation at 70 °C for 24 h. Xylanolytic activity of the XynA3 enzyme was stimulated in the presence of β-mercaptoethanol, dithiothreitol and Fe3+ ions. HPLC analysis showed that XynA3 hydrolyzes xylan forming xylobiose with lower proportion of xylotriose and xylose. Specific activity of the enzyme was 9080 U/mg for oat arabinoxylan and 5080 U/mg for beechwood xylan, respectively, without cellulase activity.
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Affiliation(s)
- Kamila Knapik
- Universidade da Coruña, Grupo EXPRELA, Facultade de Ciencias, Centro de Investigacións Científicas Avanzadas (CICA), A Coruña, Spain
| | - Manuel Becerra
- Universidade da Coruña, Grupo EXPRELA, Facultade de Ciencias, Centro de Investigacións Científicas Avanzadas (CICA), A Coruña, Spain
| | - María-Isabel González-Siso
- Universidade da Coruña, Grupo EXPRELA, Facultade de Ciencias, Centro de Investigacións Científicas Avanzadas (CICA), A Coruña, Spain.
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Improving the thermostability and catalytic efficiency of GH11 xylanase PjxA by adding disulfide bridges. Int J Biol Macromol 2019; 128:354-362. [DOI: 10.1016/j.ijbiomac.2019.01.087] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/17/2019] [Accepted: 01/19/2019] [Indexed: 11/24/2022]
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Heterologous expression, purification and biochemical characterization of a new xylanase from Myceliophthora heterothallica F.2.1.4. Int J Biol Macromol 2019; 131:798-805. [PMID: 30905755 DOI: 10.1016/j.ijbiomac.2019.03.108] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 03/16/2019] [Accepted: 03/18/2019] [Indexed: 11/21/2022]
Abstract
Myceliophthora heterothallica is a thermophilic fungus potentially relevant for the production of enzymes involved in the degradation of plant biomass. A xylanase encoding gene of this species was identified by means of RT-PCR using primers designed based on a xylanase coding sequence (GH11) of the fungus M. thermophila. The obtained gene was ligated to the vector pET28a(+) and the construct was transformed into Escherichia coli cells. The recombinant xylanase (r-ec-XylMh) was heterologously expressed, and the highest activity was observed at 55 °C and pH 6. The enzyme stability was greater than 70% between pH 4.5 and 9.5 and the inclusion of glycerol (50%) resulted in a significant increase in thermostability. Under these conditions, the enzyme retained more than 50% residual activity when incubated at 65 °C for 1 h, and approximately 30% activity when incubated at 70 °C for the same period. The tested cations did not increase xylanolytic activity, and the enzyme indicated significant tolerance to several phenolic compounds after 24 h, as well as high specificity for xylan, with no activity for other substrates such as CMC (carboxymethylcellulose), Avicel, pNPX (p-nitrophenyl-β-D-xylopyranoside) and pNPA (p-nitrophenyl-α-L-arabinofuranoside), and is thus, of potential relevance in pulp bleaching.
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Ge HH, Qiu Y, Yi ZW, Zeng RY, Zhang GY. π-π stacking interaction is a key factor for the stability of GH11 xylanases at low pH. Int J Biol Macromol 2019; 124:895-902. [DOI: 10.1016/j.ijbiomac.2018.11.282] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 11/30/2018] [Accepted: 11/30/2018] [Indexed: 01/05/2023]
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12
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Effect of disulfide bridge on hydrolytic characteristics of xylanase from Penicillium janthinellum. Int J Biol Macromol 2018; 120:405-413. [PMID: 30145159 DOI: 10.1016/j.ijbiomac.2018.08.099] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 07/02/2018] [Accepted: 08/21/2018] [Indexed: 11/20/2022]
Abstract
Highly efficient and stable enzymes are required for application in biotechnology, to meet the technical, environmental, and economic industrial demands. Xylanases are hemicellulolytic enzymes that degrade the heteroxylan constituent of the lignocellulosic plant cell wall. In this study, an acidic xylanase designated Pjxyn (pH 4.0) from Penicillium janthinellum was engineered by the introduction of a disulfide bridge. This strategy exploited the influence of the bridge on hydrolysis characteristics and enhanced hydrolysis was achieved. Three mutants [PjxynS(27)S(39), PjxynS(27)S(186), and PjxynS(39)S(186)] produced more xylose and xylobiose as hydrolysis products compared with the wild-type Pjxyn, when commercial xylans and lab-prepared water-insoluble corncob-xylan were used as the substrates, especial for the PjxynS(27)S(39) mutant, the content of xylose and xylobiose was 87.62% (using beechwood xylan) and 69.91% (using oat-spelt xylan) higher than that in the hydrolysis products of Pjxyn. Moreover, each mutant combined with the xylanase mutant T-XynFM effectively decreased the production of xylose with an optimum xylobiose yield. The findings demonstrate the potential industrial value of engineering xylanase to improve its hydrolytic properties and thermostability.
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Prajapati AS, Pawar VA, Panchal KJ, Sudhir AP, Dave BR, Patel DH, Subramanian RB. Effects of substrate binding site residue substitutions of xynA from Bacillus amyloliquefaciens on substrate specificity. BMC Biotechnol 2018; 18:9. [PMID: 29439688 PMCID: PMC5812043 DOI: 10.1186/s12896-018-0420-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/30/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The aromatic residues of xylanase enzyme, W187, Y124, W144, Y128 and W63 of substrate binding pocket from Bacillus amyloliquefaciens were investigated for their role in substrate binding by homology modelling and sequence analysis. These residues are highly conserved and play an important role in substrate binding through steric hindrance. The substitution of these residues with alanine allows the enzyme to accommodate nonspecific substrates. RESULTS Wild type and mutated genes were cloned and overexpressed in BL21. Optimum pH and temperature of rBAxn exhibited pH 9.0 and 50 °C respectively and it was stable up to 215 h. Along with the physical properties of rBAxn, kinetic parameters (Km 19.34 ± 0.72 mg/ml; kcat 6449.12 ± 155.37 min- 1 and kcat/Km 333.83 ± 6.78 ml min- 1 mg- 1) were also compared with engineered enzymes. Out of five mutations, W63A, Y128A and W144A lost almost 90% activity and Y124A and W187A retained almost 40-45% xylanase activity. CONCLUSIONS The site-specific single mutation, led to alteration in substrate specificity from xylan to CMC while in case of double mutant the substrate specificity was altered from xylan to CMC, FP and avicel, indicating the role of aromatic residues on substrate binding, catalytic process and overall catalytic efficiency.
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Affiliation(s)
- Anil S. Prajapati
- P. G. Department of Biosciences, UGC-Centre of advanced studies, Satellite campus, Sardar Patel University, Sardar Patel Maidan, Bakrol-Vadtal Road, PO Box 39, Vallabh Vidyanagar, Gujarat 388 120 India
| | - Vishakha A. Pawar
- P. G. Department of Biosciences, UGC-Centre of advanced studies, Satellite campus, Sardar Patel University, Sardar Patel Maidan, Bakrol-Vadtal Road, PO Box 39, Vallabh Vidyanagar, Gujarat 388 120 India
| | - Ketankumar J. Panchal
- P. G. Department of Biosciences, UGC-Centre of advanced studies, Satellite campus, Sardar Patel University, Sardar Patel Maidan, Bakrol-Vadtal Road, PO Box 39, Vallabh Vidyanagar, Gujarat 388 120 India
| | - Ankit P. Sudhir
- P. G. Department of Biosciences, UGC-Centre of advanced studies, Satellite campus, Sardar Patel University, Sardar Patel Maidan, Bakrol-Vadtal Road, PO Box 39, Vallabh Vidyanagar, Gujarat 388 120 India
| | - Bhaumik R. Dave
- P. G. Department of Biosciences, UGC-Centre of advanced studies, Satellite campus, Sardar Patel University, Sardar Patel Maidan, Bakrol-Vadtal Road, PO Box 39, Vallabh Vidyanagar, Gujarat 388 120 India
| | - Darshan H. Patel
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology (CHARUSAT), Changa, Anand, Gujarat India
| | - R. B. Subramanian
- P. G. Department of Biosciences, UGC-Centre of advanced studies, Satellite campus, Sardar Patel University, Sardar Patel Maidan, Bakrol-Vadtal Road, PO Box 39, Vallabh Vidyanagar, Gujarat 388 120 India
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14
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Dey P, Roy A. Molecular structure and catalytic mechanism of fungal family G acidophilic xylanases. 3 Biotech 2018; 8:78. [PMID: 29430342 PMCID: PMC5799109 DOI: 10.1007/s13205-018-1091-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Accepted: 01/04/2018] [Indexed: 10/18/2022] Open
Abstract
Industrial applications of xylanases have made this enzyme an important subject of applied research work. Function of this particular enzyme is to degrade or hydrolyze the plentiful polysaccharide xylan, an important component of hemicellulose. It mainly cleaves the backbone of xylan that is made up of a number of xylose residues connected with β-1,4-glycosidic linkages. Fungi with mycelia are regarded as the best producer of xylanases. These varied xylanases not only differ in their sizes and shapes but also differ in their physicochemical properties. Depending on the optimum pH in which they work best, they have been classified into (1) acidophilic xylanases active at low pH or acidic pH range, (2) alkaliphilic xylanases that are active at high or alkaline pH range and (3) neutral xylanases having pH optima in the neutral range between pH 5 and 7. Other researchers have classified the xylanases also on the basis of their structural properties, kinetic parameters, etc. This review discusses the molecular structures of some acidophilic xylanases and the molecular basis of low pH optima observed for their activities. It also discusses their unique catalytic mechanism and actual role of the catalytic residues found in them. Apart from these, the review also discusses different applications of these acidophilic xylanases in different industries. The article concludes with brief suggestions about how these acidophilic xylanases can be created employing the techniques of genetic engineering and concepts of synthetic evolution, using the traits of the known acidophilic xylanases discussed in the review.
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Affiliation(s)
- Protyusha Dey
- Department of Biotechnology, Visva-Bharati University, Santiniketan, 731235 West Bengal India
| | - Amit Roy
- Department of Biotechnology, Visva-Bharati University, Santiniketan, 731235 West Bengal India
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15
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Mongkorntanyatip K, Limsakul P, Ratanakhanokchai K, Khunrae P. Overexpression and characterization of alkaliphilic Bacillus firmus strain K-1 xylanase. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.anres.2018.03.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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16
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Protein homology modeling, docking, and phylogenetic analyses of an endo-1,4-β-xylanase GH11 of Colletotrichum lindemuthianum. Mycol Prog 2017. [DOI: 10.1007/s11557-017-1291-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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17
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Chakdar H, Kumar M, Pandiyan K, Singh A, Nanjappan K, Kashyap PL, Srivastava AK. Bacterial xylanases: biology to biotechnology. 3 Biotech 2016; 6:150. [PMID: 28330222 PMCID: PMC4929084 DOI: 10.1007/s13205-016-0457-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 06/10/2016] [Indexed: 12/04/2022] Open
Abstract
In this review, a comprehensive discussion exclusively on bacterial xylanases; their gene organization; different factors and conditions affecting enzyme yield and activity; and their commercial application have been deliberated in the light of recent research findings and extensive information mining. Improved understanding of biological properties and genetics of bacterial xylanase will enable exploitation of these enzymes for many more ingenious biotechnological and industrial applications.
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18
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Bagewadi ZK, Mulla SI, Shouche Y, Ninnekar HZ. Xylanase production from Penicillium citrinum isolate HZN13 using response surface methodology and characterization of immobilized xylanase on glutaraldehyde-activated calcium-alginate beads. 3 Biotech 2016; 6:164. [PMID: 28330236 PMCID: PMC4980835 DOI: 10.1007/s13205-016-0484-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 08/01/2016] [Indexed: 01/28/2023] Open
Abstract
The present study reports the production of high-level cellulase-free xylanase from Penicillium citrinum isolate HZN13. The variability in xylanase titers was assessed under both solid-state (SSF) and submerged (SmF) fermentation. SSF was initially optimized with different agro-waste residues, among them sweet sorghum bagasse was found to be the best substrate that favored maximum xylanase production (9643 U/g). Plackett–Burman and response surface methodology employing central composite design were used to optimize the process parameters for the production of xylanase under SSF. A second-order quadratic model and response surface method revealed the optimum conditions for xylanase production (sweet sorghum bagasse 25 g/50 ml; ammonium sulphate 0.36 %; yeast extract 0.6 %; pH 4; temperature 40 °C) yielding 30,144 U/g. Analysis of variance (ANOVA) showed a high correlation coefficient (R2 = 97.63 %). Glutaraldehyde-activated calcium-alginate-immobilized purified xylanase showed recycling stability (87 %) up to seven cycles. Immobilized purified xylanase showed enhanced thermo-stability in comparison to immobilized crude xylanase. Immobilization kinetics of crude and purified xylanase revealed an increase in Km (12.5 and 11.11 mg/ml) and Vmax (12,500 and 10,000 U/mg), respectively. Immobilized (crude) enzymatic hydrolysis of sweet sorghum bagasse released 8.1 g/g (48 h) of reducing sugars. Xylose and other oligosaccharides produced during hydrolysis were detected by High-Performance Liquid Chromatography. The biomass was characterized by Scanning Electron Microscopy, Energy Dispersive X-ray and Fourier Transformation Infrared Spectroscopy. However, this is one of the few reports on high-level cellulase-free xylanase from P. citrinum isolate using sweet sorghum bagasse.
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19
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Rashamuse K, Sanyika Tendai W, Mathiba K, Ngcobo T, Mtimka S, Brady D. Metagenomic mining of glycoside hydrolases from the hindgut bacterial symbionts of a termite (Trinervitermes trinervoides) and the characterization of a multimodular β-1,4-xylanase (GH11). Biotechnol Appl Biochem 2016; 64:174-186. [DOI: 10.1002/bab.1480] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 12/19/2015] [Indexed: 11/06/2022]
Affiliation(s)
| | - Walter Sanyika Tendai
- Biomanufacturing Centre; CSIR Biosciences; Pretoria South Africa
- Department of Biotechnology; Chinhoyi University of Technology; Chinhoyi Zimbabwe
| | - Kgama Mathiba
- Biomanufacturing Centre; CSIR Biosciences; Pretoria South Africa
| | - Thobile Ngcobo
- Biomanufacturing Centre; CSIR Biosciences; Pretoria South Africa
| | - Sibongile Mtimka
- Biomanufacturing Centre; CSIR Biosciences; Pretoria South Africa
| | - Dean Brady
- Biomanufacturing Centre; CSIR Biosciences; Pretoria South Africa
- Molecular Sciences Institute; School of Chemistry; University of the Witwatersrand; Johannesburg South Africa
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20
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Song Q, Wang Y, Yin C, Zhang XH. LaaA, a novel high-active alkalophilic alpha-amylase from deep-sea bacterium Luteimonas abyssi XH031(T). Enzyme Microb Technol 2016; 90:83-92. [PMID: 27241296 DOI: 10.1016/j.enzmictec.2016.05.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 04/30/2016] [Accepted: 05/06/2016] [Indexed: 10/21/2022]
Abstract
Alpha-amylase is a kind of broadly used industrial enzymes, most of which have been exploited from terrestrial organism. Comparatively, alpha-amylase from marine environment was largely undeveloped. In this study, a novel alkalophilic alpha-amylase with high activity, Luteimonas abyssi alpha-amylase (LaaA), was cloned from deep-sea bacterium L. abyssi XH031(T) and expressed in Escherichia coli BL21. The gene has a length of 1428bp and encodes 475 amino acids with a 35-residue signal peptide. The specific activity of LaaA reached 8881U/mg at the optimum pH 9.0, which is obvious higher than other reported alpha-amylase. This enzyme can remain active at pH levels ranging from 6.0 to 11.0 and temperatures below 45°C, retaining high activity even at low temperatures (almost 38% residual activity at 10°C). In addition, 1mM Na(+), K(+), and Mn(2+) enhanced the activity of LaaA. To investigate the function of potential active sites, R227G, D229K, E256Q/H, H327V and D328V mutants were generated, and the results suggested that Arg227, Asp229, Glu256 and Asp328 were total conserved and essential for the activity of alpha-amylase LaaA. This study shows that the alpha-amylase LaaA is an alkali-tolerant and high-active amylase with strong potential for use in detergent industry.
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Affiliation(s)
- Qinghao Song
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Yan Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
| | - Chong Yin
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
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21
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Lee HW, Jeon HY, Choi HJ, Kim NR, Choung WJ, Koo YS, Ko DS, You S, Shim JH. Characterization and Application of BiLA, a Psychrophilic α-Amylase from Bifidobacterium longum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:2709-2718. [PMID: 26979859 DOI: 10.1021/acs.jafc.5b05904] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
In this study, a novel α-amylase was cloned from Bifidobacterium longum and named BiLA. The enzyme exhibited optimal activity at 20 °C and a pH value of 5.0. Kinetic analysis using various carbohydrate substrates revealed that BiLA had the highest k(cat/)K(m) value for amylose. Interestingly, analysis of the enzymatic reaction products demonstrated that BiLA specifically catalyzed the hydrolysis of oligosaccharides and starches up to G5 from the nonreducing ends. To determine whether BiLA can be used to generate slowly digestible starch (SDS), starch was treated with BiLA, and the kinetic parameters were analyzed using porcine pancreatic α-amylase (PPA) and amyloglucosidase (AMG). Compared to normal starch, BiLA-treated starch showed lower k(cat)/K(m) values with PPA and AMG, suggesting that BiLA is a potential candidate for the production of SDS.
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Affiliation(s)
- Hye-Won Lee
- Department of Food Science and Nutrition and Center for Aging and Health Care, Hallym University , Hallymdaehak-gil 1, Chuncheon, Gangwon-do 200-702, South Korea
| | - Hye-Yeon Jeon
- Department of Food Science and Nutrition and Center for Aging and Health Care, Hallym University , Hallymdaehak-gil 1, Chuncheon, Gangwon-do 200-702, South Korea
| | - Hye-Jeong Choi
- Department of Food Science and Nutrition and Center for Aging and Health Care, Hallym University , Hallymdaehak-gil 1, Chuncheon, Gangwon-do 200-702, South Korea
| | - Na-Ri Kim
- Department of Food Science and Nutrition and Center for Aging and Health Care, Hallym University , Hallymdaehak-gil 1, Chuncheon, Gangwon-do 200-702, South Korea
| | - Woo-Jae Choung
- Department of Food Science and Nutrition and Center for Aging and Health Care, Hallym University , Hallymdaehak-gil 1, Chuncheon, Gangwon-do 200-702, South Korea
| | - Ye-Seul Koo
- Department of Food Science and Nutrition and Center for Aging and Health Care, Hallym University , Hallymdaehak-gil 1, Chuncheon, Gangwon-do 200-702, South Korea
| | - Dam-Seul Ko
- Department of Food Science and Nutrition and Center for Aging and Health Care, Hallym University , Hallymdaehak-gil 1, Chuncheon, Gangwon-do 200-702, South Korea
| | - SangGuan You
- Department of Marine Food Science and Technology, Gangneung-Wonju National University , 120 Gangneung Daehangno, Gangneung, Gangwon 210-702, South Korea
| | - Jae-Hoon Shim
- Department of Food Science and Nutrition and Center for Aging and Health Care, Hallym University , Hallymdaehak-gil 1, Chuncheon, Gangwon-do 200-702, South Korea
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22
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Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography. Proc Natl Acad Sci U S A 2015; 112:12384-9. [PMID: 26392527 DOI: 10.1073/pnas.1504986112] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Glycoside hydrolase (GH) enzymes apply acid/base chemistry to catalyze the decomposition of complex carbohydrates. These ubiquitous enzymes accept protons from solvent and donate them to substrates at close to neutral pH by modulating the pKa values of key side chains during catalysis. However, it is not known how the catalytic acid residue acquires a proton and transfers it efficiently to the substrate. To better understand GH chemistry, we used macromolecular neutron crystallography to directly determine protonation and ionization states of the active site residues of a family 11 GH at multiple pD (pD=pH+0.4) values. The general acid glutamate (Glu) cycles between two conformations, upward and downward, but is protonated only in the downward orientation. We performed continuum electrostatics calculations to estimate the pKa values of the catalytic Glu residues in both the apo- and substrate-bound states of the enzyme. The calculated pKa of the Glu increases substantially when the side chain moves down. The energy barrier required to rotate the catalytic Glu residue back to the upward conformation, where it can protonate the glycosidic oxygen of the substrate, is 4.3 kcal/mol according to free energy simulations. These findings shed light on the initial stage of the glycoside hydrolysis reaction in which molecular motion enables the general acid catalyst to obtain a proton from the bulk solvent and deliver it to the glycosidic oxygen.
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23
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Cheng YS, Chen CC, Huang JW, Ko TP, Huang Z, Guo RT. Improving the catalytic performance of a GH11 xylanase by rational protein engineering. Appl Microbiol Biotechnol 2015; 99:9503-10. [DOI: 10.1007/s00253-015-6712-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 05/18/2015] [Accepted: 05/21/2015] [Indexed: 11/28/2022]
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24
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Chanwicha N, Katekaew S, Aimi T, Boonlue S. Purification and characterization of alkaline xylanase from Thermoascus aurantiacus var. levisporus KKU-PN-I2-1 cultivated by solid-state fermentation. MYCOSCIENCE 2015. [DOI: 10.1016/j.myc.2014.09.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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25
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Identification of three important amino acid residues of xylanase AfxynA from Aspergillus fumigatus for enzyme activity and formation of xylobiose as the major product. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.01.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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26
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Production of xylooligosaccharides from garlic straw xylan by purified xylanase from Bacillus mojavensis UEB-FK and their in vitro evaluation as prebiotics. FOOD AND BIOPRODUCTS PROCESSING 2015. [DOI: 10.1016/j.fbp.2014.07.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Chen CC, Ko TP, Huang JW, Guo RT. Heat- and Alkaline-Stable Xylanases: Application, Protein Structure and Engineering. CHEMBIOENG REVIEWS 2015. [DOI: 10.1002/cben.201400035] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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28
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Bhattacharya AS, Bhattacharya A, Pletschke BI. Synergism of fungal and bacterial cellulases and hemicellulases: a novel perspective for enhanced bio-ethanol production. Biotechnol Lett 2015; 37:1117-29. [DOI: 10.1007/s10529-015-1779-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 01/21/2015] [Indexed: 12/15/2022]
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29
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Recombination of Thermo-Alkalistable, High Xylooligosaccharides Producing Endo-Xylanase from Thermobifida fusca and Expression in Pichia pastoris. Appl Biochem Biotechnol 2014; 175:1318-29. [DOI: 10.1007/s12010-014-1355-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 10/31/2014] [Indexed: 12/31/2022]
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30
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Kallel F, Driss D, Chaabouni SE, Ghorbel R. Biological Activities of Xylooligosaccharides Generated from Garlic Straw Xylan by Purified Xylanase from Bacillus mojavensis UEB-FK. Appl Biochem Biotechnol 2014; 175:950-64. [DOI: 10.1007/s12010-014-1308-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 10/15/2014] [Indexed: 10/24/2022]
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31
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Hiteshi K, Gupta R. Thermal adaptation of α-amylases: a review. Extremophiles 2014; 18:937-44. [DOI: 10.1007/s00792-014-0674-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 07/06/2014] [Indexed: 11/24/2022]
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32
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Lafond M, Guais O, Maestracci M, Bonnin E, Giardina T. Four GH11 xylanases from the xylanolytic fungus Talaromyces versatilis act differently on (arabino)xylans. Appl Microbiol Biotechnol 2014; 98:6339-52. [DOI: 10.1007/s00253-014-5606-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/05/2014] [Accepted: 02/07/2014] [Indexed: 12/12/2022]
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33
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Valenzuela SV, Diaz P, Pastor FIJ. Xyn11E from Paenibacillus barcinonensis BP-23: a LppX-chaperone-dependent xylanase with potential for upgrading paper pulps. Appl Microbiol Biotechnol 2014; 98:5949-57. [DOI: 10.1007/s00253-014-5565-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 12/20/2013] [Accepted: 01/21/2014] [Indexed: 12/21/2022]
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34
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35
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Tishkov VI, Gusakov AV, Cherkashina AS, Sinitsyn AP. Engineering the pH-optimum of activity of the GH12 family endoglucanase by site-directed mutagenesis. Biochimie 2013; 95:1704-10. [PMID: 23774299 DOI: 10.1016/j.biochi.2013.05.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 05/23/2013] [Indexed: 11/25/2022]
Abstract
Endo-1,4-β-glucanase from Penicillium verruculosum (PvEGIII) belongs to family 12 of glycoside hydrolases (GH12). Analysis of the enzyme 3D model structure showed that the amino acid residue Asp98 may directly affect the pH-profile of enzyme activity since it is located at the distance of hydrogen bond formation from Glu203 that plays the role of a general acid in catalysis. The gene encoding the PvEGIII was cloned into Escherichia coli. After the deletion of two introns, a plasmid construction was obtained allowing the PvEGIII expression in E. coli. Using site-directed mutagenesis, the Asp98Asn mutant of the PvEGIII was obtained. Both the wild type and mutant PvEGIIIs were expressed in E. coli with a yield of up to 1 g/L and then isolated in a highly purified form. The enzyme specific activity against soluble carboxymethylcellulose was not changed after a single amino acid substitution. However, the pH-optimum of activity of the mutant PvEGIII was shifted from pH 4.0 to 5.1, compared to the wild type enzyme. The shift in the enzyme pH-optimum to more neutral pH was also observed on insoluble cellulose, in the process of enzymatic depigmentation of denim fabric. Similar situation featuring the effect of the Asp/Asn residue, located near the Glu catalytic residue, on the enzyme activity pH-profile has previously been described for xylanases of the GH11 family. Thus, the glycoside hydrolases belonging to the GH11 and GH12 families function by a rather similar mechanism of catalysis.
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Affiliation(s)
- Vladimir I Tishkov
- Department of Chemistry, M. V. Lomonosov Moscow State University, Leninskie Gory 1/11, Moscow 119991, Russia
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36
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Sharma P, Rele MV, Kumar LS. Cloning and sequence analysis of three variants of the gene encoding alkaline xylanase C from the alkaliphilic Bacillus sp. (NCL 87-6-10). Biochem Genet 2013; 51:737-49. [PMID: 23749064 DOI: 10.1007/s10528-013-9603-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 12/03/2012] [Indexed: 10/26/2022]
Abstract
Alkaline xylanase C from the alkaliphilic Bacillus sp. (NCL 87-6-10) has a low molecular weight and alkaline pI and is cellulase-free, properties compatible with its use in the prebleaching of pulp. We report here the cloning and sequence analysis of three variants of the gene encoding xylanase C; xyl C1, xyl C2, and xyl C3. In phylogenetic analysis, the three xylanase C variants clustered into a single group along with other reported alkaline xylanases. Residues contributing to the alkaline pH were present in all three variants. DNA and protein sequence comparison of these variants with other reported alkaline xylanases revealed silent mutations, some of which are due to codon preference in the respective organisms. The recombinant Xyl C1 that was successfully expressed in E. coli BL21 (DE3) had properties similar to the native enzyme.
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Affiliation(s)
- Poonam Sharma
- Division of Biochemical Sciences, National Chemical Laboratory, Pune, 411008, India
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37
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Ludwiczek ML, D’Angelo I, Yalloway GN, Brockerman JA, Okon M, Nielsen JE, Strynadka NCJ, Withers SG, McIntosh LP. Strategies for Modulating the pH-Dependent Activity of a Family 11 Glycoside Hydrolase. Biochemistry 2013; 52:3138-56. [DOI: 10.1021/bi400034m] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Martin L. Ludwiczek
- Department of Biochemistry and
Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
- Department of Chemistry, University of British Columbia, Vancouver, British
Columbia, Canada V6T 1Z1
- Michael Smith Laboratories, University of British Columbia, Vancouver, British
Columbia, Canada V6T 1Z4
| | - Igor D’Angelo
- Department of Biochemistry and
Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Gary N. Yalloway
- Department of Biochemistry and
Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
- Department of Chemistry, University of British Columbia, Vancouver, British
Columbia, Canada V6T 1Z1
| | - Jacob A. Brockerman
- Department of Biochemistry and
Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
- Department of Chemistry, University of British Columbia, Vancouver, British
Columbia, Canada V6T 1Z1
- Michael Smith Laboratories, University of British Columbia, Vancouver, British
Columbia, Canada V6T 1Z4
| | - Mark Okon
- Department of Biochemistry and
Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
- Department of Chemistry, University of British Columbia, Vancouver, British
Columbia, Canada V6T 1Z1
- Michael Smith Laboratories, University of British Columbia, Vancouver, British
Columbia, Canada V6T 1Z4
| | - Jens E. Nielsen
- School
of Biomolecular and Biomedical
Science, Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Natalie C. J. Strynadka
- Department of Biochemistry and
Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Stephen G. Withers
- Department of Biochemistry and
Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
- Department of Chemistry, University of British Columbia, Vancouver, British
Columbia, Canada V6T 1Z1
- Centre for High-throughput Biology, University of British Columbia, Vancouver, British
Columbia, Canada V6T 1Z4
| | - Lawrence P. McIntosh
- Department of Biochemistry and
Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
- Department of Chemistry, University of British Columbia, Vancouver, British
Columbia, Canada V6T 1Z1
- Michael Smith Laboratories, University of British Columbia, Vancouver, British
Columbia, Canada V6T 1Z4
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Li JF, Gao SJ, Liu XT, Gong YY, Chen ZF, Wei XH, Zhang HM, Wu MC. Modified pPIC9K vector-mediated expression of a family 11 xylanase gene, Aoxyn11A, from Aspergillus oryzae in Pichia pastoris. ANN MICROBIOL 2012. [DOI: 10.1007/s13213-012-0568-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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39
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Probing the role of sigma π interaction and energetics in the catalytic efficiency of endo-1,4-β-xylanase. Appl Environ Microbiol 2012; 78:8817-21. [PMID: 23023743 DOI: 10.1128/aem.02261-12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chaetomium globosum endo-1,4-β-xylanase (XylCg) is distinguished from other xylanases by its high turnover rate (1,860 s(-1)), the highest ever reported for fungal xylanases. One conserved amino acid, W48, in the substrate binding pocket of wild-type XylCg was identified as an important residue affecting XylCg's catalytic efficiency.
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40
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Amino acid substitutions in the N-terminus, cord and α-helix domains improved the thermostability of a family 11 xylanase XynR8. ACTA ACUST UNITED AC 2012; 39:1279-88. [DOI: 10.1007/s10295-012-1140-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Accepted: 04/21/2012] [Indexed: 01/19/2023]
Abstract
Abstract
The thermostability of xylanase XynR8 from uncultured Neocallimastigales rumen fungal was improved by combining random point mutagenesis with site-directed mutagenesis guided by rational design, and a thermostable variant, XynR8_VNE, was identified. This variant contained three amino acid substitutions, I38V, D137N and G151E, and showed an increased melting temperature of 8.8 °C in comparison with the wild type. At 65 °C the wild-type enzyme lost all of its activity after treatment for 30 min, but XynR8_VNE retained about 65 % activity. To elucidate the mechanism of thermal stabilization, three-dimensional structures were predicted for XynR8 and its variant. We found that the tight packing density and new salt bridge caused by the substitutions may be responsible for the improved thermostability. These three substitutions are located in the N-terminus, cord and α-helix domains, respectively. Hence, the stability of these three domains may be crucial for the thermostability of family 11 xylanases.
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41
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Cui F, Zhao L. Optimization of Xylanase production from Penicillium sp.WX-Z1 by a two-step statistical strategy: Plackett-Burman and Box-Behnken experimental design. Int J Mol Sci 2012; 13:10630-10646. [PMID: 22949884 PMCID: PMC3431882 DOI: 10.3390/ijms130810630] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/23/2012] [Accepted: 08/02/2012] [Indexed: 02/07/2023] Open
Abstract
The objective of the study was to optimize the nutrition sources in a culture medium for the production of xylanase from Penicillium sp.WX-Z1 using Plackett-Burman design and Box-Behnken design. The Plackett-Burman multifactorial design was first employed to screen the important nutrient sources in the medium for xylanase production by Penicillium sp.WX-Z1 and subsequent use of the response surface methodology (RSM) was further optimized for xylanase production by Box-Behnken design. The important nutrient sources in the culture medium, identified by the initial screening method of Placket-Burman, were wheat bran, yeast extract, NaNO(3), MgSO(4), and CaCl(2). The optimal amounts (in g/L) for maximum production of xylanase were: wheat bran, 32.8; yeast extract, 1.02; NaNO(3), 12.71; MgSO(4), 0.96; and CaCl(2), 1.04. Using this statistical experimental design, the xylanase production under optimal condition reached 46.50 U/mL and an increase in xylanase activity of 1.34-fold was obtained compared with the original medium for fermentation carried out in a 30-L bioreactor.
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Affiliation(s)
- Fengjie Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; E-Mail:
| | - Liming Zhao
- Department of Respiratory Disease, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai 200003, China
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42
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Driss D, Bhiri F, Siela M, Ghorbel R, Chaabouni SE. Purification and Properties of a Thermostable Xylanase GH 11 from Penicillium occitanis Pol6. Appl Biochem Biotechnol 2012; 168:851-63. [DOI: 10.1007/s12010-012-9824-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 08/01/2012] [Indexed: 10/28/2022]
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43
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Cloning and Expression of a Novel Xylanase Gene (Auxyn11D) from Aspergillus usamii E001 in Pichia pastoris. Appl Biochem Biotechnol 2012; 167:2198-211. [DOI: 10.1007/s12010-012-9757-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 05/29/2012] [Indexed: 10/28/2022]
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44
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Cloning and constitutive expression of His-tagged xylanase GH 11 from Penicillium occitanis Pol6 in Pichia pastoris X33: Purification and characterization. Protein Expr Purif 2012; 83:8-14. [DOI: 10.1016/j.pep.2012.02.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 02/18/2012] [Accepted: 02/20/2012] [Indexed: 11/18/2022]
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45
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Deesukon W, Nishimura Y, Sakamoto T, Sukhumsirichart W. Purification, Characterization of GH11 Endo-β-1,4-xylanase from Thermotolerant Streptomyces sp. SWU10 and Overexpression in Pichia pastoris KM71H. Mol Biotechnol 2012; 54:37-46. [DOI: 10.1007/s12033-012-9541-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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46
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Ellouze OE, Loukil S, Marzouki MN. Cloning and molecular characterization of a new fungal xylanase gene from Sclerotinia sclerotiorum S2. BMB Rep 2012; 44:653-8. [PMID: 22026998 DOI: 10.5483/bmbrep.2011.44.10.653] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sclerotinia sclerotiorum fungus has three endoxylanases induced by wheat bran. In the first part, a partial xylanase sequence gene (90 bp) was isolated by PCR corresponding to catalytic domains (β 5 and β 6 strands of this protein). The high homology of this sequence with xylanase of Botryotinia fuckeliana has permitted in the second part to amplify the XYN1 gene. Sequence analysis of DNA and cDNA revealed an ORF of 746 bp interrupted by a 65 bp intron, thus encoding a predicted protein of 226 amino acids. The mature enzyme (20.06 kDa), is coded by 188 amino acid (pI 9.26). XYN1 belongs to G/11 glycosyl hydrolases family with a conserved catalytic domain containing E(86) and E(178) residues. Bioinformatics analysis revealed that there was no Asn-X-Ser/Thr motif required for N-linked glycosylation in the deduced sequence however, five O-glycosylation sites could intervene in the different folding of xylanses isoforms and in their secretary pathway.
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Affiliation(s)
- Olfa Elleuch Ellouze
- Biological Engineering Unit, National Institute of Applied Sciences and Technology (I.N.S.A.T.), Tunis Cedex, Tunisia.
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47
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Xie ZL, Gao HY, Zhang Q, Wang H, Liu Y. Cloning of a novel xylanase gene from a newly isolated Fusarium sp. Q7-31 and its expression in Escherichia coli. Braz J Microbiol 2012; 43:405-17. [PMID: 24031846 PMCID: PMC3768979 DOI: 10.1590/s1517-838220120001000049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 05/06/2011] [Accepted: 08/30/2011] [Indexed: 11/28/2022] Open
Abstract
A strain of Q7-31 was isolated from Qinghai-Tibet Plateau and was identified as Fusarium sp. based on its morphological characteristics and ITS rDNA gene sequence analysis. It has the highest capacity of degrading cell wall activity compared with other 11 strains. To do research on its xylanase activity of Fusarium sp. Q7-31 while the degrading the rice cell walls, the complete gene xyn8 that encodes endo-1, 4-β-xylanase secreted by Fusarium sp. Q7-31 was cloned and sequenced. The coding region of the gene is separated by two introns of 56bp and 55bp. It encodes 230 amino acid residues of a protein with a calculated molecular weight of 25.7 kDa. The animo acids sequence of xyn8 gene has higher similarity with those of family 11 of glycosyl hydrolases reported from other microorganisms. The nature peptide encodeing cDNA was subcloned into pGEX5x-1 expression vector. The recombinant plasmid was expressed in Escherichia coli BL21-CodonPlus (DE3)-RIL, and xylanase activity was measured. The expression fusion protein was identified by SDS-PAGE and Western blotting, a new specific band of about 52kDa was identified when induced by IPTG. Enzyme activity assay verified the recombinants proteins as a xylanase. A maxium activity of 2.34U/ mg, the xylanase had optimal activity at pH 6.0 and temperature 40℃.
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Affiliation(s)
- Zhan-Ling Xie
- Gansu Agricultural University, Lanzhou 730000, China
- Qinghai University, Xining 810016, China
| | | | - Qian Zhang
- Qinghai University, Xining 810016, China
| | - Huan Wang
- Qinghai University, Xining 810016, China
| | - Ying Liu
- Gansu Agricultural University, Lanzhou 730000, China
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48
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Paës G, Berrin JG, Beaugrand J. GH11 xylanases: Structure/function/properties relationships and applications. Biotechnol Adv 2011; 30:564-92. [PMID: 22067746 DOI: 10.1016/j.biotechadv.2011.10.003] [Citation(s) in RCA: 281] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 10/06/2011] [Accepted: 10/13/2011] [Indexed: 01/02/2023]
Abstract
For technical, environmental and economical reasons, industrial demands for process-fitted enzymes have evolved drastically in the last decade. Therefore, continuous efforts are made in order to get insights into enzyme structure/function relationships to create improved biocatalysts. Xylanases are hemicellulolytic enzymes, which are responsible for the degradation of the heteroxylans constituting the lignocellulosic plant cell wall. Due to their variety, xylanases have been classified in glycoside hydrolase families GH5, GH8, GH10, GH11, GH30 and GH43 in the CAZy database. In this review, we focus on GH11 family, which is one of the best characterized GH families with bacterial and fungal members considered as true xylanases compared to the other families because of their high substrate specificity. Based on an exhaustive analysis of the sequences and 3D structures available so far, in relation with biochemical properties, we assess biochemical aspects of GH11 xylanases: structure, catalytic machinery, focus on their "thumb" loop of major importance in catalytic efficiency and substrate selectivity, inhibition, stability to pH and temperature. GH11 xylanases have for a long time been used as biotechnological tools in various industrial applications and represent in addition promising candidates for future other uses.
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Affiliation(s)
- Gabriel Paës
- INRA, UMR614 FARE, 2 esplanade Roland-Garros, F-51686 Reims, France.
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Enhancing catalytic activity of a hybrid xylanase through single substitution of Leu to Pro near the active site. World J Microbiol Biotechnol 2011; 28:929-35. [PMID: 22805813 DOI: 10.1007/s11274-011-0890-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 09/10/2011] [Indexed: 12/21/2022]
Abstract
A modified error-prone PCR and high-throughout screening system based on 96-well plate were employed to improve catalytic activity of a hybrid xylanase (ATx). The mutant (FSI-A124) with enhanced activity was further heterologously expressed in Pichia pastoris under the control of GAP promoter. The recombinant xylanase driven by the Saccharomyces cerevisiae α-mating factor was secreted into culture medium. After growth in YPD medium for 96 h, xylanase activity in the culture supernatant reached 66.1 U ml(-1), which was 2.92 times as that of its parent. 6 × His-tagged purification increased the specific activity to 1557.61 U mg(-1). The optimum temperature and pH of recombinant xylanase were 55°C and 6.0, respectively. A single amino acid substitution (L49P) was observed within sequence of the mutant. Insight of the three dimensional structure revealed that proline possibly produced weaker hydrogen bond, van der Waals force and hydrophobic interaction with other residues nearby than leucine, especially for V174, contributing to the flexibility of catalytic residue E177. In this study, FSI-A124 exhibited higher xylanase activity but poorer thermostability than its parent, indicating that activity and stability might be negatively correlated.
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50
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Cuyvers S, Dornez E, Delcour JA, Courtin CM. Occurrence and functional significance of secondary carbohydrate binding sites in glycoside hydrolases. Crit Rev Biotechnol 2011; 32:93-107. [DOI: 10.3109/07388551.2011.561537] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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