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Role of extremophiles and their extremozymes in biorefinery process of lignocellulose degradation. Extremophiles 2021; 25:203-219. [PMID: 33768388 DOI: 10.1007/s00792-021-01225-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/10/2021] [Indexed: 12/20/2022]
Abstract
Technological advances in the field of life sciences have led to discovery of organisms that live in harsh environmental conditions referred to as extremophiles. These organisms have adapted themselves to thrive in extreme habitat giving these organisms an advantage over conventional mesophilic organisms in various industrial applications. Extremozymes produced by these extremophiles have high tolerance to inhospitable environmental conditions making them an ideal enzyme system for various industrial processes. A notable application of these extremophiles and extremozymes is their use in the degradation of recalcitrant lignocellulosic biomass and application in biorefineries. For maximum utilization of the trapped carbon source from this obstinate biomass, pretreatment is a necessary step that requires various physiochemical and enzymatic treatments. From search for novel extremophiles and extremozymes to development of various genetic and protein engineering techniques, investigation on extremozymes with enhanced stability and efficiency is been done. Since extremozymes are easily calibrated to work under such conditions, they have become an emerging topic in the research field of biofuel production. The review discusses the various extremozymes that play an important role in lignocellulose degradation along with recent studies on their molecular and genetic evolution for industrial application and production of biofuels and various value-added products.
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Souto BDM, de Araújo ACB, Hamann PRV, Bastos ADR, Cunha IDS, Peixoto J, Kruger RH, Noronha EF, Quirino BF. Functional screening of a Caatinga goat (Capra hircus) rumen metagenomic library reveals a novel GH3 β-xylosidase. PLoS One 2021; 16:e0245118. [PMID: 33449963 PMCID: PMC7810302 DOI: 10.1371/journal.pone.0245118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 12/23/2020] [Indexed: 11/18/2022] Open
Abstract
Functional screening of metagenomic libraries is an effective approach for identification of novel enzymes. A Caatinga biome goat rumen metagenomic library was screened using esculin as a substrate, and a gene from an unknown bacterium encoding a novel GH3 enzyme, BGL11, was identified. None of the BGL11 closely related genes have been previously characterized. Recombinant BGL11 was obtained and kinetically characterized. Substrate specificity of the purified protein was assessed using seven synthetic aryl substrates. Activity towards nitrophenyl-β-D-glucopyranoside (pNPG), 4-nitrophenyl-β-D-xylopyranoside (pNPX) and 4-nitrophenyl-β-D-cellobioside (pNPC) suggested that BGL11 is a multifunctional enzyme with β-glucosidase, β-xylosidase, and cellobiohydrolase activities. However, further testing with five natural substrates revealed that, although BGL11 has multiple substrate specificity, it is most active towards xylobiose. Thus, in its native goat rumen environment, BGL11 most likely functions as an extracellular β-xylosidase acting on hemicellulose. Biochemical characterization of BGL11 showed an optimal pH of 5.6, and an optimal temperature of 50°C. Enzyme stability, an important parameter for industrial application, was also investigated. At 40°C purified BGL11 remained active for more than 15 hours without reduction in activity, and at 50°C, after 7 hours of incubation, BGL11 remained 60% active. The enzyme kinetic parameters of Km and Vmax using xylobiose were determined to be 3.88 mM and 38.53 μmol.min-1.mg-1, respectively, and the Kcat was 57.79 s-1. In contrast to BLG11, most β-xylosidases kinetically studied belong to the GH43 family and have been characterized only using synthetic substrates. In industry, β-xylosidases can be used for plant biomass deconstruction, and the released sugars can be fermented into valuable bio-products, ranging from the biofuel ethanol to the sugar substitute xylitol.
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Affiliation(s)
| | | | | | | | - Isabel de Souza Cunha
- Genomic Sciences and Biotechnology Program, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Julianna Peixoto
- Department of Cellular Biology, Laboratory of Enzymology, Universidade de Brasília, Brasília, DF, Brazil
| | - Ricardo Henrique Kruger
- Department of Cellular Biology, Laboratory of Enzymology, Universidade de Brasília, Brasília, DF, Brazil
| | - Eliane Ferreira Noronha
- Department of Cellular Biology, Laboratory of Enzymology, Universidade de Brasília, Brasília, DF, Brazil
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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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Xu B, Dai L, Zhang W, Yang Y, Wu Q, Li J, Tang X, Zhou J, Ding J, Han N, Huang Z. Characterization of a novel salt-, xylose- and alkali-tolerant GH43 bifunctional β-xylosidase/α-l-arabinofuranosidase from the gut bacterial genome. J Biosci Bioeng 2019; 128:429-437. [PMID: 31109875 DOI: 10.1016/j.jbiosc.2019.03.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 02/13/2019] [Accepted: 03/30/2019] [Indexed: 10/26/2022]
Abstract
A GH43 bifunctional β-xylosidase encoding gene (XylRBM26) was cloned from Massilia sp. RBM26 and successfully expressed in Escherichia coli. Recombinant XylRBM26 exhibited β-xylosidase and α-l-arabinofuranosidase activities. When 4-nitrophenyl-β-d-xylopyranoside was used as a substrate, the enzyme reached optimal activity at pH 6.5 and 50°C and remained stable at pH 5.0-10.0. Purified XylRBM26 presented good salt tolerance and retained 96.6% activity in 3.5 M NaCl and 77.9% initial activity even in 4.0 M NaCl. In addition, it exhibited high tolerance to xylose with Ki value of 500 mM. This study was the first to identify and characterize NaCl-tolerant β-xylosidase/α-l-arabinofuranosidase from the gut microbiota. The enzyme's salt, xylose, and alkali stability and resistance to various chemicals make it a potential biocatalyst for the saccharification of lignocellulose, the food industry, and industrial processes conducted in sea water.
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Affiliation(s)
- Bo Xu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, 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; School of Life Science, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Liming Dai
- School of Life Science, Yunnan Normal University, Kunming 650500, People's Republic of China; Yunnan Institute of Tropical Crops, Jinghong 666100, People's Republic of China
| | - Wenhong Zhang
- School of Life Science, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Yunjuan Yang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, 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; School of Life Science, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Qian Wu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, 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; School of Life Science, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Junjun Li
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, 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; School of Life Science, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Xianghua Tang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, 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; School of Life Science, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Junpei Zhou
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, 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; School of Life Science, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Junmei Ding
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, 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; School of Life Science, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Nanyu Han
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, 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; School of Life Science, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Zunxi Huang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, 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; School of Life Science, Yunnan Normal University, Kunming 650500, People's Republic of China.
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Expression and characterisation of a pH and salt tolerant, thermostable and xylose tolerant recombinant GH43 β-xylosidase from Thermobifida halotolerans YIM 90462 T for promoting hemicellulose degradation. Antonie van Leeuwenhoek 2018; 112:339-350. [PMID: 30225545 DOI: 10.1007/s10482-018-1161-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 09/03/2018] [Indexed: 10/28/2022]
Abstract
A gene encoding a β-xylosidase (designated as Thxyl43A) was cloned from strain Thermobifida halotolerans YIM 90462T. The open reading frame of this gene encodes 550 amino acid residues. The gene was over-expressed in Escherichia coli and the recombinant protein was purified. The monomeric Thxyl43A protein presented a molecular mass of 61.5 kDa. When p-nitrophenyl-β-d-xylopyranoside was used as the substrate, recombinant Thxyl43A exhibited optimal activity at 55 °C and pH 4.0 to 7.0, being thermostable by maintaining 47% of its activity after 30 h incubation at 55 °C. The recombinant enzyme retained more than 80% residual activity after incubation at pH range of 4.0 to 12.0 for 24 h, respectively, which indicated notable thermostability and pH stability of Thxyl43A. Moreover, Thxyl43A displayed high catalytic activity (> 60%) in presence of 5-35% NaCl (w/v) or 1-20% ionic liquid (w/v) or 1-50 mM xylose. These properties suggest that Thxyl43A has potential for promoting hemicellulose degradation and other industrial applications.
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Rohman A, van Oosterwijk N, Puspaningsih NNT, Dijkstra BW. Structural basis of product inhibition by arabinose and xylose of the thermostable GH43 β-1,4-xylosidase from Geobacillus thermoleovorans IT-08. PLoS One 2018; 13:e0196358. [PMID: 29698436 PMCID: PMC5919610 DOI: 10.1371/journal.pone.0196358] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/11/2018] [Indexed: 11/19/2022] Open
Abstract
Complete degradation of the xylan backbone of hemicellulosic plant cell walls requires the synergistic action of endo-xylanases and β-1,4-xylosidases. While endo-xylanases produce xylooligosaccharides from xylan, β-1,4-xylosidases degrade the xylooligosaccharides into xylose monomers. The glycoside hydrolase family 43 β-1,4-xylosidase from Geobacillus thermoleovorans IT-08 is a promising, heat stable catalyst for the saccharification of hemicellulosic material into simple fermentable sugars, but it is competitively inhibited by its products arabinose and xylose. As a first step to help overcome this problem, we elucidated crystal structures of the enzyme in the unliganded form and with bound products, at 1.7-2.0 Å resolution. The structures are very similar to those of other enzymes belonging to glycoside hydrolase family 43. Unexpectedly, the monosaccharides are bound in very different ways. Arabinose preferentially binds in subsite -1, while xylose exclusively interacts with subsite +1. These structures and sugar binding preferences suggest ways for improving the catalytic performance of the enzyme by rational mutational design.
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Affiliation(s)
- Ali Rohman
- Department of Chemistry, Faculty of Sciences and Technology, Universitas Airlangga, Surabaya, Indonesia
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
- Laboratory of Biophysical Chemistry, University of Groningen, Groningen, The Netherlands
| | - Niels van Oosterwijk
- Laboratory of Biophysical Chemistry, University of Groningen, Groningen, The Netherlands
| | - Ni Nyoman Tri Puspaningsih
- Department of Chemistry, Faculty of Sciences and Technology, Universitas Airlangga, Surabaya, Indonesia
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Bauke W. Dijkstra
- Laboratory of Biophysical Chemistry, University of Groningen, Groningen, The Netherlands
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Martín Pérez L, Benítez Casanova L, Moreno Pérez AJ, Pérez Gómez D, Gavaldá Martín S, Ledesma-García L, Valbuena Crespo N, Díez García B, Reyes-Sosa FM. Coupling the pretreatment and hydrolysis of lignocellulosic biomass by the expression of beta-xylosidases. Biotechnol Bioeng 2017; 114:2497-2506. [DOI: 10.1002/bit.26386] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 07/10/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Lucía Martín Pérez
- Department of Biotechnology; Abengoa Research; Campus Palmas Altas; Seville Spain
| | | | | | - Dolores Pérez Gómez
- Department of Biotechnology; Abengoa Research; Campus Palmas Altas; Seville Spain
| | | | - Laura Ledesma-García
- Department of Biotechnology; Abengoa Research; Campus Palmas Altas; Seville Spain
| | | | - Bruno Díez García
- Department of Biotechnology; Abengoa Research; Campus Palmas Altas; Seville Spain
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Park C, Choi J, Kyung M, Seo S, Jo SE, Lee K, Kim P, Wang NHL, Jung S, Mun S. Application of Bacillus pumilus β-xylosidase reaction and simulated moving bed purification to efficient production of high-purity xylobiose from xylose. J IND ENG CHEM 2017. [DOI: 10.1016/j.jiec.2016.12.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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9
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Dehnavi E, Ranaei Siadat SO, Fathi Roudsari M, Khajeh K. Cloning and high-level expression of β-xylosidase from Selenomonas ruminantium in Pichia pastoris by optimizing of pH, methanol concentration and temperature conditions. Protein Expr Purif 2016; 124:55-61. [PMID: 27154901 DOI: 10.1016/j.pep.2016.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 04/28/2016] [Accepted: 05/02/2016] [Indexed: 10/21/2022]
Abstract
β-xylosidase and several other glycoside hydrolase family members, including xylanase, cooperate together to degrade hemicelluloses, a commonly found xylan polymer of plant-cell wall. β-d-xylosidase/α-l-arabinofuranosidase from the ruminal anaerobic bacterium Selenomonas ruminantium (SXA) has potential utility in industrial processes such as production of fuel ethanol and other bioproducts. The optimized synthetic SXA gene was overexpressed in methylotrophic Pichia pastoris under the control of alcohol oxidase I (AOX1) promoter and secreted into the medium. Recombinant protein showed an optimum pH 4.8 and optimum temperature 50 °C. Furthermore, optimization of growth and induction conditions in shake flask was carried out. Using the optimum expression condition (pH 6, temperature 20 °C and 1% methanol induction), protein production was increased by about three times in comparison to the control. The recombinant SXA we have expressed here showed higher turnover frequency using ρ-nitrophenyl β-xylopyranoside (PNPX) substrate, in contrast to most xylosidase experiments reported previously. This is the first report on the cloning and expression of a β-xylosidase gene from glycoside hydrolase (GH) family 43 in Pichia pastoris. Our results confirm that P. pastoris is an appropriate host for high level expression and production of SXA for industrial applications.
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Affiliation(s)
- Ehsan Dehnavi
- Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
| | - Seyed Omid Ranaei Siadat
- Nanobiotechnology Engineering Laboratory, Faculty of Engineering and New Technologies, Shahid Beheshti University, GC, Tehran, Iran; Protein Engineering Laboratory, Protein Research Center (PRC), Shahid Beheshti University, GC, Tehran, Iran.
| | | | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran.
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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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Bhalla A, Bischoff KM, Sani RK. Highly thermostable GH39 β-xylosidase from a Geobacillus sp. strain WSUCF1. BMC Biotechnol 2014; 14:963. [PMID: 25532585 PMCID: PMC4300165 DOI: 10.1186/s12896-014-0106-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 12/01/2014] [Indexed: 11/10/2022] Open
Abstract
Background Complete enzymatic hydrolysis of xylan to xylose requires the action of endoxylanase and β-xylosidase. β-xylosidases play an important part in hydrolyzing xylo-oligosaccharides to xylose. Thermostable β-xylosidases have been a focus of attention as industrially important enzymes due to their long shelf life and role in the relief of end-product inhibition of xylanases caused by xylo-oligosaccharides. Therefore, a highly thermostable β-xylosidase with high specific activity has significant potential in lignocellulose bioconversion. Results A gene encoding a highly thermostable GH39 β-xylosidase was cloned from Geobacillus sp. strain WSUCF1 and expressed in Escherichia coli. Recombinant β-xylosidase was active over a wide range of temperatures and pH with optimum temperature of 70°C and pH 6.5. It exhibited very high thermostability, retaining 50% activity at 70°C after 9 days. WSUCF1 β-xylosidase is more thermostable than β-xylosidases reported from other thermophiles (growth temperature ≤ 70°C). Specific activity was 133 U/mg when incubated with p-nitrophenyl xylopyranoside, with Km and Vmax values of 2.38 mM and 147 U/mg, respectively. SDS-PAGE analysis indicated that the recombinant enzyme had a mass of 58 kDa, but omitting heating prior to electrophoresis increased the apparent mass to 230 kDa, suggesting the enzyme exists as a tetramer. Enzyme exhibited high tolerance to xylose, retained approximately 70% of relative activity at 210 mM xylose concentration. Thin layer chromatography showed that the enzyme had potential to convert xylo-oligomers (xylobiose, triose, tetraose, and pentaose) into fermentable xylose. WSUCF1 β-xylosidase along with WSUCF1 endo-xylanase synergistically converted the xylan into fermentable xylose with more than 90% conversion. Conclusions Properties of the WSUCF1 β-xylosidase i.e. high tolerance to elevated temperatures, high specific activity, conversion of xylo-oligomers to xylose, and resistance to inhibition from xylose, make this enzyme potentially suitable for various biotechnological applications.
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Affiliation(s)
- Aditya Bhalla
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, 57701, USA. .,Present address: Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA.
| | - Kenneth M Bischoff
- Renewable Product Technology Research Unit, Agricultural Research Service, National Center for Agricultural Utilization Research, U.S. Department of Agriculture, Peoria, IL, 61604, USA.
| | - Rajesh K Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, 57701, USA.
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Jain I, Kumar V, Satyanarayana T. Applicability of recombinant β-xylosidase from the extremely thermophilic bacterium Geobacillus thermodenitrificans in synthesizing alkylxylosides. BIORESOURCE TECHNOLOGY 2014; 170:462-469. [PMID: 25164338 DOI: 10.1016/j.biortech.2014.07.113] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 07/26/2014] [Accepted: 07/28/2014] [Indexed: 06/03/2023]
Abstract
The β-xylosidase encoding gene (XsidB) of the extremely thermophilic bacterium Geobacillus thermodenitrificans has been cloned and expressed in Escherichia coli. The homotrimeric recombinant XsidB is of 204.0kDa, which is optimally active at 60°C and pH 7.0 with T1/2 of 58min at 70°C. The β-xylosidase remains unaffected in the presence of most metal ions and organic solvents. The Km [p-nitrophenyl β-xyloside (pNPX)], Vmax and kcat values of the enzyme are 2×10(-3)M, 1250μmolesmg(-1)min(-1) and 13.20×10(5)min(-1), respectively. The enzyme catalyzes transxylosylation reactions in the presence of alcohols as acceptors. The pharmaceutically important β-methyl-d-xylosides could be produced using pNPX as the donor and methanol as acceptor. The products of transxylosylation were identified by TLC and HPLC, and the structure was confirmed by (1)H NMR analysis. The enzyme is also useful in synthesizing transxylosylation products from the wheat bran hydrolysate.
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Affiliation(s)
- Ira Jain
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India.
| | - Vikash Kumar
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India.
| | - T Satyanarayana
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India.
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Ravanal MC, Alegría-Arcos M, Gonzalez-Nilo FD, Eyzaguirre J. Penicillium purpurogenum produces two GH family 43 enzymes with β-xylosidase activity, one monofunctional and the other bifunctional: Biochemical and structural analyses explain the difference. Arch Biochem Biophys 2013; 540:117-24. [DOI: 10.1016/j.abb.2013.10.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 10/08/2013] [Accepted: 10/21/2013] [Indexed: 11/24/2022]
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β-xylosidases and α-L-arabinofuranosidases: accessory enzymes for arabinoxylan degradation. Biotechnol Adv 2013; 32:316-32. [PMID: 24239877 DOI: 10.1016/j.biotechadv.2013.11.005] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 10/28/2013] [Accepted: 11/09/2013] [Indexed: 11/22/2022]
Abstract
Arabinoxylan (AX) is among the most abundant hemicelluloses on earth and one of the major components of feedstocks that are currently investigated as a source for advanced biofuels. As global research into these sustainable biofuels is increasing, scientific knowledge about the enzymatic breakdown of AX advanced significantly over the last decade. This review focuses on the exo-acting AX hydrolases, such as α-arabinofuranosidases and β-xylosidases. It aims to provide a comprehensive overview of the diverse substrate specificities and corresponding structural features found in the different glycoside hydrolase families. A careful review of the available literature reveals a marked difference in activity between synthetically labeled and naturally occurring substrates, often leading to erroneous enzymatic annotations. Therefore, special attention is given to enzymes with experimental evidence on the hydrolysis of natural polymers.
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Ratnadewi AAI, Fanani M, Kurniasih SD, Sakka M, Wasito EB, Sakka K, Nurachman Z, Puspaningsih NNT. β-D-xylosidase from Geobacillus thermoleovorans IT-08: biochemical characterization and bioinformatics of the enzyme. Appl Biochem Biotechnol 2013; 170:1950-64. [PMID: 23797510 DOI: 10.1007/s12010-013-0329-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 06/11/2013] [Indexed: 11/24/2022]
Abstract
The gene encoding a thermostable β-D-xylosidase (GbtXyl43B) from Geobacillus thermoleovorans IT-08 was cloned in pET30a and expressed in Escherichia coli; additionally, characterization and kinetic analysis of GbtXyl43B were carried out. The gene product was purified to apparent homogeneity showing M r of 72 by sodium dodecyl sulfate polyacrylamide gel electrophoresis. The enzyme exhibited an optimum temperature and pH of 60 °C and 6.0, respectively. In terms of stability, GbtXyl43B was stable at 60 °C at pH 6.0 for 1 h as well as at pH 6-8 at 4 °C for 24 h. The enzyme had a catalytic efficiency (k cat/K M) of 0.0048 ± 0.0010 s(-1) mM(-1) on p-nitrophenyl-β-D-xylopyranoside substrate. Thin layer chromatography product analysis indicated that GbtXyl43B was exoglycosidase cleaving single xylose units from the nonreducing end of xylan. The activity of GbtXyl43B on insoluble xylan was eightfold higher than on soluble xylan. Bioinformatics analysis showed that GbtXyl43B belonging to glycoside hydrolase family 43 contained carbohydrate-binding module (CBM; residues 15 to 149 forming eight antiparallel β-strands) and catalytic module (residues 157 to 604 forming five-bladed β-propeller fold with predicted catalytic residues to be Asp287 and Glu476). CBM of GbtXyl43B dominated by the Phe residues which grip the carbohydrate is proposed as a novel CBM36 subfamily.
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Affiliation(s)
- Anak Agung Istri Ratnadewi
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Jember, Jalan Kalimantan 37, Jember, 68121, Indonesia
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Jordan DB, Vermillion KE, Grigorescu AA, Braker JD. Rehabilitation of faulty kinetic determinations and misassigned glycoside hydrolase family of retaining mechanism β-xylosidases. Arch Biochem Biophys 2013; 537:176-84. [PMID: 23916587 DOI: 10.1016/j.abb.2013.07.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 07/19/2013] [Accepted: 07/22/2013] [Indexed: 11/16/2022]
Abstract
We obtained Cx1 from a commercial supplier, whose catalog listed it as a β-xylosidase of glycoside hydrolase family 43. NMR experiments indicate retention of anomeric configuration in its reaction stereochemistry, opposing the assignment of GH43, which follows an inverting mechanism. Partial protein sequencing indicates Cx1 is similar to but not identical to β-xylosidases of GH52, including Q09LZ0, that have retaining mechanisms. Q09LZ0 β-xylosidase had been characterized biochemically in kinetic reactions that contained Tris. We overproduced Q09LZ0 and demonstrated that Tris is a competitive inhibitor of the β-xylosidase. Also, the previous work used grossly incorrect extinction coefficients for product 4-nitrophenol. We redetermined kinetic parameters using reactions that omitted Tris and using correct extinction coefficients for 4-nitrophenol. Cx1 and Q09LZ0 β-xylosidases were thus shown to possess similar kinetic properties when acting on 4-nitrophenyl-β-d-xylopyranoside and xylobiose. kcat pH profiles of Cx1 and Q09LZ0 acting on 4-nitrophenyl-β-d-xylopyranoside and xylobiose have patterns containing two rate increases with increasing acidity, not reported before for glycoside hydrolases. The dexylosylation step of 4-nitrophenyl-β-d-xylopyranoside hydrolysis mediated by Q09LZ0 is not rate determining for kcat(4NPX).
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Affiliation(s)
- Douglas B Jordan
- USDA-ARS-National Center for Agricultural Utilization Research, Peoria, IL 61604, USA.
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Viborg AH, Sørensen KI, Gilad O, Steen-Jensen DB, Dilokpimol A, Jacobsen S, Svensson B. Biochemical and kinetic characterisation of a novel xylooligosaccharide-upregulated GH43 β-d-xylosidase/α-l-arabinofuranosidase (BXA43) from the probiotic Bifidobacterium animalis subsp. lactis BB-12. AMB Express 2013; 3:56. [PMID: 24025736 PMCID: PMC3847938 DOI: 10.1186/2191-0855-3-56] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 09/02/2013] [Indexed: 12/28/2022] Open
Abstract
The Bifidobacterium animalis subsp. lactis BB-12 gene BIF_00092, assigned to encode a β-d-xylosidase (BXA43) of glycoside hydrolase family 43 (GH43), was cloned with a C-terminal His-tag and expressed in Escherichia coli. BXA43 was purified to homogeneity from the cell lysate and found to be a dual-specificity exo-hydrolase active on para-nitrophenyl-β-d-xylopyranoside (pNPX), para-nitrophenyl-α-L-arabinofuranoside (pNPA), β-(1 → 4)-xylopyranosyl oligomers (XOS) of degree of polymerisation (DP) 2-4, and birchwood xylan. A phylogenetic tree of the 92 characterised GH43 enzymes displayed five distinct groups (I - V) showing specificity differences. BXA43 belonged to group IV and had an activity ratio for pNPA:pNPX of 1:25. BXA43 was stable below 40°C and at pH 4.0-8.0 and showed maximum activity at pH 5.5 and 50°C. Km and kcat for pNPX were 15.6 ± 4.2 mM and 60.6 ± 10.8 s-1, respectively, and substrate inhibition became apparent above 18 mM pNPX. Similar kinetic parameters and catalytic efficiency values were reported for β-d-xylosidase (XynB3) from Geobacillus stearothermophilus T‒6 also belonging to group IV. The activity of BXA43 for xylooligosaccharides increased with the size and was 2.3 and 5.6 fold higher, respectively for xylobiose and xylotetraose compared to pNPX. BXA43 showed clearly metal inhibition for Zn2+ and Ag+, which is different to its close homologues. Multiple sequence alignment and homology modelling indicated that Arg505Tyr506 present in BXA43 are probably important for binding to xylotetraose at subsite +3 and occur only in GH43 from the Bifidobacterium genus.
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Affiliation(s)
- Alexander Holm Viborg
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs, Lyngby, Denmark
| | - Kim Ib Sørensen
- Department for Strains, Chr. Hansen A/S, 2970 Hørsholm, Denmark
| | - Ofir Gilad
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs, Lyngby, Denmark
- Department for Identification, Chr. Hansen A/S, 2970 Hørsholm, Denmark
| | - Daniel Bisgaard Steen-Jensen
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs, Lyngby, Denmark
| | - Adiphol Dilokpimol
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs, Lyngby, Denmark
| | - Susanne Jacobsen
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs, Lyngby, Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs, Lyngby, Denmark
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Jordan DB, Lee CC, Wagschal K, Braker JD. Activation of a GH43 β-xylosidase by divalent metal cations: slow binding of divalent metal and high substrate specificity. Arch Biochem Biophys 2013; 533:79-87. [PMID: 23500142 DOI: 10.1016/j.abb.2013.02.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 02/26/2013] [Accepted: 02/27/2013] [Indexed: 11/19/2022]
Abstract
RS223-BX of glycoside hydrolase family 43 is a β-d-xylosidase that is strongly activated (k(cat)/K(m) as much as 116-fold) by the addition of divalent metal cations, Ca(2+), Co(2+), Fe(2+), Mg(2+), Mn(2+) and Ni(2+). Slow activation by Mg(2+) was demonstrated (k(on) 0.013 s(-1) mM(-1), k(off) 0.008 s(-1)) at pH 7.0 and 25 °C. k(off) and k(on) values are independent of Mg(2+) concentration, but k(off) and k(on) are slower in the presence of increasing levels of substrate 4-nitrophenyl-β-D-xylopyranoside. The kinetics strongly suggest that M(2+) binds to the enzyme rapidly, forming E M(2+), followed by slow isomerization to the activated enzyme, E* M(2+). Moderately high values of kcat (7-30 s(-1)) were found for M(2+)-activated RS223-BX acting on xylobiose (natural substrate) at pH 7.0 and 25 °C. Certain M(2+)-activated RS223-BX exhibit the highest reported values of k(cat)/K(m) of any β-xylosidase acting on natural substrates: for example, at pH 7.0 and 25°C, xylobiose (Mn(2+), 190 s(-1) mM(-1)), xylotriose (Ca(2+), 150 s(-1) mM(-1)) and xylotetraose (Ca(2+), 260 s(-1) mM(-1)). There is potential for the enzyme to add value to industrial saccharification operations at low substrate and high d-glucose and high d-xylose concentrations.
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Affiliation(s)
- Douglas B Jordan
- USDA-ARS-National Center for Agricultural Utilization Research, Peoria, IL 61604, USA.
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19
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Distinct actions by Paenibacillus sp. strain E18 α-L-arabinofuranosidases and xylanase in xylan degradation. Appl Environ Microbiol 2013; 79:1990-5. [PMID: 23335774 DOI: 10.1128/aem.03276-12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We cloned a Paenibacillus sp. strain E18 5.3-kb xylanolytic gene cluster that contains three open reading frames encoding two family 43 α-L-arabinofuranosidases (Abf43A and Abf43B) and one family 10 xylanase (XynBE18). The deduced amino acid sequences of Abf43A and Abf43B were at most 68% and 63% identical to those of two putative family 43 proteins from Clostridium sp. strain DL-VIII (EHI98634.1 and EHI98635.1), respectively, but were only 11% identical to each other. Recombinant Abf43A and Abf43B had similar activities at 45°C and pH 6.0 but varied in thermostabilities and substrate specificities. Abf43B was active against only 4-nitrophenyl α-L-arabinofuranoside, whereas Abf43A acted on 4-nitrophenyl α-L-arabinofuranoside, wheat arabinoxylan, 4-nitrophenyl α-D-xylopyranoside, and sugar beet arabinan. The sequential and combined effects on xylan degradation by XynBE18, Abf43A, and Abf43B were characterized. For beechwood, birchwood, and oat spelt xylans as the substrates, synergistic effects were found when XynBE18 and Abf43A or Abf43B were incubated together and when the substrates were first incubated with Abf43A or Abf43B and then with XynBE18. Further high-performance liquid chromatography (HPLC) analysis showed that the amounts of xylobiose and xylose increased sharply in the aforementioned reactions. For water-soluble wheat arabinoxylan as the substrate, Abf43A not only released arabinose but also had a synergistic effect with XynBE18. Synergy may arise as the result of removal of arabinose residues from xylans by α-L-arabinofuranosidases, which eliminates steric hindrance caused by the arabinose side chains and which allows xylanases to then degrade the xylan backbone, producing short xylooligosaccharides.
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20
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Highly active β-xylosidases of glycoside hydrolase family 43 operating on natural and artificial substrates. Appl Microbiol Biotechnol 2012; 97:4415-28. [PMID: 23053115 DOI: 10.1007/s00253-012-4475-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 09/24/2012] [Accepted: 09/25/2012] [Indexed: 10/27/2022]
Abstract
The hemicellulose xylan constitutes a major portion of plant biomass, a renewable feedstock available for conversion to biofuels and other bioproducts. β-xylosidase operates in the deconstruction of the polysaccharide to fermentable sugars. Glycoside hydrolase family 43 is recognized as a source of highly active β-xylosidases, some of which could have practical applications. The biochemical details of four GH43 β-xylosidases (those from Alkaliphilus metalliredigens QYMF, Bacillus pumilus, Bacillus subtilis subsp. subtilis str. 168, and Lactobacillus brevis ATCC 367) are examined here. Sedimentation equilibrium experiments indicate that the quaternary states of three of the enzymes are mixtures of monomers and homodimers (B. pumilus) or mixtures of homodimers and homotetramers (B. subtilis and L. brevis). k cat and k cat/K m values of the four enzymes are higher for xylobiose than for xylotriose, suggesting that the enzyme active sites comprise two subsites, as has been demonstrated by the X-ray structures of other GH43 β-xylosidases. The K i values for D-glucose (83.3-357 mM) and D-xylose (15.6-70.0 mM) of the four enzymes are moderately high. The four enzymes display good temperature (K t (0.5) ∼ 45 °C) and pH stabilities (>4.6 to <10.3). At pH 6.0 and 25 °C, the enzyme from L. brevis ATCC 367 displays the highest reported k cat and k cat/K m on natural substrates xylobiose (407 s(-1), 138 s(-1) mM(-1)), xylotriose (235 s(-1), 80.8 s(-1) mM(-1)), and xylotetraose (146 s(-1), 32.6 s(-1) mM(-1)).
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21
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Chen Z, Jia H, Yang Y, Yan Q, Jiang Z, Teng C. Secretory expression of a β-xylosidase gene fromThermomyces lanuginosusinEscherichia coliand characterization of its recombinant enzyme. Lett Appl Microbiol 2012; 55:330-7. [DOI: 10.1111/j.1472-765x.2012.03299.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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Assessment of the biomass hydrolysis potential in bacterial isolates from a volcanic environment: biosynthesis of the corresponding activities. World J Microbiol Biotechnol 2012; 28:2889-902. [DOI: 10.1007/s11274-012-1100-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 06/05/2012] [Indexed: 11/25/2022]
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Abstract
Conversion of plant cell walls to ethanol constitutes second generation bioethanol production. The process consists of several steps: biomass selection/genetic modification, physiochemical pretreatment, enzymatic saccharification, fermentation and separation. Ultimately, it is desirable to combine as many of the biochemical steps as possible in a single organism to achieve CBP (consolidated bioprocessing). A commercially ready CBP organism is currently unreported. Production of second generation bioethanol is hindered by economics, particularly in the cost of pretreatment (including waste management and solvent recovery), the cost of saccharification enzymes (particularly exocellulases and endocellulases displaying kcat ~1 s−1 on crystalline cellulose), and the inefficiency of co-fermentation of 5- and 6-carbon monosaccharides (owing in part to redox cofactor imbalances in Saccharomyces cerevisiae).
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Biochemical and kinetic characterization of GH43 β-d-xylosidase/α-l-arabinofuranosidase and GH30 α-l-arabinofuranosidase/β-d-xylosidase from rumen metagenome. ACTA ACUST UNITED AC 2012; 39:143-52. [DOI: 10.1007/s10295-011-1009-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 06/15/2011] [Indexed: 10/18/2022]
Abstract
Abstract
The present study focuses on characterization of two hemicellulases, RuXyn1 and RuXyn2, from rumen bacterial metagenome and their capabilities for degradation of xylans. Glycosyl hydrolase (GH) family 43 β-d-xylosidase/α-l-arabinofuranosidase RuXyn1 can hydrolyze p-nitrophenyl-β-d-xylopyranoside (pNPX), p-nitrophenyl-α-l-arabinofuranoside (pNPA), and xylo-oligosaccharide substrates, while GH30 1,5-α-l-arabinofuranosidase/β-d-xylosidase RuXyn2, the first α-l-arabinofuranosidase assigned to this GH family, shows activities towards 1,5-α-l-arabinobiose and pNPX substrates but no activity for pNPA. Kinetic analysis for aryl-glycosides revealed that RuXyn2 had higher catalytic efficiency than RuXyn1 toward pNPX substrate. RuXyn1 shows high synergism with endoxylanase, elevating by 73% the reducing sugars released from brichwood xylans, and converted most intermediate xylo-oligosaccharide hydrolysate into xylose. The high xylose conversion capability of RuXyn1 suggests it has potential applications in enzymatic production of xylose and improvement of hemicellulose saccharification for production of biofuels. RuXyn2 shows no obviously synergistic effect in the endoxylanase-coupled assay for enzymatic saccharification of xylan. Further cosmid DNA sequencing revealed a neighboring putative GH43 α-l-arabinofuranosidase RuAra1 and two putative GH3 β-xylosidase/arabinosidases, RuXyn3 and RuXyn5, downstream of RuXyn2, indicating that this hemicellulase gene cluster may be responsible for production of end-product, xylose and arabinose, from hemicellulose biomass.
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Engineering lower inhibitor affinities in β-d-xylosidase of Selenomonas ruminantium by site-directed mutagenesis of Trp145. J Ind Microbiol Biotechnol 2011; 38:1821-35. [DOI: 10.1007/s10295-011-0971-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 04/01/2011] [Indexed: 10/18/2022]
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Gold H, Munneke S, Dinkelaar J, Overkleeft HS, Aerts JMFG, Codée JDC, van der Marel GA. A practical synthesis of capped 4-methylumbelliferyl hyaluronan disaccharides and tetrasaccharides as potential hyaluronidase substrates. Carbohydr Res 2011; 346:1467-78. [PMID: 21536258 DOI: 10.1016/j.carres.2011.03.042] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Revised: 03/24/2011] [Accepted: 03/29/2011] [Indexed: 10/18/2022]
Abstract
The synthesis of hyaluronan dimers and tetramers equipped with a 4-methylumbelliferyl group at the reducing end to potentially allow monitoring of hyaluronidase activities is described. The 4-OH at the non-reducing glucuronate in the presented series is either removed or methylated to prohibit transglycosylase reactions, leading to a total of four probes.
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Affiliation(s)
- Henrik Gold
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2300 RA Leiden, The Netherlands
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Yoshida S, Hespen CW, Beverly RL, Mackie RI, Cann IKO. Domain analysis of a modular alpha-L-Arabinofuranosidase with a unique carbohydrate binding strategy from the fiber-degrading bacterium Fibrobacter succinogenes S85. J Bacteriol 2010; 192:5424-36. [PMID: 20709893 PMCID: PMC2950500 DOI: 10.1128/jb.00503-10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Accepted: 08/03/2010] [Indexed: 11/20/2022] Open
Abstract
Family 43 glycoside hydrolases (GH43s) are known to exhibit various activities involved in hemicellulose hydrolysis. Thus, these enzymes contribute to efficient plant cell wall degradation, a topic of much interest for biofuel production. In this study, we characterized a unique GH43 protein from Fibrobacter succinogenes S85. The recombinant protein showed α-l-arabinofuranosidase activity, specifically with arabinoxylan. The enzyme is, therefore, an arabinoxylan arabinofuranohydrolase (AXH). The F. succinogenes AXH (FSUAXH1) is a modular protein that is composed of a signal peptide, a GH43 catalytic module, a unique β-sandwich module (XX domain), a family 6 carbohydrate-binding module (CBM6), and F. succinogenes-specific paralogous module 1 (FPm-1). Truncational analysis and site-directed mutagenesis of the protein revealed that the GH43 domain/XX domain constitute a new form of carbohydrate-binding module and that residue Y484 in the XX domain is essential for binding to arabinoxylan, although protein structural analyses may be required to confirm some of the observations. Kinetic studies demonstrated that the Y484A mutation leads to a higher k(cat) for a truncated derivative of FSUAXH1 composed of only the GH43 catalytic module and the XX domain. However, an increase in the K(m) for arabinoxylan led to a 3-fold decrease in catalytic efficiency. Based on the knowledge that most XX domains are found only in GH43 proteins, the evolutionary relationships within the GH43 family were investigated. These analyses showed that in GH43 members with a XX domain, the two modules have coevolved and that the length of a loop within the XX domain may serve as an important determinant of substrate specificity.
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Affiliation(s)
- Shosuke Yoshida
- Energy Biosciences Institute, Institute for Genomic Biology, Department of Biochemistry, Department of Microbiology, Department of Animal Sciences, University of Illinois, Urbana, Illinois 61801
| | - Charles W. Hespen
- Energy Biosciences Institute, Institute for Genomic Biology, Department of Biochemistry, Department of Microbiology, Department of Animal Sciences, University of Illinois, Urbana, Illinois 61801
| | - Robert L. Beverly
- Energy Biosciences Institute, Institute for Genomic Biology, Department of Biochemistry, Department of Microbiology, Department of Animal Sciences, University of Illinois, Urbana, Illinois 61801
| | - Roderick I. Mackie
- Energy Biosciences Institute, Institute for Genomic Biology, Department of Biochemistry, Department of Microbiology, Department of Animal Sciences, University of Illinois, Urbana, Illinois 61801
| | - Isaac K. O. Cann
- Energy Biosciences Institute, Institute for Genomic Biology, Department of Biochemistry, Department of Microbiology, Department of Animal Sciences, University of Illinois, Urbana, Illinois 61801
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Fan Z, Yuan L. Production of multifunctional chimaeric enzymes in plants: a promising approach for degrading plant cell wall from within. PLANT BIOTECHNOLOGY JOURNAL 2010; 8:308-15. [PMID: 20070871 DOI: 10.1111/j.1467-7652.2009.00484.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Multifunctional chimaeric hydrolases can be created by covalently linking heterologous catalytic and functional domains in a single polypeptide. Previously, we have generated a number of chimaeric lignocellulosic hydrolases that contain two to five modules [Biotechnol Bioeng (2009) 102: 1045; Appl Environ Microbiol (2009) 75: 1754]. These chimaeras closely resemble the parental enzymes in kinetics and other enzymatic properties, and some exhibit improved synergy in degrading natural substrates when compared to mixtures of parental enzymes. In addition to the applications in fermentative enzyme production, the chimaeric genes can be used in the construction of a single plant transformation binary vector carrying several genes that encode a complete set of lignocellulosic hydrolase activities. The advantages of this approach include ease in vector construction and transformation, as well as downstream plant analysis and breeding. The hydrolases sequestered in biomass feedstock can potentially assist enzymatic pretreatment and sugar conversion. Here, we report the gene expression and functional characterization of a chimaeric hemicellulase in transgenic tobacco plants. T1 transgenic plants produced up to 19-mg active enzymes per gram of total-soluble leaf proteins. The results demonstrate the feasibility of producing multifunctional lignocellulosic hydrolases in plants. Key considerations in the design, construction and plant expression of the chimaeric genes are discussed.
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Affiliation(s)
- Zhanmin Fan
- The Department of Plant and Soil Sciences, and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, USA
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29
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Jordan DB, Wagschal K. Properties and applications of microbial β-D-xylosidases featuring the catalytically efficient enzyme from Selenomonas ruminantium. Appl Microbiol Biotechnol 2010; 86:1647-58. [DOI: 10.1007/s00253-010-2538-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Revised: 03/02/2010] [Accepted: 03/03/2010] [Indexed: 11/28/2022]
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30
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Engineering lower inhibitor affinities in β-d-xylosidase. Appl Microbiol Biotechnol 2009; 86:1099-113. [DOI: 10.1007/s00253-009-2335-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Revised: 10/13/2009] [Accepted: 10/26/2009] [Indexed: 10/20/2022]
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